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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Feb '14

26 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7f7da7248d4d/ Changeset: 7f7da7248d4d Branch: stable User: greg Date: 2014-02-26 21:09:43 Summary: Fixes for handling complex repository dependency definitions in tool dependency recipes. Affected #: 2 files diff -r 66aa6798e55303abc40fbb585c75e8c77638cca3 -r 7f7da7248d4de5d9f039639db77721d0b22fa6c5 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -274,7 +274,11 @@ return False, None, error_message def handle_repository_dependency_elem( trans, elem, unpopulate=False ): + """Populate or unpopulate repository tags.""" # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> + # <repository changeset_revision="xxx" name="package_xorg_macros_1_17_1" owner="test" toolshed="yyy"> + # <package name="xorg_macros" version="1.17.1" /> + # </repository> error_message = '' name = elem.get( 'name' ) owner = elem.get( 'owner' ) @@ -285,6 +289,23 @@ revised = False toolshed = elem.get( 'toolshed' ) changeset_revision = elem.get( 'changeset_revision' ) + sub_elems = elem.findall( './/' ) + if sub_elems: + # At this point, a <repository> tag will point only to a package. + # <package name="xorg_macros" version="1.17.1" /> + # Coerce the list to an odict(). + sub_elements = odict() + packages = [] + for sub_elem in sub_elems: + sub_elem_type = sub_elem.tag + sub_elem_name = sub_elem.get( 'name' ) + sub_elem_version = sub_elem.get( 'version' ) + if sub_elem_type and sub_elem_name and sub_elem_version: + packages.append( ( sub_elem_name, sub_elem_version ) ) + sub_elements[ 'packages' ] = packages + else: + # Set to None. + sub_elements = None if unpopulate: # We're exporting the repository, so eliminate all toolshed and changeset_revision attributes from the <repository> tag. if toolshed or changeset_revision: @@ -292,7 +313,7 @@ attributes[ 'name' ] = name attributes[ 'owner' ] = owner attributes[ 'prior_installation_required' ] = elem.get( 'prior_installation_required', 'False' ) - elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=None ) + elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) revised = True return revised, elem, error_message # From here on we're populating the toolshed and changeset_revisions if necessary. @@ -321,10 +342,12 @@ return revised, elem, error_message def handle_repository_dependency_sub_elem( trans, package_altered, altered, actions_elem, action_index, action_elem, unpopulate=False ): - # This method populates the toolshed and changeset_revision attributes for each of the following. - # <action type="set_environment_for_install"> - # <action type="setup_r_environment"> - # <action type="setup_ruby_environment"> + """ + Populate or unpopulate the toolshed and changeset_revision attributes for each of the following tag sets. + <action type="set_environment_for_install"> + <action type="setup_r_environment"> + <action type="setup_ruby_environment"> + """ error_message = '' for repo_index, repo_elem in enumerate( action_elem ): # Make sure to skip comments and tags that are not <repository>. @@ -343,7 +366,8 @@ def handle_tool_dependencies_definition( trans, tool_dependencies_config, unpopulate=False ): """ - Populate or unpopulate the tooshed and changeset_revision attributes of each <repository> tag defined within a tool_dependencies.xml file. + Populate or unpopulate the tooshed and changeset_revision attributes of each <repository> + tag defined within a tool_dependencies.xml file. """ altered = False error_message = '' diff -r 66aa6798e55303abc40fbb585c75e8c77638cca3 -r 7f7da7248d4de5d9f039639db77721d0b22fa6c5 lib/tool_shed/util/xml_util.py --- a/lib/tool_shed/util/xml_util.py +++ b/lib/tool_shed/util/xml_util.py @@ -47,7 +47,7 @@ def create_element( tag, attributes=None, sub_elements=None ): """ Create a new element whose tag is the value of the received tag, and whose attributes are all - key / value pairs in the received the attributes and sub_elements. + key / value pairs in the received attributes and sub_elements. """ if tag: elem = XmlET.Element( tag ) @@ -56,14 +56,22 @@ for k, v in attributes.items(): elem.set( k, v ) if sub_elements: - # The received attributes is an odict as well. These handle information that tends to be + # The received attributes is an odict. These handle information that tends to be # long text including paragraphs (e.g., description and long_description. for k, v in sub_elements.items(): # Don't include fields that are blank. if v: - sub_elem = XmlET.SubElement( elem, k ) - if isinstance( v, list ): - # If the sub_elem is a list, then it must be a list of tuples where the first + if k == 'packages': + # The received sub_elements is an odict whose key is 'packages' and whose + # value is a list of ( name, version ) tuples. + for v_tuple in v: + sub_elem = XmlET.SubElement( elem, 'package' ) + sub_elem_name, sub_elem_version = v_tuple + sub_elem.set( 'name', sub_elem_name ) + sub_elem.set( 'version', sub_elem_version ) + elif isinstance( v, list ): + sub_elem = XmlET.SubElement( elem, k ) + # If v is a list, then it must be a list of tuples where the first # item is the tag and the second item is the text value. for v_tuple in v: if len( v_tuple ) == 2: @@ -74,6 +82,7 @@ v_elem = XmlET.SubElement( sub_elem, v_tag ) v_elem.text = v_text else: + sub_elem = XmlET.SubElement( elem, k ) sub_elem.text = v return elem return None https://bitbucket.org/galaxy/galaxy-central/commits/ce7e90f9576b/ Changeset: ce7e90f9576b User: davebgx Date: 2014-02-26 21:11:47 Summary: Merge stable. Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fixes for handling complex repository dependency definitions in tool dependency recipes.
by commits-noreply＠bitbucket.org 26 Feb '14

26 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/11cde97a48eb/ Changeset: 11cde97a48eb User: greg Date: 2014-02-26 21:09:43 Summary: Fixes for handling complex repository dependency definitions in tool dependency recipes. Affected #: 2 files diff -r 7225183f34d12b1ed3d879a85054ee98a7750729 -r 11cde97a48eb4a7b2934bef3a507d1a2c5ea3379 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -274,7 +274,11 @@ return False, None, error_message def handle_repository_dependency_elem( trans, elem, unpopulate=False ): + """Populate or unpopulate repository tags.""" # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> + # <repository changeset_revision="xxx" name="package_xorg_macros_1_17_1" owner="test" toolshed="yyy"> + # <package name="xorg_macros" version="1.17.1" /> + # </repository> error_message = '' name = elem.get( 'name' ) owner = elem.get( 'owner' ) @@ -285,6 +289,23 @@ revised = False toolshed = elem.get( 'toolshed' ) changeset_revision = elem.get( 'changeset_revision' ) + sub_elems = elem.findall( './/' ) + if sub_elems: + # At this point, a <repository> tag will point only to a package. + # <package name="xorg_macros" version="1.17.1" /> + # Coerce the list to an odict(). + sub_elements = odict() + packages = [] + for sub_elem in sub_elems: + sub_elem_type = sub_elem.tag + sub_elem_name = sub_elem.get( 'name' ) + sub_elem_version = sub_elem.get( 'version' ) + if sub_elem_type and sub_elem_name and sub_elem_version: + packages.append( ( sub_elem_name, sub_elem_version ) ) + sub_elements[ 'packages' ] = packages + else: + # Set to None. + sub_elements = None if unpopulate: # We're exporting the repository, so eliminate all toolshed and changeset_revision attributes from the <repository> tag. if toolshed or changeset_revision: @@ -292,7 +313,7 @@ attributes[ 'name' ] = name attributes[ 'owner' ] = owner attributes[ 'prior_installation_required' ] = elem.get( 'prior_installation_required', 'False' ) - elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=None ) + elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) revised = True return revised, elem, error_message # From here on we're populating the toolshed and changeset_revisions if necessary. @@ -321,10 +342,12 @@ return revised, elem, error_message def handle_repository_dependency_sub_elem( trans, package_altered, altered, actions_elem, action_index, action_elem, unpopulate=False ): - # This method populates the toolshed and changeset_revision attributes for each of the following. - # <action type="set_environment_for_install"> - # <action type="setup_r_environment"> - # <action type="setup_ruby_environment"> + """ + Populate or unpopulate the toolshed and changeset_revision attributes for each of the following tag sets. + <action type="set_environment_for_install"> + <action type="setup_r_environment"> + <action type="setup_ruby_environment"> + """ error_message = '' for repo_index, repo_elem in enumerate( action_elem ): # Make sure to skip comments and tags that are not <repository>. @@ -343,7 +366,8 @@ def handle_tool_dependencies_definition( trans, tool_dependencies_config, unpopulate=False ): """ - Populate or unpopulate the tooshed and changeset_revision attributes of each <repository> tag defined within a tool_dependencies.xml file. + Populate or unpopulate the tooshed and changeset_revision attributes of each <repository> + tag defined within a tool_dependencies.xml file. """ altered = False error_message = '' diff -r 7225183f34d12b1ed3d879a85054ee98a7750729 -r 11cde97a48eb4a7b2934bef3a507d1a2c5ea3379 lib/tool_shed/util/xml_util.py --- a/lib/tool_shed/util/xml_util.py +++ b/lib/tool_shed/util/xml_util.py @@ -47,7 +47,7 @@ def create_element( tag, attributes=None, sub_elements=None ): """ Create a new element whose tag is the value of the received tag, and whose attributes are all - key / value pairs in the received the attributes and sub_elements. + key / value pairs in the received attributes and sub_elements. """ if tag: elem = XmlET.Element( tag ) @@ -56,14 +56,22 @@ for k, v in attributes.items(): elem.set( k, v ) if sub_elements: - # The received attributes is an odict as well. These handle information that tends to be + # The received attributes is an odict. These handle information that tends to be # long text including paragraphs (e.g., description and long_description. for k, v in sub_elements.items(): # Don't include fields that are blank. if v: - sub_elem = XmlET.SubElement( elem, k ) - if isinstance( v, list ): - # If the sub_elem is a list, then it must be a list of tuples where the first + if k == 'packages': + # The received sub_elements is an odict whose key is 'packages' and whose + # value is a list of ( name, version ) tuples. + for v_tuple in v: + sub_elem = XmlET.SubElement( elem, 'package' ) + sub_elem_name, sub_elem_version = v_tuple + sub_elem.set( 'name', sub_elem_name ) + sub_elem.set( 'version', sub_elem_version ) + elif isinstance( v, list ): + sub_elem = XmlET.SubElement( elem, k ) + # If v is a list, then it must be a list of tuples where the first # item is the tag and the second item is the text value. for v_tuple in v: if len( v_tuple ) == 2: @@ -74,6 +82,7 @@ v_elem = XmlET.SubElement( sub_elem, v_tag ) v_elem.text = v_text else: + sub_elem = XmlET.SubElement( elem, k ) sub_elem.text = v return elem return None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Feb '14

26 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/66aa6798e553/ Changeset: 66aa6798e553 Branch: stable User: jeremy goecks Date: 2014-02-26 20:05:50 Summary: Trackster: location parsing/interpretation fix. Affected #: 2 files diff -r 9c915a92142d3b796b0df82b8d097e5a5aae678f -r 66aa6798e55303abc40fbb585c75e8c77638cca3 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ad,af,ae){af=".group";n[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=n[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=n[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}n[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);n[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));n[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. 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ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){R.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:ad.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=(ae.type==="color"&&!ae.default_value?l.get_random_color():ae.default_value)});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input/>").attr({id:am,name:am}).val(ax).addClass("color-input").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.prefs.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.prefs.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(o);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ad,af,ae){af=".group";n[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=n[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=n[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}n[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);n[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));n[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){R.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:ad.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=(ae.type==="color"&&!ae.default_value?l.get_random_color():ae.default_value)});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input/>").attr({id:am,name:am}).val(ax).addClass("color-input").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.prefs.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.prefs.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(o);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file diff -r 9c915a92142d3b796b0df82b8d097e5a5aae678f -r 66aa6798e55303abc40fbb585c75e8c77638cca3 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1302,15 +1302,28 @@ view.reference_track.init(); } } - if (low !== undefined && high !== undefined) { - view.low = Math.max(low, 0); - view.high = Math.min(high, view.max_high); - } - else { - // Low and high undefined, so view is whole chome. + + // Resolve low, high. + if (low === undefined && high === undefined) { + // Both are undefined, so view is whole chromosome. view.low = 0; view.high = view.max_high; } + else { + // Low and/or high is defined. + view.low = (low !== undefined ? Math.max(low, 0) : 0); + if (high === undefined) { + // Center visualization around low. + // HACK: max resolution is currently 30 bases. + view.low = Math.max(view.low - 15, 0); + view.high = view.low + 30; + } + else { + // High is defined. + view.high = Math.min(high, view.max_high); + } + } + view.reset_overview(); view.request_redraw(); } @@ -1338,16 +1351,8 @@ // Parse new location. var chrom_pos = str.split(/\s+/), chrom = chrom_pos[0], - new_low = (chrom_pos[1] ? parseInt(chrom_pos[1], 10) : null), - new_high = (chrom_pos[2] ? parseInt(chrom_pos[2], 10) : null); - - // If no new high, new_low is the position of focus, so adjust low, high - // accordingly. - if (!new_high) { - // HACK: max resolution is 30 bases,so adjust low, high accordingly. - new_low = new_low - 15; - new_high = new_low + 15; - } + new_low = (chrom_pos[1] ? parseInt(chrom_pos[1], 10) : undefined), + new_high = (chrom_pos[2] ? parseInt(chrom_pos[2], 10) : undefined); this.change_chrom(chrom, new_low, new_high); }, https://bitbucket.org/galaxy/galaxy-central/commits/7225183f34d1/ Changeset: 7225183f34d1 User: jeremy goecks Date: 2014-02-26 20:06:19 Summary: Automated merge of stable to default. Affected #: 2 files diff -r ead13267cf213e10e76d2478b477b729e6f6129a -r 7225183f34d12b1ed3d879a85054ee98a7750729 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ad,af,ae){af=".group";n[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=n[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=n[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}n[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);n[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));n[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){R.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:ad.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=(ae.type==="color"&&!ae.default_value?l.get_random_color():ae.default_value)});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input/>").attr({id:am,name:am}).val(ax).addClass("color-input").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.prefs.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.prefs.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(o);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ad,af,ae){af=".group";n[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=n[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=n[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}n[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);n[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));n[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){R.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:ad.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=(ae.type==="color"&&!ae.default_value?l.get_random_color():ae.default_value)});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input/>").attr({id:am,name:am}).val(ax).addClass("color-input").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.prefs.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.prefs.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(o);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file diff -r ead13267cf213e10e76d2478b477b729e6f6129a -r 7225183f34d12b1ed3d879a85054ee98a7750729 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1302,15 +1302,28 @@ view.reference_track.init(); } } - if (low !== undefined && high !== undefined) { - view.low = Math.max(low, 0); - view.high = Math.min(high, view.max_high); - } - else { - // Low and high undefined, so view is whole chome. + + // Resolve low, high. + if (low === undefined && high === undefined) { + // Both are undefined, so view is whole chromosome. view.low = 0; view.high = view.max_high; } + else { + // Low and/or high is defined. + view.low = (low !== undefined ? Math.max(low, 0) : 0); + if (high === undefined) { + // Center visualization around low. + // HACK: max resolution is currently 30 bases. + view.low = Math.max(view.low - 15, 0); + view.high = view.low + 30; + } + else { + // High is defined. + view.high = Math.min(high, view.max_high); + } + } + view.reset_overview(); view.request_redraw(); } @@ -1338,16 +1351,8 @@ // Parse new location. var chrom_pos = str.split(/\s+/), chrom = chrom_pos[0], - new_low = (chrom_pos[1] ? parseInt(chrom_pos[1], 10) : null), - new_high = (chrom_pos[2] ? parseInt(chrom_pos[2], 10) : null); - - // If no new high, new_low is the position of focus, so adjust low, high - // accordingly. - if (!new_high) { - // HACK: max resolution is 30 bases,so adjust low, high accordingly. - new_low = new_low - 15; - new_high = new_low + 15; - } + new_low = (chrom_pos[1] ? parseInt(chrom_pos[1], 10) : undefined), + new_high = (chrom_pos[2] ? parseInt(chrom_pos[2], 10) : undefined); this.change_chrom(chrom, new_low, new_high); }, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: UI: Add click-event handler to tabs, Ui: Improve table wrapper, Charts: Hide tooltips on element hide, improve UI
by commits-noreply＠bitbucket.org 26 Feb '14

26 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ead13267cf21/ Changeset: ead13267cf21 User: guerler Date: 2014-02-26 19:09:23 Summary: UI: Add click-event handler to tabs, Ui: Improve table wrapper, Charts: Hide tooltips on element hide, improve UI Affected #: 8 files diff -r f26afae68417905a7f662671a18ca551f39ecf5f -r ead13267cf213e10e76d2478b477b729e6f6129a config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -61,9 +61,6 @@ // events var self = this; - this.config.on('change:current_view', function() { - self._showCurrent(); - }); this.config.on('change:title', function() { self._refreshTitle(); }); @@ -86,11 +83,6 @@ this.portlet.title('Charts' + title); }, - // current view - _showCurrent: function() { - - }, - // execute command execute: function(options) { }, diff -r f26afae68417905a7f662671a18ca551f39ecf5f -r ead13267cf213e10e76d2478b477b729e6f6129a config/plugins/visualizations/charts/static/library/table.js --- a/config/plugins/visualizations/charts/static/library/table.js +++ b/config/plugins/visualizations/charts/static/library/table.js @@ -33,7 +33,15 @@ this.options = Utils.merge(options, this.optionsDefault); // create new element - this.setElement(this._template(options)); + var $el = $(this._template(options)); + + // link sub-elements + this.$thead = $el.find('thead'); + this.$tbody = $el.find('tbody'); + this.$tmessage = $el.find('tmessage'); + + // set element + this.setElement($el); // initialize row this.row = $('<tr></tr>'); @@ -49,7 +57,7 @@ // header appendHeader: function() { // append header row - $(this.el).find('thead').append(this.row); + this.$thead.append(this.row); // row this.row = $('<tr></tr>'); @@ -74,14 +82,14 @@ // remove remove: function(id) { - $(this.el).find('#' + id).remove(); + this.$tbody.find('#' + id).remove(); this.row_count--; this._refresh(); }, // remove removeAll: function() { - $(this.el).find('tbody').html(''); + this.$tbody.html(''); this.row_count = 0; this._refresh(); }, @@ -89,18 +97,18 @@ // value value: function(new_value) { // get current id/value - this.before = this.$el.find('.current').attr('id'); + this.before = this.$tbody.find('.current').attr('id'); // check if new_value is defined if (new_value !== undefined) { - this.$el.find('tr').removeClass('current'); + this.$tbody.find('tr').removeClass('current'); if (new_value) { - this.$el.find('#' + new_value).addClass('current'); + this.$tbody.find('#' + new_value).addClass('current'); } } // get current id/value - var after = this.$el.find('.current').attr('id'); + var after = this.$tbody.find('.current').attr('id'); if(after === undefined) { return null; } else { @@ -114,6 +122,11 @@ } }, + // size + size: function() { + return this.$tbody.find('tr').length; + }, + // commit _commit: function(id, prepend) { // add @@ -121,9 +134,9 @@ // add row if (prepend) { - $(this.el).find('tbody').prepend(this.row); + this.$tbody.prepend(this.row); } else { - $(this.el).find('tbody').append(this.row); + this.$tbody.append(this.row); } // row @@ -161,9 +174,9 @@ // refresh _refresh: function() { if (this.row_count == 0) { - this.$el.find('tmessage').show(); + this.$tmessage.show(); } else { - this.$el.find('tmessage').hide(); + this.$tmessage.hide(); } }, diff -r f26afae68417905a7f662671a18ca551f39ecf5f -r ead13267cf213e10e76d2478b477b729e6f6129a config/plugins/visualizations/charts/static/library/ui.js --- a/config/plugins/visualizations/charts/static/library/ui.js +++ b/config/plugins/visualizations/charts/static/library/ui.js @@ -111,7 +111,7 @@ if (options.title) { str += '<div style="margin-right: 5px; margin-left: 5px;">' + '<i class="icon fa ' + options.icon + '"/> ' + - '<span style="position: relative; font-size: 0.8em; top: -1px;">' + options.title + '</span>' + + '<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">' + options.title + '</span>' + '</div>'; } else { str += '<i class="icon fa ' + options.icon + '"/>'; diff -r f26afae68417905a7f662671a18ca551f39ecf5f -r ead13267cf213e10e76d2478b477b729e6f6129a config/plugins/visualizations/charts/static/views/chart.js --- a/config/plugins/visualizations/charts/static/views/chart.js +++ b/config/plugins/visualizations/charts/static/views/chart.js @@ -96,6 +96,10 @@ // save chart self._saveChart(); + + // show viewport + self.hide(); + self.app.charts_view.$el.show(); } }), 'back' : new Ui.ButtonIcon({ @@ -103,7 +107,7 @@ tooltip : 'Return to Viewer', title : 'Return', onclick : function() { - self.$el.hide(); + self.hide(); self.app.charts_view.$el.show(); } }) @@ -161,7 +165,7 @@ self.tabs.showOperation('back'); }); this.app.charts.on('remove', function(chart) { - if (self.app.charts.length == 1) { + if (self.app.charts.length == 0) { self.tabs.hideOperation('back'); } }); @@ -187,6 +191,12 @@ this._resetChart(); }, + // hide + hide: function() { + $('.tooltip').hide(); + this.$el.hide(); + }, + // update _refreshLabels: function() { var self = this; @@ -275,12 +285,6 @@ // update chart model current.copy(this.chart); - - // hide - this.$el.hide(); - - // update main - this.app.charts_view.$el.show(); } }); diff -r f26afae68417905a7f662671a18ca551f39ecf5f -r ead13267cf213e10e76d2478b477b729e6f6129a config/plugins/visualizations/charts/static/views/charts.js --- a/config/plugins/visualizations/charts/static/views/charts.js +++ b/config/plugins/visualizations/charts/static/views/charts.js @@ -19,7 +19,7 @@ self.app.chart.copy(chart); // hide this element - self.$el.hide(); + self.hide(); // show chart view self.app.chart_view.$el.show(); @@ -44,17 +44,19 @@ height : 100, operations : { 'new' : new Ui.ButtonIcon({ - icon : 'fa-plus', - tooltip: 'Create', + icon : 'fa-magic', + tooltip: 'Create a new Chart', + title: 'New', onclick: function() { - self.$el.hide(); + self.hide(); self.app.chart.reset(); self.app.chart_view.$el.show(); } }), 'delete' : new Ui.ButtonIcon({ - icon : 'fa-minus', - tooltip: 'Delete', + icon : 'fa-trash-o', + tooltip: 'Delete this Chart', + title: 'Delete', onclick: function() { // check if element has been selected @@ -109,6 +111,12 @@ }); }, + // hide + hide: function() { + $('.tooltip').hide(); + this.$el.hide(); + }, + // append append : function($el) { this.$el.append(Utils.wrap('')); @@ -134,6 +142,15 @@ _removeChart: function(chart) { // remove from to table this.table.remove(chart.id); + + // check if table is empty + if (this.table.size() == 0) { + this.hide(); + this.app.chart_view.$el.show(); + } else { + // select available chart + this.table.value(this.app.charts.last().id); + } } }); diff -r f26afae68417905a7f662671a18ca551f39ecf5f -r ead13267cf213e10e76d2478b477b729e6f6129a config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -31,7 +31,8 @@ operations : { 'edit' : new Ui.ButtonIcon({ icon : 'fa-gear', - tooltip : 'Configure' + tooltip : 'Customize Chart', + title : 'Customize' }) } }); @@ -80,7 +81,7 @@ self.app.chart.copy(chart); // show edit - self.app.charts_view.$el.hide(); + self.app.charts_view.hide(); self.app.chart_view.$el.show(); }); @@ -89,6 +90,12 @@ } }, + // hide + hide: function() { + $('.tooltip').hide(); + this.$el.hide(); + }, + // add _addChart: function(chart) { // link this diff -r f26afae68417905a7f662671a18ca551f39ecf5f -r ead13267cf213e10e76d2478b477b729e6f6129a static/scripts/mvc/ui/ui-tabs.js --- a/static/scripts/mvc/ui/ui-tabs.js +++ b/static/scripts/mvc/ui/ui-tabs.js @@ -37,9 +37,14 @@ // create new element this.setElement($tabs); + // clear list + this.list = {}; + + // link this + var self = this; + // append operations if (this.options.operations) { - var self = this; $.each(this.options.operations, function(name, item) { item.$el.prop('id', name); self.$nav.append(item.$el); @@ -69,7 +74,7 @@ add: function(options) { // get tab id var id = options.id; - + // create tab object var tab = { $title : $(this._template_tab(options)), @@ -79,7 +84,7 @@ // add to list this.list[id] = tab; - + // add a new tab either before the add-new-tab tab or behind the last tab if (this.options.onnew) { this.$nav.find('#new-tab').before(tab.$title); @@ -102,12 +107,19 @@ if (options.ondel) { var $del_icon = tab.$title.find('#delete'); $del_icon.tooltip({title: 'Delete this tab', placement: 'bottom'}); - $del_icon.on('click', function(e) { + $del_icon.on('click', function() { $del_icon.tooltip('destroy'); options.ondel(); return false; }); } + + // add custom click event handler + if (options.onclick) { + tab.$title.on('click', function() { + options.onclick(); + }); + } }, // delete tab diff -r f26afae68417905a7f662671a18ca551f39ecf5f -r ead13267cf213e10e76d2478b477b729e6f6129a static/scripts/packed/mvc/ui/ui-tabs.js --- a/static/scripts/packed/mvc/ui/ui-tabs.js +++ b/static/scripts/packed/mvc/ui/ui-tabs.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(e){this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);if(this.options.operations){var d=this;$.each(this.options.operations,function(g,h){h.$el.prop("id",g);d.$nav.append(h.$el)})}if(this.options.onnew){var f=$(this._template_tab_new(this.options));this.$nav.append(f);f.tooltip({title:"Add a new tab",placement:"bottom"});f.on("click",function(g){f.tooltip("hide");d.options.onnew()})}},add:function(d){var f=d.id;var e={$title:$(this._template_tab(d)),$content:$(this._template_tab_content(d)),removable:d.ondel?true:false};this.list[f]=e;if(this.options.onnew){this.$nav.find("#new-tab").before(e.$title)}else{this.$nav.append(e.$title)}e.$content.append(d.$el);this.$content.append(e.$content);if(_.size(this.list)==1){e.$title.addClass("active");e.$content.addClass("active");this.first_tab=f}if(d.ondel){var c=e.$title.find("#delete");c.tooltip({title:"Delete this tab",placement:"bottom"});c.on("click",function(g){c.tooltip("destroy");d.ondel();return false})}},del:function(d){var c=this.list[d];c.$title.remove();c.$content.remove();delete c;if(this.first_tab==d){this.first_tab=null}if(this.first_tab!=null){this.show(this.first_tab)}},delRemovable:function(){for(var d in this.list){var c=this.list[d];if(c.removable){this.del(d)}}},show:function(c){this.$el.fadeIn("fast");this.visible=true;if(c){this.list[c].$title.find("a").tab("show")}},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,d){var c=this.list[e].$title.find("#text");if(d){c.html(d)}return c.html()},_template:function(c){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"/><div class="tab-content"/></div>'},_template_tab_new:function(c){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+c.title_new+"</a></li>"},_template_tab:function(d){var c='<li id="title-'+d.id+'"><a title="" href="#tab-'+d.id+'" data-toggle="tab" data-original-title=""><span id="text">'+d.title+"</span>";if(d.ondel){c+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'}c+="</a></li>";return c},_template_tab_content:function(c){return'<div id="tab-'+c.id+'" class="tab-pane"/>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(e){this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);this.list={};var d=this;if(this.options.operations){$.each(this.options.operations,function(g,h){h.$el.prop("id",g);d.$nav.append(h.$el)})}if(this.options.onnew){var f=$(this._template_tab_new(this.options));this.$nav.append(f);f.tooltip({title:"Add a new tab",placement:"bottom"});f.on("click",function(g){f.tooltip("hide");d.options.onnew()})}},add:function(d){var f=d.id;var e={$title:$(this._template_tab(d)),$content:$(this._template_tab_content(d)),removable:d.ondel?true:false};this.list[f]=e;if(this.options.onnew){this.$nav.find("#new-tab").before(e.$title)}else{this.$nav.append(e.$title)}e.$content.append(d.$el);this.$content.append(e.$content);if(_.size(this.list)==1){e.$title.addClass("active");e.$content.addClass("active");this.first_tab=f}if(d.ondel){var c=e.$title.find("#delete");c.tooltip({title:"Delete this tab",placement:"bottom"});c.on("click",function(){c.tooltip("destroy");d.ondel();return false})}if(d.onclick){e.$title.on("click",function(){d.onclick()})}},del:function(d){var c=this.list[d];c.$title.remove();c.$content.remove();delete c;if(this.first_tab==d){this.first_tab=null}if(this.first_tab!=null){this.show(this.first_tab)}},delRemovable:function(){for(var d in this.list){var c=this.list[d];if(c.removable){this.del(d)}}},show:function(c){this.$el.fadeIn("fast");this.visible=true;if(c){this.list[c].$title.find("a").tab("show")}},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,d){var c=this.list[e].$title.find("#text");if(d){c.html(d)}return c.html()},_template:function(c){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"/><div class="tab-content"/></div>'},_template_tab_new:function(c){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+c.title_new+"</a></li>"},_template_tab:function(d){var c='<li id="title-'+d.id+'"><a title="" href="#tab-'+d.id+'" data-toggle="tab" data-original-title=""><span id="text">'+d.title+"</span>";if(d.ondel){c+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'}c+="</a></li>";return c},_template_tab_content:function(c){return'<div id="tab-'+c.id+'" class="tab-pane"/>'}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Merge latest stable.
by commits-noreply＠bitbucket.org 26 Feb '14

26 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f26afae68417/ Changeset: f26afae68417 User: jmchilton Date: 2014-02-26 17:32:13 Summary: Merge latest stable. Affected #: 3 files diff -r 2295745a2888e74a518bdd6d7189d10031cbbf7d -r f26afae68417905a7f662671a18ca551f39ecf5f lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -207,6 +207,7 @@ self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) + self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) ) self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") diff -r 2295745a2888e74a518bdd6d7189d10031cbbf7d -r f26afae68417905a7f662671a18ca551f39ecf5f lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -21,6 +21,12 @@ eggs.require( "Paste" ) import paste +XSS_VULNERABLE_MIME_TYPES = [ + 'image/svg+xml', # Unfiltered by Galaxy and may contain JS that would be executed by some browsers. + 'application/xml', # Some browsers will evalute SVG embedded JS in such XML documents. +] +DEFAULT_MIME_TYPE = 'text/plain' # Vulnerable mime types will be replaced with this. + log = logging.getLogger(__name__) comptypes=[] # Is this being used anywhere, why was this here? -JohnC @@ -334,11 +340,12 @@ mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] ) except: mime = "text/plain" - trans.response.set_content_type( mime ) + self._clean_and_set_mime_type( trans, mime ) return open( file_path ) else: return trans.show_error_message( "Could not find '%s' on the extra files path %s." % ( filename, file_path ) ) - trans.response.set_content_type(data.get_mime()) + self._clean_and_set_mime_type( trans, data.get_mime() ) + trans.log_event( "Display dataset id: %s" % str( data.id ) ) from galaxy import datatypes #DBTODO REMOVE THIS AT REFACTOR if to_ext or isinstance(data.datatype, datatypes.binary.Binary): # Saving the file, or binary file @@ -624,6 +631,12 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.chunk.Base64ChunkDataProvider( dataset_source, **settings ) + def _clean_and_set_mime_type(self, trans, mime): + if mime.lower() in XSS_VULNERABLE_MIME_TYPES: + if not getattr( trans.app.config, "serve_xss_vulnerable_mimetypes", True ): + mime = DEFAULT_MIME_TYPE + trans.response.set_content_type( mime ) + @dataproviders.decorators.has_dataproviders class Text( Data ): diff -r 2295745a2888e74a518bdd6d7189d10031cbbf7d -r f26afae68417905a7f662671a18ca551f39ecf5f universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -507,6 +507,12 @@ # unaltered output. #sanitize_all_html = True +# By default Galaxy will serve non-HTML tool output that may potentially +# contain browser executable JavaScript content as plain text. This will for +# instance cause SVG datasets to not render properly and so may be disabled +# by setting the following option to True. +#serve_xss_vulnerable_mimetypes = False + # Debug enables access to various config options useful for development and # debugging: use_lint, use_profile, use_printdebug and use_interactive. It # also causes the files used by PBS/SGE (submission script, output, and error) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Feb '14

26 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3a3c1a860c30/ Changeset: 3a3c1a860c30 Branch: stable User: jmchilton Date: 2014-02-21 16:54:53 Summary: Do not serve non-HTML content that may contain JavaScript in such a way that web browsers execute it. This option will prevent Galaxy from correctly rendering SVG files generated from tools or uploaded by users and so can be disabled with by setting the new option serve_xss_vulnerable_mimetypes in universe_wsgi.ini to True. Thanks to Tobias Sargeant for pointing out this problem. Affected #: 3 files diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r 3a3c1a860c306df8d8176b0d2d455a5ed663f597 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -207,6 +207,7 @@ self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) + self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) ) self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r 3a3c1a860c306df8d8176b0d2d455a5ed663f597 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -21,6 +21,12 @@ eggs.require( "Paste" ) import paste +XSS_VULNERABLE_MIME_TYPES = [ + 'image/svg+xml', # Unfiltered by Galaxy and may contain JS that would be executed by some browsers. + 'application/xml', # Some browsers will evalute SVG embedded JS in such XML documents. +] +DEFAULT_MIME_TYPE = 'text/plain' # Vulnerable mime types will be replaced with this. + log = logging.getLogger(__name__) comptypes=[] # Is this being used anywhere, why was this here? -JohnC @@ -334,11 +340,12 @@ mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] ) except: mime = "text/plain" - trans.response.set_content_type( mime ) + self._clean_and_set_mime_type( trans, mime ) return open( file_path ) else: return trans.show_error_message( "Could not find '%s' on the extra files path %s." % ( filename, file_path ) ) - trans.response.set_content_type(data.get_mime()) + self._clean_and_set_mime_type( trans, data.get_mime() ) + trans.log_event( "Display dataset id: %s" % str( data.id ) ) from galaxy import datatypes #DBTODO REMOVE THIS AT REFACTOR if to_ext or isinstance(data.datatype, datatypes.binary.Binary): # Saving the file, or binary file @@ -624,6 +631,12 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.chunk.Base64ChunkDataProvider( dataset_source, **settings ) + def _clean_and_set_mime_type(self, trans, mime): + if mime.lower() in XSS_VULNERABLE_MIME_TYPES: + if not getattr( trans.app.config, "serve_xss_vulnerable_mimetypes", True ): + mime = DEFAULT_MIME_TYPE + trans.response.set_content_type( mime ) + @dataproviders.decorators.has_dataproviders class Text( Data ): diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r 3a3c1a860c306df8d8176b0d2d455a5ed663f597 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -497,6 +497,12 @@ # unaltered output. #sanitize_all_html = True +# By default Galaxy will serve non-HTML tool output that may potentially +# contain browser executable JavaScript content as plain text. This will for +# instance cause SVG datasets to not render properly and so may be disabled +# by setting the following option to True. +#serve_xss_vulnerable_mimetypes = False + # Debug enables access to various config options useful for development and # debugging: use_lint, use_profile, use_printdebug and use_interactive. It # also causes the files used by PBS/SGE (submission script, output, and error) https://bitbucket.org/galaxy/galaxy-central/commits/9c915a92142d/ Changeset: 9c915a92142d Branch: stable User: jmchilton Date: 2014-02-26 17:30:09 Summary: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #333) Disable rendering of user uploaded/tool generated SVG files. Affected #: 3 files diff -r 520c006a361987cf89f77c0e31e259a4a894ef60 -r 9c915a92142d3b796b0df82b8d097e5a5aae678f lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -207,6 +207,7 @@ self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) + self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) ) self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") diff -r 520c006a361987cf89f77c0e31e259a4a894ef60 -r 9c915a92142d3b796b0df82b8d097e5a5aae678f lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -21,6 +21,12 @@ eggs.require( "Paste" ) import paste +XSS_VULNERABLE_MIME_TYPES = [ + 'image/svg+xml', # Unfiltered by Galaxy and may contain JS that would be executed by some browsers. + 'application/xml', # Some browsers will evalute SVG embedded JS in such XML documents. +] +DEFAULT_MIME_TYPE = 'text/plain' # Vulnerable mime types will be replaced with this. + log = logging.getLogger(__name__) comptypes=[] # Is this being used anywhere, why was this here? -JohnC @@ -334,11 +340,12 @@ mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] ) except: mime = "text/plain" - trans.response.set_content_type( mime ) + self._clean_and_set_mime_type( trans, mime ) return open( file_path ) else: return trans.show_error_message( "Could not find '%s' on the extra files path %s." % ( filename, file_path ) ) - trans.response.set_content_type(data.get_mime()) + self._clean_and_set_mime_type( trans, data.get_mime() ) + trans.log_event( "Display dataset id: %s" % str( data.id ) ) from galaxy import datatypes #DBTODO REMOVE THIS AT REFACTOR if to_ext or isinstance(data.datatype, datatypes.binary.Binary): # Saving the file, or binary file @@ -624,6 +631,12 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.chunk.Base64ChunkDataProvider( dataset_source, **settings ) + def _clean_and_set_mime_type(self, trans, mime): + if mime.lower() in XSS_VULNERABLE_MIME_TYPES: + if not getattr( trans.app.config, "serve_xss_vulnerable_mimetypes", True ): + mime = DEFAULT_MIME_TYPE + trans.response.set_content_type( mime ) + @dataproviders.decorators.has_dataproviders class Text( Data ): diff -r 520c006a361987cf89f77c0e31e259a4a894ef60 -r 9c915a92142d3b796b0df82b8d097e5a5aae678f universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -497,6 +497,12 @@ # unaltered output. #sanitize_all_html = True +# By default Galaxy will serve non-HTML tool output that may potentially +# contain browser executable JavaScript content as plain text. This will for +# instance cause SVG datasets to not render properly and so may be disabled +# by setting the following option to True. +#serve_xss_vulnerable_mimetypes = False + # Debug enables access to various config options useful for development and # debugging: use_lint, use_profile, use_printdebug and use_interactive. It # also causes the files used by PBS/SGE (submission script, output, and error) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Feb '14

26 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/520c006a3619/ Changeset: 520c006a3619 Branch: stable User: carlfeberhard Date: 2014-02-26 16:52:56 Summary: Improve embedded item editing in pages: a) preserve empty paragraphs, b) when the cursor is in an embedded title and enter is pressed: create a new paragraph before the item, when the cursor is in an embedded content and enter is pressed: create a new paragraph after the item Affected #: 4 files diff -r cf7ff18cb3573c42c4bd77459112b40298df0ff6 -r 520c006a361987cf89f77c0e31e259a4a894ef60 static/scripts/galaxy.pages.js --- a/static/scripts/galaxy.pages.js +++ b/static/scripts/galaxy.pages.js @@ -452,14 +452,14 @@ // item_class='History'). var item_elt_id = item_info.iclass + "-" + item_id; var item_embed_html = - "<p><div id='" + item_elt_id + "' class='embedded-item " + item_info.singular.toLowerCase() + + "<div id='" + item_elt_id + "' class='embedded-item " + item_info.singular.toLowerCase() + " placeholder'> \ <p class='title'>Embedded Galaxy " + item_info.singular + " '" + item_name + "'</p> \ <p class='content'> \ [Do not edit this block; Galaxy will fill it in with the annotated " + item_info.singular.toLowerCase() + " when it is displayed.] \ </p> \ - </div></p>"; + </div>"; // Insert embedded item into document. wym.insert(" "); // Needed to prevent insertion from occurring in child element in webkit browsers. @@ -468,18 +468,18 @@ // TODO: can we fix this? // Due to oddities of wym.insert() [likely due to inserting a <div> and/or a complete paragraph], an // empty paragraph (or two!) may be included either before an embedded item. Remove these paragraphs. - $("#" + item_elt_id, wym._doc.body).each( function() { - // Remove previous empty paragraphs. - var removing = true; - while (removing) - { - var prev_elt = $(this).prev(); - if ( prev_elt.length != 0 && jQuery.trim(prev_elt.text()) == "" ) - prev_elt.remove(); - else - removing = false; - } - }); + //$("#" + item_elt_id, wym._doc.body).each( function() { + // // Remove previous empty paragraphs. + // var removing = true; + // while (removing) + // { + // var prev_elt = $(this).prev(); + // if ( prev_elt.length != 0 && jQuery.trim(prev_elt.text()) == "" ) + // prev_elt.remove(); + // else + // removing = false; + // } + //}); }); hide_modal(); @@ -706,4 +706,4 @@ // editor.dialog(Galaxy.DIALOG_EMBED_PAGE); //} }); -}); \ No newline at end of file +}); diff -r cf7ff18cb3573c42c4bd77459112b40298df0ff6 -r 520c006a361987cf89f77c0e31e259a4a894ef60 static/scripts/libs/jquery/jquery.wymeditor.js --- a/static/scripts/libs/jquery/jquery.wymeditor.js +++ b/static/scripts/libs/jquery/jquery.wymeditor.js @@ -3432,9 +3432,17 @@ replace(new RegExp('(\s*<('+tags+')>\s*){2}(.*)(\s*<\/\\2>\s*){2}' ,''),'<\$2>\$3<\$2>'); }; +// keep empty paragraphs +// from: http://forum.wymeditor.org/forum/viewtopic.php?f=2&t=711#p2430 +//WYMeditor.XhtmlSaxListener.prototype.removeEmptyTags = function(xhtml) +//{ +// return xhtml.replace(new RegExp('<('+this.block_tags.join("|").replace(/\|td/,'') +// .replace(/\|th/, '')+')>(<br \/>| | |\\s)*<\/\\1>' ,'g'),''); +//}; WYMeditor.XhtmlSaxListener.prototype.removeEmptyTags = function(xhtml) { - return xhtml.replace(new RegExp('<('+this.block_tags.join("|").replace(/\|td/,'').replace(/\|th/, '')+')>(<br \/>| | |\\s)*<\/\\1>' ,'g'),''); + return xhtml.replace(new RegExp('<('+this.block_tags.join("|").replace(/\|td/,'').replace(/\|p/,'') + .replace(/\|th/, '')+')>(<br \/>| | |\\s)*<\/\\1>' ,'g'),''); }; WYMeditor.XhtmlSaxListener.prototype.removeBrInPre = function(xhtml) @@ -4197,6 +4205,28 @@ var wym = WYMeditor.INSTANCES[this.title]; var container = null; + if( evt.keyCode === WYMeditor.KEY.ENTER ){ + container = wym.selected(); + if( container ){ + var $container = $( container ), + $parent = $container.parent(), + $embedded = $container.parents( '.embedded-item' ); + if( $embedded.size() ){ + // if the cursor is in the title, add a para before + var $newNode = $( '<p/>' ); + if( $container.hasClass( 'title' ) ){ + $embedded.before( $newNode ); + // if the cursor is in the content, add after + } else if( $container.hasClass( 'content' ) ){ + $embedded.after( $newNode ); + } + wym.setFocusToNode( $newNode.get(0) ); + // prevent the default - wym's chop the text and split it up into paras + return false; + } + } + } + if(evt.ctrlKey){ if(evt.keyCode == 66){ //CTRL+b => STRONG @@ -4227,27 +4257,27 @@ //'this' is the doc var wym = WYMeditor.INSTANCES[this.title]; - + wym._selected_image = null; var container = null; if(evt.keyCode == 13 && !evt.shiftKey) { - + //RETURN key //cleanup <br><br> between paragraphs jQuery(wym._doc.body).children(WYMeditor.BR).remove(); } - + else if(evt.keyCode != 8 && evt.keyCode != 17 && evt.keyCode != 46 && evt.keyCode != 224 && !evt.metaKey && !evt.ctrlKey) { - + //NOT BACKSPACE, NOT DELETE, NOT CTRL, NOT COMMAND //text nodes replaced by P - + container = wym.selected(); var name = container.tagName.toLowerCase(); @@ -4301,7 +4331,7 @@ return; } } - + this.output += this.helper.tag(tag, attributes, true); }; @@ -4343,9 +4373,9 @@ this._iframe = iframe; this._doc = iframe.contentWindow.document; - + //add css rules from options - var styles = this._doc.styleSheets[0]; + var styles = this._doc.styleSheets[0]; var aCss = eval(this._options.editorStyles); this.addCssRules(this._doc, aCss); @@ -4354,28 +4384,28 @@ //set the text direction jQuery('html', this._doc).attr('dir', this._options.direction); - + //init designMode this._doc.designMode = "on"; //init html value this.html(this._wym._html); - + //pre-bind functions if(jQuery.isFunction(this._options.preBind)) this._options.preBind(this); - + //bind external events this._wym.bindEvents(); - + //bind editor keydown events jQuery(this._doc).bind("keydown", this.keydown); - + //bind editor events jQuery(this._doc).bind("keyup", this.keyup); - + //post-init functions if(jQuery.isFunction(this._options.postInit)) this._options.postInit(this); - + //add event listeners to doc elements, e.g. images this.listen(); }; @@ -4384,7 +4414,7 @@ if(param) this._doc.execCommand(cmd,false,param); else this._doc.execCommand(cmd); - + this.listen(); }; @@ -4406,7 +4436,7 @@ //keydown handler WYMeditor.WymClassOpera.prototype.keydown = function(evt) { - + //'this' is the doc var wym = WYMeditor.INSTANCES[this.title]; var sel = wym._iframe.contentWindow.getSelection(); @@ -4470,12 +4500,12 @@ this._iframe = iframe; this._doc = iframe.contentDocument; - + //add css rules from options - - var styles = this._doc.styleSheets[0]; + + var styles = this._doc.styleSheets[0]; var aCss = eval(this._options.editorStyles); - + this.addCssRules(this._doc, aCss); this._doc.title = this._wym._index; @@ -4485,25 +4515,25 @@ //init designMode this._doc.designMode = "on"; - + //init html value this.html(this._wym._html); - + //pre-bind functions if(jQuery.isFunction(this._options.preBind)) this._options.preBind(this); - + //bind external events this._wym.bindEvents(); - + //bind editor keydown events jQuery(this._doc).bind("keydown", this.keydown); - + //bind editor keyup events jQuery(this._doc).bind("keyup", this.keyup); - + //post-init functions if(jQuery.isFunction(this._options.postInit)) this._options.postInit(this); - + //add event listeners to doc elements, e.g. images this.listen(); }; @@ -4513,17 +4543,17 @@ if(!this.selected()) return(false); switch(cmd) { - + case WYMeditor.INDENT: case WYMeditor.OUTDENT: - - var focusNode = this.selected(); + + var focusNode = this.selected(); var sel = this._iframe.contentWindow.getSelection(); var anchorNode = sel.anchorNode; if(anchorNode.nodeName == "#text") anchorNode = anchorNode.parentNode; - + focusNode = this.findUp(focusNode, WYMeditor.BLOCKS); anchorNode = this.findUp(anchorNode, WYMeditor.BLOCKS); - + if(focusNode && focusNode == anchorNode && focusNode.tagName.toLowerCase() == WYMeditor.LI) { @@ -4548,13 +4578,13 @@ if(container) jQuery(container).replaceWith(jQuery(container).html()); break; - + default: if(param) this._doc.execCommand(cmd,'',param); else this._doc.execCommand(cmd,'',null); } - + //set to P if parent = BODY var container = this.selected(); if(container && container.tagName.toLowerCase() == WYMeditor.BODY) @@ -4586,9 +4616,31 @@ //keydown handler, mainly used for keyboard shortcuts WYMeditor.WymClassSafari.prototype.keydown = function(evt) { - + //'this' is the doc var wym = WYMeditor.INSTANCES[this.title]; + + if( evt.keyCode === WYMeditor.KEY.ENTER ){ + var container = wym.selected(); + if( container ){ + var $container = $( container ), + $parent = $container.parent(), + $embedded = $container.parents( '.embedded-item' ); + if( $embedded.size() ){ + // if the cursor is in the title, add a para before + var $newNode = $( '<p/>' ); + if( $container.hasClass( 'title' ) ){ + $embedded.before( $newNode ); + // if the cursor is in the content, add after + } else if( $container.hasClass( 'content' ) ){ + $embedded.after( $newNode ); + } + wym.setFocusToNode( $newNode.get(0) ); + // prevent the default - wym's chop the text and split it up into paras + return false; + } + } + } if(evt.ctrlKey){ if(evt.keyCode == 66){ diff -r cf7ff18cb3573c42c4bd77459112b40298df0ff6 -r 520c006a361987cf89f77c0e31e259a4a894ef60 static/scripts/packed/galaxy.pages.js --- a/static/scripts/packed/galaxy.pages.js +++ b/static/scripts/packed/galaxy.pages.js @@ -1,1 +1,1 @@ -var Galaxy={ITEM_HISTORY:"item_history",ITEM_DATASET:"item_dataset",ITEM_WORKFLOW:"item_workflow",ITEM_PAGE:"item_page",ITEM_VISUALIZATION:"item_visualization",DIALOG_HISTORY_LINK:"link_history",DIALOG_DATASET_LINK:"link_dataset",DIALOG_WORKFLOW_LINK:"link_workflow",DIALOG_PAGE_LINK:"link_page",DIALOG_VISUALIZATION_LINK:"link_visualization",DIALOG_EMBED_HISTORY:"embed_history",DIALOG_EMBED_DATASET:"embed_dataset",DIALOG_EMBED_WORKFLOW:"embed_workflow",DIALOG_EMBED_PAGE:"embed_page",DIALOG_EMBED_VISUALIZATION:"embed_visualization",DIALOG_HISTORY_ANNOTATE:"history_annotate",};function init_galaxy_elts(a){$(".annotation",a._doc.body).each(function(){$(this).click(function(){var b=a._doc.createRange();b.selectNodeContents(this);var d=window.getSelection();d.removeAllRanges();d.addRange(b);var c=""})})}function get_item_info(d){var f,c,b;switch(d){case (Galaxy.ITEM_HISTORY):f="History";c="Histories";b="history";item_class="History";break;case (Galaxy.ITEM_DATASET):f="Dataset";c="Datasets";b="dataset";item_class="HistoryDatasetAssociation";break;case (Galaxy.ITEM_WORKFLOW):f="Workflow";c="Workflows";b="workflow";item_class="StoredWorkflow";break;case (Galaxy.ITEM_PAGE):f="Page";c="Pages";b="page";item_class="Page";break;case (Galaxy.ITEM_VISUALIZATION):f="Visualization";c="Visualizations";b="visualization";item_class="Visualization";break}var e="list_"+c.toLowerCase()+"_for_selection";var a=list_objects_url.replace("LIST_ACTION",e);return{singular:f,plural:c,controller:b,iclass:item_class,list_ajax_url:a}}function make_item_importable(a,c,b){ajax_url=set_accessible_url.replace("ITEM_CONTROLLER",a);$.ajax({type:"POST",url:ajax_url,data:{id:c,accessible:"True"},error:function(){alert("Making "+b+" accessible failed")}})}WYMeditor.editor.prototype.dialog=function(i,e,g){var a=this;var b=a.uniqueStamp();var f=a.selected();function h(){$("#set_link_id").click(function(){$("#link_attribute_label").text("ID/Name");var k=$(".wym_href");k.addClass("wym_id").removeClass("wym_href");if(f){k.val($(f).attr("id"))}$(this).remove()})}if(i==WYMeditor.DIALOG_LINK){if(f){$(a._options.hrefSelector).val($(f).attr(WYMeditor.HREF));$(a._options.srcSelector).val($(f).attr(WYMeditor.SRC));$(a._options.titleSelector).val($(f).attr(WYMeditor.TITLE));$(a._options.altSelector).val($(f).attr(WYMeditor.ALT))}var c,d;if(f){c=$(f).attr("href");if(c==undefined){c=""}d=$(f).attr("title");if(d==undefined){d=""}}show_modal("Create Link","<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='"+c+"' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='"+d+"' size='40' /></div><div>",{"Make link":function(){var m=$(a._options.hrefSelector).val()||"",k=$(".wym_id").val()||"",n=$(a._options.titleSelector).val()||"";if(m||k){a._exec(WYMeditor.CREATE_LINK,b);var l=$("a[href="+b+"]",a._doc.body);l.attr(WYMeditor.HREF,m).attr(WYMeditor.TITLE,n).attr("id",k);if(l.text().indexOf("wym-")===0){l.text(n)}}hide_modal()},Cancel:function(){hide_modal()}},{},h)}if(i==WYMeditor.DIALOG_IMAGE){if(a._selected_image){$(a._options.dialogImageSelector+" "+a._options.srcSelector).val($(a._selected_image).attr(WYMeditor.SRC));$(a._options.dialogImageSelector+" "+a._options.titleSelector).val($(a._selected_image).attr(WYMeditor.TITLE));$(a._options.dialogImageSelector+" "+a._options.altSelector).val($(a._selected_image).attr(WYMeditor.ALT))}show_modal("Image","<div class='row'><label>URL</label><br><input type='text' class='wym_src' value='' size='40' /></div><div class='row'><label>Alt text</label><br><input type='text' class='wym_alt' value='' size='40' /></div><div class='row'><label>Title</label><br><input type='text' class='wym_title' value='' size='40' /></div>",{Insert:function(){var k=$(a._options.srcSelector).val();if(k.length>0){a._exec(WYMeditor.INSERT_IMAGE,b);$("img[src$="+b+"]",a._doc.body).attr(WYMeditor.SRC,k).attr(WYMeditor.TITLE,$(a._options.titleSelector).val()).attr(WYMeditor.ALT,$(a._options.altSelector).val())}hide_modal()},Cancel:function(){hide_modal()}});return}if(i==WYMeditor.DIALOG_TABLE){show_modal("Table","<div class='row'><label>Caption</label><br><input type='text' class='wym_caption' value='' size='40' /></div><div class='row'><label>Summary</label><br><input type='text' class='wym_summary' value='' size='40' /></div><div class='row'><label>Number Of Rows<br></label><input type='text' class='wym_rows' value='3' size='3' /></div><div class='row'><label>Number Of Cols<br></label><input type='text' class='wym_cols' value='2' size='3' /></div>",{Insert:function(){var o=$(a._options.rowsSelector).val();var r=$(a._options.colsSelector).val();if(o>0&&r>0){var n=a._doc.createElement(WYMeditor.TABLE);var l=null;var q=null;var k=$(a._options.captionSelector).val();var p=n.createCaption();p.innerHTML=k;for(x=0;x<o;x++){l=n.insertRow(x);for(y=0;y<r;y++){l.insertCell(y)}}$(n).attr("summary",$(a._options.summarySelector).val());var m=$(a.findUp(a.container(),WYMeditor.MAIN_CONTAINERS)).get(0);if(!m||!m.parentNode){$(a._doc.body).append(n)}else{$(m).after(n)}}hide_modal()},Cancel:function(){hide_modal()}})}if(i==Galaxy.DIALOG_HISTORY_LINK||i==Galaxy.DIALOG_DATASET_LINK||i==Galaxy.DIALOG_WORKFLOW_LINK||i==Galaxy.DIALOG_PAGE_LINK||i==Galaxy.DIALOG_VISUALIZATION_LINK){var j;switch(i){case (Galaxy.DIALOG_HISTORY_LINK):j=get_item_info(Galaxy.ITEM_HISTORY);break;case (Galaxy.DIALOG_DATASET_LINK):j=get_item_info(Galaxy.ITEM_DATASET);break;case (Galaxy.DIALOG_WORKFLOW_LINK):j=get_item_info(Galaxy.ITEM_WORKFLOW);break;case (Galaxy.DIALOG_PAGE_LINK):j=get_item_info(Galaxy.ITEM_PAGE);break;case 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Galaxy={ITEM_HISTORY:"item_history",ITEM_DATASET:"item_dataset",ITEM_WORKFLOW:"item_workflow",ITEM_PAGE:"item_page",ITEM_VISUALIZATION:"item_visualization",DIALOG_HISTORY_LINK:"link_history",DIALOG_DATASET_LINK:"link_dataset",DIALOG_WORKFLOW_LINK:"link_workflow",DIALOG_PAGE_LINK:"link_page",DIALOG_VISUALIZATION_LINK:"link_visualization",DIALOG_EMBED_HISTORY:"embed_history",DIALOG_EMBED_DATASET:"embed_dataset",DIALOG_EMBED_WORKFLOW:"embed_workflow",DIALOG_EMBED_PAGE:"embed_page",DIALOG_EMBED_VISUALIZATION:"embed_visualization",DIALOG_HISTORY_ANNOTATE:"history_annotate",};function init_galaxy_elts(a){$(".annotation",a._doc.body).each(function(){$(this).click(function(){var b=a._doc.createRange();b.selectNodeContents(this);var d=window.getSelection();d.removeAllRanges();d.addRange(b);var c=""})})}function get_item_info(d){var f,c,b;switch(d){case (Galaxy.ITEM_HISTORY):f="History";c="Histories";b="history";item_class="History";break;case 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Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(c);make_popupmenu(c,{"Insert History Link":function(){d.dialog(Galaxy.DIALOG_HISTORY_LINK)},"Insert Dataset Link":function(){d.dialog(Galaxy.DIALOG_DATASET_LINK)},"Insert Workflow Link":function(){d.dialog(Galaxy.DIALOG_WORKFLOW_LINK)},"Insert Page Link":function(){d.dialog(Galaxy.DIALOG_PAGE_LINK)},"Insert Visualization Link":function(){d.dialog(Galaxy.DIALOG_VISUALIZATION_LINK)},});var e=$("<div><a id='embed-galaxy-object' class='action-button popup' href='#'>Embed Galaxy Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(e);make_popupmenu(e,{"Embed History":function(){d.dialog(Galaxy.DIALOG_EMBED_HISTORY)},"Embed Dataset":function(){d.dialog(Galaxy.DIALOG_EMBED_DATASET)},"Embed Workflow":function(){d.dialog(Galaxy.DIALOG_EMBED_WORKFLOW)},"Embed Visualization":function(){d.dialog(Galaxy.DIALOG_EMBED_VISUALIZATION)},})}); \ No newline at end of file diff -r cf7ff18cb3573c42c4bd77459112b40298df0ff6 -r 520c006a361987cf89f77c0e31e259a4a894ef60 static/scripts/packed/libs/jquery/jquery.wymeditor.js --- a/static/scripts/packed/libs/jquery/jquery.wymeditor.js +++ b/static/scripts/packed/libs/jquery/jquery.wymeditor.js @@ -1,1 +1,1 @@ -if(!WYMeditor){var WYMeditor={}}(function(){if(!window.console||!console.firebug){var b=["log","debug","info","warn","error","assert","dir","dirxml","group","groupEnd","time","timeEnd","count","trace","profile","profileEnd"];WYMeditor.console={};for(var a=0;a<b.length;++a){WYMeditor.console[b[a]]=function(){}}}else{WYMeditor.console=window.console}})();jQuery.extend(WYMeditor,{VERSION:"0.5-rc1",INSTANCES:[],STRINGS:[],SKINS:[],NAME:"name",INDEX:"{Wym_Index}",WYM_INDEX:"wym_index",BASE_PATH:"{Wym_Base_Path}",CSS_PATH:"{Wym_Css_Path}",WYM_PATH:"{Wym_Wym_Path}",SKINS_DEFAULT_PATH:"skins/",SKINS_DEFAULT_CSS:"skin.css",SKINS_DEFAULT_JS:"skin.js",LANG_DEFAULT_PATH:"lang/",IFRAME_BASE_PATH:"{Wym_Iframe_Base_Path}",IFRAME_DEFAULT:"iframe/default/",JQUERY_PATH:"{Wym_Jquery_Path}",DIRECTION:"{Wym_Direction}",LOGO:"{Wym_Logo}",TOOLS:"{Wym_Tools}",TOOLS_ITEMS:"{Wym_Tools_Items}",TOOL_NAME:"{Wym_Tool_Name}",TOOL_TITLE:"{Wym_Tool_Title}",TOOL_CLASS:"{Wym_Tool_Class}",CLASSES:"{Wym_Classes}",CLASSES_ITEMS:"{Wym_Classes_Items}",CLASS_NAME:"{Wym_Class_Name}",CLASS_TITLE:"{Wym_Class_Title}",CONTAINERS:"{Wym_Containers}",CONTAINERS_ITEMS:"{Wym_Containers_Items}",CONTAINER_NAME:"{Wym_Container_Name}",CONTAINER_TITLE:"{Wym_Containers_Title}",CONTAINER_CLASS:"{Wym_Container_Class}",HTML:"{Wym_Html}",IFRAME:"{Wym_Iframe}",STATUS:"{Wym_Status}",DIALOG_TITLE:"{Wym_Dialog_Title}",DIALOG_BODY:"{Wym_Dialog_Body}",STRING:"string",BODY:"body",DIV:"div",P:"p",H1:"h1",H2:"h2",H3:"h3",H4:"h4",H5:"h5",H6:"h6",PRE:"pre",BLOCKQUOTE:"blockquote",A:"a",BR:"br",IMG:"img",TABLE:"table",TD:"td",TH:"th",UL:"ul",OL:"ol",LI:"li",CLASS:"class",HREF:"href",SRC:"src",TITLE:"title",ALT:"alt",DIALOG_LINK:"Link",DIALOG_IMAGE:"Image",DIALOG_TABLE:"Table",DIALOG_PASTE:"Paste_From_Word",BOLD:"Bold",ITALIC:"Italic",CREATE_LINK:"CreateLink",INSERT_IMAGE:"InsertImage",INSERT_TABLE:"InsertTable",INSERT_HTML:"InsertHTML",PASTE:"Paste",INDENT:"Indent",OUTDENT:"Outdent",TOGGLE_HTML:"ToggleHtml",FORMAT_BLOCK:"FormatBlock",PREVIEW:"Preview",UNLINK:"Unlink",INSERT_UNORDEREDLIST:"InsertUnorderedList",INSERT_ORDEREDLIST:"InsertOrderedList",MAIN_CONTAINERS:new Array("p","h1","h2","h3","h4","h5","h6","pre","blockquote"),BLOCKS:new Array("address","blockquote","div","dl","fieldset","form","h1","h2","h3","h4","h5","h6","hr","noscript","ol","p","pre","table","ul","dd","dt","li","tbody","td","tfoot","th","thead","tr"),KEY:{BACKSPACE:8,ENTER:13,END:35,HOME:36,LEFT:37,UP:38,RIGHT:39,DOWN:40,CURSOR:new Array(37,38,39,40),DELETE:46},NODE:{ELEMENT:1,ATTRIBUTE:2,TEXT:3},editor:function(b,a){this._index=WYMeditor.INSTANCES.push(this)-1;this._element=b;this._options=a;this._html=jQuery(b).val();if(this._options.html){this._html=this._options.html}this._options.basePath=this._options.basePath||this.computeBasePath();this._options.skinPath=this._options.skinPath||this._options.basePath+WYMeditor.SKINS_DEFAULT_PATH+this._options.skin+"/";this._options.wymPath=this._options.wymPath||this.computeWymPath();this._options.langPath=this._options.langPath||this._options.basePath+WYMeditor.LANG_DEFAULT_PATH;this._options.iframeBasePath=this._options.iframeBasePath||this._options.basePath+WYMeditor.IFRAME_DEFAULT;this._options.jQueryPath=this._options.jQueryPath||this.computeJqueryPath();this.init()}});jQuery.fn.wymeditor=function(a){a=jQuery.extend({html:"",basePath:false,skinPath:false,wymPath:false,iframeBasePath:false,jQueryPath:false,styles:false,stylesheet:false,skin:"default",initSkin:true,loadSkin:true,lang:"en",direction:"ltr",boxHtml:"<div class='wym_box'><div class='wym_area_top'>"+WYMeditor.TOOLS+"</div><div class='wym_area_left'></div><div class='wym_area_right'>"+WYMeditor.CONTAINERS+WYMeditor.CLASSES+"</div><div class='wym_area_main'>"+WYMeditor.HTML+WYMeditor.IFRAME+WYMeditor.STATUS+"</div><div class='wym_area_bottom'>"+WYMeditor.LOGO+"</div></div>",logoHtml:"<a class='wym_wymeditor_link' href='http://www.wymeditor.org/'>WYMeditor</a>",iframeHtml:"<div class='wym_iframe wym_section'><iframe src='/page/get_editor_iframe' onload='this.contentWindow.parent.WYMeditor.INSTANCES["+WYMeditor.INDEX+"].initIframe(this)'></iframe></div>",editorStyles:[],toolsHtml:"<div class='wym_tools wym_section'><h2>{Tools}</h2><ul>"+WYMeditor.TOOLS_ITEMS+"</ul></div>",toolsItemHtml:"<li class='"+WYMeditor.TOOL_CLASS+"'><a href='#' name='"+WYMeditor.TOOL_NAME+"' title='"+WYMeditor.TOOL_TITLE+"'>"+WYMeditor.TOOL_TITLE+"</a></li>",toolsItems:[{name:"Bold",title:"Strong",css:"wym_tools_strong"},{name:"Italic",title:"Emphasis",css:"wym_tools_emphasis"},{name:"Superscript",title:"Superscript",css:"wym_tools_superscript"},{name:"Subscript",title:"Subscript",css:"wym_tools_subscript"},{name:"InsertOrderedList",title:"Ordered_List",css:"wym_tools_ordered_list"},{name:"InsertUnorderedList",title:"Unordered_List",css:"wym_tools_unordered_list"},{name:"Indent",title:"Indent",css:"wym_tools_indent"},{name:"Outdent",title:"Outdent",css:"wym_tools_outdent"},{name:"Undo",title:"Undo",css:"wym_tools_undo"},{name:"Redo",title:"Redo",css:"wym_tools_redo"},{name:"CreateLink",title:"Link",css:"wym_tools_link"},{name:"Unlink",title:"Unlink",css:"wym_tools_unlink"},{name:"InsertImage",title:"Image",css:"wym_tools_image"},{name:"InsertTable",title:"Table",css:"wym_tools_table"},{name:"Paste",title:"Paste_From_Word",css:"wym_tools_paste"},{name:"ToggleHtml",title:"HTML",css:"wym_tools_html"},{name:"Preview",title:"Preview",css:"wym_tools_preview"}],containersHtml:"<div class='wym_containers wym_section'><h2>{Containers}</h2><ul>"+WYMeditor.CONTAINERS_ITEMS+"</ul></div>",containersItemHtml:"<li class='"+WYMeditor.CONTAINER_CLASS+"'><a href='#' name='"+WYMeditor.CONTAINER_NAME+"'>"+WYMeditor.CONTAINER_TITLE+"</a></li>",containersItems:[{name:"P",title:"Paragraph",css:"wym_containers_p"},{name:"H1",title:"Heading_1",css:"wym_containers_h1"},{name:"H2",title:"Heading_2",css:"wym_containers_h2"},{name:"H3",title:"Heading_3",css:"wym_containers_h3"},{name:"H4",title:"Heading_4",css:"wym_containers_h4"},{name:"H5",title:"Heading_5",css:"wym_containers_h5"},{name:"H6",title:"Heading_6",css:"wym_containers_h6"},{name:"PRE",title:"Preformatted",css:"wym_containers_pre"},{name:"BLOCKQUOTE",title:"Blockquote",css:"wym_containers_blockquote"},{name:"TH",title:"Table_Header",css:"wym_containers_th"}],classesHtml:"<div class='wym_classes wym_section'><h2>{Classes}</h2><ul>"+WYMeditor.CLASSES_ITEMS+"</ul></div>",classesItemHtml:"<li><a href='#' name='"+WYMeditor.CLASS_NAME+"'>"+WYMeditor.CLASS_TITLE+"</a></li>",classesItems:[],statusHtml:"<div class='wym_status wym_section'><h2>{Status}</h2></div>",htmlHtml:"<div class='wym_html wym_section'><h2>{Source_Code}</h2><textarea class='wym_html_val'></textarea></div>",boxSelector:".wym_box",toolsSelector:".wym_tools",toolsListSelector:" ul",containersSelector:".wym_containers",classesSelector:".wym_classes",htmlSelector:".wym_html",iframeSelector:".wym_iframe iframe",iframeBodySelector:".wym_iframe",statusSelector:".wym_status",toolSelector:".wym_tools a",containerSelector:".wym_containers a",classSelector:".wym_classes a",htmlValSelector:".wym_html_val",hrefSelector:".wym_href",srcSelector:".wym_src",titleSelector:".wym_title",altSelector:".wym_alt",textSelector:".wym_text",rowsSelector:".wym_rows",colsSelector:".wym_cols",captionSelector:".wym_caption",summarySelector:".wym_summary",submitSelector:".wym_submit",cancelSelector:".wym_cancel",previewSelector:"",dialogTypeSelector:".wym_dialog_type",dialogLinkSelector:".wym_dialog_link",dialogImageSelector:".wym_dialog_image",dialogTableSelector:".wym_dialog_table",dialogPasteSelector:".wym_dialog_paste",dialogPreviewSelector:".wym_dialog_preview",updateSelector:".wymupdate",updateEvent:"click",dialogFeatures:"menubar=no,titlebar=no,toolbar=no,resizable=no,width=560,height=300,top=0,left=0",dialogFeaturesPreview:"menubar=no,titlebar=no,toolbar=no,resizable=no,scrollbars=yes,width=560,height=300,top=0,left=0",dialogHtml:"<!DOCTYPE html PUBLIC '-//W3C//DTD XHTML 1.0 Strict//EN' 'http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd'><html dir='"+WYMeditor.DIRECTION+"'><head><link rel='stylesheet' type='text/css' media='screen' href='"+WYMeditor.CSS_PATH+"' /><title>"+WYMeditor.DIALOG_TITLE+"</title><script type='text/javascript' src='"+WYMeditor.JQUERY_PATH+"'><\/script><script type='text/javascript' src='"+WYMeditor.WYM_PATH+"'><\/script></head>"+WYMeditor.DIALOG_BODY+"</html>",dialogLinkHtml:"<body class='wym_dialog wym_dialog_link' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><fieldset><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_LINK+"' /><legend>{Link}</legend><div class='row'><label>{URL}</label><input type='text' class='wym_href' value='' size='40' /></div><div class='row'><label>{Title}</label><input type='text' class='wym_title' value='' size='40' /></div><div class='row row-indent'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogImageHtml:"<body class='wym_dialog wym_dialog_image' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><fieldset><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_IMAGE+"' /><legend>{Image}</legend><div class='row'><label>{URL}</label><input type='text' class='wym_src' value='' size='40' /></div><div class='row'><label>{Alternative_Text}</label><input type='text' class='wym_alt' value='' size='40' /></div><div class='row'><label>{Title}</label><input type='text' class='wym_title' value='' size='40' /></div><div class='row row-indent'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogTableHtml:"<body class='wym_dialog wym_dialog_table' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><fieldset><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_TABLE+"' /><legend>{Table}</legend><div class='row'><label>{Caption}</label><input type='text' class='wym_caption' value='' size='40' /></div><div class='row'><label>{Summary}</label><input type='text' class='wym_summary' value='' size='40' /></div><div class='row'><label>{Number_Of_Rows}</label><input type='text' class='wym_rows' value='3' size='3' /></div><div class='row'><label>{Number_Of_Cols}</label><input type='text' class='wym_cols' value='2' size='3' /></div><div class='row row-indent'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogPasteHtml:"<body class='wym_dialog wym_dialog_paste' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_PASTE+"' /><fieldset><legend>{Paste_From_Word}</legend><div class='row'><textarea class='wym_text' rows='10' cols='50'></textarea></div><div class='row'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogPreviewHtml:"<body class='wym_dialog wym_dialog_preview' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'></body>",dialogStyles:[],stringDelimiterLeft:"{",stringDelimiterRight:"}",preInit:null,preBind:null,postInit:null,preInitDialog:null,postInitDialog:null},a);return this.each(function(){new WYMeditor.editor(jQuery(this),a)})};jQuery.extend({wymeditors:function(a){return(WYMeditor.INSTANCES[a])}});WYMeditor.editor.prototype.init=function(){if(jQuery.browser.msie){var WymClass=new WYMeditor.WymClassExplorer(this)}else{if(jQuery.browser.mozilla){var WymClass=new WYMeditor.WymClassMozilla(this)}else{if(jQuery.browser.opera){var WymClass=new WYMeditor.WymClassOpera(this)}else{if(jQuery.browser.safari||jQuery.browser.chrome){var WymClass=new WYMeditor.WymClassSafari(this)}}}}if(WymClass){if(jQuery.isFunction(this._options.preInit)){this._options.preInit(this)}var SaxListener=new WYMeditor.XhtmlSaxListener();jQuery.extend(SaxListener,WymClass);this.parser=new WYMeditor.XhtmlParser(SaxListener);if(this._options.styles||this._options.stylesheet){this.configureEditorUsingRawCss()}this.helper=new WYMeditor.XmlHelper();for(var prop in WymClass){this[prop]=WymClass[prop]}this._box=jQuery(this._element).hide().after(this._options.boxHtml).next().addClass("wym_box_"+this._index);if(jQuery.isFunction(jQuery.fn.data)){jQuery.data(this._box.get(0),WYMeditor.WYM_INDEX,this._index);jQuery.data(this._element.get(0),WYMeditor.WYM_INDEX,this._index)}var h=WYMeditor.Helper;var iframeHtml=this._options.iframeHtml;iframeHtml=h.replaceAll(iframeHtml,WYMeditor.INDEX,this._index);iframeHtml=h.replaceAll(iframeHtml,WYMeditor.IFRAME_BASE_PATH,this._options.iframeBasePath);var boxHtml=jQuery(this._box).html();boxHtml=h.replaceAll(boxHtml,WYMeditor.LOGO,this._options.logoHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.TOOLS,this._options.toolsHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.CONTAINERS,this._options.containersHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.CLASSES,this._options.classesHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.HTML,this._options.htmlHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.IFRAME,iframeHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.STATUS,this._options.statusHtml);var aTools=eval(this._options.toolsItems);var sTools="";for(var i=0;i<aTools.length;i++){var oTool=aTools[i];if(oTool.name&&oTool.title){var sTool=this._options.toolsItemHtml}var sTool=h.replaceAll(sTool,WYMeditor.TOOL_NAME,oTool.name);sTool=h.replaceAll(sTool,WYMeditor.TOOL_TITLE,this._options.stringDelimiterLeft+oTool.title+this._options.stringDelimiterRight);sTool=h.replaceAll(sTool,WYMeditor.TOOL_CLASS,oTool.css);sTools+=sTool}boxHtml=h.replaceAll(boxHtml,WYMeditor.TOOLS_ITEMS,sTools);var aClasses=eval(this._options.classesItems);var sClasses="";for(var i=0;i<aClasses.length;i++){var oClass=aClasses[i];if(oClass.name&&oClass.title){var sClass=this._options.classesItemHtml}sClass=h.replaceAll(sClass,WYMeditor.CLASS_NAME,oClass.name);sClass=h.replaceAll(sClass,WYMeditor.CLASS_TITLE,oClass.title);sClasses+=sClass}boxHtml=h.replaceAll(boxHtml,WYMeditor.CLASSES_ITEMS,sClasses);var aContainers=eval(this._options.containersItems);var sContainers="";for(var i=0;i<aContainers.length;i++){var oContainer=aContainers[i];if(oContainer.name&&oContainer.title){var sContainer=this._options.containersItemHtml}sContainer=h.replaceAll(sContainer,WYMeditor.CONTAINER_NAME,oContainer.name);sContainer=h.replaceAll(sContainer,WYMeditor.CONTAINER_TITLE,this._options.stringDelimiterLeft+oContainer.title+this._options.stringDelimiterRight);sContainer=h.replaceAll(sContainer,WYMeditor.CONTAINER_CLASS,oContainer.css);sContainers+=sContainer}boxHtml=h.replaceAll(boxHtml,WYMeditor.CONTAINERS_ITEMS,sContainers);boxHtml=this.replaceStrings(boxHtml);jQuery(this._box).html(boxHtml);jQuery(this._box).find(this._options.htmlSelector).hide();this.loadSkin()}};WYMeditor.editor.prototype.bindEvents=function(){var wym=this;jQuery(this._box).find(this._options.toolSelector).click(function(){wym._iframe.contentWindow.focus();wym.exec(jQuery(this).attr(WYMeditor.NAME));return(false)});jQuery(this._box).find(this._options.containerSelector).click(function(){wym.container(jQuery(this).attr(WYMeditor.NAME));return(false)});jQuery(this._box).find(this._options.htmlValSelector).keyup(function(){jQuery(wym._doc.body).html(jQuery(this).val())}).focus(function(){jQuery(this).toggleClass("hasfocus")}).blur(function(){jQuery(this).toggleClass("hasfocus")});jQuery(this._box).find(this._options.classSelector).click(function(){var aClasses=eval(wym._options.classesItems);var sName=jQuery(this).attr(WYMeditor.NAME);var oClass=WYMeditor.Helper.findByName(aClasses,sName);if(oClass){var jqexpr=oClass.expr;wym.toggleClass(sName,jqexpr)}wym._iframe.contentWindow.focus();return(false)});jQuery(this._options.updateSelector).bind(this._options.updateEvent,function(){wym.update()})};WYMeditor.editor.prototype.ready=function(){return(this._doc!=null)};WYMeditor.editor.prototype.box=function(){return(this._box)};WYMeditor.editor.prototype.html=function(a){if(typeof a==="string"){jQuery(this._doc.body).html(a)}else{return(jQuery(this._doc.body).html())}};WYMeditor.editor.prototype.xhtml=function(){return this.parser.parse(this.html())};WYMeditor.editor.prototype.exec=function(b){switch(b){case WYMeditor.CREATE_LINK:var a=this.container();if(a||this._selected_image){this.dialog(WYMeditor.DIALOG_LINK)}break;case WYMeditor.INSERT_IMAGE:this.dialog(WYMeditor.DIALOG_IMAGE);break;case WYMeditor.INSERT_TABLE:this.dialog(WYMeditor.DIALOG_TABLE);break;case WYMeditor.PASTE:this.dialog(WYMeditor.DIALOG_PASTE);break;case WYMeditor.TOGGLE_HTML:this.update();this.toggleHtml();if(!jQuery(this._box).find(this._options.htmlSelector).is(":visible")){this.listen()}break;case WYMeditor.PREVIEW:this.dialog(WYMeditor.PREVIEW,this._options.dialogFeaturesPreview);break;default:this._exec(b);break}};WYMeditor.editor.prototype.container=function(a){if(a){var d=null;if(a.toLowerCase()==WYMeditor.TH){d=this.container();switch(d.tagName.toLowerCase()){case WYMeditor.TD:case WYMeditor.TH:break;default:var e=new Array(WYMeditor.TD,WYMeditor.TH);d=this.findUp(this.container(),e);break}if(d!=null){a=(d.tagName.toLowerCase()==WYMeditor.TD)?WYMeditor.TH:WYMeditor.TD;this.switchTo(d,a);this.update()}}else{var e=new Array(WYMeditor.P,WYMeditor.H1,WYMeditor.H2,WYMeditor.H3,WYMeditor.H4,WYMeditor.H5,WYMeditor.H6,WYMeditor.PRE,WYMeditor.BLOCKQUOTE);d=this.findUp(this.container(),e);if(d){var i=null;if(a.toLowerCase()==WYMeditor.BLOCKQUOTE){var f=this.findUp(this.container(),WYMeditor.BLOCKQUOTE);if(f==null){i=this._doc.createElement(a);d.parentNode.insertBefore(i,d);i.appendChild(d);this.setFocusToNode(i.firstChild)}else{var c=f.childNodes;var g=c.length;var b=null;if(g>0){b=c.item(0)}for(var h=0;h<g;h++){f.parentNode.insertBefore(c.item(0),f)}f.parentNode.removeChild(f);if(b){this.setFocusToNode(b)}}}else{this.switchTo(d,a)}this.update()}}}else{return(this.selected())}};WYMeditor.editor.prototype.toggleClass=function(c,b){var a=(this._selected_image?this._selected_image:jQuery(this.selected()));a=jQuery(a).parentsOrSelf(b);jQuery(a).toggleClass(c);if(!jQuery(a).attr(WYMeditor.CLASS)){jQuery(a).removeAttr(this._class)}};WYMeditor.editor.prototype.findUp=function(d,c){if(d){var e=d.tagName.toLowerCase();if(typeof(c)==WYMeditor.STRING){while(e!=c&&e!=WYMeditor.BODY){d=d.parentNode;e=d.tagName.toLowerCase()}}else{var b=false;while(!b&&e!=WYMeditor.BODY){for(var a=0;a<c.length;a++){if(e==c[a]){b=true;break}}if(!b){d=d.parentNode;e=d.tagName.toLowerCase()}}}if(e!=WYMeditor.BODY){return(d)}else{return(null)}}else{return(null)}};WYMeditor.editor.prototype.switchTo=function(c,d){var b=this._doc.createElement(d);var a=jQuery(c).html();c.parentNode.replaceChild(b,c);jQuery(b).html(a);this.setFocusToNode(b)};WYMeditor.editor.prototype.replaceStrings=function(sVal){if(!WYMeditor.STRINGS[this._options.lang]){try{eval(jQuery.ajax({url:this._options.langPath+this._options.lang+".js",async:false}).responseText)}catch(e){WYMeditor.console.error("WYMeditor: error while parsing language file.");return sVal}}for(var key in WYMeditor.STRINGS[this._options.lang]){sVal=WYMeditor.Helper.replaceAll(sVal,this._options.stringDelimiterLeft+key+this._options.stringDelimiterRight,WYMeditor.STRINGS[this._options.lang][key])}return(sVal)};WYMeditor.editor.prototype.encloseString=function(a){return(this._options.stringDelimiterLeft+a+this._options.stringDelimiterRight)};WYMeditor.editor.prototype.status=function(a){jQuery(this._box).find(this._options.statusSelector).html(a)};WYMeditor.editor.prototype.update=function(){var a=this.xhtml();jQuery(this._element).val(a);jQuery(this._box).find(this._options.htmlValSelector).not(".hasfocus").val(a)};WYMeditor.editor.prototype.dialog=function(j,c,f){var a=c||this._wym._options.dialogFeatures;var d=window.open("","dialog",a);if(d){var b="";switch(j){case (WYMeditor.DIALOG_LINK):b=this._options.dialogLinkHtml;break;case (WYMeditor.DIALOG_IMAGE):b=this._options.dialogImageHtml;break;case (WYMeditor.DIALOG_TABLE):b=this._options.dialogTableHtml;break;case (WYMeditor.DIALOG_PASTE):b=this._options.dialogPasteHtml;break;case (WYMeditor.PREVIEW):b=this._options.dialogPreviewHtml;break;default:b=f}var e=WYMeditor.Helper;var g=this._options.dialogHtml;g=e.replaceAll(g,WYMeditor.BASE_PATH,this._options.basePath);g=e.replaceAll(g,WYMeditor.DIRECTION,this._options.direction);g=e.replaceAll(g,WYMeditor.CSS_PATH,this._options.skinPath+WYMeditor.SKINS_DEFAULT_CSS);g=e.replaceAll(g,WYMeditor.WYM_PATH,this._options.wymPath);g=e.replaceAll(g,WYMeditor.JQUERY_PATH,this._options.jQueryPath);g=e.replaceAll(g,WYMeditor.DIALOG_TITLE,this.encloseString(j));g=e.replaceAll(g,WYMeditor.DIALOG_BODY,b);g=e.replaceAll(g,WYMeditor.INDEX,this._index);g=this.replaceStrings(g);var i=d.document;i.write(g);i.close()}};WYMeditor.editor.prototype.toggleHtml=function(){jQuery(this._box).find(this._options.htmlSelector).toggle()};WYMeditor.editor.prototype.uniqueStamp=function(){var a=new Date();return("wym-"+a.getTime())};WYMeditor.editor.prototype.paste=function(b){var e;var a=this.selected();var c=b.split(this._newLine+this._newLine);var d=new RegExp(this._newLine,"g");if(a&&a.tagName.toLowerCase()!=WYMeditor.BODY){for(x=c.length-1;x>=0;x--){e=c[x];e=e.replace(d,"<br />");jQuery(a).after("<p>"+e+"</p>")}}else{for(x=0;x<c.length;x++){e=c[x];e=e.replace(d,"<br />");jQuery(this._doc.body).append("<p>"+e+"</p>")}}};WYMeditor.editor.prototype.insert=function(a){if(this._iframe.contentWindow.getSelection().focusNode!=null){this._exec(WYMeditor.INSERT_HTML,a)}else{this.paste(a)}};WYMeditor.editor.prototype.wrap=function(b,a){if(this._iframe.contentWindow.getSelection().focusNode!=null){this._exec(WYMeditor.INSERT_HTML,b+this._iframe.contentWindow.getSelection().toString()+a)}};WYMeditor.editor.prototype.unwrap=function(){if(this._iframe.contentWindow.getSelection().focusNode!=null){this._exec(WYMeditor.INSERT_HTML,this._iframe.contentWindow.getSelection().toString())}};WYMeditor.editor.prototype.addCssRules=function(e,c){var b=e.styleSheets[0];if(b){for(var a=0;a<c.length;a++){var d=c[a];if(d.name&&d.css){this.addCssRule(b,d)}}}};WYMeditor.editor.prototype.computeBasePath=function(){return jQuery(jQuery.grep(jQuery("script"),function(a){return(a.src&&a.src.match(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/))})).attr("src").replace(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/,"")};WYMeditor.editor.prototype.computeWymPath=function(){return jQuery(jQuery.grep(jQuery("script"),function(a){return(a.src&&a.src.match(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/))})).attr("src")};WYMeditor.editor.prototype.computeJqueryPath=function(){return jQuery(jQuery.grep(jQuery("script"),function(a){return(a.src&&a.src.match(/jquery(-(.*)){0,1}(\.pack|\.min|\.packed)?\.js(\?.*)?$/))})).attr("src")};WYMeditor.editor.prototype.computeCssPath=function(){return jQuery(jQuery.grep(jQuery("link"),function(a){return(a.href&&a.href.match(/wymeditor\/skins\/(.*)screen\.css(\?.*)?$/))})).attr("href")};WYMeditor.editor.prototype.configureEditorUsingRawCss=function(){var a=new WYMeditor.WymCssParser();if(this._options.stylesheet){a.parse(jQuery.ajax({url:this._options.stylesheet,async:false}).responseText)}else{a.parse(this._options.styles,false)}if(this._options.classesItems.length==0){this._options.classesItems=a.css_settings.classesItems}if(this._options.editorStyles.length==0){this._options.editorStyles=a.css_settings.editorStyles}if(this._options.dialogStyles.length==0){this._options.dialogStyles=a.css_settings.dialogStyles}};WYMeditor.editor.prototype.listen=function(){jQuery(this._doc.body).bind("mousedown",this.mousedown);var a=this._doc.body.getElementsByTagName("img");for(var b=0;b<a.length;b++){jQuery(a[b]).bind("mousedown",this.mousedown)}};WYMeditor.editor.prototype.mousedown=function(a){var b=WYMeditor.INSTANCES[this.ownerDocument.title];b._selected_image=(this.tagName.toLowerCase()==WYMeditor.IMG)?this:null;a.stopPropagation()};WYMeditor.loadCss=function(a){var c=document.createElement("link");c.rel="stylesheet";c.href=a;var b=jQuery("head").get(0);b.appendChild(c)};WYMeditor.editor.prototype.loadSkin=function(){if(this._options.loadSkin&&!WYMeditor.SKINS[this._options.skin]){var found=false;var rExp=new RegExp(this._options.skin+"/"+WYMeditor.SKINS_DEFAULT_CSS+"$");jQuery("link").each(function(){if(this.href.match(rExp)){found=true}});if(!found){WYMeditor.loadCss(this._options.skinPath+WYMeditor.SKINS_DEFAULT_CSS)}}jQuery(this._box).addClass("wym_skin_"+this._options.skin);if(this._options.initSkin&&!WYMeditor.SKINS[this._options.skin]){eval(jQuery.ajax({url:this._options.skinPath+WYMeditor.SKINS_DEFAULT_JS,async:false}).responseText)}if(WYMeditor.SKINS[this._options.skin]&&WYMeditor.SKINS[this._options.skin].init){WYMeditor.SKINS[this._options.skin].init(this)}};WYMeditor.INIT_DIALOG=function(index){var wym=window.opener.WYMeditor.INSTANCES[index];var doc=window.document;var selected=wym.selected();var dialogType=jQuery(wym._options.dialogTypeSelector).val();var sStamp=wym.uniqueStamp();switch(dialogType){case WYMeditor.DIALOG_LINK:if(selected&&selected.tagName&&selected.tagName.toLowerCase!=WYMeditor.A){selected=jQuery(selected).parentsOrSelf(WYMeditor.A)}if(!selected&&wym._selected_image){selected=jQuery(wym._selected_image).parentsOrSelf(WYMeditor.A)}break}if(jQuery.isFunction(wym._options.preInitDialog)){wym._options.preInitDialog(wym,window)}var styles=doc.styleSheets[0];var aCss=eval(wym._options.dialogStyles);wym.addCssRules(doc,aCss);if(selected){jQuery(wym._options.hrefSelector).val(jQuery(selected).attr(WYMeditor.HREF));jQuery(wym._options.srcSelector).val(jQuery(selected).attr(WYMeditor.SRC));jQuery(wym._options.titleSelector).val(jQuery(selected).attr(WYMeditor.TITLE));jQuery(wym._options.altSelector).val(jQuery(selected).attr(WYMeditor.ALT))}if(wym._selected_image){jQuery(wym._options.dialogImageSelector+" "+wym._options.srcSelector).val(jQuery(wym._selected_image).attr(WYMeditor.SRC));jQuery(wym._options.dialogImageSelector+" "+wym._options.titleSelector).val(jQuery(wym._selected_image).attr(WYMeditor.TITLE));jQuery(wym._options.dialogImageSelector+" "+wym._options.altSelector).val(jQuery(wym._selected_image).attr(WYMeditor.ALT))}jQuery(wym._options.dialogLinkSelector+" "+wym._options.submitSelector).click(function(){var sUrl=jQuery(wym._options.hrefSelector).val();if(sUrl.length>0){wym._exec(WYMeditor.CREATE_LINK,sStamp);jQuery("a[href="+sStamp+"]",wym._doc.body).attr(WYMeditor.HREF,sUrl).attr(WYMeditor.TITLE,jQuery(wym._options.titleSelector).val())}window.close()});jQuery(wym._options.dialogImageSelector+" "+wym._options.submitSelector).click(function(){var sUrl=jQuery(wym._options.srcSelector).val();if(sUrl.length>0){wym._exec(WYMeditor.INSERT_IMAGE,sStamp);jQuery("img[src$="+sStamp+"]",wym._doc.body).attr(WYMeditor.SRC,sUrl).attr(WYMeditor.TITLE,jQuery(wym._options.titleSelector).val()).attr(WYMeditor.ALT,jQuery(wym._options.altSelector).val())}window.close()});jQuery(wym._options.dialogTableSelector+" "+wym._options.submitSelector).click(function(){var iRows=jQuery(wym._options.rowsSelector).val();var iCols=jQuery(wym._options.colsSelector).val();if(iRows>0&&iCols>0){var table=wym._doc.createElement(WYMeditor.TABLE);var newRow=null;var newCol=null;var sCaption=jQuery(wym._options.captionSelector).val();var newCaption=table.createCaption();newCaption.innerHTML=sCaption;for(x=0;x<iRows;x++){newRow=table.insertRow(x);for(y=0;y<iCols;y++){newRow.insertCell(y)}}jQuery(table).attr("summary",jQuery(wym._options.summarySelector).val());var node=jQuery(wym.findUp(wym.container(),WYMeditor.MAIN_CONTAINERS)).get(0);if(!node||!node.parentNode){jQuery(wym._doc.body).append(table)}else{jQuery(node).after(table)}}window.close()});jQuery(wym._options.dialogPasteSelector+" "+wym._options.submitSelector).click(function(){var sText=jQuery(wym._options.textSelector).val();wym.paste(sText);window.close()});jQuery(wym._options.dialogPreviewSelector+" "+wym._options.previewSelector).html(wym.xhtml());jQuery(wym._options.cancelSelector).mousedown(function(){window.close()});if(jQuery.isFunction(wym._options.postInitDialog)){wym._options.postInitDialog(wym,window)}};WYMeditor.XmlHelper=function(){this._entitiesDiv=document.createElement("div");return this};WYMeditor.XmlHelper.prototype.tag=function(c,b,a){b=b||false;a=a||false;return"<"+c+(b?this.tagOptions(b):"")+(a?">":" />")};WYMeditor.XmlHelper.prototype.contentTag=function(b,c,a){a=a||false;return"<"+b+(a?this.tagOptions(a):"")+">"+c+"</"+b+">"};WYMeditor.XmlHelper.prototype.cdataSection=function(a){return"<![CDATA["+a+"]]>"};WYMeditor.XmlHelper.prototype.escapeOnce=function(a){return this._fixDoubleEscape(this.escapeEntities(a))};WYMeditor.XmlHelper.prototype._fixDoubleEscape=function(a){return a.replace(/&([a-z]+|(#\d+));/ig,"&$1;")};WYMeditor.XmlHelper.prototype.tagOptions=function(b){var a=this;a._formated_options="";for(var c in b){var d="";var e=b[c];if(typeof e!="function"&&e.length>0){if(parseInt(c)==c&&typeof e=="object"){c=e.shift();e=e.pop()}if(c!=""&&e!=""){a._formated_options+=" "+c+'="'+a.escapeOnce(e)+'"'}}}return a._formated_options};WYMeditor.XmlHelper.prototype.escapeEntities=function(c,b){this._entitiesDiv.innerHTML=c;this._entitiesDiv.textContent=c;var a=this._entitiesDiv.innerHTML;if(typeof b=="undefined"){if(b!=false){a=a.replace('"',""")}if(b==true){a=a.replace('"',"'")}}return a};WYMeditor.XmlHelper.prototype.parseAttributes=function(h){var a=[];var g=h.split(/((=\s*")(")("))|((=\s*\')(\')(\'))|((=\s*[^>\s]*))/g);if(g.toString()!=h){for(var d in g){var c=g[d];if(typeof c!="function"&&c.length!=0){var e=new RegExp("(\\w+)\\s*"+c);if(match=h.match(e)){var f=c.replace(/^[\s=]+/,"");var b=f.charAt(0);b=b=='"'?'"':(b=="'"?"'":"");if(b!=""){f=b=='"'?f.replace(/^"|"+$/g,""):f.replace(/^'|'+$/g,"")}h=h.replace(match[0],"");a.push([match[1],f])}}}}return a};WYMeditor.XhtmlValidator={_attributes:{core:{except:["base","head","html","meta","param","script","style","title"],attributes:["class","id","style","title","accesskey","tabindex"]},language:{except:["base","br","hr","iframe","param","script"],attributes:{dir:["ltr","rtl"],"0":"lang","1":"xml:lang"}},keyboard:{attributes:{accesskey:/^(\w){1}$/,tabindex:/^(\d)+$/}}},_events:{window:{only:["body"],attributes:["onload","onunload"]},form:{only:["form","input","textarea","select","a","label","button"],attributes:["onchange","onsubmit","onreset","onselect","onblur","onfocus"]},keyboard:{except:["base","bdo","br","frame","frameset","head","html","iframe","meta","param","script","style","title"],attributes:["onkeydown","onkeypress","onkeyup"]},mouse:{except:["base","bdo","br","head","html","meta","param","script","style","title"],attributes:["onclick","ondblclick","onmousedown","onmousemove","onmouseover","onmouseout","onmouseup"]}},_tags:{a:{attributes:{"0":"charset","1":"coords","2":"href","3":"hreflang","4":"name",rel:/^(alternate|designates|stylesheet|start|next|prev|contents|index|glossary|copyright|chapter|section|subsection|appendix|help|bookmark| |shortcut|icon)+$/,rev:/^(alternate|designates|stylesheet|start|next|prev|contents|index|glossary|copyright|chapter|section|subsection|appendix|help|bookmark| 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)+$/i,rel:/^(alternate|appendix|bookmark|chapter|contents|copyright|glossary|help|home|index|next|prev|section|start|stylesheet|subsection| |shortcut|icon)+$/i,rev:/^(alternate|appendix|bookmark|chapter|contents|copyright|glossary|help|home|index|next|prev|section|start|stylesheet|subsection| |shortcut|icon)+$/i,"3":"type"},inside:"head"},map:{attributes:["id","name"],required:["id"]},meta:{attributes:{"0":"content","http-equiv":/^(content\-type|expires|refresh|set\-cookie)$/i,"1":"name","2":"scheme"},required:["content"]},"27":"noscript",object:{attributes:["archive","classid","codebase","codetype","data","declare","height","name","standby","type","usemap","width"]},"28":"ol",optgroup:{attributes:{"0":"label",disabled:/^(disabled)$/},required:["label"]},option:{attributes:{"0":"label",disabled:/^(disabled)$/,selected:/^(selected)$/,"1":"value"},inside:"select"},"29":"p",param:{attributes:{"0":"type",valuetype:/^(data|ref|object)$/,"1":"valuetype","2":"value"},required:["name"]},"30":"pre",q:{attributes:["cite"]},"31":"samp",script:{attributes:{type:/^(text\/ecmascript|text\/javascript|text\/jscript|text\/vbscript|text\/vbs|text\/xml)$/,"0":"charset",defer:/^(defer)$/,"1":"src"},required:["type"]},select:{attributes:{disabled:/^(disabled)$/,multiple:/^(multiple)$/,"0":"name","1":"size"},inside:"form"},"32":"small","33":"span","34":"strong",style:{attributes:{"0":"type",media:/^(screen|tty|tv|projection|handheld|print|braille|aural|all)$/},required:["type"]},"35":"sub","36":"sup",table:{attributes:{"0":"border","1":"cellpadding","2":"cellspacing",frame:/^(void|above|below|hsides|lhs|rhs|vsides|box|border)$/,rules:/^(none|groups|rows|cols|all)$/,"3":"summary","4":"width"}},tbody:{attributes:{align:/^(right|left|center|justify)$/,"0":"char","1":"charoff",valign:/^(top|middle|bottom|baseline)$/}},td:{attributes:{"0":"abbr",align:/^(left|right|center|justify|char)$/,"1":"axis","2":"char","3":"charoff",colspan:/^(\d)+$/,"4":"headers",rowspan:/^(\d)+$/,scope:/^(col|colgroup|row|rowgroup)$/,valign:/^(top|middle|bottom|baseline)$/}},textarea:{attributes:["cols","rows","disabled","name","readonly"],required:["cols","rows"],inside:"form"},tfoot:{attributes:{align:/^(right|left|center|justify)$/,"0":"char","1":"charoff",valign:/^(top|middle|bottom)$/,"2":"baseline"}},th:{attributes:{"0":"abbr",align:/^(left|right|center|justify|char)$/,"1":"axis","2":"char","3":"charoff",colspan:/^(\d)+$/,"4":"headers",rowspan:/^(\d)+$/,scope:/^(col|colgroup|row|rowgroup)$/,valign:/^(top|middle|bottom|baseline)$/}},thead:{attributes:{align:/^(right|left|center|justify)$/,"0":"char","1":"charoff",valign:/^(top|middle|bottom|baseline)$/}},"37":"title",tr:{attributes:{align:/^(right|left|center|justify|char)$/,"0":"char","1":"charoff",valign:/^(top|middle|bottom|baseline)$/}},"38":"tt","39":"ul","40":"var"},skiped_attributes:[],skiped_attribute_values:[],getValidTagAttributes:function(a,b){var c={};var g=this.getPossibleTagAttributes(a);for(var e in b){var f=b[e];var d=WYMeditor.Helper;if(!d.contains(this.skiped_attributes,e)&&!d.contains(this.skiped_attribute_values,f)){if(typeof f!="function"&&d.contains(g,e)){if(this.doesAttributeNeedsValidation(a,e)){if(this.validateAttribute(a,e,f)){c[e]=f}}else{c[e]=f}}}}return c},getUniqueAttributesAndEventsForTag:function(b){var a=[];if(this._tags[b]&&this._tags[b]["attributes"]){for(k in this._tags[b]["attributes"]){a.push(parseInt(k)==k?this._tags[b]["attributes"][k]:k)}}return a},getDefaultAttributesAndEventsForTags:function(){var a=[];for(var b in this._events){a.push(this._events[b])}for(var b in this._attributes){a.push(this._attributes[b])}return a},isValidTag:function(a){if(this._tags[a]){return true}for(var b in this._tags){if(this._tags[b]==a){return true}}return false},getDefaultAttributesAndEventsForTag:function(a){var i=[];if(this.isValidTag(a)){var g=this.getDefaultAttributesAndEventsForTags();for(var d in g){var f=g[d];if(typeof f=="object"){var e=WYMeditor.Helper;if((f.except&&e.contains(f.except,a))||(f.only&&!e.contains(f.only,a))){continue}var c=f.attributes?f.attributes:f.events;for(var b in c){i.push(typeof c[b]!="string"?b:c[b])}}}}return i},doesAttributeNeedsValidation:function(a,b){return this._tags[a]&&((this._tags[a]["attributes"]&&this._tags[a]["attributes"][b])||(this._tags[a]["required"]&&WYMeditor.Helper.contains(this._tags[a]["required"],b)))},validateAttribute:function(a,b,c){if(this._tags[a]&&(this._tags[a]["attributes"]&&this._tags[a]["attributes"][b]&&c.length>0&&!c.match(this._tags[a]["attributes"][b]))||(this._tags[a]&&this._tags[a]["required"]&&WYMeditor.Helper.contains(this._tags[a]["required"],b)&&c.length==0)){return false}return typeof this._tags[a]!="undefined"},getPossibleTagAttributes:function(a){if(!this._possible_tag_attributes){this._possible_tag_attributes={}}if(!this._possible_tag_attributes[a]){this._possible_tag_attributes[a]=this.getUniqueAttributesAndEventsForTag(a).concat(this.getDefaultAttributesAndEventsForTag(a))}return this._possible_tag_attributes[a]}};WYMeditor.ParallelRegex=function(a){this._case=a;this._patterns=[];this._labels=[];this._regex=null;return this};WYMeditor.ParallelRegex.prototype.addPattern=function(c,a){a=a||true;var b=this._patterns.length;this._patterns[b]=c;this._labels[b]=a;this._regex=null};WYMeditor.ParallelRegex.prototype.match=function(c){if(this._patterns.length==0){return[false,""]}var d=c.match(this._getCompoundedRegex());if(!d){return[false,""]}var a=d[0];for(var b=1;b<d.length;b++){if(d[b]){return[this._labels[b-1],a]}}return[true,d[0]]};WYMeditor.ParallelRegex.prototype._getCompoundedRegex=function(){if(this._regex==null){for(var a=0,b=this._patterns.length;a<b;a++){this._patterns[a]="("+this._untokenizeRegex(this._tokenizeRegex(this._patterns[a]).replace(/([\/])/g,"\\$1"))+")"}this._regex=new RegExp(this._patterns.join("|"),this._getPerlMatchingFlags())}return this._regex};WYMeditor.ParallelRegex.prototype._tokenizeRegex=function(a){return a.replace(/$\?(i|m|s|x|U)$/,"~~~~~~Tk1$1~~~~~~").replace(/$\?(\-[i|m|s|x|U])$/,"~~~~~~Tk2$1~~~~~~").replace(/$\?\=(.*)$/,"~~~~~~Tk3$1~~~~~~").replace(/$\?\!(.*)$/,"~~~~~~Tk4$1~~~~~~").replace(/$\?\<\=(.*)$/,"~~~~~~Tk5$1~~~~~~").replace(/$\?\<\!(.*)$/,"~~~~~~Tk6$1~~~~~~").replace(/$\?\:(.*)$/,"~~~~~~Tk7$1~~~~~~")};WYMeditor.ParallelRegex.prototype._untokenizeRegex=function(a){return a.replace(/~~~~~~Tk1(.{1})~~~~~~/,"(?$1)").replace(/~~~~~~Tk2(.{2})~~~~~~/,"(?$1)").replace(/~~~~~~Tk3(.*)~~~~~~/,"(?=$1)").replace(/~~~~~~Tk4(.*)~~~~~~/,"(?!$1)").replace(/~~~~~~Tk5(.*)~~~~~~/,"(?<=$1)").replace(/~~~~~~Tk6(.*)~~~~~~/,"(?<!$1)").replace(/~~~~~~Tk7(.*)~~~~~~/,"(?:$1)")};WYMeditor.ParallelRegex.prototype._getPerlMatchingFlags=function(){return(this._case?"m":"mi")};WYMeditor.StateStack=function(a){this._stack=[a];return this};WYMeditor.StateStack.prototype.getCurrent=function(){return this._stack[this._stack.length-1]};WYMeditor.StateStack.prototype.enter=function(a){this._stack.push(a)};WYMeditor.StateStack.prototype.leave=function(){if(this._stack.length==1){return false}this._stack.pop();return true};WYMeditor.LEXER_ENTER=1;WYMeditor.LEXER_MATCHED=2;WYMeditor.LEXER_UNMATCHED=3;WYMeditor.LEXER_EXIT=4;WYMeditor.LEXER_SPECIAL=5;WYMeditor.Lexer=function(c,b,a){b=b||"accept";this._case=a||false;this._regexes={};this._parser=c;this._mode=new WYMeditor.StateStack(b);this._mode_handlers={};this._mode_handlers[b]=b;return this};WYMeditor.Lexer.prototype.addPattern=function(a,b){var b=b||"accept";if(typeof this._regexes[b]=="undefined"){this._regexes[b]=new WYMeditor.ParallelRegex(this._case)}this._regexes[b].addPattern(a);if(typeof this._mode_handlers[b]=="undefined"){this._mode_handlers[b]=b}};WYMeditor.Lexer.prototype.addEntryPattern=function(b,c,a){if(typeof this._regexes[c]=="undefined"){this._regexes[c]=new WYMeditor.ParallelRegex(this._case)}this._regexes[c].addPattern(b,a);if(typeof this._mode_handlers[a]=="undefined"){this._mode_handlers[a]=a}};WYMeditor.Lexer.prototype.addExitPattern=function(a,b){if(typeof this._regexes[b]=="undefined"){this._regexes[b]=new WYMeditor.ParallelRegex(this._case)}this._regexes[b].addPattern(a,"__exit");if(typeof this._mode_handlers[b]=="undefined"){this._mode_handlers[b]=b}};WYMeditor.Lexer.prototype.addSpecialPattern=function(b,c,a){if(typeof this._regexes[c]=="undefined"){this._regexes[c]=new WYMeditor.ParallelRegex(this._case)}this._regexes[c].addPattern(b,"_"+a);if(typeof this._mode_handlers[a]=="undefined"){this._mode_handlers[a]=a}};WYMeditor.Lexer.prototype.mapHandler=function(b,a){this._mode_handlers[b]=a};WYMeditor.Lexer.prototype.parse=function(d){if(typeof this._parser=="undefined"){return false}var e=d.length;var c;while(typeof(c=this._reduce(d))=="object"){var d=c[0];var b=c[1];var a=c[2];var f=c[3];if(!this._dispatchTokens(b,a,f)){return false}if(d==""){return true}if(d.length==e){return false}e=d.length}if(!c){return false}return this._invokeParser(d,WYMeditor.LEXER_UNMATCHED)};WYMeditor.Lexer.prototype._dispatchTokens=function(b,a,c){c=c||false;if(!this._invokeParser(b,WYMeditor.LEXER_UNMATCHED)){return false}if(typeof c=="boolean"){return this._invokeParser(a,WYMeditor.LEXER_MATCHED)}if(this._isModeEnd(c)){if(!this._invokeParser(a,WYMeditor.LEXER_EXIT)){return false}return this._mode.leave()}if(this._isSpecialMode(c)){this._mode.enter(this._decodeSpecial(c));if(!this._invokeParser(a,WYMeditor.LEXER_SPECIAL)){return false}return this._mode.leave()}this._mode.enter(c);return this._invokeParser(a,WYMeditor.LEXER_ENTER)};WYMeditor.Lexer.prototype._isModeEnd=function(a){return(a==="__exit")};WYMeditor.Lexer.prototype._isSpecialMode=function(a){return(a.substring(0,1)=="_")};WYMeditor.Lexer.prototype._decodeSpecial=function(a){return a.substring(1)};WYMeditor.Lexer.prototype._invokeParser=function(content,is_match){if(!/ +/.test(content)&&((content==="")||(content==false))){return true}var current=this._mode.getCurrent();var handler=this._mode_handlers[current];var result;eval("result = this._parser."+handler+"(content, is_match);");return result};WYMeditor.Lexer.prototype._reduce=function(c){var a=this._regexes[this._mode.getCurrent()].match(c);var b=a[1];var e=a[0];if(e){var f=c.indexOf(b);var d=c.substr(0,f);c=c.substring(f+b.length);return[c,d,b,e]}return true};WYMeditor.XhtmlLexer=function(a){jQuery.extend(this,new WYMeditor.Lexer(a,"Text"));this.mapHandler("Text","Text");this.addTokens();this.init();return this};WYMeditor.XhtmlLexer.prototype.init=function(){};WYMeditor.XhtmlLexer.prototype.addTokens=function(){this.addCommentTokens("Text");this.addScriptTokens("Text");this.addCssTokens("Text");this.addTagTokens("Text")};WYMeditor.XhtmlLexer.prototype.addCommentTokens=function(a){this.addEntryPattern("","Comment")};WYMeditor.XhtmlLexer.prototype.addScriptTokens=function(a){this.addEntryPattern("<script",a,"Script");this.addExitPattern("<\/script>","Script")};WYMeditor.XhtmlLexer.prototype.addCssTokens=function(a){this.addEntryPattern("<style",a,"Css");this.addExitPattern("</style>","Css")};WYMeditor.XhtmlLexer.prototype.addTagTokens=function(a){this.addSpecialPattern("<\\s*[a-z0-9:-]+\\s*>",a,"OpeningTag");this.addEntryPattern("<[a-z0-9:-]+[\\/ \\>]+",a,"OpeningTag");this.addInTagDeclarationTokens("OpeningTag");this.addSpecialPattern("</\\s*[a-z0-9:-]+\\s*>",a,"ClosingTag")};WYMeditor.XhtmlLexer.prototype.addInTagDeclarationTokens=function(a){this.addSpecialPattern("\\s+",a,"Ignore");this.addAttributeTokens(a);this.addExitPattern("/>",a);this.addExitPattern(">",a)};WYMeditor.XhtmlLexer.prototype.addAttributeTokens=function(a){this.addSpecialPattern("\\s*[a-z-_0-9]*:?[a-z-_0-9]+\\s*(?==)\\s*",a,"TagAttributes");this.addEntryPattern('=\\s*"',a,"DoubleQuotedAttribute");this.addPattern('\\\\"',"DoubleQuotedAttribute");this.addExitPattern('"',"DoubleQuotedAttribute");this.addEntryPattern("=\\s*'",a,"SingleQuotedAttribute");this.addPattern("\\\\'","SingleQuotedAttribute");this.addExitPattern("'","SingleQuotedAttribute");this.addSpecialPattern("=\\s*[^>\\s]*",a,"UnquotedAttribute")};WYMeditor.XhtmlParser=function(a,b){var b=b||"Text";this._Lexer=new WYMeditor.XhtmlLexer(this);this._Listener=a;this._mode=b;this._matches=[];this._last_match="";this._current_match="";return this};WYMeditor.XhtmlParser.prototype.parse=function(a){this._Lexer.parse(this.beforeParsing(a));return this.afterParsing(this._Listener.getResult())};WYMeditor.XhtmlParser.prototype.beforeParsing=function(a){if(a.match(/class="MsoNormal"/)||a.match(/ns = "urn:schemas-microsoft-com/)){this._Listener.avoidStylingTagsAndAttributes()}return this._Listener.beforeParsing(a)};WYMeditor.XhtmlParser.prototype.afterParsing=function(a){if(this._Listener._avoiding_tags_implicitly){this._Listener.allowStylingTagsAndAttributes()}return this._Listener.afterParsing(a)};WYMeditor.XhtmlParser.prototype.Ignore=function(a,b){return true};WYMeditor.XhtmlParser.prototype.Text=function(a){this._Listener.addContent(a);return true};WYMeditor.XhtmlParser.prototype.Comment=function(b,a){return this._addNonTagBlock(b,a,"addComment")};WYMeditor.XhtmlParser.prototype.Script=function(b,a){return this._addNonTagBlock(b,a,"addScript")};WYMeditor.XhtmlParser.prototype.Css=function(b,a){return this._addNonTagBlock(b,a,"addCss")};WYMeditor.XhtmlParser.prototype._addNonTagBlock=function(a,c,b){switch(c){case WYMeditor.LEXER_ENTER:this._non_tag=a;break;case WYMeditor.LEXER_UNMATCHED:this._non_tag+=a;break;case WYMeditor.LEXER_EXIT:switch(b){case"addComment":this._Listener.addComment(this._non_tag+a);break;case"addScript":this._Listener.addScript(this._non_tag+a);break;case"addCss":this._Listener.addCss(this._non_tag+a);break}}return true};WYMeditor.XhtmlParser.prototype.OpeningTag=function(a,b){switch(b){case WYMeditor.LEXER_ENTER:this._tag=this.normalizeTag(a);this._tag_attributes={};break;case WYMeditor.LEXER_SPECIAL:this._callOpenTagListener(this.normalizeTag(a));break;case WYMeditor.LEXER_EXIT:this._callOpenTagListener(this._tag,this._tag_attributes)}return true};WYMeditor.XhtmlParser.prototype.ClosingTag=function(a,b){this._callCloseTagListener(this.normalizeTag(a));return true};WYMeditor.XhtmlParser.prototype._callOpenTagListener=function(a,b){var b=b||{};this.autoCloseUnclosedBeforeNewOpening(a);if(this._Listener.isBlockTag(a)){this._Listener._tag_stack.push(a);this._Listener.fixNestingBeforeOpeningBlockTag(a,b);this._Listener.openBlockTag(a,b);this._increaseOpenTagCounter(a)}else{if(this._Listener.isInlineTag(a)){this._Listener.inlineTag(a,b)}else{this._Listener.openUnknownTag(a,b);this._increaseOpenTagCounter(a)}}this._Listener.last_tag=a;this._Listener.last_tag_opened=true;this._Listener.last_tag_attributes=b};WYMeditor.XhtmlParser.prototype._callCloseTagListener=function(a){if(this._decreaseOpenTagCounter(a)){this.autoCloseUnclosedBeforeTagClosing(a);if(this._Listener.isBlockTag(a)){var b=this._Listener._tag_stack.pop();if(b==false){return}else{if(b!=a){a=b}}this._Listener.closeBlockTag(a)}else{this._Listener.closeUnknownTag(a)}}else{this._Listener.closeUnopenedTag(a)}this._Listener.last_tag=a;this._Listener.last_tag_opened=false};WYMeditor.XhtmlParser.prototype._increaseOpenTagCounter=function(a){this._Listener._open_tags[a]=this._Listener._open_tags[a]||0;this._Listener._open_tags[a]++};WYMeditor.XhtmlParser.prototype._decreaseOpenTagCounter=function(a){if(this._Listener._open_tags[a]){this._Listener._open_tags[a]--;if(this._Listener._open_tags[a]==0){this._Listener._open_tags[a]=undefined}return true}return false};WYMeditor.XhtmlParser.prototype.autoCloseUnclosedBeforeNewOpening=function(a){this._autoCloseUnclosed(a,false)};WYMeditor.XhtmlParser.prototype.autoCloseUnclosedBeforeTagClosing=function(a){this._autoCloseUnclosed(a,true)};WYMeditor.XhtmlParser.prototype._autoCloseUnclosed=function(c,d){var d=d||false;if(this._Listener._open_tags){for(var a in this._Listener._open_tags){var b=this._Listener._open_tags[a];if(b>0&&this._Listener.shouldCloseTagAutomatically(a,c,d)){this._callCloseTagListener(a,true)}}}};WYMeditor.XhtmlParser.prototype.getTagReplacements=function(){return this._Listener.getTagReplacements()};WYMeditor.XhtmlParser.prototype.normalizeTag=function(a){a=a.replace(/^([\s<\/>]*)|([\s<\/>]*)$/gm,"").toLowerCase();var b=this._Listener.getTagReplacements();if(b[a]){return b[a]}return a};WYMeditor.XhtmlParser.prototype.TagAttributes=function(a,b){if(WYMeditor.LEXER_SPECIAL==b){this._current_attribute=a}return true};WYMeditor.XhtmlParser.prototype.DoubleQuotedAttribute=function(a,b){if(WYMeditor.LEXER_UNMATCHED==b){this._tag_attributes[this._current_attribute]=a}return true};WYMeditor.XhtmlParser.prototype.SingleQuotedAttribute=function(a,b){if(WYMeditor.LEXER_UNMATCHED==b){this._tag_attributes[this._current_attribute]=a}return true};WYMeditor.XhtmlParser.prototype.UnquotedAttribute=function(a,b){this._tag_attributes[this._current_attribute]=a.replace(/^=/,"");return true};WYMeditor.XhtmlSaxListener=function(){this.output="";this.helper=new WYMeditor.XmlHelper();this._open_tags={};this.validator=WYMeditor.XhtmlValidator;this._tag_stack=[];this.avoided_tags=[];this.entities={" ":" ","¡":"¡","¢":"¢","£":"£","¤":"¤","¥":"¥","¦":"¦","§":"§","¨":"¨","©":"©","ª":"ª","«":"«","¬":"¬","":"","®":"®","¯":"¯","°":"°","±":"±","²":"²","³":"³","´":"´","µ":"µ","¶":"¶","·":"·","¸":"¸","¹":"¹","º":"º","»":"»","¼":"¼","½":"½","¾":"¾","¿":"¿","À":"À","Á":"Á","Â":"Â","Ã":"Ã","Ä":"Ä","Å":"Å","Æ":"Æ","Ç":"Ç","È":"È","É":"É","Ê":"Ê","Ë":"Ë","Ì":"Ì","Í":"Í","Î":"Î","Ï":"Ï","Ð":"Ð","Ñ":"Ñ","Ò":"Ò","Ó":"Ó","Ô":"Ô","Õ":"Õ","Ö":"Ö","×":"×","Ø":"Ø","Ù":"Ù","Ú":"Ú","Û":"Û","Ü":"Ü","Ý":"Ý","Þ":"Þ","ß":"ß","à":"à","á":"á","â":"â","ã":"ã","ä":"ä","å":"å","æ":"æ","ç":"ç","è":"è","é":"é","ê":"ê","ë":"ë","ì":"ì","í":"í","î":"î","ï":"ï","ð":"ð","ñ":"ñ","ò":"ò","ó":"ó","ô":"ô","õ":"õ","ö":"ö","÷":"÷","ø":"ø","ù":"ù","ú":"ú","û":"û","ü":"ü","ý":"ý","þ":"þ","ÿ":"ÿ","&OElig;":"Œ","&oelig;":"œ","&Scaron;":"Š","&scaron;":"š","&Yuml;":"Ÿ","&fnof;":"ƒ","&circ;":"ˆ","&tilde;":"˜","Α":"Α","Β":"Β","Γ":"Γ","Δ":"Δ","Ε":"Ε","Ζ":"Ζ","Η":"Η","Θ":"Θ","Ι":"Ι","Κ":"Κ","Λ":"Λ","Μ":"Μ","Ν":"Ν","Ξ":"Ξ","Ο":"Ο","Π":"Π","Ρ":"Ρ","Σ":"Σ","Τ":"Τ","Υ":"Υ","Φ":"Φ","Χ":"Χ","Ψ":"Ψ","Ω":"Ω","α":"α","β":"β","γ":"γ","δ":"δ","ε":"ε","ζ":"ζ","η":"η","θ":"θ","ι":"ι","κ":"κ","λ":"λ","μ":"μ","ν":"ν","ξ":"ξ","ο":"ο","π":"π","ρ":"ρ","&sigmaf;":"ς","σ":"σ","τ":"τ","υ":"υ","φ":"φ","χ":"χ","ψ":"ψ","ω":"ω","&thetasym;":"ϑ","&upsih;":"ϒ","ϖ":"ϖ","&ensp;":" ","&emsp;":" "," ":" ","&zwnj;":"‌","&zwj;":"‍","&lrm;":"‎","&rlm;":"‏","–":"–","—":"—","‘":"‘","’":"’","&sbquo;":"‚","“":"“","”":"”","&bdquo;":"„","&dagger;":"†","&Dagger;":"‡","•":"•","…":"…","&permil;":"‰","′":"′","″":"″","&lsaquo;":"‹","&rsaquo;":"›","&oline;":"‾","&frasl;":"⁄","€":"€","&image;":"ℑ","&weierp;":"℘","&real;":"ℜ","™":"™","&alefsym;":"ℵ","←":"←","↑":"↑","→":"→","↓":"↓","↔":"↔","&crarr;":"↵","⇐":"⇐","&uArr;":"⇑","⇒":"⇒","&dArr;":"⇓","⇔":"⇔","∀":"∀","∂":"∂","∃":"∃","∅":"∅","∇":"∇","∈":"∈","∉":"∉","&ni;":"∋","∏":"∏","∑":"∑","−":"−","&lowast;":"∗","√":"√","&prop;":"∝","∞":"∞","&ang;":"∠","&and;":"∧","&or;":"∨","∩":"∩","∪":"∪","∫":"∫","&there4;":"∴","&sim;":"∼","&cong;":"≅","≈":"≈","≠":"≠","&equiv;":"≡","≤":"≤","≥":"≥","⊂":"⊂","⊃":"⊃","&nsub;":"⊄","&sube;":"⊆","&supe;":"⊇","&oplus;":"⊕","&otimes;":"⊗","&perp;":"⊥","⋅":"⋅","&lceil;":"⌈","&rceil;":"⌉","&lfloor;":"⌊","&rfloor;":"⌋","&lang;":"〈","&rang;":"〉","&loz;":"◊","&spades;":"♠","&clubs;":"♣","&hearts;":"♥","&diams;":"♦"};this.block_tags=["a","abbr","acronym","address","area","b","base","bdo","big","blockquote","body","button","caption","cite","code","col","colgroup","dd","del","div","dfn","dl","dt","em","fieldset","form","head","h1","h2","h3","h4","h5","h6","html","i","ins","kbd","label","legend","li","map","noscript","object","ol","optgroup","option","p","param","pre","q","samp","script","select","small","span","strong","style","sub","sup","table","tbody","td","textarea","tfoot","th","thead","title","tr","tt","ul","var","extends"];this.inline_tags=["br","hr","img","input"];return this};WYMeditor.XhtmlSaxListener.prototype.shouldCloseTagAutomatically=function(a,c,b){var b=b||false;if(a=="td"){if((b&&c=="tr")||(!b&&c=="td")){return true}}if(a=="option"){if((b&&c=="select")||(!b&&c=="option")){return true}}return false};WYMeditor.XhtmlSaxListener.prototype.beforeParsing=function(a){this.output="";return a};WYMeditor.XhtmlSaxListener.prototype.afterParsing=function(a){a=this.replaceNamedEntities(a);a=this.joinRepeatedEntities(a);a=this.removeEmptyTags(a);a=this.removeBrInPre(a);return a};WYMeditor.XhtmlSaxListener.prototype.replaceNamedEntities=function(b){for(var a in this.entities){b=b.replace(new RegExp(a,"g"),this.entities[a])}return b};WYMeditor.XhtmlSaxListener.prototype.joinRepeatedEntities=function(b){var a="em|strong|sub|sup|acronym|pre|del|address";return b.replace(new RegExp("</("+a+")><\\1>",""),"").replace(new RegExp("(s*<("+a+")>s*){2}(.*)(s*</\\2>s*){2}",""),"<$2>$3<$2>")};WYMeditor.XhtmlSaxListener.prototype.removeEmptyTags=function(a){return a.replace(new RegExp("<("+this.block_tags.join("|").replace(/\|td/,"").replace(/\|th/,"")+")>(<br />| | |\\s)*</\\1>","g"),"")};WYMeditor.XhtmlSaxListener.prototype.removeBrInPre=function(c){var b=c.match(new RegExp("<pre[^>]*>(.*?)</pre>","gmi"));if(b){for(var a=0;a<b.length;a++){c=c.replace(b[a],b[a].replace(new RegExp("<br />","g"),String.fromCharCode(13,10)))}}return c};WYMeditor.XhtmlSaxListener.prototype.getResult=function(){return this.output};WYMeditor.XhtmlSaxListener.prototype.getTagReplacements=function(){return{b:"strong",i:"em"}};WYMeditor.XhtmlSaxListener.prototype.addContent=function(a){this.output+=a};WYMeditor.XhtmlSaxListener.prototype.addComment=function(a){if(this.remove_comments){this.output+=a}};WYMeditor.XhtmlSaxListener.prototype.addScript=function(a){if(!this.remove_scripts){this.output+=a}};WYMeditor.XhtmlSaxListener.prototype.addCss=function(a){if(!this.remove_embeded_styles){this.output+=a}};WYMeditor.XhtmlSaxListener.prototype.openBlockTag=function(a,b){this.output+=this.helper.tag(a,this.validator.getValidTagAttributes(a,b),true)};WYMeditor.XhtmlSaxListener.prototype.inlineTag=function(a,b){this.output+=this.helper.tag(a,this.validator.getValidTagAttributes(a,b))};WYMeditor.XhtmlSaxListener.prototype.openUnknownTag=function(a,b){};WYMeditor.XhtmlSaxListener.prototype.closeBlockTag=function(a){this.output=this.output.replace(/<br \/>$/,"")+this._getClosingTagContent("before",a)+"</"+a+">"+this._getClosingTagContent("after",a)};WYMeditor.XhtmlSaxListener.prototype.closeUnknownTag=function(a){};WYMeditor.XhtmlSaxListener.prototype.closeUnopenedTag=function(a){this.output+="</"+a+">"};WYMeditor.XhtmlSaxListener.prototype.avoidStylingTagsAndAttributes=function(){this.avoided_tags=["div","span"];this.validator.skiped_attributes=["style"];this.validator.skiped_attribute_values=["MsoNormal","main1"];this._avoiding_tags_implicitly=true};WYMeditor.XhtmlSaxListener.prototype.allowStylingTagsAndAttributes=function(){this.avoided_tags=[];this.validator.skiped_attributes=[];this.validator.skiped_attribute_values=[];this._avoiding_tags_implicitly=false};WYMeditor.XhtmlSaxListener.prototype.isBlockTag=function(a){return !WYMeditor.Helper.contains(this.avoided_tags,a)&&WYMeditor.Helper.contains(this.block_tags,a)};WYMeditor.XhtmlSaxListener.prototype.isInlineTag=function(a){return !WYMeditor.Helper.contains(this.avoided_tags,a)&&WYMeditor.Helper.contains(this.inline_tags,a)};WYMeditor.XhtmlSaxListener.prototype.insertContentAfterClosingTag=function(a,b){this._insertContentWhenClosingTag("after",a,b)};WYMeditor.XhtmlSaxListener.prototype.insertContentBeforeClosingTag=function(a,b){this._insertContentWhenClosingTag("before",a,b)};WYMeditor.XhtmlSaxListener.prototype.fixNestingBeforeOpeningBlockTag=function(a,b){if(a!="li"&&(a=="ul"||a=="ol")&&this.last_tag&&!this.last_tag_opened&&this.last_tag=="li"){this.output=this.output.replace(/<\/li>$/,"");this.insertContentAfterClosingTag(a,"</li>")}};WYMeditor.XhtmlSaxListener.prototype._insertContentWhenClosingTag=function(b,a,c){if(!this["_insert_"+b+"_closing"]){this["_insert_"+b+"_closing"]=[]}if(!this["_insert_"+b+"_closing"][a]){this["_insert_"+b+"_closing"][a]=[]}this["_insert_"+b+"_closing"][a].push(c)};WYMeditor.XhtmlSaxListener.prototype._getClosingTagContent=function(b,a){if(this["_insert_"+b+"_closing"]&&this["_insert_"+b+"_closing"][a]&&this["_insert_"+b+"_closing"][a].length>0){return this["_insert_"+b+"_closing"][a].pop()}return""};WYMeditor.WymCssLexer=function(b,a){var a=(typeof a=="undefined"?true:a);jQuery.extend(this,new WYMeditor.Lexer(b,(a?"Ignore":"WymCss")));this.mapHandler("WymCss","Ignore");if(a==true){this.addEntryPattern("/\\\x2a[<\\s]*WYMeditor[>\\s]*\\\x2a/","Ignore","WymCss");this.addExitPattern("/\\\x2a[</\\s]*WYMeditor[>\\s]*\\\x2a/","WymCss")}this.addSpecialPattern("[\\sa-z1-6]*\\\x2e[a-z-_0-9]+","WymCss","WymCssStyleDeclaration");this.addEntryPattern("/\\\x2a","WymCss","WymCssComment");this.addExitPattern("\\\x2a/","WymCssComment");this.addEntryPattern("\x7b","WymCss","WymCssStyle");this.addExitPattern("\x7d","WymCssStyle");this.addEntryPattern("/\\\x2a","WymCssStyle","WymCssFeedbackStyle");this.addExitPattern("\\\x2a/","WymCssFeedbackStyle");return this};WYMeditor.WymCssParser=function(){this._in_style=false;this._has_title=false;this.only_wym_blocks=true;this.css_settings={classesItems:[],editorStyles:[],dialogStyles:[]};return this};WYMeditor.WymCssParser.prototype.parse=function(a,b){var b=(typeof b=="undefined"?this.only_wym_blocks:b);this._Lexer=new WYMeditor.WymCssLexer(this,b);this._Lexer.parse(a)};WYMeditor.WymCssParser.prototype.Ignore=function(a,b){return true};WYMeditor.WymCssParser.prototype.WymCssComment=function(b,a){if(b.match(/end[a-z0-9\s]*wym[a-z0-9\s]*/mi)){return false}if(a==WYMeditor.LEXER_UNMATCHED){if(!this._in_style){this._has_title=true;this._current_item={title:WYMeditor.Helper.trim(b)}}else{if(this._current_item[this._current_element]){if(!this._current_item[this._current_element].expressions){this._current_item[this._current_element].expressions=[b]}else{this._current_item[this._current_element].expressions.push(b)}}}this._in_style=true}return true};WYMeditor.WymCssParser.prototype.WymCssStyle=function(b,a){if(a==WYMeditor.LEXER_UNMATCHED){b=WYMeditor.Helper.trim(b);if(b!=""){this._current_item[this._current_element].style=b}}else{if(a==WYMeditor.LEXER_EXIT){this._in_style=false;this._has_title=false;this.addStyleSetting(this._current_item)}}return true};WYMeditor.WymCssParser.prototype.WymCssFeedbackStyle=function(b,a){if(a==WYMeditor.LEXER_UNMATCHED){this._current_item[this._current_element].feedback_style=b.replace(/^([\s\/\*]*)|([\s\/\*]*)$/gm,"")}return true};WYMeditor.WymCssParser.prototype.WymCssStyleDeclaration=function(b){b=b.replace(/^([\s\.]*)|([\s\.*]*)$/gm,"");var a="";if(b.indexOf(".")>0){var c=b.split(".");this._current_element=c[1];var a=c[0]}else{this._current_element=b}if(!this._has_title){this._current_item={title:(!a?"":a.toUpperCase()+": ")+this._current_element};this._has_title=true}if(!this._current_item[this._current_element]){this._current_item[this._current_element]={name:this._current_element}}if(a){if(!this._current_item[this._current_element].tags){this._current_item[this._current_element].tags=[a]}else{this._current_item[this._current_element].tags.push(a)}}return true};WYMeditor.WymCssParser.prototype.addStyleSetting=function(a){for(var b in a){var c=a[b];if(typeof c=="object"&&b!="title"){this.css_settings.classesItems.push({name:WYMeditor.Helper.trim(c.name),title:a.title,expr:WYMeditor.Helper.trim((c.expressions||c.tags).join(", "))});if(c.feedback_style){this.css_settings.editorStyles.push({name:"."+WYMeditor.Helper.trim(c.name),css:c.feedback_style})}if(c.style){this.css_settings.dialogStyles.push({name:"."+WYMeditor.Helper.trim(c.name),css:c.style})}}}};jQuery.fn.isPhantomNode=function(){if(this[0].nodeType==3){return !(/[^\t\n\r ]/.test(this[0].data))}return false};WYMeditor.isPhantomNode=function(a){if(a.nodeType==3){return !(/[^\t\n\r ]/.test(a.data))}return false};WYMeditor.isPhantomString=function(a){return !(/[^\t\n\r ]/.test(a))};jQuery.fn.parentsOrSelf=function(b){var a=this;if(a[0].nodeType==3){a=a.parents().slice(0,1)}if(a.filter(b).size()==1){return a}else{return a.parents(b).slice(0,1)}};WYMeditor.Helper={replaceAll:function(d,a,c){var b=new RegExp(a,"g");return(d.replace(b,c))},insertAt:function(b,a,c){return(b.substr(0,c)+a+b.substring(c))},trim:function(a){return a.replace(/^(\s*)|(\s*)$/gm,"")},contains:function(a,c){for(var b=0;b<a.length;b++){if(a[b]===c){return true}}return false},indexOf:function(a,d){var b=-1;for(var c=0;c<a.length;c++){if(a[c]==d){b=c;break}}return(b)},findByName:function(a,b){for(var c=0;c<a.length;c++){var d=a[c];if(d.name==b){return(d)}}return(null)}};WYMeditor.WymClassExplorer=function(a){this._wym=a;this._class="className";this._newLine="\r\n"};WYMeditor.WymClassExplorer.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentWindow.document;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);jQuery(this._doc.body).html(this._wym._html);var wym=this;this._doc.body.onfocus=function(){wym._doc.designMode="on";wym._doc=iframe.contentWindow.document};this._doc.onbeforedeactivate=function(){wym.saveCaret()};this._doc.onkeyup=function(){wym.saveCaret();wym.keyup()};this._doc.onclick=function(){wym.saveCaret()};this._doc.body.onbeforepaste=function(){wym._iframe.contentWindow.event.returnValue=false};this._doc.body.onpaste=function(){wym._iframe.contentWindow.event.returnValue=false;wym.paste(window.clipboardData.getData("Text"))};if(this._initialized){if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()}this._initialized=true;this._doc.designMode="on";try{this._doc=iframe.contentWindow.document}catch(e){}};WYMeditor.WymClassExplorer.prototype._exec=function(c,d){switch(c){case WYMeditor.INDENT:case WYMeditor.OUTDENT:var a=this.findUp(this.container(),WYMeditor.LI);if(a){var b=a.parentNode.parentNode;if(a.parentNode.childNodes.length>1||b.tagName.toLowerCase()==WYMeditor.OL||b.tagName.toLowerCase()==WYMeditor.UL){this._doc.execCommand(c)}}break;default:if(d){this._doc.execCommand(c,false,d)}else{this._doc.execCommand(c)}break}this.listen()};WYMeditor.WymClassExplorer.prototype.selected=function(){var a=this._iframe.contentWindow.document.caretPos;if(a!=null){if(a.parentElement!=undefined){return(a.parentElement())}}};WYMeditor.WymClassExplorer.prototype.saveCaret=function(){this._doc.caretPos=this._doc.selection.createRange()};WYMeditor.WymClassExplorer.prototype.addCssRule=function(a,b){a.addRule(b.name,b.css)};WYMeditor.WymClassExplorer.prototype.insert=function(b){var a=this._doc.selection.createRange();if(jQuery(a.parentElement()).parents(this._options.iframeBodySelector).is("*")){try{a.pasteHTML(b)}catch(c){}}else{this.paste(b)}};WYMeditor.WymClassExplorer.prototype.wrap=function(d,b){var a=this._doc.selection.createRange();if(jQuery(a.parentElement()).parents(this._options.iframeBodySelector).is("*")){try{a.pasteHTML(d+a.text+b)}catch(c){}}};WYMeditor.WymClassExplorer.prototype.unwrap=function(){var a=this._doc.selection.createRange();if(jQuery(a.parentElement()).parents(this._options.iframeBodySelector).is("*")){try{var c=a.text;this._exec("Cut");a.pasteHTML(c)}catch(b){}}};WYMeditor.WymClassExplorer.prototype.keyup=function(){this._selected_image=null};WYMeditor.WymClassExplorer.prototype.setFocusToNode=function(b){var a=this._doc.selection.createRange();a.moveToElementText(b);a.collapse(false);a.move("character",-1);a.select();b.focus()};WYMeditor.WymClassMozilla=function(a){this._wym=a;this._class="class";this._newLine="\n"};WYMeditor.WymClassMozilla.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentDocument;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);this.html(this._wym._html);this.enableDesignMode();if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();jQuery(this._doc).bind("keydown",this.keydown);jQuery(this._doc).bind("keyup",this.keyup);jQuery(this._doc).bind("focus",this.enableDesignMode);if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()};WYMeditor.WymClassMozilla.prototype.html=function(a){if(typeof a==="string"){try{this._doc.designMode="off"}catch(b){}a=a.replace(/<em(\b[^>]*)>/gi,"<i$1>").replace(/<\/em>/gi,"</i>").replace(/<strong(\b[^>]*)>/gi,"<b$1>").replace(/<\/strong>/gi,"</b>");jQuery(this._doc.body).html(a);this.enableDesignMode()}else{return(jQuery(this._doc.body).html())}};WYMeditor.WymClassMozilla.prototype._exec=function(e,g){if(!this.selected()){return(false)}switch(e){case WYMeditor.INDENT:case WYMeditor.OUTDENT:var f=this.selected();var d=this._iframe.contentWindow.getSelection();var b=d.anchorNode;if(b.nodeName=="#text"){b=b.parentNode}f=this.findUp(f,WYMeditor.BLOCKS);b=this.findUp(b,WYMeditor.BLOCKS);if(f&&f==b&&f.tagName.toLowerCase()==WYMeditor.LI){var c=f.parentNode.parentNode;if(f.parentNode.childNodes.length>1||c.tagName.toLowerCase()==WYMeditor.OL||c.tagName.toLowerCase()==WYMeditor.UL){this._doc.execCommand(e,"",null)}}break;default:if(g){this._doc.execCommand(e,"",g)}else{this._doc.execCommand(e,"",null)}}var a=this.selected();if(a.tagName.toLowerCase()==WYMeditor.BODY){this._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}this.listen()};WYMeditor.WymClassMozilla.prototype.selected=function(){var b=this._iframe.contentWindow.getSelection();var a=b.focusNode;if(a){if(a.nodeName=="#text"){return(a.parentNode)}else{return(a)}}else{return(null)}};WYMeditor.WymClassMozilla.prototype.addCssRule=function(a,b){a.insertRule(b.name+" {"+b.css+"}",a.cssRules.length)};WYMeditor.WymClassMozilla.prototype.keydown=function(b){var c=WYMeditor.INSTANCES[this.title];var a=null;if(b.ctrlKey){if(b.keyCode==66){c._exec(WYMeditor.BOLD);return false}if(b.keyCode==73){c._exec(WYMeditor.ITALIC);return false}}else{if(b.keyCode==13){if(!b.shiftKey){a=c.selected();if(a&&a.tagName.toLowerCase()==WYMeditor.PRE){b.preventDefault();c.insert("<p></p>")}}}}};WYMeditor.WymClassMozilla.prototype.keyup=function(b){var d=WYMeditor.INSTANCES[this.title];d._selected_image=null;var a=null;if(b.keyCode==13&&!b.shiftKey){jQuery(d._doc.body).children(WYMeditor.BR).remove()}else{if(b.keyCode!=8&&b.keyCode!=17&&b.keyCode!=46&&b.keyCode!=224&&!b.metaKey&&!b.ctrlKey){a=d.selected();var c=a.tagName.toLowerCase();if(c=="strong"||c=="b"||c=="em"||c=="i"||c=="sub"||c=="sup"||c=="a"){c=a.parentNode.tagName.toLowerCase()}if(c==WYMeditor.BODY){d._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}}}};WYMeditor.WymClassMozilla.prototype.enableDesignMode=function(){if(this.designMode=="off"){try{this.designMode="on";this.execCommand("styleWithCSS","",false)}catch(a){}}};WYMeditor.WymClassMozilla.prototype.setFocusToNode=function(c){var a=document.createRange();a.selectNode(c);var b=this._iframe.contentWindow.getSelection();b.addRange(a);b.collapse(c,c.childNodes.length);this._iframe.contentWindow.focus()};WYMeditor.WymClassMozilla.prototype.openBlockTag=function(a,c){var c=this.validator.getValidTagAttributes(a,c);if(a=="span"&&c.style){var b=this.getTagForStyle(c.style);if(b){this._tag_stack.pop();var a=b;this._tag_stack.push(b);c.style=""}else{return}}this.output+=this.helper.tag(a,c,true)};WYMeditor.WymClassMozilla.prototype.getTagForStyle=function(a){if(/bold/.test(a)){return"strong"}if(/italic/.test(a)){return"em"}if(/sub/.test(a)){return"sub"}if(/sub/.test(a)){return"super"}return false};WYMeditor.WymClassOpera=function(a){this._wym=a;this._class="class";this._newLine="\r\n"};WYMeditor.WymClassOpera.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentWindow.document;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);this._doc.designMode="on";this.html(this._wym._html);if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();jQuery(this._doc).bind("keydown",this.keydown);jQuery(this._doc).bind("keyup",this.keyup);if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()};WYMeditor.WymClassOpera.prototype._exec=function(a,b){if(b){this._doc.execCommand(a,false,b)}else{this._doc.execCommand(a)}this.listen()};WYMeditor.WymClassOpera.prototype.selected=function(){var b=this._iframe.contentWindow.getSelection();var a=b.focusNode;if(a){if(a.nodeName=="#text"){return(a.parentNode)}else{return(a)}}else{return(null)}};WYMeditor.WymClassOpera.prototype.addCssRule=function(a,b){a.insertRule(b.name+" {"+b.css+"}",a.cssRules.length)};WYMeditor.WymClassOpera.prototype.keydown=function(a){var c=WYMeditor.INSTANCES[this.title];var b=c._iframe.contentWindow.getSelection();startNode=b.getRangeAt(0).startContainer;if(!jQuery(startNode).parentsOrSelf(WYMeditor.MAIN_CONTAINERS.join(","))[0]&&!jQuery(startNode).parentsOrSelf("li")&&a.keyCode!=WYMeditor.KEY.ENTER&&a.keyCode!=WYMeditor.KEY.LEFT&&a.keyCode!=WYMeditor.KEY.UP&&a.keyCode!=WYMeditor.KEY.RIGHT&&a.keyCode!=WYMeditor.KEY.DOWN&&a.keyCode!=WYMeditor.KEY.BACKSPACE&&a.keyCode!=WYMeditor.KEY.DELETE){c._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}};WYMeditor.WymClassOpera.prototype.keyup=function(a){var b=WYMeditor.INSTANCES[this.title];b._selected_image=null};WYMeditor.WymClassOpera.prototype.setFocusToNode=function(a){};WYMeditor.WymClassSafari=function(a){this._wym=a;this._class="class";this._newLine="\n"};WYMeditor.WymClassSafari.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentDocument;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);this._doc.designMode="on";this.html(this._wym._html);if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();jQuery(this._doc).bind("keydown",this.keydown);jQuery(this._doc).bind("keyup",this.keyup);if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()};WYMeditor.WymClassSafari.prototype._exec=function(e,g){if(!this.selected()){return(false)}switch(e){case WYMeditor.INDENT:case WYMeditor.OUTDENT:var f=this.selected();var d=this._iframe.contentWindow.getSelection();var b=d.anchorNode;if(b.nodeName=="#text"){b=b.parentNode}f=this.findUp(f,WYMeditor.BLOCKS);b=this.findUp(b,WYMeditor.BLOCKS);if(f&&f==b&&f.tagName.toLowerCase()==WYMeditor.LI){var c=f.parentNode.parentNode;if(f.parentNode.childNodes.length>1||c.tagName.toLowerCase()==WYMeditor.OL||c.tagName.toLowerCase()==WYMeditor.UL){this._doc.execCommand(e,"",null)}}break;case WYMeditor.INSERT_ORDEREDLIST:case WYMeditor.INSERT_UNORDEREDLIST:this._doc.execCommand(e,"",null);var f=this.selected();var a=this.findUp(f,WYMeditor.MAIN_CONTAINERS);if(a){jQuery(a).replaceWith(jQuery(a).html())}break;default:if(g){this._doc.execCommand(e,"",g)}else{this._doc.execCommand(e,"",null)}}var a=this.selected();if(a&&a.tagName.toLowerCase()==WYMeditor.BODY){this._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}this.listen()};WYMeditor.WymClassSafari.prototype.selected=function(){var b=this._iframe.contentWindow.getSelection();var a=b.focusNode;if(a){if(a.nodeName=="#text"){return(a.parentNode)}else{return(a)}}else{return(null)}};WYMeditor.WymClassSafari.prototype.addCssRule=function(a,b){a.insertRule(b.name+" {"+b.css+"}",a.cssRules.length)};WYMeditor.WymClassSafari.prototype.keydown=function(a){var b=WYMeditor.INSTANCES[this.title];if(a.ctrlKey){if(a.keyCode==66){b._exec(WYMeditor.BOLD);return false}if(a.keyCode==73){b._exec(WYMeditor.ITALIC);return false}}};WYMeditor.WymClassSafari.prototype.keyup=function(b){var d=WYMeditor.INSTANCES[this.title];d._selected_image=null;var a=null;if(b.keyCode==13&&!b.shiftKey){jQuery(d._doc.body).children(WYMeditor.BR).remove();a=d.selected();if(a&&a.tagName.toLowerCase()==WYMeditor.PRE){d._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}}if(b.keyCode==13&&b.shiftKey){d._exec("InsertLineBreak")}if(b.keyCode!=8&&b.keyCode!=17&&b.keyCode!=46&&b.keyCode!=224&&!b.metaKey&&!b.ctrlKey){a=d.selected();var c=a.tagName.toLowerCase();if(c=="strong"||c=="b"||c=="em"||c=="i"||c=="sub"||c=="sup"||c=="a"||c=="span"){c=a.parentNode.tagName.toLowerCase()}if(c==WYMeditor.BODY||c==WYMeditor.DIV){d._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}}};WYMeditor.WymClassSafari.prototype.setFocusToNode=function(c){var a=this._iframe.contentDocument.createRange();a.selectNode(c);var b=this._iframe.contentWindow.getSelection();b.addRange(a);b.collapse(c,c.childNodes.length);this._iframe.contentWindow.focus()};WYMeditor.WymClassSafari.prototype.openBlockTag=function(a,c){var c=this.validator.getValidTagAttributes(a,c);if(a=="span"&&c.style){var b=this.getTagForStyle(c.style);if(b){this._tag_stack.pop();var a=b;this._tag_stack.push(b);c.style="";if(typeof c["class"]=="string"){c["class"]=c["class"].replace(/apple-style-span/gi,"")}}else{return}}this.output+=this.helper.tag(a,c,true)};WYMeditor.WymClassSafari.prototype.getTagForStyle=function(a){if(/bold/.test(a)){return"strong"}if(/italic/.test(a)){return"em"}if(/sub/.test(a)){return"sub"}if(/super/.test(a)){return"sup"}return false}; \ No newline at end of file +if(!WYMeditor){var WYMeditor={}}(function(){if(!window.console||!console.firebug){var b=["log","debug","info","warn","error","assert","dir","dirxml","group","groupEnd","time","timeEnd","count","trace","profile","profileEnd"];WYMeditor.console={};for(var a=0;a<b.length;++a){WYMeditor.console[b[a]]=function(){}}}else{WYMeditor.console=window.console}})();jQuery.extend(WYMeditor,{VERSION:"0.5-rc1",INSTANCES:[],STRINGS:[],SKINS:[],NAME:"name",INDEX:"{Wym_Index}",WYM_INDEX:"wym_index",BASE_PATH:"{Wym_Base_Path}",CSS_PATH:"{Wym_Css_Path}",WYM_PATH:"{Wym_Wym_Path}",SKINS_DEFAULT_PATH:"skins/",SKINS_DEFAULT_CSS:"skin.css",SKINS_DEFAULT_JS:"skin.js",LANG_DEFAULT_PATH:"lang/",IFRAME_BASE_PATH:"{Wym_Iframe_Base_Path}",IFRAME_DEFAULT:"iframe/default/",JQUERY_PATH:"{Wym_Jquery_Path}",DIRECTION:"{Wym_Direction}",LOGO:"{Wym_Logo}",TOOLS:"{Wym_Tools}",TOOLS_ITEMS:"{Wym_Tools_Items}",TOOL_NAME:"{Wym_Tool_Name}",TOOL_TITLE:"{Wym_Tool_Title}",TOOL_CLASS:"{Wym_Tool_Class}",CLASSES:"{Wym_Classes}",CLASSES_ITEMS:"{Wym_Classes_Items}",CLASS_NAME:"{Wym_Class_Name}",CLASS_TITLE:"{Wym_Class_Title}",CONTAINERS:"{Wym_Containers}",CONTAINERS_ITEMS:"{Wym_Containers_Items}",CONTAINER_NAME:"{Wym_Container_Name}",CONTAINER_TITLE:"{Wym_Containers_Title}",CONTAINER_CLASS:"{Wym_Container_Class}",HTML:"{Wym_Html}",IFRAME:"{Wym_Iframe}",STATUS:"{Wym_Status}",DIALOG_TITLE:"{Wym_Dialog_Title}",DIALOG_BODY:"{Wym_Dialog_Body}",STRING:"string",BODY:"body",DIV:"div",P:"p",H1:"h1",H2:"h2",H3:"h3",H4:"h4",H5:"h5",H6:"h6",PRE:"pre",BLOCKQUOTE:"blockquote",A:"a",BR:"br",IMG:"img",TABLE:"table",TD:"td",TH:"th",UL:"ul",OL:"ol",LI:"li",CLASS:"class",HREF:"href",SRC:"src",TITLE:"title",ALT:"alt",DIALOG_LINK:"Link",DIALOG_IMAGE:"Image",DIALOG_TABLE:"Table",DIALOG_PASTE:"Paste_From_Word",BOLD:"Bold",ITALIC:"Italic",CREATE_LINK:"CreateLink",INSERT_IMAGE:"InsertImage",INSERT_TABLE:"InsertTable",INSERT_HTML:"InsertHTML",PASTE:"Paste",INDENT:"Indent",OUTDENT:"Outdent",TOGGLE_HTML:"ToggleHtml",FORMAT_BLOCK:"FormatBlock",PREVIEW:"Preview",UNLINK:"Unlink",INSERT_UNORDEREDLIST:"InsertUnorderedList",INSERT_ORDEREDLIST:"InsertOrderedList",MAIN_CONTAINERS:new Array("p","h1","h2","h3","h4","h5","h6","pre","blockquote"),BLOCKS:new Array("address","blockquote","div","dl","fieldset","form","h1","h2","h3","h4","h5","h6","hr","noscript","ol","p","pre","table","ul","dd","dt","li","tbody","td","tfoot","th","thead","tr"),KEY:{BACKSPACE:8,ENTER:13,END:35,HOME:36,LEFT:37,UP:38,RIGHT:39,DOWN:40,CURSOR:new Array(37,38,39,40),DELETE:46},NODE:{ELEMENT:1,ATTRIBUTE:2,TEXT:3},editor:function(b,a){this._index=WYMeditor.INSTANCES.push(this)-1;this._element=b;this._options=a;this._html=jQuery(b).val();if(this._options.html){this._html=this._options.html}this._options.basePath=this._options.basePath||this.computeBasePath();this._options.skinPath=this._options.skinPath||this._options.basePath+WYMeditor.SKINS_DEFAULT_PATH+this._options.skin+"/";this._options.wymPath=this._options.wymPath||this.computeWymPath();this._options.langPath=this._options.langPath||this._options.basePath+WYMeditor.LANG_DEFAULT_PATH;this._options.iframeBasePath=this._options.iframeBasePath||this._options.basePath+WYMeditor.IFRAME_DEFAULT;this._options.jQueryPath=this._options.jQueryPath||this.computeJqueryPath();this.init()}});jQuery.fn.wymeditor=function(a){a=jQuery.extend({html:"",basePath:false,skinPath:false,wymPath:false,iframeBasePath:false,jQueryPath:false,styles:false,stylesheet:false,skin:"default",initSkin:true,loadSkin:true,lang:"en",direction:"ltr",boxHtml:"<div class='wym_box'><div class='wym_area_top'>"+WYMeditor.TOOLS+"</div><div class='wym_area_left'></div><div class='wym_area_right'>"+WYMeditor.CONTAINERS+WYMeditor.CLASSES+"</div><div class='wym_area_main'>"+WYMeditor.HTML+WYMeditor.IFRAME+WYMeditor.STATUS+"</div><div class='wym_area_bottom'>"+WYMeditor.LOGO+"</div></div>",logoHtml:"<a class='wym_wymeditor_link' href='http://www.wymeditor.org/'>WYMeditor</a>",iframeHtml:"<div class='wym_iframe wym_section'><iframe src='/page/get_editor_iframe' onload='this.contentWindow.parent.WYMeditor.INSTANCES["+WYMeditor.INDEX+"].initIframe(this)'></iframe></div>",editorStyles:[],toolsHtml:"<div class='wym_tools wym_section'><h2>{Tools}</h2><ul>"+WYMeditor.TOOLS_ITEMS+"</ul></div>",toolsItemHtml:"<li class='"+WYMeditor.TOOL_CLASS+"'><a href='#' name='"+WYMeditor.TOOL_NAME+"' title='"+WYMeditor.TOOL_TITLE+"'>"+WYMeditor.TOOL_TITLE+"</a></li>",toolsItems:[{name:"Bold",title:"Strong",css:"wym_tools_strong"},{name:"Italic",title:"Emphasis",css:"wym_tools_emphasis"},{name:"Superscript",title:"Superscript",css:"wym_tools_superscript"},{name:"Subscript",title:"Subscript",css:"wym_tools_subscript"},{name:"InsertOrderedList",title:"Ordered_List",css:"wym_tools_ordered_list"},{name:"InsertUnorderedList",title:"Unordered_List",css:"wym_tools_unordered_list"},{name:"Indent",title:"Indent",css:"wym_tools_indent"},{name:"Outdent",title:"Outdent",css:"wym_tools_outdent"},{name:"Undo",title:"Undo",css:"wym_tools_undo"},{name:"Redo",title:"Redo",css:"wym_tools_redo"},{name:"CreateLink",title:"Link",css:"wym_tools_link"},{name:"Unlink",title:"Unlink",css:"wym_tools_unlink"},{name:"InsertImage",title:"Image",css:"wym_tools_image"},{name:"InsertTable",title:"Table",css:"wym_tools_table"},{name:"Paste",title:"Paste_From_Word",css:"wym_tools_paste"},{name:"ToggleHtml",title:"HTML",css:"wym_tools_html"},{name:"Preview",title:"Preview",css:"wym_tools_preview"}],containersHtml:"<div class='wym_containers wym_section'><h2>{Containers}</h2><ul>"+WYMeditor.CONTAINERS_ITEMS+"</ul></div>",containersItemHtml:"<li class='"+WYMeditor.CONTAINER_CLASS+"'><a href='#' name='"+WYMeditor.CONTAINER_NAME+"'>"+WYMeditor.CONTAINER_TITLE+"</a></li>",containersItems:[{name:"P",title:"Paragraph",css:"wym_containers_p"},{name:"H1",title:"Heading_1",css:"wym_containers_h1"},{name:"H2",title:"Heading_2",css:"wym_containers_h2"},{name:"H3",title:"Heading_3",css:"wym_containers_h3"},{name:"H4",title:"Heading_4",css:"wym_containers_h4"},{name:"H5",title:"Heading_5",css:"wym_containers_h5"},{name:"H6",title:"Heading_6",css:"wym_containers_h6"},{name:"PRE",title:"Preformatted",css:"wym_containers_pre"},{name:"BLOCKQUOTE",title:"Blockquote",css:"wym_containers_blockquote"},{name:"TH",title:"Table_Header",css:"wym_containers_th"}],classesHtml:"<div class='wym_classes wym_section'><h2>{Classes}</h2><ul>"+WYMeditor.CLASSES_ITEMS+"</ul></div>",classesItemHtml:"<li><a href='#' name='"+WYMeditor.CLASS_NAME+"'>"+WYMeditor.CLASS_TITLE+"</a></li>",classesItems:[],statusHtml:"<div class='wym_status wym_section'><h2>{Status}</h2></div>",htmlHtml:"<div class='wym_html wym_section'><h2>{Source_Code}</h2><textarea class='wym_html_val'></textarea></div>",boxSelector:".wym_box",toolsSelector:".wym_tools",toolsListSelector:" ul",containersSelector:".wym_containers",classesSelector:".wym_classes",htmlSelector:".wym_html",iframeSelector:".wym_iframe iframe",iframeBodySelector:".wym_iframe",statusSelector:".wym_status",toolSelector:".wym_tools a",containerSelector:".wym_containers a",classSelector:".wym_classes a",htmlValSelector:".wym_html_val",hrefSelector:".wym_href",srcSelector:".wym_src",titleSelector:".wym_title",altSelector:".wym_alt",textSelector:".wym_text",rowsSelector:".wym_rows",colsSelector:".wym_cols",captionSelector:".wym_caption",summarySelector:".wym_summary",submitSelector:".wym_submit",cancelSelector:".wym_cancel",previewSelector:"",dialogTypeSelector:".wym_dialog_type",dialogLinkSelector:".wym_dialog_link",dialogImageSelector:".wym_dialog_image",dialogTableSelector:".wym_dialog_table",dialogPasteSelector:".wym_dialog_paste",dialogPreviewSelector:".wym_dialog_preview",updateSelector:".wymupdate",updateEvent:"click",dialogFeatures:"menubar=no,titlebar=no,toolbar=no,resizable=no,width=560,height=300,top=0,left=0",dialogFeaturesPreview:"menubar=no,titlebar=no,toolbar=no,resizable=no,scrollbars=yes,width=560,height=300,top=0,left=0",dialogHtml:"<!DOCTYPE html PUBLIC '-//W3C//DTD XHTML 1.0 Strict//EN' 'http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd'><html dir='"+WYMeditor.DIRECTION+"'><head><link rel='stylesheet' type='text/css' media='screen' href='"+WYMeditor.CSS_PATH+"' /><title>"+WYMeditor.DIALOG_TITLE+"</title><script type='text/javascript' src='"+WYMeditor.JQUERY_PATH+"'><\/script><script type='text/javascript' src='"+WYMeditor.WYM_PATH+"'><\/script></head>"+WYMeditor.DIALOG_BODY+"</html>",dialogLinkHtml:"<body class='wym_dialog wym_dialog_link' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><fieldset><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_LINK+"' /><legend>{Link}</legend><div class='row'><label>{URL}</label><input type='text' class='wym_href' value='' size='40' /></div><div class='row'><label>{Title}</label><input type='text' class='wym_title' value='' size='40' /></div><div class='row row-indent'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogImageHtml:"<body class='wym_dialog wym_dialog_image' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><fieldset><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_IMAGE+"' /><legend>{Image}</legend><div class='row'><label>{URL}</label><input type='text' class='wym_src' value='' size='40' /></div><div class='row'><label>{Alternative_Text}</label><input type='text' class='wym_alt' value='' size='40' /></div><div class='row'><label>{Title}</label><input type='text' class='wym_title' value='' size='40' /></div><div class='row row-indent'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogTableHtml:"<body class='wym_dialog wym_dialog_table' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><fieldset><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_TABLE+"' /><legend>{Table}</legend><div class='row'><label>{Caption}</label><input type='text' class='wym_caption' value='' size='40' /></div><div class='row'><label>{Summary}</label><input type='text' class='wym_summary' value='' size='40' /></div><div class='row'><label>{Number_Of_Rows}</label><input type='text' class='wym_rows' value='3' size='3' /></div><div class='row'><label>{Number_Of_Cols}</label><input type='text' class='wym_cols' value='2' size='3' /></div><div class='row row-indent'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogPasteHtml:"<body class='wym_dialog wym_dialog_paste' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_PASTE+"' /><fieldset><legend>{Paste_From_Word}</legend><div class='row'><textarea class='wym_text' rows='10' cols='50'></textarea></div><div class='row'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogPreviewHtml:"<body class='wym_dialog wym_dialog_preview' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'></body>",dialogStyles:[],stringDelimiterLeft:"{",stringDelimiterRight:"}",preInit:null,preBind:null,postInit:null,preInitDialog:null,postInitDialog:null},a);return this.each(function(){new WYMeditor.editor(jQuery(this),a)})};jQuery.extend({wymeditors:function(a){return(WYMeditor.INSTANCES[a])}});WYMeditor.editor.prototype.init=function(){if(jQuery.browser.msie){var WymClass=new WYMeditor.WymClassExplorer(this)}else{if(jQuery.browser.mozilla){var WymClass=new WYMeditor.WymClassMozilla(this)}else{if(jQuery.browser.opera){var WymClass=new WYMeditor.WymClassOpera(this)}else{if(jQuery.browser.safari||jQuery.browser.chrome){var WymClass=new WYMeditor.WymClassSafari(this)}}}}if(WymClass){if(jQuery.isFunction(this._options.preInit)){this._options.preInit(this)}var SaxListener=new WYMeditor.XhtmlSaxListener();jQuery.extend(SaxListener,WymClass);this.parser=new WYMeditor.XhtmlParser(SaxListener);if(this._options.styles||this._options.stylesheet){this.configureEditorUsingRawCss()}this.helper=new WYMeditor.XmlHelper();for(var prop in WymClass){this[prop]=WymClass[prop]}this._box=jQuery(this._element).hide().after(this._options.boxHtml).next().addClass("wym_box_"+this._index);if(jQuery.isFunction(jQuery.fn.data)){jQuery.data(this._box.get(0),WYMeditor.WYM_INDEX,this._index);jQuery.data(this._element.get(0),WYMeditor.WYM_INDEX,this._index)}var h=WYMeditor.Helper;var iframeHtml=this._options.iframeHtml;iframeHtml=h.replaceAll(iframeHtml,WYMeditor.INDEX,this._index);iframeHtml=h.replaceAll(iframeHtml,WYMeditor.IFRAME_BASE_PATH,this._options.iframeBasePath);var boxHtml=jQuery(this._box).html();boxHtml=h.replaceAll(boxHtml,WYMeditor.LOGO,this._options.logoHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.TOOLS,this._options.toolsHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.CONTAINERS,this._options.containersHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.CLASSES,this._options.classesHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.HTML,this._options.htmlHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.IFRAME,iframeHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.STATUS,this._options.statusHtml);var aTools=eval(this._options.toolsItems);var sTools="";for(var i=0;i<aTools.length;i++){var oTool=aTools[i];if(oTool.name&&oTool.title){var sTool=this._options.toolsItemHtml}var sTool=h.replaceAll(sTool,WYMeditor.TOOL_NAME,oTool.name);sTool=h.replaceAll(sTool,WYMeditor.TOOL_TITLE,this._options.stringDelimiterLeft+oTool.title+this._options.stringDelimiterRight);sTool=h.replaceAll(sTool,WYMeditor.TOOL_CLASS,oTool.css);sTools+=sTool}boxHtml=h.replaceAll(boxHtml,WYMeditor.TOOLS_ITEMS,sTools);var aClasses=eval(this._options.classesItems);var sClasses="";for(var i=0;i<aClasses.length;i++){var oClass=aClasses[i];if(oClass.name&&oClass.title){var sClass=this._options.classesItemHtml}sClass=h.replaceAll(sClass,WYMeditor.CLASS_NAME,oClass.name);sClass=h.replaceAll(sClass,WYMeditor.CLASS_TITLE,oClass.title);sClasses+=sClass}boxHtml=h.replaceAll(boxHtml,WYMeditor.CLASSES_ITEMS,sClasses);var aContainers=eval(this._options.containersItems);var sContainers="";for(var i=0;i<aContainers.length;i++){var oContainer=aContainers[i];if(oContainer.name&&oContainer.title){var sContainer=this._options.containersItemHtml}sContainer=h.replaceAll(sContainer,WYMeditor.CONTAINER_NAME,oContainer.name);sContainer=h.replaceAll(sContainer,WYMeditor.CONTAINER_TITLE,this._options.stringDelimiterLeft+oContainer.title+this._options.stringDelimiterRight);sContainer=h.replaceAll(sContainer,WYMeditor.CONTAINER_CLASS,oContainer.css);sContainers+=sContainer}boxHtml=h.replaceAll(boxHtml,WYMeditor.CONTAINERS_ITEMS,sContainers);boxHtml=this.replaceStrings(boxHtml);jQuery(this._box).html(boxHtml);jQuery(this._box).find(this._options.htmlSelector).hide();this.loadSkin()}};WYMeditor.editor.prototype.bindEvents=function(){var wym=this;jQuery(this._box).find(this._options.toolSelector).click(function(){wym._iframe.contentWindow.focus();wym.exec(jQuery(this).attr(WYMeditor.NAME));return(false)});jQuery(this._box).find(this._options.containerSelector).click(function(){wym.container(jQuery(this).attr(WYMeditor.NAME));return(false)});jQuery(this._box).find(this._options.htmlValSelector).keyup(function(){jQuery(wym._doc.body).html(jQuery(this).val())}).focus(function(){jQuery(this).toggleClass("hasfocus")}).blur(function(){jQuery(this).toggleClass("hasfocus")});jQuery(this._box).find(this._options.classSelector).click(function(){var aClasses=eval(wym._options.classesItems);var sName=jQuery(this).attr(WYMeditor.NAME);var oClass=WYMeditor.Helper.findByName(aClasses,sName);if(oClass){var jqexpr=oClass.expr;wym.toggleClass(sName,jqexpr)}wym._iframe.contentWindow.focus();return(false)});jQuery(this._options.updateSelector).bind(this._options.updateEvent,function(){wym.update()})};WYMeditor.editor.prototype.ready=function(){return(this._doc!=null)};WYMeditor.editor.prototype.box=function(){return(this._box)};WYMeditor.editor.prototype.html=function(a){if(typeof a==="string"){jQuery(this._doc.body).html(a)}else{return(jQuery(this._doc.body).html())}};WYMeditor.editor.prototype.xhtml=function(){return this.parser.parse(this.html())};WYMeditor.editor.prototype.exec=function(b){switch(b){case WYMeditor.CREATE_LINK:var a=this.container();if(a||this._selected_image){this.dialog(WYMeditor.DIALOG_LINK)}break;case WYMeditor.INSERT_IMAGE:this.dialog(WYMeditor.DIALOG_IMAGE);break;case WYMeditor.INSERT_TABLE:this.dialog(WYMeditor.DIALOG_TABLE);break;case WYMeditor.PASTE:this.dialog(WYMeditor.DIALOG_PASTE);break;case WYMeditor.TOGGLE_HTML:this.update();this.toggleHtml();if(!jQuery(this._box).find(this._options.htmlSelector).is(":visible")){this.listen()}break;case WYMeditor.PREVIEW:this.dialog(WYMeditor.PREVIEW,this._options.dialogFeaturesPreview);break;default:this._exec(b);break}};WYMeditor.editor.prototype.container=function(a){if(a){var d=null;if(a.toLowerCase()==WYMeditor.TH){d=this.container();switch(d.tagName.toLowerCase()){case WYMeditor.TD:case WYMeditor.TH:break;default:var e=new Array(WYMeditor.TD,WYMeditor.TH);d=this.findUp(this.container(),e);break}if(d!=null){a=(d.tagName.toLowerCase()==WYMeditor.TD)?WYMeditor.TH:WYMeditor.TD;this.switchTo(d,a);this.update()}}else{var e=new Array(WYMeditor.P,WYMeditor.H1,WYMeditor.H2,WYMeditor.H3,WYMeditor.H4,WYMeditor.H5,WYMeditor.H6,WYMeditor.PRE,WYMeditor.BLOCKQUOTE);d=this.findUp(this.container(),e);if(d){var i=null;if(a.toLowerCase()==WYMeditor.BLOCKQUOTE){var f=this.findUp(this.container(),WYMeditor.BLOCKQUOTE);if(f==null){i=this._doc.createElement(a);d.parentNode.insertBefore(i,d);i.appendChild(d);this.setFocusToNode(i.firstChild)}else{var c=f.childNodes;var g=c.length;var b=null;if(g>0){b=c.item(0)}for(var h=0;h<g;h++){f.parentNode.insertBefore(c.item(0),f)}f.parentNode.removeChild(f);if(b){this.setFocusToNode(b)}}}else{this.switchTo(d,a)}this.update()}}}else{return(this.selected())}};WYMeditor.editor.prototype.toggleClass=function(c,b){var a=(this._selected_image?this._selected_image:jQuery(this.selected()));a=jQuery(a).parentsOrSelf(b);jQuery(a).toggleClass(c);if(!jQuery(a).attr(WYMeditor.CLASS)){jQuery(a).removeAttr(this._class)}};WYMeditor.editor.prototype.findUp=function(d,c){if(d){var e=d.tagName.toLowerCase();if(typeof(c)==WYMeditor.STRING){while(e!=c&&e!=WYMeditor.BODY){d=d.parentNode;e=d.tagName.toLowerCase()}}else{var b=false;while(!b&&e!=WYMeditor.BODY){for(var a=0;a<c.length;a++){if(e==c[a]){b=true;break}}if(!b){d=d.parentNode;e=d.tagName.toLowerCase()}}}if(e!=WYMeditor.BODY){return(d)}else{return(null)}}else{return(null)}};WYMeditor.editor.prototype.switchTo=function(c,d){var b=this._doc.createElement(d);var a=jQuery(c).html();c.parentNode.replaceChild(b,c);jQuery(b).html(a);this.setFocusToNode(b)};WYMeditor.editor.prototype.replaceStrings=function(sVal){if(!WYMeditor.STRINGS[this._options.lang]){try{eval(jQuery.ajax({url:this._options.langPath+this._options.lang+".js",async:false}).responseText)}catch(e){WYMeditor.console.error("WYMeditor: error while parsing language file.");return sVal}}for(var key in WYMeditor.STRINGS[this._options.lang]){sVal=WYMeditor.Helper.replaceAll(sVal,this._options.stringDelimiterLeft+key+this._options.stringDelimiterRight,WYMeditor.STRINGS[this._options.lang][key])}return(sVal)};WYMeditor.editor.prototype.encloseString=function(a){return(this._options.stringDelimiterLeft+a+this._options.stringDelimiterRight)};WYMeditor.editor.prototype.status=function(a){jQuery(this._box).find(this._options.statusSelector).html(a)};WYMeditor.editor.prototype.update=function(){var a=this.xhtml();jQuery(this._element).val(a);jQuery(this._box).find(this._options.htmlValSelector).not(".hasfocus").val(a)};WYMeditor.editor.prototype.dialog=function(j,c,f){var a=c||this._wym._options.dialogFeatures;var d=window.open("","dialog",a);if(d){var b="";switch(j){case (WYMeditor.DIALOG_LINK):b=this._options.dialogLinkHtml;break;case (WYMeditor.DIALOG_IMAGE):b=this._options.dialogImageHtml;break;case (WYMeditor.DIALOG_TABLE):b=this._options.dialogTableHtml;break;case (WYMeditor.DIALOG_PASTE):b=this._options.dialogPasteHtml;break;case (WYMeditor.PREVIEW):b=this._options.dialogPreviewHtml;break;default:b=f}var e=WYMeditor.Helper;var g=this._options.dialogHtml;g=e.replaceAll(g,WYMeditor.BASE_PATH,this._options.basePath);g=e.replaceAll(g,WYMeditor.DIRECTION,this._options.direction);g=e.replaceAll(g,WYMeditor.CSS_PATH,this._options.skinPath+WYMeditor.SKINS_DEFAULT_CSS);g=e.replaceAll(g,WYMeditor.WYM_PATH,this._options.wymPath);g=e.replaceAll(g,WYMeditor.JQUERY_PATH,this._options.jQueryPath);g=e.replaceAll(g,WYMeditor.DIALOG_TITLE,this.encloseString(j));g=e.replaceAll(g,WYMeditor.DIALOG_BODY,b);g=e.replaceAll(g,WYMeditor.INDEX,this._index);g=this.replaceStrings(g);var i=d.document;i.write(g);i.close()}};WYMeditor.editor.prototype.toggleHtml=function(){jQuery(this._box).find(this._options.htmlSelector).toggle()};WYMeditor.editor.prototype.uniqueStamp=function(){var a=new Date();return("wym-"+a.getTime())};WYMeditor.editor.prototype.paste=function(b){var e;var a=this.selected();var c=b.split(this._newLine+this._newLine);var d=new RegExp(this._newLine,"g");if(a&&a.tagName.toLowerCase()!=WYMeditor.BODY){for(x=c.length-1;x>=0;x--){e=c[x];e=e.replace(d,"<br />");jQuery(a).after("<p>"+e+"</p>")}}else{for(x=0;x<c.length;x++){e=c[x];e=e.replace(d,"<br />");jQuery(this._doc.body).append("<p>"+e+"</p>")}}};WYMeditor.editor.prototype.insert=function(a){if(this._iframe.contentWindow.getSelection().focusNode!=null){this._exec(WYMeditor.INSERT_HTML,a)}else{this.paste(a)}};WYMeditor.editor.prototype.wrap=function(b,a){if(this._iframe.contentWindow.getSelection().focusNode!=null){this._exec(WYMeditor.INSERT_HTML,b+this._iframe.contentWindow.getSelection().toString()+a)}};WYMeditor.editor.prototype.unwrap=function(){if(this._iframe.contentWindow.getSelection().focusNode!=null){this._exec(WYMeditor.INSERT_HTML,this._iframe.contentWindow.getSelection().toString())}};WYMeditor.editor.prototype.addCssRules=function(e,c){var b=e.styleSheets[0];if(b){for(var a=0;a<c.length;a++){var d=c[a];if(d.name&&d.css){this.addCssRule(b,d)}}}};WYMeditor.editor.prototype.computeBasePath=function(){return jQuery(jQuery.grep(jQuery("script"),function(a){return(a.src&&a.src.match(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/))})).attr("src").replace(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/,"")};WYMeditor.editor.prototype.computeWymPath=function(){return jQuery(jQuery.grep(jQuery("script"),function(a){return(a.src&&a.src.match(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/))})).attr("src")};WYMeditor.editor.prototype.computeJqueryPath=function(){return jQuery(jQuery.grep(jQuery("script"),function(a){return(a.src&&a.src.match(/jquery(-(.*)){0,1}(\.pack|\.min|\.packed)?\.js(\?.*)?$/))})).attr("src")};WYMeditor.editor.prototype.computeCssPath=function(){return jQuery(jQuery.grep(jQuery("link"),function(a){return(a.href&&a.href.match(/wymeditor\/skins\/(.*)screen\.css(\?.*)?$/))})).attr("href")};WYMeditor.editor.prototype.configureEditorUsingRawCss=function(){var a=new WYMeditor.WymCssParser();if(this._options.stylesheet){a.parse(jQuery.ajax({url:this._options.stylesheet,async:false}).responseText)}else{a.parse(this._options.styles,false)}if(this._options.classesItems.length==0){this._options.classesItems=a.css_settings.classesItems}if(this._options.editorStyles.length==0){this._options.editorStyles=a.css_settings.editorStyles}if(this._options.dialogStyles.length==0){this._options.dialogStyles=a.css_settings.dialogStyles}};WYMeditor.editor.prototype.listen=function(){jQuery(this._doc.body).bind("mousedown",this.mousedown);var a=this._doc.body.getElementsByTagName("img");for(var b=0;b<a.length;b++){jQuery(a[b]).bind("mousedown",this.mousedown)}};WYMeditor.editor.prototype.mousedown=function(a){var b=WYMeditor.INSTANCES[this.ownerDocument.title];b._selected_image=(this.tagName.toLowerCase()==WYMeditor.IMG)?this:null;a.stopPropagation()};WYMeditor.loadCss=function(a){var c=document.createElement("link");c.rel="stylesheet";c.href=a;var b=jQuery("head").get(0);b.appendChild(c)};WYMeditor.editor.prototype.loadSkin=function(){if(this._options.loadSkin&&!WYMeditor.SKINS[this._options.skin]){var found=false;var rExp=new RegExp(this._options.skin+"/"+WYMeditor.SKINS_DEFAULT_CSS+"$");jQuery("link").each(function(){if(this.href.match(rExp)){found=true}});if(!found){WYMeditor.loadCss(this._options.skinPath+WYMeditor.SKINS_DEFAULT_CSS)}}jQuery(this._box).addClass("wym_skin_"+this._options.skin);if(this._options.initSkin&&!WYMeditor.SKINS[this._options.skin]){eval(jQuery.ajax({url:this._options.skinPath+WYMeditor.SKINS_DEFAULT_JS,async:false}).responseText)}if(WYMeditor.SKINS[this._options.skin]&&WYMeditor.SKINS[this._options.skin].init){WYMeditor.SKINS[this._options.skin].init(this)}};WYMeditor.INIT_DIALOG=function(index){var wym=window.opener.WYMeditor.INSTANCES[index];var doc=window.document;var selected=wym.selected();var dialogType=jQuery(wym._options.dialogTypeSelector).val();var sStamp=wym.uniqueStamp();switch(dialogType){case WYMeditor.DIALOG_LINK:if(selected&&selected.tagName&&selected.tagName.toLowerCase!=WYMeditor.A){selected=jQuery(selected).parentsOrSelf(WYMeditor.A)}if(!selected&&wym._selected_image){selected=jQuery(wym._selected_image).parentsOrSelf(WYMeditor.A)}break}if(jQuery.isFunction(wym._options.preInitDialog)){wym._options.preInitDialog(wym,window)}var styles=doc.styleSheets[0];var aCss=eval(wym._options.dialogStyles);wym.addCssRules(doc,aCss);if(selected){jQuery(wym._options.hrefSelector).val(jQuery(selected).attr(WYMeditor.HREF));jQuery(wym._options.srcSelector).val(jQuery(selected).attr(WYMeditor.SRC));jQuery(wym._options.titleSelector).val(jQuery(selected).attr(WYMeditor.TITLE));jQuery(wym._options.altSelector).val(jQuery(selected).attr(WYMeditor.ALT))}if(wym._selected_image){jQuery(wym._options.dialogImageSelector+" "+wym._options.srcSelector).val(jQuery(wym._selected_image).attr(WYMeditor.SRC));jQuery(wym._options.dialogImageSelector+" "+wym._options.titleSelector).val(jQuery(wym._selected_image).attr(WYMeditor.TITLE));jQuery(wym._options.dialogImageSelector+" "+wym._options.altSelector).val(jQuery(wym._selected_image).attr(WYMeditor.ALT))}jQuery(wym._options.dialogLinkSelector+" "+wym._options.submitSelector).click(function(){var sUrl=jQuery(wym._options.hrefSelector).val();if(sUrl.length>0){wym._exec(WYMeditor.CREATE_LINK,sStamp);jQuery("a[href="+sStamp+"]",wym._doc.body).attr(WYMeditor.HREF,sUrl).attr(WYMeditor.TITLE,jQuery(wym._options.titleSelector).val())}window.close()});jQuery(wym._options.dialogImageSelector+" "+wym._options.submitSelector).click(function(){var sUrl=jQuery(wym._options.srcSelector).val();if(sUrl.length>0){wym._exec(WYMeditor.INSERT_IMAGE,sStamp);jQuery("img[src$="+sStamp+"]",wym._doc.body).attr(WYMeditor.SRC,sUrl).attr(WYMeditor.TITLE,jQuery(wym._options.titleSelector).val()).attr(WYMeditor.ALT,jQuery(wym._options.altSelector).val())}window.close()});jQuery(wym._options.dialogTableSelector+" 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c={};var g=this.getPossibleTagAttributes(a);for(var e in b){var f=b[e];var d=WYMeditor.Helper;if(!d.contains(this.skiped_attributes,e)&&!d.contains(this.skiped_attribute_values,f)){if(typeof f!="function"&&d.contains(g,e)){if(this.doesAttributeNeedsValidation(a,e)){if(this.validateAttribute(a,e,f)){c[e]=f}}else{c[e]=f}}}}return c},getUniqueAttributesAndEventsForTag:function(b){var a=[];if(this._tags[b]&&this._tags[b]["attributes"]){for(k in this._tags[b]["attributes"]){a.push(parseInt(k)==k?this._tags[b]["attributes"][k]:k)}}return a},getDefaultAttributesAndEventsForTags:function(){var a=[];for(var b in this._events){a.push(this._events[b])}for(var b in this._attributes){a.push(this._attributes[b])}return a},isValidTag:function(a){if(this._tags[a]){return true}for(var b in this._tags){if(this._tags[b]==a){return true}}return false},getDefaultAttributesAndEventsForTag:function(a){var i=[];if(this.isValidTag(a)){var g=this.getDefaultAttributesAndEventsForTags();for(var d in g){var f=g[d];if(typeof f=="object"){var e=WYMeditor.Helper;if((f.except&&e.contains(f.except,a))||(f.only&&!e.contains(f.only,a))){continue}var c=f.attributes?f.attributes:f.events;for(var b in c){i.push(typeof c[b]!="string"?b:c[b])}}}}return i},doesAttributeNeedsValidation:function(a,b){return this._tags[a]&&((this._tags[a]["attributes"]&&this._tags[a]["attributes"][b])||(this._tags[a]["required"]&&WYMeditor.Helper.contains(this._tags[a]["required"],b)))},validateAttribute:function(a,b,c){if(this._tags[a]&&(this._tags[a]["attributes"]&&this._tags[a]["attributes"][b]&&c.length>0&&!c.match(this._tags[a]["attributes"][b]))||(this._tags[a]&&this._tags[a]["required"]&&WYMeditor.Helper.contains(this._tags[a]["required"],b)&&c.length==0)){return false}return typeof this._tags[a]!="undefined"},getPossibleTagAttributes:function(a){if(!this._possible_tag_attributes){this._possible_tag_attributes={}}if(!this._possible_tag_attributes[a]){this._possible_tag_attributes[a]=this.getUniqueAttributesAndEventsForTag(a).concat(this.getDefaultAttributesAndEventsForTag(a))}return this._possible_tag_attributes[a]}};WYMeditor.ParallelRegex=function(a){this._case=a;this._patterns=[];this._labels=[];this._regex=null;return this};WYMeditor.ParallelRegex.prototype.addPattern=function(c,a){a=a||true;var b=this._patterns.length;this._patterns[b]=c;this._labels[b]=a;this._regex=null};WYMeditor.ParallelRegex.prototype.match=function(c){if(this._patterns.length==0){return[false,""]}var d=c.match(this._getCompoundedRegex());if(!d){return[false,""]}var a=d[0];for(var b=1;b<d.length;b++){if(d[b]){return[this._labels[b-1],a]}}return[true,d[0]]};WYMeditor.ParallelRegex.prototype._getCompoundedRegex=function(){if(this._regex==null){for(var a=0,b=this._patterns.length;a<b;a++){this._patterns[a]="("+this._untokenizeRegex(this._tokenizeRegex(this._patterns[a]).replace(/([\/])/g,"\\$1"))+")"}this._regex=new RegExp(this._patterns.join("|"),this._getPerlMatchingFlags())}return this._regex};WYMeditor.ParallelRegex.prototype._tokenizeRegex=function(a){return a.replace(/$\?(i|m|s|x|U)$/,"~~~~~~Tk1$1~~~~~~").replace(/$\?(\-[i|m|s|x|U])$/,"~~~~~~Tk2$1~~~~~~").replace(/$\?\=(.*)$/,"~~~~~~Tk3$1~~~~~~").replace(/$\?\!(.*)$/,"~~~~~~Tk4$1~~~~~~").replace(/$\?\<\=(.*)$/,"~~~~~~Tk5$1~~~~~~").replace(/$\?\<\!(.*)$/,"~~~~~~Tk6$1~~~~~~").replace(/$\?\:(.*)$/,"~~~~~~Tk7$1~~~~~~")};WYMeditor.ParallelRegex.prototype._untokenizeRegex=function(a){return a.replace(/~~~~~~Tk1(.{1})~~~~~~/,"(?$1)").replace(/~~~~~~Tk2(.{2})~~~~~~/,"(?$1)").replace(/~~~~~~Tk3(.*)~~~~~~/,"(?=$1)").replace(/~~~~~~Tk4(.*)~~~~~~/,"(?!$1)").replace(/~~~~~~Tk5(.*)~~~~~~/,"(?<=$1)").replace(/~~~~~~Tk6(.*)~~~~~~/,"(?<!$1)").replace(/~~~~~~Tk7(.*)~~~~~~/,"(?:$1)")};WYMeditor.ParallelRegex.prototype._getPerlMatchingFlags=function(){return(this._case?"m":"mi")};WYMeditor.StateStack=function(a){this._stack=[a];return this};WYMeditor.StateStack.prototype.getCurrent=function(){return this._stack[this._stack.length-1]};WYMeditor.StateStack.prototype.enter=function(a){this._stack.push(a)};WYMeditor.StateStack.prototype.leave=function(){if(this._stack.length==1){return false}this._stack.pop();return true};WYMeditor.LEXER_ENTER=1;WYMeditor.LEXER_MATCHED=2;WYMeditor.LEXER_UNMATCHED=3;WYMeditor.LEXER_EXIT=4;WYMeditor.LEXER_SPECIAL=5;WYMeditor.Lexer=function(c,b,a){b=b||"accept";this._case=a||false;this._regexes={};this._parser=c;this._mode=new WYMeditor.StateStack(b);this._mode_handlers={};this._mode_handlers[b]=b;return this};WYMeditor.Lexer.prototype.addPattern=function(a,b){var b=b||"accept";if(typeof this._regexes[b]=="undefined"){this._regexes[b]=new WYMeditor.ParallelRegex(this._case)}this._regexes[b].addPattern(a);if(typeof this._mode_handlers[b]=="undefined"){this._mode_handlers[b]=b}};WYMeditor.Lexer.prototype.addEntryPattern=function(b,c,a){if(typeof this._regexes[c]=="undefined"){this._regexes[c]=new WYMeditor.ParallelRegex(this._case)}this._regexes[c].addPattern(b,a);if(typeof this._mode_handlers[a]=="undefined"){this._mode_handlers[a]=a}};WYMeditor.Lexer.prototype.addExitPattern=function(a,b){if(typeof this._regexes[b]=="undefined"){this._regexes[b]=new WYMeditor.ParallelRegex(this._case)}this._regexes[b].addPattern(a,"__exit");if(typeof this._mode_handlers[b]=="undefined"){this._mode_handlers[b]=b}};WYMeditor.Lexer.prototype.addSpecialPattern=function(b,c,a){if(typeof this._regexes[c]=="undefined"){this._regexes[c]=new WYMeditor.ParallelRegex(this._case)}this._regexes[c].addPattern(b,"_"+a);if(typeof this._mode_handlers[a]=="undefined"){this._mode_handlers[a]=a}};WYMeditor.Lexer.prototype.mapHandler=function(b,a){this._mode_handlers[b]=a};WYMeditor.Lexer.prototype.parse=function(d){if(typeof this._parser=="undefined"){return false}var e=d.length;var c;while(typeof(c=this._reduce(d))=="object"){var d=c[0];var b=c[1];var a=c[2];var f=c[3];if(!this._dispatchTokens(b,a,f)){return false}if(d==""){return true}if(d.length==e){return false}e=d.length}if(!c){return false}return this._invokeParser(d,WYMeditor.LEXER_UNMATCHED)};WYMeditor.Lexer.prototype._dispatchTokens=function(b,a,c){c=c||false;if(!this._invokeParser(b,WYMeditor.LEXER_UNMATCHED)){return false}if(typeof c=="boolean"){return this._invokeParser(a,WYMeditor.LEXER_MATCHED)}if(this._isModeEnd(c)){if(!this._invokeParser(a,WYMeditor.LEXER_EXIT)){return false}return this._mode.leave()}if(this._isSpecialMode(c)){this._mode.enter(this._decodeSpecial(c));if(!this._invokeParser(a,WYMeditor.LEXER_SPECIAL)){return false}return this._mode.leave()}this._mode.enter(c);return this._invokeParser(a,WYMeditor.LEXER_ENTER)};WYMeditor.Lexer.prototype._isModeEnd=function(a){return(a==="__exit")};WYMeditor.Lexer.prototype._isSpecialMode=function(a){return(a.substring(0,1)=="_")};WYMeditor.Lexer.prototype._decodeSpecial=function(a){return a.substring(1)};WYMeditor.Lexer.prototype._invokeParser=function(content,is_match){if(!/ +/.test(content)&&((content==="")||(content==false))){return true}var current=this._mode.getCurrent();var handler=this._mode_handlers[current];var result;eval("result = this._parser."+handler+"(content, is_match);");return result};WYMeditor.Lexer.prototype._reduce=function(c){var a=this._regexes[this._mode.getCurrent()].match(c);var b=a[1];var e=a[0];if(e){var f=c.indexOf(b);var d=c.substr(0,f);c=c.substring(f+b.length);return[c,d,b,e]}return true};WYMeditor.XhtmlLexer=function(a){jQuery.extend(this,new WYMeditor.Lexer(a,"Text"));this.mapHandler("Text","Text");this.addTokens();this.init();return this};WYMeditor.XhtmlLexer.prototype.init=function(){};WYMeditor.XhtmlLexer.prototype.addTokens=function(){this.addCommentTokens("Text");this.addScriptTokens("Text");this.addCssTokens("Text");this.addTagTokens("Text")};WYMeditor.XhtmlLexer.prototype.addCommentTokens=function(a){this.addEntryPattern("","Comment")};WYMeditor.XhtmlLexer.prototype.addScriptTokens=function(a){this.addEntryPattern("<script",a,"Script");this.addExitPattern("<\/script>","Script")};WYMeditor.XhtmlLexer.prototype.addCssTokens=function(a){this.addEntryPattern("<style",a,"Css");this.addExitPattern("</style>","Css")};WYMeditor.XhtmlLexer.prototype.addTagTokens=function(a){this.addSpecialPattern("<\\s*[a-z0-9:-]+\\s*>",a,"OpeningTag");this.addEntryPattern("<[a-z0-9:-]+[\\/ \\>]+",a,"OpeningTag");this.addInTagDeclarationTokens("OpeningTag");this.addSpecialPattern("</\\s*[a-z0-9:-]+\\s*>",a,"ClosingTag")};WYMeditor.XhtmlLexer.prototype.addInTagDeclarationTokens=function(a){this.addSpecialPattern("\\s+",a,"Ignore");this.addAttributeTokens(a);this.addExitPattern("/>",a);this.addExitPattern(">",a)};WYMeditor.XhtmlLexer.prototype.addAttributeTokens=function(a){this.addSpecialPattern("\\s*[a-z-_0-9]*:?[a-z-_0-9]+\\s*(?==)\\s*",a,"TagAttributes");this.addEntryPattern('=\\s*"',a,"DoubleQuotedAttribute");this.addPattern('\\\\"',"DoubleQuotedAttribute");this.addExitPattern('"',"DoubleQuotedAttribute");this.addEntryPattern("=\\s*'",a,"SingleQuotedAttribute");this.addPattern("\\\\'","SingleQuotedAttribute");this.addExitPattern("'","SingleQuotedAttribute");this.addSpecialPattern("=\\s*[^>\\s]*",a,"UnquotedAttribute")};WYMeditor.XhtmlParser=function(a,b){var b=b||"Text";this._Lexer=new WYMeditor.XhtmlLexer(this);this._Listener=a;this._mode=b;this._matches=[];this._last_match="";this._current_match="";return this};WYMeditor.XhtmlParser.prototype.parse=function(a){this._Lexer.parse(this.beforeParsing(a));return this.afterParsing(this._Listener.getResult())};WYMeditor.XhtmlParser.prototype.beforeParsing=function(a){if(a.match(/class="MsoNormal"/)||a.match(/ns = "urn:schemas-microsoft-com/)){this._Listener.avoidStylingTagsAndAttributes()}return this._Listener.beforeParsing(a)};WYMeditor.XhtmlParser.prototype.afterParsing=function(a){if(this._Listener._avoiding_tags_implicitly){this._Listener.allowStylingTagsAndAttributes()}return this._Listener.afterParsing(a)};WYMeditor.XhtmlParser.prototype.Ignore=function(a,b){return true};WYMeditor.XhtmlParser.prototype.Text=function(a){this._Listener.addContent(a);return true};WYMeditor.XhtmlParser.prototype.Comment=function(b,a){return this._addNonTagBlock(b,a,"addComment")};WYMeditor.XhtmlParser.prototype.Script=function(b,a){return this._addNonTagBlock(b,a,"addScript")};WYMeditor.XhtmlParser.prototype.Css=function(b,a){return this._addNonTagBlock(b,a,"addCss")};WYMeditor.XhtmlParser.prototype._addNonTagBlock=function(a,c,b){switch(c){case WYMeditor.LEXER_ENTER:this._non_tag=a;break;case WYMeditor.LEXER_UNMATCHED:this._non_tag+=a;break;case WYMeditor.LEXER_EXIT:switch(b){case"addComment":this._Listener.addComment(this._non_tag+a);break;case"addScript":this._Listener.addScript(this._non_tag+a);break;case"addCss":this._Listener.addCss(this._non_tag+a);break}}return true};WYMeditor.XhtmlParser.prototype.OpeningTag=function(a,b){switch(b){case WYMeditor.LEXER_ENTER:this._tag=this.normalizeTag(a);this._tag_attributes={};break;case WYMeditor.LEXER_SPECIAL:this._callOpenTagListener(this.normalizeTag(a));break;case WYMeditor.LEXER_EXIT:this._callOpenTagListener(this._tag,this._tag_attributes)}return true};WYMeditor.XhtmlParser.prototype.ClosingTag=function(a,b){this._callCloseTagListener(this.normalizeTag(a));return true};WYMeditor.XhtmlParser.prototype._callOpenTagListener=function(a,b){var b=b||{};this.autoCloseUnclosedBeforeNewOpening(a);if(this._Listener.isBlockTag(a)){this._Listener._tag_stack.push(a);this._Listener.fixNestingBeforeOpeningBlockTag(a,b);this._Listener.openBlockTag(a,b);this._increaseOpenTagCounter(a)}else{if(this._Listener.isInlineTag(a)){this._Listener.inlineTag(a,b)}else{this._Listener.openUnknownTag(a,b);this._increaseOpenTagCounter(a)}}this._Listener.last_tag=a;this._Listener.last_tag_opened=true;this._Listener.last_tag_attributes=b};WYMeditor.XhtmlParser.prototype._callCloseTagListener=function(a){if(this._decreaseOpenTagCounter(a)){this.autoCloseUnclosedBeforeTagClosing(a);if(this._Listener.isBlockTag(a)){var b=this._Listener._tag_stack.pop();if(b==false){return}else{if(b!=a){a=b}}this._Listener.closeBlockTag(a)}else{this._Listener.closeUnknownTag(a)}}else{this._Listener.closeUnopenedTag(a)}this._Listener.last_tag=a;this._Listener.last_tag_opened=false};WYMeditor.XhtmlParser.prototype._increaseOpenTagCounter=function(a){this._Listener._open_tags[a]=this._Listener._open_tags[a]||0;this._Listener._open_tags[a]++};WYMeditor.XhtmlParser.prototype._decreaseOpenTagCounter=function(a){if(this._Listener._open_tags[a]){this._Listener._open_tags[a]--;if(this._Listener._open_tags[a]==0){this._Listener._open_tags[a]=undefined}return true}return false};WYMeditor.XhtmlParser.prototype.autoCloseUnclosedBeforeNewOpening=function(a){this._autoCloseUnclosed(a,false)};WYMeditor.XhtmlParser.prototype.autoCloseUnclosedBeforeTagClosing=function(a){this._autoCloseUnclosed(a,true)};WYMeditor.XhtmlParser.prototype._autoCloseUnclosed=function(c,d){var d=d||false;if(this._Listener._open_tags){for(var a in this._Listener._open_tags){var b=this._Listener._open_tags[a];if(b>0&&this._Listener.shouldCloseTagAutomatically(a,c,d)){this._callCloseTagListener(a,true)}}}};WYMeditor.XhtmlParser.prototype.getTagReplacements=function(){return this._Listener.getTagReplacements()};WYMeditor.XhtmlParser.prototype.normalizeTag=function(a){a=a.replace(/^([\s<\/>]*)|([\s<\/>]*)$/gm,"").toLowerCase();var b=this._Listener.getTagReplacements();if(b[a]){return b[a]}return a};WYMeditor.XhtmlParser.prototype.TagAttributes=function(a,b){if(WYMeditor.LEXER_SPECIAL==b){this._current_attribute=a}return true};WYMeditor.XhtmlParser.prototype.DoubleQuotedAttribute=function(a,b){if(WYMeditor.LEXER_UNMATCHED==b){this._tag_attributes[this._current_attribute]=a}return true};WYMeditor.XhtmlParser.prototype.SingleQuotedAttribute=function(a,b){if(WYMeditor.LEXER_UNMATCHED==b){this._tag_attributes[this._current_attribute]=a}return true};WYMeditor.XhtmlParser.prototype.UnquotedAttribute=function(a,b){this._tag_attributes[this._current_attribute]=a.replace(/^=/,"");return true};WYMeditor.XhtmlSaxListener=function(){this.output="";this.helper=new WYMeditor.XmlHelper();this._open_tags={};this.validator=WYMeditor.XhtmlValidator;this._tag_stack=[];this.avoided_tags=[];this.entities={" ":" ","¡":"¡","¢":"¢","£":"£","¤":"¤","¥":"¥","¦":"¦","§":"§","¨":"¨","©":"©","ª":"ª","«":"«","¬":"¬","":"","®":"®","¯":"¯","°":"°","±":"±","²":"²","³":"³","´":"´","µ":"µ","¶":"¶","·":"·","¸":"¸","¹":"¹","º":"º","»":"»","¼":"¼","½":"½","¾":"¾","¿":"¿","À":"À","Á":"Á","Â":"Â","Ã":"Ã","Ä":"Ä","Å":"Å","Æ":"Æ","Ç":"Ç","È":"È","É":"É","Ê":"Ê","Ë":"Ë","Ì":"Ì","Í":"Í","Î":"Î","Ï":"Ï","Ð":"Ð","Ñ":"Ñ","Ò":"Ò","Ó":"Ó","Ô":"Ô","Õ":"Õ","Ö":"Ö","×":"×","Ø":"Ø","Ù":"Ù","Ú":"Ú","Û":"Û","Ü":"Ü","Ý":"Ý","Þ":"Þ","ß":"ß","à":"à","á":"á","â":"â","ã":"ã","ä":"ä","å":"å","æ":"æ","ç":"ç","è":"è","é":"é","ê":"ê","ë":"ë","ì":"ì","í":"í","î":"î","ï":"ï","ð":"ð","ñ":"ñ","ò":"ò","ó":"ó","ô":"ô","õ":"õ","ö":"ö","÷":"÷","ø":"ø","ù":"ù","ú":"ú","û":"û","ü":"ü","ý":"ý","þ":"þ","ÿ":"ÿ","&OElig;":"Œ","&oelig;":"œ","&Scaron;":"Š","&scaron;":"š","&Yuml;":"Ÿ","&fnof;":"ƒ","&circ;":"ˆ","&tilde;":"˜","Α":"Α","Β":"Β","Γ":"Γ","Δ":"Δ","Ε":"Ε","Ζ":"Ζ","Η":"Η","Θ":"Θ","Ι":"Ι","Κ":"Κ","Λ":"Λ","Μ":"Μ","Ν":"Ν","Ξ":"Ξ","Ο":"Ο","Π":"Π","Ρ":"Ρ","Σ":"Σ","Τ":"Τ","Υ":"Υ","Φ":"Φ","Χ":"Χ","Ψ":"Ψ","Ω":"Ω","α":"α","β":"β","γ":"γ","δ":"δ","ε":"ε","ζ":"ζ","η":"η","θ":"θ","ι":"ι","κ":"κ","λ":"λ","μ":"μ","ν":"ν","ξ":"ξ","ο":"ο","π":"π","ρ":"ρ","&sigmaf;":"ς","σ":"σ","τ":"τ","υ":"υ","φ":"φ","χ":"χ","ψ":"ψ","ω":"ω","&thetasym;":"ϑ","&upsih;":"ϒ","ϖ":"ϖ","&ensp;":" ","&emsp;":" "," ":" ","&zwnj;":"‌","&zwj;":"‍","&lrm;":"‎","&rlm;":"‏","–":"–","—":"—","‘":"‘","’":"’","&sbquo;":"‚","“":"“","”":"”","&bdquo;":"„","&dagger;":"†","&Dagger;":"‡","•":"•","…":"…","&permil;":"‰","′":"′","″":"″","&lsaquo;":"‹","&rsaquo;":"›","&oline;":"‾","&frasl;":"⁄","€":"€","&image;":"ℑ","&weierp;":"℘","&real;":"ℜ","™":"™","&alefsym;":"ℵ","←":"←","↑":"↑","→":"→","↓":"↓","↔":"↔","&crarr;":"↵","⇐":"⇐","&uArr;":"⇑","⇒":"⇒","&dArr;":"⇓","⇔":"⇔","∀":"∀","∂":"∂","∃":"∃","∅":"∅","∇":"∇","∈":"∈","∉":"∉","&ni;":"∋","∏":"∏","∑":"∑","−":"−","&lowast;":"∗","√":"√","&prop;":"∝","∞":"∞","&ang;":"∠","&and;":"∧","&or;":"∨","∩":"∩","∪":"∪","∫":"∫","&there4;":"∴","&sim;":"∼","&cong;":"≅","≈":"≈","≠":"≠","&equiv;":"≡","≤":"≤","≥":"≥","⊂":"⊂","⊃":"⊃","&nsub;":"⊄","&sube;":"⊆","&supe;":"⊇","&oplus;":"⊕","&otimes;":"⊗","&perp;":"⊥","⋅":"⋅","&lceil;":"⌈","&rceil;":"⌉","&lfloor;":"⌊","&rfloor;":"⌋","&lang;":"〈","&rang;":"〉","&loz;":"◊","&spades;":"♠","&clubs;":"♣","&hearts;":"♥","&diams;":"♦"};this.block_tags=["a","abbr","acronym","address","area","b","base","bdo","big","blockquote","body","button","caption","cite","code","col","colgroup","dd","del","div","dfn","dl","dt","em","fieldset","form","head","h1","h2","h3","h4","h5","h6","html","i","ins","kbd","label","legend","li","map","noscript","object","ol","optgroup","option","p","param","pre","q","samp","script","select","small","span","strong","style","sub","sup","table","tbody","td","textarea","tfoot","th","thead","title","tr","tt","ul","var","extends"];this.inline_tags=["br","hr","img","input"];return this};WYMeditor.XhtmlSaxListener.prototype.shouldCloseTagAutomatically=function(a,c,b){var b=b||false;if(a=="td"){if((b&&c=="tr")||(!b&&c=="td")){return true}}if(a=="option"){if((b&&c=="select")||(!b&&c=="option")){return true}}return false};WYMeditor.XhtmlSaxListener.prototype.beforeParsing=function(a){this.output="";return a};WYMeditor.XhtmlSaxListener.prototype.afterParsing=function(a){a=this.replaceNamedEntities(a);a=this.joinRepeatedEntities(a);a=this.removeEmptyTags(a);a=this.removeBrInPre(a);return a};WYMeditor.XhtmlSaxListener.prototype.replaceNamedEntities=function(b){for(var a in this.entities){b=b.replace(new RegExp(a,"g"),this.entities[a])}return b};WYMeditor.XhtmlSaxListener.prototype.joinRepeatedEntities=function(b){var a="em|strong|sub|sup|acronym|pre|del|address";return b.replace(new RegExp("</("+a+")><\\1>",""),"").replace(new RegExp("(s*<("+a+")>s*){2}(.*)(s*</\\2>s*){2}",""),"<$2>$3<$2>")};WYMeditor.XhtmlSaxListener.prototype.removeEmptyTags=function(a){return a.replace(new RegExp("<("+this.block_tags.join("|").replace(/\|td/,"").replace(/\|p/,"").replace(/\|th/,"")+")>(<br />| | |\\s)*</\\1>","g"),"")};WYMeditor.XhtmlSaxListener.prototype.removeBrInPre=function(c){var b=c.match(new RegExp("<pre[^>]*>(.*?)</pre>","gmi"));if(b){for(var a=0;a<b.length;a++){c=c.replace(b[a],b[a].replace(new RegExp("<br />","g"),String.fromCharCode(13,10)))}}return c};WYMeditor.XhtmlSaxListener.prototype.getResult=function(){return this.output};WYMeditor.XhtmlSaxListener.prototype.getTagReplacements=function(){return{b:"strong",i:"em"}};WYMeditor.XhtmlSaxListener.prototype.addContent=function(a){this.output+=a};WYMeditor.XhtmlSaxListener.prototype.addComment=function(a){if(this.remove_comments){this.output+=a}};WYMeditor.XhtmlSaxListener.prototype.addScript=function(a){if(!this.remove_scripts){this.output+=a}};WYMeditor.XhtmlSaxListener.prototype.addCss=function(a){if(!this.remove_embeded_styles){this.output+=a}};WYMeditor.XhtmlSaxListener.prototype.openBlockTag=function(a,b){this.output+=this.helper.tag(a,this.validator.getValidTagAttributes(a,b),true)};WYMeditor.XhtmlSaxListener.prototype.inlineTag=function(a,b){this.output+=this.helper.tag(a,this.validator.getValidTagAttributes(a,b))};WYMeditor.XhtmlSaxListener.prototype.openUnknownTag=function(a,b){};WYMeditor.XhtmlSaxListener.prototype.closeBlockTag=function(a){this.output=this.output.replace(/<br \/>$/,"")+this._getClosingTagContent("before",a)+"</"+a+">"+this._getClosingTagContent("after",a)};WYMeditor.XhtmlSaxListener.prototype.closeUnknownTag=function(a){};WYMeditor.XhtmlSaxListener.prototype.closeUnopenedTag=function(a){this.output+="</"+a+">"};WYMeditor.XhtmlSaxListener.prototype.avoidStylingTagsAndAttributes=function(){this.avoided_tags=["div","span"];this.validator.skiped_attributes=["style"];this.validator.skiped_attribute_values=["MsoNormal","main1"];this._avoiding_tags_implicitly=true};WYMeditor.XhtmlSaxListener.prototype.allowStylingTagsAndAttributes=function(){this.avoided_tags=[];this.validator.skiped_attributes=[];this.validator.skiped_attribute_values=[];this._avoiding_tags_implicitly=false};WYMeditor.XhtmlSaxListener.prototype.isBlockTag=function(a){return !WYMeditor.Helper.contains(this.avoided_tags,a)&&WYMeditor.Helper.contains(this.block_tags,a)};WYMeditor.XhtmlSaxListener.prototype.isInlineTag=function(a){return !WYMeditor.Helper.contains(this.avoided_tags,a)&&WYMeditor.Helper.contains(this.inline_tags,a)};WYMeditor.XhtmlSaxListener.prototype.insertContentAfterClosingTag=function(a,b){this._insertContentWhenClosingTag("after",a,b)};WYMeditor.XhtmlSaxListener.prototype.insertContentBeforeClosingTag=function(a,b){this._insertContentWhenClosingTag("before",a,b)};WYMeditor.XhtmlSaxListener.prototype.fixNestingBeforeOpeningBlockTag=function(a,b){if(a!="li"&&(a=="ul"||a=="ol")&&this.last_tag&&!this.last_tag_opened&&this.last_tag=="li"){this.output=this.output.replace(/<\/li>$/,"");this.insertContentAfterClosingTag(a,"</li>")}};WYMeditor.XhtmlSaxListener.prototype._insertContentWhenClosingTag=function(b,a,c){if(!this["_insert_"+b+"_closing"]){this["_insert_"+b+"_closing"]=[]}if(!this["_insert_"+b+"_closing"][a]){this["_insert_"+b+"_closing"][a]=[]}this["_insert_"+b+"_closing"][a].push(c)};WYMeditor.XhtmlSaxListener.prototype._getClosingTagContent=function(b,a){if(this["_insert_"+b+"_closing"]&&this["_insert_"+b+"_closing"][a]&&this["_insert_"+b+"_closing"][a].length>0){return this["_insert_"+b+"_closing"][a].pop()}return""};WYMeditor.WymCssLexer=function(b,a){var a=(typeof a=="undefined"?true:a);jQuery.extend(this,new WYMeditor.Lexer(b,(a?"Ignore":"WymCss")));this.mapHandler("WymCss","Ignore");if(a==true){this.addEntryPattern("/\\\x2a[<\\s]*WYMeditor[>\\s]*\\\x2a/","Ignore","WymCss");this.addExitPattern("/\\\x2a[</\\s]*WYMeditor[>\\s]*\\\x2a/","WymCss")}this.addSpecialPattern("[\\sa-z1-6]*\\\x2e[a-z-_0-9]+","WymCss","WymCssStyleDeclaration");this.addEntryPattern("/\\\x2a","WymCss","WymCssComment");this.addExitPattern("\\\x2a/","WymCssComment");this.addEntryPattern("\x7b","WymCss","WymCssStyle");this.addExitPattern("\x7d","WymCssStyle");this.addEntryPattern("/\\\x2a","WymCssStyle","WymCssFeedbackStyle");this.addExitPattern("\\\x2a/","WymCssFeedbackStyle");return this};WYMeditor.WymCssParser=function(){this._in_style=false;this._has_title=false;this.only_wym_blocks=true;this.css_settings={classesItems:[],editorStyles:[],dialogStyles:[]};return this};WYMeditor.WymCssParser.prototype.parse=function(a,b){var b=(typeof b=="undefined"?this.only_wym_blocks:b);this._Lexer=new WYMeditor.WymCssLexer(this,b);this._Lexer.parse(a)};WYMeditor.WymCssParser.prototype.Ignore=function(a,b){return true};WYMeditor.WymCssParser.prototype.WymCssComment=function(b,a){if(b.match(/end[a-z0-9\s]*wym[a-z0-9\s]*/mi)){return false}if(a==WYMeditor.LEXER_UNMATCHED){if(!this._in_style){this._has_title=true;this._current_item={title:WYMeditor.Helper.trim(b)}}else{if(this._current_item[this._current_element]){if(!this._current_item[this._current_element].expressions){this._current_item[this._current_element].expressions=[b]}else{this._current_item[this._current_element].expressions.push(b)}}}this._in_style=true}return true};WYMeditor.WymCssParser.prototype.WymCssStyle=function(b,a){if(a==WYMeditor.LEXER_UNMATCHED){b=WYMeditor.Helper.trim(b);if(b!=""){this._current_item[this._current_element].style=b}}else{if(a==WYMeditor.LEXER_EXIT){this._in_style=false;this._has_title=false;this.addStyleSetting(this._current_item)}}return true};WYMeditor.WymCssParser.prototype.WymCssFeedbackStyle=function(b,a){if(a==WYMeditor.LEXER_UNMATCHED){this._current_item[this._current_element].feedback_style=b.replace(/^([\s\/\*]*)|([\s\/\*]*)$/gm,"")}return true};WYMeditor.WymCssParser.prototype.WymCssStyleDeclaration=function(b){b=b.replace(/^([\s\.]*)|([\s\.*]*)$/gm,"");var a="";if(b.indexOf(".")>0){var c=b.split(".");this._current_element=c[1];var a=c[0]}else{this._current_element=b}if(!this._has_title){this._current_item={title:(!a?"":a.toUpperCase()+": ")+this._current_element};this._has_title=true}if(!this._current_item[this._current_element]){this._current_item[this._current_element]={name:this._current_element}}if(a){if(!this._current_item[this._current_element].tags){this._current_item[this._current_element].tags=[a]}else{this._current_item[this._current_element].tags.push(a)}}return true};WYMeditor.WymCssParser.prototype.addStyleSetting=function(a){for(var b in a){var c=a[b];if(typeof c=="object"&&b!="title"){this.css_settings.classesItems.push({name:WYMeditor.Helper.trim(c.name),title:a.title,expr:WYMeditor.Helper.trim((c.expressions||c.tags).join(", "))});if(c.feedback_style){this.css_settings.editorStyles.push({name:"."+WYMeditor.Helper.trim(c.name),css:c.feedback_style})}if(c.style){this.css_settings.dialogStyles.push({name:"."+WYMeditor.Helper.trim(c.name),css:c.style})}}}};jQuery.fn.isPhantomNode=function(){if(this[0].nodeType==3){return !(/[^\t\n\r ]/.test(this[0].data))}return false};WYMeditor.isPhantomNode=function(a){if(a.nodeType==3){return !(/[^\t\n\r ]/.test(a.data))}return false};WYMeditor.isPhantomString=function(a){return !(/[^\t\n\r ]/.test(a))};jQuery.fn.parentsOrSelf=function(b){var a=this;if(a[0].nodeType==3){a=a.parents().slice(0,1)}if(a.filter(b).size()==1){return a}else{return a.parents(b).slice(0,1)}};WYMeditor.Helper={replaceAll:function(d,a,c){var b=new RegExp(a,"g");return(d.replace(b,c))},insertAt:function(b,a,c){return(b.substr(0,c)+a+b.substring(c))},trim:function(a){return a.replace(/^(\s*)|(\s*)$/gm,"")},contains:function(a,c){for(var b=0;b<a.length;b++){if(a[b]===c){return true}}return false},indexOf:function(a,d){var b=-1;for(var c=0;c<a.length;c++){if(a[c]==d){b=c;break}}return(b)},findByName:function(a,b){for(var c=0;c<a.length;c++){var d=a[c];if(d.name==b){return(d)}}return(null)}};WYMeditor.WymClassExplorer=function(a){this._wym=a;this._class="className";this._newLine="\r\n"};WYMeditor.WymClassExplorer.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentWindow.document;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);jQuery(this._doc.body).html(this._wym._html);var wym=this;this._doc.body.onfocus=function(){wym._doc.designMode="on";wym._doc=iframe.contentWindow.document};this._doc.onbeforedeactivate=function(){wym.saveCaret()};this._doc.onkeyup=function(){wym.saveCaret();wym.keyup()};this._doc.onclick=function(){wym.saveCaret()};this._doc.body.onbeforepaste=function(){wym._iframe.contentWindow.event.returnValue=false};this._doc.body.onpaste=function(){wym._iframe.contentWindow.event.returnValue=false;wym.paste(window.clipboardData.getData("Text"))};if(this._initialized){if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()}this._initialized=true;this._doc.designMode="on";try{this._doc=iframe.contentWindow.document}catch(e){}};WYMeditor.WymClassExplorer.prototype._exec=function(c,d){switch(c){case WYMeditor.INDENT:case WYMeditor.OUTDENT:var a=this.findUp(this.container(),WYMeditor.LI);if(a){var b=a.parentNode.parentNode;if(a.parentNode.childNodes.length>1||b.tagName.toLowerCase()==WYMeditor.OL||b.tagName.toLowerCase()==WYMeditor.UL){this._doc.execCommand(c)}}break;default:if(d){this._doc.execCommand(c,false,d)}else{this._doc.execCommand(c)}break}this.listen()};WYMeditor.WymClassExplorer.prototype.selected=function(){var a=this._iframe.contentWindow.document.caretPos;if(a!=null){if(a.parentElement!=undefined){return(a.parentElement())}}};WYMeditor.WymClassExplorer.prototype.saveCaret=function(){this._doc.caretPos=this._doc.selection.createRange()};WYMeditor.WymClassExplorer.prototype.addCssRule=function(a,b){a.addRule(b.name,b.css)};WYMeditor.WymClassExplorer.prototype.insert=function(b){var a=this._doc.selection.createRange();if(jQuery(a.parentElement()).parents(this._options.iframeBodySelector).is("*")){try{a.pasteHTML(b)}catch(c){}}else{this.paste(b)}};WYMeditor.WymClassExplorer.prototype.wrap=function(d,b){var a=this._doc.selection.createRange();if(jQuery(a.parentElement()).parents(this._options.iframeBodySelector).is("*")){try{a.pasteHTML(d+a.text+b)}catch(c){}}};WYMeditor.WymClassExplorer.prototype.unwrap=function(){var a=this._doc.selection.createRange();if(jQuery(a.parentElement()).parents(this._options.iframeBodySelector).is("*")){try{var c=a.text;this._exec("Cut");a.pasteHTML(c)}catch(b){}}};WYMeditor.WymClassExplorer.prototype.keyup=function(){this._selected_image=null};WYMeditor.WymClassExplorer.prototype.setFocusToNode=function(b){var a=this._doc.selection.createRange();a.moveToElementText(b);a.collapse(false);a.move("character",-1);a.select();b.focus()};WYMeditor.WymClassMozilla=function(a){this._wym=a;this._class="class";this._newLine="\n"};WYMeditor.WymClassMozilla.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentDocument;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);this.html(this._wym._html);this.enableDesignMode();if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();jQuery(this._doc).bind("keydown",this.keydown);jQuery(this._doc).bind("keyup",this.keyup);jQuery(this._doc).bind("focus",this.enableDesignMode);if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()};WYMeditor.WymClassMozilla.prototype.html=function(a){if(typeof a==="string"){try{this._doc.designMode="off"}catch(b){}a=a.replace(/<em(\b[^>]*)>/gi,"<i$1>").replace(/<\/em>/gi,"</i>").replace(/<strong(\b[^>]*)>/gi,"<b$1>").replace(/<\/strong>/gi,"</b>");jQuery(this._doc.body).html(a);this.enableDesignMode()}else{return(jQuery(this._doc.body).html())}};WYMeditor.WymClassMozilla.prototype._exec=function(e,g){if(!this.selected()){return(false)}switch(e){case WYMeditor.INDENT:case WYMeditor.OUTDENT:var f=this.selected();var d=this._iframe.contentWindow.getSelection();var b=d.anchorNode;if(b.nodeName=="#text"){b=b.parentNode}f=this.findUp(f,WYMeditor.BLOCKS);b=this.findUp(b,WYMeditor.BLOCKS);if(f&&f==b&&f.tagName.toLowerCase()==WYMeditor.LI){var c=f.parentNode.parentNode;if(f.parentNode.childNodes.length>1||c.tagName.toLowerCase()==WYMeditor.OL||c.tagName.toLowerCase()==WYMeditor.UL){this._doc.execCommand(e,"",null)}}break;default:if(g){this._doc.execCommand(e,"",g)}else{this._doc.execCommand(e,"",null)}}var a=this.selected();if(a.tagName.toLowerCase()==WYMeditor.BODY){this._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}this.listen()};WYMeditor.WymClassMozilla.prototype.selected=function(){var b=this._iframe.contentWindow.getSelection();var a=b.focusNode;if(a){if(a.nodeName=="#text"){return(a.parentNode)}else{return(a)}}else{return(null)}};WYMeditor.WymClassMozilla.prototype.addCssRule=function(a,b){a.insertRule(b.name+" {"+b.css+"}",a.cssRules.length)};WYMeditor.WymClassMozilla.prototype.keydown=function(b){var f=WYMeditor.INSTANCES[this.title];var a=null;if(b.keyCode===WYMeditor.KEY.ENTER){a=f.selected();if(a){var g=$(a),e=g.parent(),d=g.parents(".embedded-item");if(d.size()){var c=$("<p/>");if(g.hasClass("title")){d.before(c)}else{if(g.hasClass("content")){d.after(c)}}f.setFocusToNode(c.get(0));return false}}}if(b.ctrlKey){if(b.keyCode==66){f._exec(WYMeditor.BOLD);return false}if(b.keyCode==73){f._exec(WYMeditor.ITALIC);return false}}else{if(b.keyCode==13){if(!b.shiftKey){a=f.selected();if(a&&a.tagName.toLowerCase()==WYMeditor.PRE){b.preventDefault();f.insert("<p></p>")}}}}};WYMeditor.WymClassMozilla.prototype.keyup=function(b){var d=WYMeditor.INSTANCES[this.title];d._selected_image=null;var a=null;if(b.keyCode==13&&!b.shiftKey){jQuery(d._doc.body).children(WYMeditor.BR).remove()}else{if(b.keyCode!=8&&b.keyCode!=17&&b.keyCode!=46&&b.keyCode!=224&&!b.metaKey&&!b.ctrlKey){a=d.selected();var c=a.tagName.toLowerCase();if(c=="strong"||c=="b"||c=="em"||c=="i"||c=="sub"||c=="sup"||c=="a"){c=a.parentNode.tagName.toLowerCase()}if(c==WYMeditor.BODY){d._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}}}};WYMeditor.WymClassMozilla.prototype.enableDesignMode=function(){if(this.designMode=="off"){try{this.designMode="on";this.execCommand("styleWithCSS","",false)}catch(a){}}};WYMeditor.WymClassMozilla.prototype.setFocusToNode=function(c){var a=document.createRange();a.selectNode(c);var b=this._iframe.contentWindow.getSelection();b.addRange(a);b.collapse(c,c.childNodes.length);this._iframe.contentWindow.focus()};WYMeditor.WymClassMozilla.prototype.openBlockTag=function(a,c){var c=this.validator.getValidTagAttributes(a,c);if(a=="span"&&c.style){var b=this.getTagForStyle(c.style);if(b){this._tag_stack.pop();var a=b;this._tag_stack.push(b);c.style=""}else{return}}this.output+=this.helper.tag(a,c,true)};WYMeditor.WymClassMozilla.prototype.getTagForStyle=function(a){if(/bold/.test(a)){return"strong"}if(/italic/.test(a)){return"em"}if(/sub/.test(a)){return"sub"}if(/sub/.test(a)){return"super"}return false};WYMeditor.WymClassOpera=function(a){this._wym=a;this._class="class";this._newLine="\r\n"};WYMeditor.WymClassOpera.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentWindow.document;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);this._doc.designMode="on";this.html(this._wym._html);if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();jQuery(this._doc).bind("keydown",this.keydown);jQuery(this._doc).bind("keyup",this.keyup);if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()};WYMeditor.WymClassOpera.prototype._exec=function(a,b){if(b){this._doc.execCommand(a,false,b)}else{this._doc.execCommand(a)}this.listen()};WYMeditor.WymClassOpera.prototype.selected=function(){var b=this._iframe.contentWindow.getSelection();var a=b.focusNode;if(a){if(a.nodeName=="#text"){return(a.parentNode)}else{return(a)}}else{return(null)}};WYMeditor.WymClassOpera.prototype.addCssRule=function(a,b){a.insertRule(b.name+" {"+b.css+"}",a.cssRules.length)};WYMeditor.WymClassOpera.prototype.keydown=function(a){var c=WYMeditor.INSTANCES[this.title];var b=c._iframe.contentWindow.getSelection();startNode=b.getRangeAt(0).startContainer;if(!jQuery(startNode).parentsOrSelf(WYMeditor.MAIN_CONTAINERS.join(","))[0]&&!jQuery(startNode).parentsOrSelf("li")&&a.keyCode!=WYMeditor.KEY.ENTER&&a.keyCode!=WYMeditor.KEY.LEFT&&a.keyCode!=WYMeditor.KEY.UP&&a.keyCode!=WYMeditor.KEY.RIGHT&&a.keyCode!=WYMeditor.KEY.DOWN&&a.keyCode!=WYMeditor.KEY.BACKSPACE&&a.keyCode!=WYMeditor.KEY.DELETE){c._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}};WYMeditor.WymClassOpera.prototype.keyup=function(a){var b=WYMeditor.INSTANCES[this.title];b._selected_image=null};WYMeditor.WymClassOpera.prototype.setFocusToNode=function(a){};WYMeditor.WymClassSafari=function(a){this._wym=a;this._class="class";this._newLine="\n"};WYMeditor.WymClassSafari.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentDocument;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);this._doc.designMode="on";this.html(this._wym._html);if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();jQuery(this._doc).bind("keydown",this.keydown);jQuery(this._doc).bind("keyup",this.keyup);if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()};WYMeditor.WymClassSafari.prototype._exec=function(e,g){if(!this.selected()){return(false)}switch(e){case WYMeditor.INDENT:case WYMeditor.OUTDENT:var f=this.selected();var d=this._iframe.contentWindow.getSelection();var b=d.anchorNode;if(b.nodeName=="#text"){b=b.parentNode}f=this.findUp(f,WYMeditor.BLOCKS);b=this.findUp(b,WYMeditor.BLOCKS);if(f&&f==b&&f.tagName.toLowerCase()==WYMeditor.LI){var c=f.parentNode.parentNode;if(f.parentNode.childNodes.length>1||c.tagName.toLowerCase()==WYMeditor.OL||c.tagName.toLowerCase()==WYMeditor.UL){this._doc.execCommand(e,"",null)}}break;case WYMeditor.INSERT_ORDEREDLIST:case WYMeditor.INSERT_UNORDEREDLIST:this._doc.execCommand(e,"",null);var f=this.selected();var a=this.findUp(f,WYMeditor.MAIN_CONTAINERS);if(a){jQuery(a).replaceWith(jQuery(a).html())}break;default:if(g){this._doc.execCommand(e,"",g)}else{this._doc.execCommand(e,"",null)}}var a=this.selected();if(a&&a.tagName.toLowerCase()==WYMeditor.BODY){this._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}this.listen()};WYMeditor.WymClassSafari.prototype.selected=function(){var b=this._iframe.contentWindow.getSelection();var a=b.focusNode;if(a){if(a.nodeName=="#text"){return(a.parentNode)}else{return(a)}}else{return(null)}};WYMeditor.WymClassSafari.prototype.addCssRule=function(a,b){a.insertRule(b.name+" {"+b.css+"}",a.cssRules.length)};WYMeditor.WymClassSafari.prototype.keydown=function(b){var f=WYMeditor.INSTANCES[this.title];if(b.keyCode===WYMeditor.KEY.ENTER){var a=f.selected();if(a){var g=$(a),e=g.parent(),d=g.parents(".embedded-item");if(d.size()){var c=$("<p/>");if(g.hasClass("title")){d.before(c)}else{if(g.hasClass("content")){d.after(c)}}f.setFocusToNode(c.get(0));return false}}}if(b.ctrlKey){if(b.keyCode==66){f._exec(WYMeditor.BOLD);return false}if(b.keyCode==73){f._exec(WYMeditor.ITALIC);return false}}};WYMeditor.WymClassSafari.prototype.keyup=function(b){var d=WYMeditor.INSTANCES[this.title];d._selected_image=null;var a=null;if(b.keyCode==13&&!b.shiftKey){jQuery(d._doc.body).children(WYMeditor.BR).remove();a=d.selected();if(a&&a.tagName.toLowerCase()==WYMeditor.PRE){d._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}}if(b.keyCode==13&&b.shiftKey){d._exec("InsertLineBreak")}if(b.keyCode!=8&&b.keyCode!=17&&b.keyCode!=46&&b.keyCode!=224&&!b.metaKey&&!b.ctrlKey){a=d.selected();var c=a.tagName.toLowerCase();if(c=="strong"||c=="b"||c=="em"||c=="i"||c=="sub"||c=="sup"||c=="a"||c=="span"){c=a.parentNode.tagName.toLowerCase()}if(c==WYMeditor.BODY||c==WYMeditor.DIV){d._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}}};WYMeditor.WymClassSafari.prototype.setFocusToNode=function(c){var a=this._iframe.contentDocument.createRange();a.selectNode(c);var b=this._iframe.contentWindow.getSelection();b.addRange(a);b.collapse(c,c.childNodes.length);this._iframe.contentWindow.focus()};WYMeditor.WymClassSafari.prototype.openBlockTag=function(a,c){var c=this.validator.getValidTagAttributes(a,c);if(a=="span"&&c.style){var b=this.getTagForStyle(c.style);if(b){this._tag_stack.pop();var a=b;this._tag_stack.push(b);c.style="";if(typeof c["class"]=="string"){c["class"]=c["class"].replace(/apple-style-span/gi,"")}}else{return}}this.output+=this.helper.tag(a,c,true)};WYMeditor.WymClassSafari.prototype.getTagForStyle=function(a){if(/bold/.test(a)){return"strong"}if(/italic/.test(a)){return"em"}if(/sub/.test(a)){return"sub"}if(/super/.test(a)){return"sup"}return false}; \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/2295745a2888/ Changeset: 2295745a2888 User: carlfeberhard Date: 2014-02-26 16:53:13 Summary: merge Affected #: 4 files diff -r a24050956e787690b7a37564a932fdfb194cdb6a -r 2295745a2888e74a518bdd6d7189d10031cbbf7d static/scripts/galaxy.pages.js --- a/static/scripts/galaxy.pages.js +++ b/static/scripts/galaxy.pages.js @@ -452,14 +452,14 @@ // item_class='History'). var item_elt_id = item_info.iclass + "-" + item_id; var item_embed_html = - "<p><div id='" + item_elt_id + "' class='embedded-item " + item_info.singular.toLowerCase() + + "<div id='" + item_elt_id + "' class='embedded-item " + item_info.singular.toLowerCase() + " placeholder'> \ <p class='title'>Embedded Galaxy " + item_info.singular + " '" + item_name + "'</p> \ <p class='content'> \ [Do not edit this block; Galaxy will fill it in with the annotated " + item_info.singular.toLowerCase() + " when it is displayed.] \ </p> \ - </div></p>"; + </div>"; // Insert embedded item into document. wym.insert(" "); // Needed to prevent insertion from occurring in child element in webkit browsers. @@ -468,18 +468,18 @@ // TODO: can we fix this? // Due to oddities of wym.insert() [likely due to inserting a <div> and/or a complete paragraph], an // empty paragraph (or two!) may be included either before an embedded item. Remove these paragraphs. - $("#" + item_elt_id, wym._doc.body).each( function() { - // Remove previous empty paragraphs. - var removing = true; - while (removing) - { - var prev_elt = $(this).prev(); - if ( prev_elt.length != 0 && jQuery.trim(prev_elt.text()) == "" ) - prev_elt.remove(); - else - removing = false; - } - }); + //$("#" + item_elt_id, wym._doc.body).each( function() { + // // Remove previous empty paragraphs. + // var removing = true; + // while (removing) + // { + // var prev_elt = $(this).prev(); + // if ( prev_elt.length != 0 && jQuery.trim(prev_elt.text()) == "" ) + // prev_elt.remove(); + // else + // removing = false; + // } + //}); }); hide_modal(); @@ -706,4 +706,4 @@ // editor.dialog(Galaxy.DIALOG_EMBED_PAGE); //} }); -}); \ No newline at end of file +}); diff -r a24050956e787690b7a37564a932fdfb194cdb6a -r 2295745a2888e74a518bdd6d7189d10031cbbf7d static/scripts/libs/jquery/jquery.wymeditor.js --- a/static/scripts/libs/jquery/jquery.wymeditor.js +++ b/static/scripts/libs/jquery/jquery.wymeditor.js @@ -3432,9 +3432,17 @@ replace(new RegExp('(\s*<('+tags+')>\s*){2}(.*)(\s*<\/\\2>\s*){2}' ,''),'<\$2>\$3<\$2>'); }; +// keep empty paragraphs +// from: http://forum.wymeditor.org/forum/viewtopic.php?f=2&t=711#p2430 +//WYMeditor.XhtmlSaxListener.prototype.removeEmptyTags = function(xhtml) +//{ +// return xhtml.replace(new RegExp('<('+this.block_tags.join("|").replace(/\|td/,'') +// .replace(/\|th/, '')+')>(<br \/>| | |\\s)*<\/\\1>' ,'g'),''); +//}; WYMeditor.XhtmlSaxListener.prototype.removeEmptyTags = function(xhtml) { - return xhtml.replace(new RegExp('<('+this.block_tags.join("|").replace(/\|td/,'').replace(/\|th/, '')+')>(<br \/>| | |\\s)*<\/\\1>' ,'g'),''); + return xhtml.replace(new RegExp('<('+this.block_tags.join("|").replace(/\|td/,'').replace(/\|p/,'') + .replace(/\|th/, '')+')>(<br \/>| | |\\s)*<\/\\1>' ,'g'),''); }; WYMeditor.XhtmlSaxListener.prototype.removeBrInPre = function(xhtml) @@ -4197,6 +4205,28 @@ var wym = WYMeditor.INSTANCES[this.title]; var container = null; + if( evt.keyCode === WYMeditor.KEY.ENTER ){ + container = wym.selected(); + if( container ){ + var $container = $( container ), + $parent = $container.parent(), + $embedded = $container.parents( '.embedded-item' ); + if( $embedded.size() ){ + // if the cursor is in the title, add a para before + var $newNode = $( '<p/>' ); + if( $container.hasClass( 'title' ) ){ + $embedded.before( $newNode ); + // if the cursor is in the content, add after + } else if( $container.hasClass( 'content' ) ){ + $embedded.after( $newNode ); + } + wym.setFocusToNode( $newNode.get(0) ); + // prevent the default - wym's chop the text and split it up into paras + return false; + } + } + } + if(evt.ctrlKey){ if(evt.keyCode == 66){ //CTRL+b => STRONG @@ -4227,27 +4257,27 @@ //'this' is the doc var wym = WYMeditor.INSTANCES[this.title]; - + wym._selected_image = null; var container = null; if(evt.keyCode == 13 && !evt.shiftKey) { - + //RETURN key //cleanup <br><br> between paragraphs jQuery(wym._doc.body).children(WYMeditor.BR).remove(); } - + else if(evt.keyCode != 8 && evt.keyCode != 17 && evt.keyCode != 46 && evt.keyCode != 224 && !evt.metaKey && !evt.ctrlKey) { - + //NOT BACKSPACE, NOT DELETE, NOT CTRL, NOT COMMAND //text nodes replaced by P - + container = wym.selected(); var name = container.tagName.toLowerCase(); @@ -4301,7 +4331,7 @@ return; } } - + this.output += this.helper.tag(tag, attributes, true); }; @@ -4343,9 +4373,9 @@ this._iframe = iframe; this._doc = iframe.contentWindow.document; - + //add css rules from options - var styles = this._doc.styleSheets[0]; + var styles = this._doc.styleSheets[0]; var aCss = eval(this._options.editorStyles); this.addCssRules(this._doc, aCss); @@ -4354,28 +4384,28 @@ //set the text direction jQuery('html', this._doc).attr('dir', this._options.direction); - + //init designMode this._doc.designMode = "on"; //init html value this.html(this._wym._html); - + //pre-bind functions if(jQuery.isFunction(this._options.preBind)) this._options.preBind(this); - + //bind external events this._wym.bindEvents(); - + //bind editor keydown events jQuery(this._doc).bind("keydown", this.keydown); - + //bind editor events jQuery(this._doc).bind("keyup", this.keyup); - + //post-init functions if(jQuery.isFunction(this._options.postInit)) this._options.postInit(this); - + //add event listeners to doc elements, e.g. images this.listen(); }; @@ -4384,7 +4414,7 @@ if(param) this._doc.execCommand(cmd,false,param); else this._doc.execCommand(cmd); - + this.listen(); }; @@ -4406,7 +4436,7 @@ //keydown handler WYMeditor.WymClassOpera.prototype.keydown = function(evt) { - + //'this' is the doc var wym = WYMeditor.INSTANCES[this.title]; var sel = wym._iframe.contentWindow.getSelection(); @@ -4470,12 +4500,12 @@ this._iframe = iframe; this._doc = iframe.contentDocument; - + //add css rules from options - - var styles = this._doc.styleSheets[0]; + + var styles = this._doc.styleSheets[0]; var aCss = eval(this._options.editorStyles); - + this.addCssRules(this._doc, aCss); this._doc.title = this._wym._index; @@ -4485,25 +4515,25 @@ //init designMode this._doc.designMode = "on"; - + //init html value this.html(this._wym._html); - + //pre-bind functions if(jQuery.isFunction(this._options.preBind)) this._options.preBind(this); - + //bind external events this._wym.bindEvents(); - + //bind editor keydown events jQuery(this._doc).bind("keydown", this.keydown); - + //bind editor keyup events jQuery(this._doc).bind("keyup", this.keyup); - + //post-init functions if(jQuery.isFunction(this._options.postInit)) this._options.postInit(this); - + //add event listeners to doc elements, e.g. images this.listen(); }; @@ -4513,17 +4543,17 @@ if(!this.selected()) return(false); switch(cmd) { - + case WYMeditor.INDENT: case WYMeditor.OUTDENT: - - var focusNode = this.selected(); + + var focusNode = this.selected(); var sel = this._iframe.contentWindow.getSelection(); var anchorNode = sel.anchorNode; if(anchorNode.nodeName == "#text") anchorNode = anchorNode.parentNode; - + focusNode = this.findUp(focusNode, WYMeditor.BLOCKS); anchorNode = this.findUp(anchorNode, WYMeditor.BLOCKS); - + if(focusNode && focusNode == anchorNode && focusNode.tagName.toLowerCase() == WYMeditor.LI) { @@ -4548,13 +4578,13 @@ if(container) jQuery(container).replaceWith(jQuery(container).html()); break; - + default: if(param) this._doc.execCommand(cmd,'',param); else this._doc.execCommand(cmd,'',null); } - + //set to P if parent = BODY var container = this.selected(); if(container && container.tagName.toLowerCase() == WYMeditor.BODY) @@ -4586,9 +4616,31 @@ //keydown handler, mainly used for keyboard shortcuts WYMeditor.WymClassSafari.prototype.keydown = function(evt) { - + //'this' is the doc var wym = WYMeditor.INSTANCES[this.title]; + + if( evt.keyCode === WYMeditor.KEY.ENTER ){ + var container = wym.selected(); + if( container ){ + var $container = $( container ), + $parent = $container.parent(), + $embedded = $container.parents( '.embedded-item' ); + if( $embedded.size() ){ + // if the cursor is in the title, add a para before + var $newNode = $( '<p/>' ); + if( $container.hasClass( 'title' ) ){ + $embedded.before( $newNode ); + // if the cursor is in the content, add after + } else if( $container.hasClass( 'content' ) ){ + $embedded.after( $newNode ); + } + wym.setFocusToNode( $newNode.get(0) ); + // prevent the default - wym's chop the text and split it up into paras + return false; + } + } + } if(evt.ctrlKey){ if(evt.keyCode == 66){ diff -r a24050956e787690b7a37564a932fdfb194cdb6a -r 2295745a2888e74a518bdd6d7189d10031cbbf7d static/scripts/packed/galaxy.pages.js --- a/static/scripts/packed/galaxy.pages.js +++ b/static/scripts/packed/galaxy.pages.js @@ -1,1 +1,1 @@ -var Galaxy={ITEM_HISTORY:"item_history",ITEM_DATASET:"item_dataset",ITEM_WORKFLOW:"item_workflow",ITEM_PAGE:"item_page",ITEM_VISUALIZATION:"item_visualization",DIALOG_HISTORY_LINK:"link_history",DIALOG_DATASET_LINK:"link_dataset",DIALOG_WORKFLOW_LINK:"link_workflow",DIALOG_PAGE_LINK:"link_page",DIALOG_VISUALIZATION_LINK:"link_visualization",DIALOG_EMBED_HISTORY:"embed_history",DIALOG_EMBED_DATASET:"embed_dataset",DIALOG_EMBED_WORKFLOW:"embed_workflow",DIALOG_EMBED_PAGE:"embed_page",DIALOG_EMBED_VISUALIZATION:"embed_visualization",DIALOG_HISTORY_ANNOTATE:"history_annotate",};function init_galaxy_elts(a){$(".annotation",a._doc.body).each(function(){$(this).click(function(){var b=a._doc.createRange();b.selectNodeContents(this);var d=window.getSelection();d.removeAllRanges();d.addRange(b);var c=""})})}function get_item_info(d){var f,c,b;switch(d){case (Galaxy.ITEM_HISTORY):f="History";c="Histories";b="history";item_class="History";break;case (Galaxy.ITEM_DATASET):f="Dataset";c="Datasets";b="dataset";item_class="HistoryDatasetAssociation";break;case (Galaxy.ITEM_WORKFLOW):f="Workflow";c="Workflows";b="workflow";item_class="StoredWorkflow";break;case (Galaxy.ITEM_PAGE):f="Page";c="Pages";b="page";item_class="Page";break;case (Galaxy.ITEM_VISUALIZATION):f="Visualization";c="Visualizations";b="visualization";item_class="Visualization";break}var e="list_"+c.toLowerCase()+"_for_selection";var a=list_objects_url.replace("LIST_ACTION",e);return{singular:f,plural:c,controller:b,iclass:item_class,list_ajax_url:a}}function make_item_importable(a,c,b){ajax_url=set_accessible_url.replace("ITEM_CONTROLLER",a);$.ajax({type:"POST",url:ajax_url,data:{id:c,accessible:"True"},error:function(){alert("Making "+b+" accessible failed")}})}WYMeditor.editor.prototype.dialog=function(i,e,g){var a=this;var b=a.uniqueStamp();var f=a.selected();function h(){$("#set_link_id").click(function(){$("#link_attribute_label").text("ID/Name");var k=$(".wym_href");k.addClass("wym_id").removeClass("wym_href");if(f){k.val($(f).attr("id"))}$(this).remove()})}if(i==WYMeditor.DIALOG_LINK){if(f){$(a._options.hrefSelector).val($(f).attr(WYMeditor.HREF));$(a._options.srcSelector).val($(f).attr(WYMeditor.SRC));$(a._options.titleSelector).val($(f).attr(WYMeditor.TITLE));$(a._options.altSelector).val($(f).attr(WYMeditor.ALT))}var c,d;if(f){c=$(f).attr("href");if(c==undefined){c=""}d=$(f).attr("title");if(d==undefined){d=""}}show_modal("Create Link","<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='"+c+"' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='"+d+"' size='40' /></div><div>",{"Make link":function(){var m=$(a._options.hrefSelector).val()||"",k=$(".wym_id").val()||"",n=$(a._options.titleSelector).val()||"";if(m||k){a._exec(WYMeditor.CREATE_LINK,b);var l=$("a[href="+b+"]",a._doc.body);l.attr(WYMeditor.HREF,m).attr(WYMeditor.TITLE,n).attr("id",k);if(l.text().indexOf("wym-")===0){l.text(n)}}hide_modal()},Cancel:function(){hide_modal()}},{},h)}if(i==WYMeditor.DIALOG_IMAGE){if(a._selected_image){$(a._options.dialogImageSelector+" "+a._options.srcSelector).val($(a._selected_image).attr(WYMeditor.SRC));$(a._options.dialogImageSelector+" "+a._options.titleSelector).val($(a._selected_image).attr(WYMeditor.TITLE));$(a._options.dialogImageSelector+" "+a._options.altSelector).val($(a._selected_image).attr(WYMeditor.ALT))}show_modal("Image","<div class='row'><label>URL</label><br><input type='text' class='wym_src' value='' size='40' /></div><div class='row'><label>Alt text</label><br><input type='text' class='wym_alt' value='' size='40' /></div><div class='row'><label>Title</label><br><input type='text' class='wym_title' value='' size='40' /></div>",{Insert:function(){var k=$(a._options.srcSelector).val();if(k.length>0){a._exec(WYMeditor.INSERT_IMAGE,b);$("img[src$="+b+"]",a._doc.body).attr(WYMeditor.SRC,k).attr(WYMeditor.TITLE,$(a._options.titleSelector).val()).attr(WYMeditor.ALT,$(a._options.altSelector).val())}hide_modal()},Cancel:function(){hide_modal()}});return}if(i==WYMeditor.DIALOG_TABLE){show_modal("Table","<div class='row'><label>Caption</label><br><input type='text' class='wym_caption' value='' size='40' /></div><div class='row'><label>Summary</label><br><input type='text' class='wym_summary' value='' size='40' /></div><div class='row'><label>Number Of Rows<br></label><input type='text' class='wym_rows' value='3' size='3' /></div><div class='row'><label>Number Of Cols<br></label><input type='text' class='wym_cols' value='2' size='3' /></div>",{Insert:function(){var o=$(a._options.rowsSelector).val();var r=$(a._options.colsSelector).val();if(o>0&&r>0){var n=a._doc.createElement(WYMeditor.TABLE);var l=null;var q=null;var k=$(a._options.captionSelector).val();var p=n.createCaption();p.innerHTML=k;for(x=0;x<o;x++){l=n.insertRow(x);for(y=0;y<r;y++){l.insertCell(y)}}$(n).attr("summary",$(a._options.summarySelector).val());var m=$(a.findUp(a.container(),WYMeditor.MAIN_CONTAINERS)).get(0);if(!m||!m.parentNode){$(a._doc.body).append(n)}else{$(m).after(n)}}hide_modal()},Cancel:function(){hide_modal()}})}if(i==Galaxy.DIALOG_HISTORY_LINK||i==Galaxy.DIALOG_DATASET_LINK||i==Galaxy.DIALOG_WORKFLOW_LINK||i==Galaxy.DIALOG_PAGE_LINK||i==Galaxy.DIALOG_VISUALIZATION_LINK){var j;switch(i){case (Galaxy.DIALOG_HISTORY_LINK):j=get_item_info(Galaxy.ITEM_HISTORY);break;case (Galaxy.DIALOG_DATASET_LINK):j=get_item_info(Galaxy.ITEM_DATASET);break;case (Galaxy.DIALOG_WORKFLOW_LINK):j=get_item_info(Galaxy.ITEM_WORKFLOW);break;case (Galaxy.DIALOG_PAGE_LINK):j=get_item_info(Galaxy.ITEM_PAGE);break;case (Galaxy.DIALOG_VISUALIZATION_LINK):j=get_item_info(Galaxy.ITEM_VISUALIZATION);break}$.ajax({url:j.list_ajax_url,data:{},error:function(){alert("Failed to list "+j.plural.toLowerCase()+" for selection")},success:function(k){show_modal("Insert Link to "+j.singular,k+"<div><input id='make-importable' type='checkbox' checked/>Make the selected "+j.plural.toLowerCase()+" accessible so that they can viewed by everyone.</div>",{Insert:function(){var m=false;if($("#make-importable:checked").val()!==null){m=true}var l=new Array();$("input[name=id]:checked").each(function(){var n=$(this).val();if(m){make_item_importable(j.controller,n,j.singular)}url_template=get_name_and_link_url+n;ajax_url=url_template.replace("ITEM_CONTROLLER",j.controller);$.getJSON(ajax_url,function(p){a._exec(WYMeditor.CREATE_LINK,b);var o=$("a[href="+b+"]",a._doc.body).text();if(o==""||o==b){a.insert("<a href='"+p.link+"'>"+j.singular+" '"+p.name+"'</a>")}else{$("a[href="+b+"]",a._doc.body).attr(WYMeditor.HREF,p.link).attr(WYMeditor.TITLE,j.singular+n)}})});hide_modal()},Cancel:function(){hide_modal()}})}})}if(i==Galaxy.DIALOG_EMBED_HISTORY||i==Galaxy.DIALOG_EMBED_DATASET||i==Galaxy.DIALOG_EMBED_WORKFLOW||i==Galaxy.DIALOG_EMBED_PAGE||i==Galaxy.DIALOG_EMBED_VISUALIZATION){var j;switch(i){case (Galaxy.DIALOG_EMBED_HISTORY):j=get_item_info(Galaxy.ITEM_HISTORY);break;case (Galaxy.DIALOG_EMBED_DATASET):j=get_item_info(Galaxy.ITEM_DATASET);break;case (Galaxy.DIALOG_EMBED_WORKFLOW):j=get_item_info(Galaxy.ITEM_WORKFLOW);break;case (Galaxy.DIALOG_EMBED_PAGE):j=get_item_info(Galaxy.ITEM_PAGE);break;case (Galaxy.DIALOG_EMBED_VISUALIZATION):j=get_item_info(Galaxy.ITEM_VISUALIZATION);break}$.ajax({url:j.list_ajax_url,data:{},error:function(){alert("Failed to list "+j.plural.toLowerCase()+" for selection")},success:function(k){if(i==Galaxy.DIALOG_EMBED_HISTORY||i==Galaxy.DIALOG_EMBED_WORKFLOW||i==Galaxy.DIALOG_EMBED_VISUALIZATION){k=k+"<div><input id='make-importable' type='checkbox' checked/>Make the selected "+j.plural.toLowerCase()+" accessible so that they can viewed by everyone.</div>"}show_modal("Embed "+j.plural,k,{Embed:function(){var l=false;if($("#make-importable:checked").val()!=null){l=true}$("input[name=id]:checked").each(function(){var m=$(this).val();var p=$("label[for='"+m+"']:first").text();if(l){make_item_importable(j.controller,m,j.singular)}var n=j.iclass+"-"+m;var o="<p><div id='"+n+"' class='embedded-item "+j.singular.toLowerCase()+" placeholder'><p class='title'>Embedded Galaxy "+j.singular+" '"+p+"'</p><p class='content'> [Do not edit this block; Galaxy will fill it in with the annotated "+j.singular.toLowerCase()+" when it is displayed.] </p></div></p>";a.insert(" ");a.insert(o);$("#"+n,a._doc.body).each(function(){var q=true;while(q){var r=$(this).prev();if(r.length!=0&&jQuery.trim(r.text())==""){r.remove()}else{q=false}}})});hide_modal()},Cancel:function(){hide_modal()}})}})}if(i==Galaxy.DIALOG_ANNOTATE_HISTORY){$.ajax({url:list_histories_for_selection_url,data:{},error:function(){alert("Grid refresh failed")},success:function(k){show_modal("Insert Link to History",k,{Annotate:function(){var l=new Array();$("input[name=id]:checked").each(function(){var m=$(this).val();$.ajax({url:get_history_annotation_table_url,data:{id:m},error:function(){alert("Grid refresh failed")},success:function(n){a.insert(n);init_galaxy_elts(a)}})});hide_modal()},Cancel:function(){hide_modal()}})}})}};$(function(){$(document).ajaxError(function(i,g){var h=g.responseText||g.statusText||"Could not connect to server";show_modal("Server error",h,{"Ignore error":hide_modal});return false});$("[name=page_content]").wymeditor({skin:"galaxy",basePath:editor_base_path,iframeBasePath:iframe_base_path,boxHtml:"<table class='wym_box' width='100%' height='100%'><tr><td><div class='wym_area_top'>"+WYMeditor.TOOLS+"</div></td></tr><tr height='100%'><td><div class='wym_area_main' style='height: 100%;'>"+WYMeditor.IFRAME+WYMeditor.STATUS+"</div></div></td></tr></table>",toolsItems:[{name:"Bold",title:"Strong",css:"wym_tools_strong"},{name:"Italic",title:"Emphasis",css:"wym_tools_emphasis"},{name:"Superscript",title:"Superscript",css:"wym_tools_superscript"},{name:"Subscript",title:"Subscript",css:"wym_tools_subscript"},{name:"InsertOrderedList",title:"Ordered_List",css:"wym_tools_ordered_list"},{name:"InsertUnorderedList",title:"Unordered_List",css:"wym_tools_unordered_list"},{name:"Indent",title:"Indent",css:"wym_tools_indent"},{name:"Outdent",title:"Outdent",css:"wym_tools_outdent"},{name:"Undo",title:"Undo",css:"wym_tools_undo"},{name:"Redo",title:"Redo",css:"wym_tools_redo"},{name:"CreateLink",title:"Link",css:"wym_tools_link"},{name:"Unlink",title:"Unlink",css:"wym_tools_unlink"},{name:"InsertImage",title:"Image",css:"wym_tools_image"},{name:"InsertTable",title:"Table",css:"wym_tools_table"},]});var d=$.wymeditors(0);var f=function(g){show_modal("Saving page","progress");$.ajax({url:save_url,type:"POST",data:{id:page_id,content:d.xhtml(),annotations:JSON.stringify(new Object()),_:"true"},success:function(){g()}})};$("#save-button").click(function(){f(function(){hide_modal()})});$("#close-button").click(function(){var h=false;if(h){var g=function(){window.onbeforeunload=undefined;window.document.location=page_list_url};show_modal("Close editor","There are unsaved changes to your page which will be lost.",{Cancel:hide_modal,"Save Changes":function(){f(g)}},{"Don't Save":g})}else{window.document.location=page_list_url}});var a=$("<div class='galaxy-page-editor-button'><a id='insert-galaxy-link' class='action-button popup' href='#'>Paragraph type</a></div>");$(".wym_area_top").append(a);var b={};$.each(d._options.containersItems,function(h,g){var i=g.name;b[g.title.replace("_"," ")]=function(){d.container(i)}});make_popupmenu(a,b);var c=$("<div><a id='insert-galaxy-link' class='action-button popup' href='#'>Insert Link to Galaxy Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(c);make_popupmenu(c,{"Insert History Link":function(){d.dialog(Galaxy.DIALOG_HISTORY_LINK)},"Insert Dataset Link":function(){d.dialog(Galaxy.DIALOG_DATASET_LINK)},"Insert Workflow Link":function(){d.dialog(Galaxy.DIALOG_WORKFLOW_LINK)},"Insert Page Link":function(){d.dialog(Galaxy.DIALOG_PAGE_LINK)},"Insert Visualization Link":function(){d.dialog(Galaxy.DIALOG_VISUALIZATION_LINK)},});var e=$("<div><a id='embed-galaxy-object' class='action-button popup' href='#'>Embed Galaxy Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(e);make_popupmenu(e,{"Embed History":function(){d.dialog(Galaxy.DIALOG_EMBED_HISTORY)},"Embed Dataset":function(){d.dialog(Galaxy.DIALOG_EMBED_DATASET)},"Embed Workflow":function(){d.dialog(Galaxy.DIALOG_EMBED_WORKFLOW)},"Embed Visualization":function(){d.dialog(Galaxy.DIALOG_EMBED_VISUALIZATION)},})}); \ No newline at end of file +var Galaxy={ITEM_HISTORY:"item_history",ITEM_DATASET:"item_dataset",ITEM_WORKFLOW:"item_workflow",ITEM_PAGE:"item_page",ITEM_VISUALIZATION:"item_visualization",DIALOG_HISTORY_LINK:"link_history",DIALOG_DATASET_LINK:"link_dataset",DIALOG_WORKFLOW_LINK:"link_workflow",DIALOG_PAGE_LINK:"link_page",DIALOG_VISUALIZATION_LINK:"link_visualization",DIALOG_EMBED_HISTORY:"embed_history",DIALOG_EMBED_DATASET:"embed_dataset",DIALOG_EMBED_WORKFLOW:"embed_workflow",DIALOG_EMBED_PAGE:"embed_page",DIALOG_EMBED_VISUALIZATION:"embed_visualization",DIALOG_HISTORY_ANNOTATE:"history_annotate",};function init_galaxy_elts(a){$(".annotation",a._doc.body).each(function(){$(this).click(function(){var b=a._doc.createRange();b.selectNodeContents(this);var d=window.getSelection();d.removeAllRanges();d.addRange(b);var c=""})})}function get_item_info(d){var f,c,b;switch(d){case (Galaxy.ITEM_HISTORY):f="History";c="Histories";b="history";item_class="History";break;case (Galaxy.ITEM_DATASET):f="Dataset";c="Datasets";b="dataset";item_class="HistoryDatasetAssociation";break;case (Galaxy.ITEM_WORKFLOW):f="Workflow";c="Workflows";b="workflow";item_class="StoredWorkflow";break;case (Galaxy.ITEM_PAGE):f="Page";c="Pages";b="page";item_class="Page";break;case (Galaxy.ITEM_VISUALIZATION):f="Visualization";c="Visualizations";b="visualization";item_class="Visualization";break}var e="list_"+c.toLowerCase()+"_for_selection";var a=list_objects_url.replace("LIST_ACTION",e);return{singular:f,plural:c,controller:b,iclass:item_class,list_ajax_url:a}}function make_item_importable(a,c,b){ajax_url=set_accessible_url.replace("ITEM_CONTROLLER",a);$.ajax({type:"POST",url:ajax_url,data:{id:c,accessible:"True"},error:function(){alert("Making "+b+" accessible failed")}})}WYMeditor.editor.prototype.dialog=function(i,e,g){var a=this;var b=a.uniqueStamp();var f=a.selected();function h(){$("#set_link_id").click(function(){$("#link_attribute_label").text("ID/Name");var 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a",htmlValSelector:".wym_html_val",hrefSelector:".wym_href",srcSelector:".wym_src",titleSelector:".wym_title",altSelector:".wym_alt",textSelector:".wym_text",rowsSelector:".wym_rows",colsSelector:".wym_cols",captionSelector:".wym_caption",summarySelector:".wym_summary",submitSelector:".wym_submit",cancelSelector:".wym_cancel",previewSelector:"",dialogTypeSelector:".wym_dialog_type",dialogLinkSelector:".wym_dialog_link",dialogImageSelector:".wym_dialog_image",dialogTableSelector:".wym_dialog_table",dialogPasteSelector:".wym_dialog_paste",dialogPreviewSelector:".wym_dialog_preview",updateSelector:".wymupdate",updateEvent:"click",dialogFeatures:"menubar=no,titlebar=no,toolbar=no,resizable=no,width=560,height=300,top=0,left=0",dialogFeaturesPreview:"menubar=no,titlebar=no,toolbar=no,resizable=no,scrollbars=yes,width=560,height=300,top=0,left=0",dialogHtml:"<!DOCTYPE html PUBLIC '-//W3C//DTD XHTML 1.0 Strict//EN' 'http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd'><html dir='"+WYMeditor.DIRECTION+"'><head><link rel='stylesheet' type='text/css' media='screen' href='"+WYMeditor.CSS_PATH+"' /><title>"+WYMeditor.DIALOG_TITLE+"</title><script type='text/javascript' src='"+WYMeditor.JQUERY_PATH+"'><\/script><script type='text/javascript' src='"+WYMeditor.WYM_PATH+"'><\/script></head>"+WYMeditor.DIALOG_BODY+"</html>",dialogLinkHtml:"<body class='wym_dialog wym_dialog_link' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><fieldset><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_LINK+"' /><legend>{Link}</legend><div class='row'><label>{URL}</label><input type='text' class='wym_href' value='' size='40' /></div><div class='row'><label>{Title}</label><input type='text' class='wym_title' value='' size='40' /></div><div class='row row-indent'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogImageHtml:"<body class='wym_dialog wym_dialog_image' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><fieldset><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_IMAGE+"' /><legend>{Image}</legend><div class='row'><label>{URL}</label><input type='text' class='wym_src' value='' size='40' /></div><div class='row'><label>{Alternative_Text}</label><input type='text' class='wym_alt' value='' size='40' /></div><div class='row'><label>{Title}</label><input type='text' class='wym_title' value='' size='40' /></div><div class='row row-indent'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogTableHtml:"<body class='wym_dialog wym_dialog_table' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><fieldset><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_TABLE+"' /><legend>{Table}</legend><div class='row'><label>{Caption}</label><input type='text' class='wym_caption' value='' size='40' /></div><div class='row'><label>{Summary}</label><input type='text' class='wym_summary' value='' size='40' /></div><div class='row'><label>{Number_Of_Rows}</label><input type='text' class='wym_rows' value='3' size='3' /></div><div class='row'><label>{Number_Of_Cols}</label><input type='text' class='wym_cols' value='2' size='3' /></div><div class='row row-indent'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogPasteHtml:"<body class='wym_dialog wym_dialog_paste' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_PASTE+"' /><fieldset><legend>{Paste_From_Word}</legend><div class='row'><textarea class='wym_text' rows='10' cols='50'></textarea></div><div class='row'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogPreviewHtml:"<body class='wym_dialog wym_dialog_preview' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'></body>",dialogStyles:[],stringDelimiterLeft:"{",stringDelimiterRight:"}",preInit:null,preBind:null,postInit:null,preInitDialog:null,postInitDialog:null},a);return this.each(function(){new WYMeditor.editor(jQuery(this),a)})};jQuery.extend({wymeditors:function(a){return(WYMeditor.INSTANCES[a])}});WYMeditor.editor.prototype.init=function(){if(jQuery.browser.msie){var WymClass=new WYMeditor.WymClassExplorer(this)}else{if(jQuery.browser.mozilla){var WymClass=new WYMeditor.WymClassMozilla(this)}else{if(jQuery.browser.opera){var WymClass=new WYMeditor.WymClassOpera(this)}else{if(jQuery.browser.safari||jQuery.browser.chrome){var WymClass=new WYMeditor.WymClassSafari(this)}}}}if(WymClass){if(jQuery.isFunction(this._options.preInit)){this._options.preInit(this)}var SaxListener=new WYMeditor.XhtmlSaxListener();jQuery.extend(SaxListener,WymClass);this.parser=new WYMeditor.XhtmlParser(SaxListener);if(this._options.styles||this._options.stylesheet){this.configureEditorUsingRawCss()}this.helper=new WYMeditor.XmlHelper();for(var prop in WymClass){this[prop]=WymClass[prop]}this._box=jQuery(this._element).hide().after(this._options.boxHtml).next().addClass("wym_box_"+this._index);if(jQuery.isFunction(jQuery.fn.data)){jQuery.data(this._box.get(0),WYMeditor.WYM_INDEX,this._index);jQuery.data(this._element.get(0),WYMeditor.WYM_INDEX,this._index)}var h=WYMeditor.Helper;var iframeHtml=this._options.iframeHtml;iframeHtml=h.replaceAll(iframeHtml,WYMeditor.INDEX,this._index);iframeHtml=h.replaceAll(iframeHtml,WYMeditor.IFRAME_BASE_PATH,this._options.iframeBasePath);var boxHtml=jQuery(this._box).html();boxHtml=h.replaceAll(boxHtml,WYMeditor.LOGO,this._options.logoHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.TOOLS,this._options.toolsHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.CONTAINERS,this._options.containersHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.CLASSES,this._options.classesHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.HTML,this._options.htmlHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.IFRAME,iframeHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.STATUS,this._options.statusHtml);var aTools=eval(this._options.toolsItems);var sTools="";for(var i=0;i<aTools.length;i++){var oTool=aTools[i];if(oTool.name&&oTool.title){var sTool=this._options.toolsItemHtml}var sTool=h.replaceAll(sTool,WYMeditor.TOOL_NAME,oTool.name);sTool=h.replaceAll(sTool,WYMeditor.TOOL_TITLE,this._options.stringDelimiterLeft+oTool.title+this._options.stringDelimiterRight);sTool=h.replaceAll(sTool,WYMeditor.TOOL_CLASS,oTool.css);sTools+=sTool}boxHtml=h.replaceAll(boxHtml,WYMeditor.TOOLS_ITEMS,sTools);var aClasses=eval(this._options.classesItems);var sClasses="";for(var i=0;i<aClasses.length;i++){var oClass=aClasses[i];if(oClass.name&&oClass.title){var sClass=this._options.classesItemHtml}sClass=h.replaceAll(sClass,WYMeditor.CLASS_NAME,oClass.name);sClass=h.replaceAll(sClass,WYMeditor.CLASS_TITLE,oClass.title);sClasses+=sClass}boxHtml=h.replaceAll(boxHtml,WYMeditor.CLASSES_ITEMS,sClasses);var aContainers=eval(this._options.containersItems);var sContainers="";for(var i=0;i<aContainers.length;i++){var oContainer=aContainers[i];if(oContainer.name&&oContainer.title){var sContainer=this._options.containersItemHtml}sContainer=h.replaceAll(sContainer,WYMeditor.CONTAINER_NAME,oContainer.name);sContainer=h.replaceAll(sContainer,WYMeditor.CONTAINER_TITLE,this._options.stringDelimiterLeft+oContainer.title+this._options.stringDelimiterRight);sContainer=h.replaceAll(sContainer,WYMeditor.CONTAINER_CLASS,oContainer.css);sContainers+=sContainer}boxHtml=h.replaceAll(boxHtml,WYMeditor.CONTAINERS_ITEMS,sContainers);boxHtml=this.replaceStrings(boxHtml);jQuery(this._box).html(boxHtml);jQuery(this._box).find(this._options.htmlSelector).hide();this.loadSkin()}};WYMeditor.editor.prototype.bindEvents=function(){var wym=this;jQuery(this._box).find(this._options.toolSelector).click(function(){wym._iframe.contentWindow.focus();wym.exec(jQuery(this).attr(WYMeditor.NAME));return(false)});jQuery(this._box).find(this._options.containerSelector).click(function(){wym.container(jQuery(this).attr(WYMeditor.NAME));return(false)});jQuery(this._box).find(this._options.htmlValSelector).keyup(function(){jQuery(wym._doc.body).html(jQuery(this).val())}).focus(function(){jQuery(this).toggleClass("hasfocus")}).blur(function(){jQuery(this).toggleClass("hasfocus")});jQuery(this._box).find(this._options.classSelector).click(function(){var aClasses=eval(wym._options.classesItems);var sName=jQuery(this).attr(WYMeditor.NAME);var oClass=WYMeditor.Helper.findByName(aClasses,sName);if(oClass){var jqexpr=oClass.expr;wym.toggleClass(sName,jqexpr)}wym._iframe.contentWindow.focus();return(false)});jQuery(this._options.updateSelector).bind(this._options.updateEvent,function(){wym.update()})};WYMeditor.editor.prototype.ready=function(){return(this._doc!=null)};WYMeditor.editor.prototype.box=function(){return(this._box)};WYMeditor.editor.prototype.html=function(a){if(typeof a==="string"){jQuery(this._doc.body).html(a)}else{return(jQuery(this._doc.body).html())}};WYMeditor.editor.prototype.xhtml=function(){return this.parser.parse(this.html())};WYMeditor.editor.prototype.exec=function(b){switch(b){case WYMeditor.CREATE_LINK:var a=this.container();if(a||this._selected_image){this.dialog(WYMeditor.DIALOG_LINK)}break;case WYMeditor.INSERT_IMAGE:this.dialog(WYMeditor.DIALOG_IMAGE);break;case WYMeditor.INSERT_TABLE:this.dialog(WYMeditor.DIALOG_TABLE);break;case WYMeditor.PASTE:this.dialog(WYMeditor.DIALOG_PASTE);break;case WYMeditor.TOGGLE_HTML:this.update();this.toggleHtml();if(!jQuery(this._box).find(this._options.htmlSelector).is(":visible")){this.listen()}break;case WYMeditor.PREVIEW:this.dialog(WYMeditor.PREVIEW,this._options.dialogFeaturesPreview);break;default:this._exec(b);break}};WYMeditor.editor.prototype.container=function(a){if(a){var d=null;if(a.toLowerCase()==WYMeditor.TH){d=this.container();switch(d.tagName.toLowerCase()){case WYMeditor.TD:case WYMeditor.TH:break;default:var e=new Array(WYMeditor.TD,WYMeditor.TH);d=this.findUp(this.container(),e);break}if(d!=null){a=(d.tagName.toLowerCase()==WYMeditor.TD)?WYMeditor.TH:WYMeditor.TD;this.switchTo(d,a);this.update()}}else{var e=new Array(WYMeditor.P,WYMeditor.H1,WYMeditor.H2,WYMeditor.H3,WYMeditor.H4,WYMeditor.H5,WYMeditor.H6,WYMeditor.PRE,WYMeditor.BLOCKQUOTE);d=this.findUp(this.container(),e);if(d){var i=null;if(a.toLowerCase()==WYMeditor.BLOCKQUOTE){var f=this.findUp(this.container(),WYMeditor.BLOCKQUOTE);if(f==null){i=this._doc.createElement(a);d.parentNode.insertBefore(i,d);i.appendChild(d);this.setFocusToNode(i.firstChild)}else{var c=f.childNodes;var g=c.length;var b=null;if(g>0){b=c.item(0)}for(var h=0;h<g;h++){f.parentNode.insertBefore(c.item(0),f)}f.parentNode.removeChild(f);if(b){this.setFocusToNode(b)}}}else{this.switchTo(d,a)}this.update()}}}else{return(this.selected())}};WYMeditor.editor.prototype.toggleClass=function(c,b){var a=(this._selected_image?this._selected_image:jQuery(this.selected()));a=jQuery(a).parentsOrSelf(b);jQuery(a).toggleClass(c);if(!jQuery(a).attr(WYMeditor.CLASS)){jQuery(a).removeAttr(this._class)}};WYMeditor.editor.prototype.findUp=function(d,c){if(d){var e=d.tagName.toLowerCase();if(typeof(c)==WYMeditor.STRING){while(e!=c&&e!=WYMeditor.BODY){d=d.parentNode;e=d.tagName.toLowerCase()}}else{var b=false;while(!b&&e!=WYMeditor.BODY){for(var a=0;a<c.length;a++){if(e==c[a]){b=true;break}}if(!b){d=d.parentNode;e=d.tagName.toLowerCase()}}}if(e!=WYMeditor.BODY){return(d)}else{return(null)}}else{return(null)}};WYMeditor.editor.prototype.switchTo=function(c,d){var b=this._doc.createElement(d);var a=jQuery(c).html();c.parentNode.replaceChild(b,c);jQuery(b).html(a);this.setFocusToNode(b)};WYMeditor.editor.prototype.replaceStrings=function(sVal){if(!WYMeditor.STRINGS[this._options.lang]){try{eval(jQuery.ajax({url:this._options.langPath+this._options.lang+".js",async:false}).responseText)}catch(e){WYMeditor.console.error("WYMeditor: error while parsing language file.");return sVal}}for(var key in WYMeditor.STRINGS[this._options.lang]){sVal=WYMeditor.Helper.replaceAll(sVal,this._options.stringDelimiterLeft+key+this._options.stringDelimiterRight,WYMeditor.STRINGS[this._options.lang][key])}return(sVal)};WYMeditor.editor.prototype.encloseString=function(a){return(this._options.stringDelimiterLeft+a+this._options.stringDelimiterRight)};WYMeditor.editor.prototype.status=function(a){jQuery(this._box).find(this._options.statusSelector).html(a)};WYMeditor.editor.prototype.update=function(){var a=this.xhtml();jQuery(this._element).val(a);jQuery(this._box).find(this._options.htmlValSelector).not(".hasfocus").val(a)};WYMeditor.editor.prototype.dialog=function(j,c,f){var a=c||this._wym._options.dialogFeatures;var d=window.open("","dialog",a);if(d){var b="";switch(j){case (WYMeditor.DIALOG_LINK):b=this._options.dialogLinkHtml;break;case (WYMeditor.DIALOG_IMAGE):b=this._options.dialogImageHtml;break;case (WYMeditor.DIALOG_TABLE):b=this._options.dialogTableHtml;break;case (WYMeditor.DIALOG_PASTE):b=this._options.dialogPasteHtml;break;case (WYMeditor.PREVIEW):b=this._options.dialogPreviewHtml;break;default:b=f}var e=WYMeditor.Helper;var g=this._options.dialogHtml;g=e.replaceAll(g,WYMeditor.BASE_PATH,this._options.basePath);g=e.replaceAll(g,WYMeditor.DIRECTION,this._options.direction);g=e.replaceAll(g,WYMeditor.CSS_PATH,this._options.skinPath+WYMeditor.SKINS_DEFAULT_CSS);g=e.replaceAll(g,WYMeditor.WYM_PATH,this._options.wymPath);g=e.replaceAll(g,WYMeditor.JQUERY_PATH,this._options.jQueryPath);g=e.replaceAll(g,WYMeditor.DIALOG_TITLE,this.encloseString(j));g=e.replaceAll(g,WYMeditor.DIALOG_BODY,b);g=e.replaceAll(g,WYMeditor.INDEX,this._index);g=this.replaceStrings(g);var i=d.document;i.write(g);i.close()}};WYMeditor.editor.prototype.toggleHtml=function(){jQuery(this._box).find(this._options.htmlSelector).toggle()};WYMeditor.editor.prototype.uniqueStamp=function(){var a=new Date();return("wym-"+a.getTime())};WYMeditor.editor.prototype.paste=function(b){var e;var a=this.selected();var c=b.split(this._newLine+this._newLine);var d=new RegExp(this._newLine,"g");if(a&&a.tagName.toLowerCase()!=WYMeditor.BODY){for(x=c.length-1;x>=0;x--){e=c[x];e=e.replace(d,"<br />");jQuery(a).after("<p>"+e+"</p>")}}else{for(x=0;x<c.length;x++){e=c[x];e=e.replace(d,"<br />");jQuery(this._doc.body).append("<p>"+e+"</p>")}}};WYMeditor.editor.prototype.insert=function(a){if(this._iframe.contentWindow.getSelection().focusNode!=null){this._exec(WYMeditor.INSERT_HTML,a)}else{this.paste(a)}};WYMeditor.editor.prototype.wrap=function(b,a){if(this._iframe.contentWindow.getSelection().focusNode!=null){this._exec(WYMeditor.INSERT_HTML,b+this._iframe.contentWindow.getSelection().toString()+a)}};WYMeditor.editor.prototype.unwrap=function(){if(this._iframe.contentWindow.getSelection().focusNode!=null){this._exec(WYMeditor.INSERT_HTML,this._iframe.contentWindow.getSelection().toString())}};WYMeditor.editor.prototype.addCssRules=function(e,c){var b=e.styleSheets[0];if(b){for(var a=0;a<c.length;a++){var d=c[a];if(d.name&&d.css){this.addCssRule(b,d)}}}};WYMeditor.editor.prototype.computeBasePath=function(){return jQuery(jQuery.grep(jQuery("script"),function(a){return(a.src&&a.src.match(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/))})).attr("src").replace(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/,"")};WYMeditor.editor.prototype.computeWymPath=function(){return jQuery(jQuery.grep(jQuery("script"),function(a){return(a.src&&a.src.match(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/))})).attr("src")};WYMeditor.editor.prototype.computeJqueryPath=function(){return jQuery(jQuery.grep(jQuery("script"),function(a){return(a.src&&a.src.match(/jquery(-(.*)){0,1}(\.pack|\.min|\.packed)?\.js(\?.*)?$/))})).attr("src")};WYMeditor.editor.prototype.computeCssPath=function(){return jQuery(jQuery.grep(jQuery("link"),function(a){return(a.href&&a.href.match(/wymeditor\/skins\/(.*)screen\.css(\?.*)?$/))})).attr("href")};WYMeditor.editor.prototype.configureEditorUsingRawCss=function(){var a=new WYMeditor.WymCssParser();if(this._options.stylesheet){a.parse(jQuery.ajax({url:this._options.stylesheet,async:false}).responseText)}else{a.parse(this._options.styles,false)}if(this._options.classesItems.length==0){this._options.classesItems=a.css_settings.classesItems}if(this._options.editorStyles.length==0){this._options.editorStyles=a.css_settings.editorStyles}if(this._options.dialogStyles.length==0){this._options.dialogStyles=a.css_settings.dialogStyles}};WYMeditor.editor.prototype.listen=function(){jQuery(this._doc.body).bind("mousedown",this.mousedown);var a=this._doc.body.getElementsByTagName("img");for(var b=0;b<a.length;b++){jQuery(a[b]).bind("mousedown",this.mousedown)}};WYMeditor.editor.prototype.mousedown=function(a){var b=WYMeditor.INSTANCES[this.ownerDocument.title];b._selected_image=(this.tagName.toLowerCase()==WYMeditor.IMG)?this:null;a.stopPropagation()};WYMeditor.loadCss=function(a){var c=document.createElement("link");c.rel="stylesheet";c.href=a;var b=jQuery("head").get(0);b.appendChild(c)};WYMeditor.editor.prototype.loadSkin=function(){if(this._options.loadSkin&&!WYMeditor.SKINS[this._options.skin]){var found=false;var rExp=new RegExp(this._options.skin+"/"+WYMeditor.SKINS_DEFAULT_CSS+"$");jQuery("link").each(function(){if(this.href.match(rExp)){found=true}});if(!found){WYMeditor.loadCss(this._options.skinPath+WYMeditor.SKINS_DEFAULT_CSS)}}jQuery(this._box).addClass("wym_skin_"+this._options.skin);if(this._options.initSkin&&!WYMeditor.SKINS[this._options.skin]){eval(jQuery.ajax({url:this._options.skinPath+WYMeditor.SKINS_DEFAULT_JS,async:false}).responseText)}if(WYMeditor.SKINS[this._options.skin]&&WYMeditor.SKINS[this._options.skin].init){WYMeditor.SKINS[this._options.skin].init(this)}};WYMeditor.INIT_DIALOG=function(index){var wym=window.opener.WYMeditor.INSTANCES[index];var doc=window.document;var selected=wym.selected();var dialogType=jQuery(wym._options.dialogTypeSelector).val();var sStamp=wym.uniqueStamp();switch(dialogType){case WYMeditor.DIALOG_LINK:if(selected&&selected.tagName&&selected.tagName.toLowerCase!=WYMeditor.A){selected=jQuery(selected).parentsOrSelf(WYMeditor.A)}if(!selected&&wym._selected_image){selected=jQuery(wym._selected_image).parentsOrSelf(WYMeditor.A)}break}if(jQuery.isFunction(wym._options.preInitDialog)){wym._options.preInitDialog(wym,window)}var styles=doc.styleSheets[0];var aCss=eval(wym._options.dialogStyles);wym.addCssRules(doc,aCss);if(selected){jQuery(wym._options.hrefSelector).val(jQuery(selected).attr(WYMeditor.HREF));jQuery(wym._options.srcSelector).val(jQuery(selected).attr(WYMeditor.SRC));jQuery(wym._options.titleSelector).val(jQuery(selected).attr(WYMeditor.TITLE));jQuery(wym._options.altSelector).val(jQuery(selected).attr(WYMeditor.ALT))}if(wym._selected_image){jQuery(wym._options.dialogImageSelector+" "+wym._options.srcSelector).val(jQuery(wym._selected_image).attr(WYMeditor.SRC));jQuery(wym._options.dialogImageSelector+" "+wym._options.titleSelector).val(jQuery(wym._selected_image).attr(WYMeditor.TITLE));jQuery(wym._options.dialogImageSelector+" "+wym._options.altSelector).val(jQuery(wym._selected_image).attr(WYMeditor.ALT))}jQuery(wym._options.dialogLinkSelector+" "+wym._options.submitSelector).click(function(){var sUrl=jQuery(wym._options.hrefSelector).val();if(sUrl.length>0){wym._exec(WYMeditor.CREATE_LINK,sStamp);jQuery("a[href="+sStamp+"]",wym._doc.body).attr(WYMeditor.HREF,sUrl).attr(WYMeditor.TITLE,jQuery(wym._options.titleSelector).val())}window.close()});jQuery(wym._options.dialogImageSelector+" "+wym._options.submitSelector).click(function(){var sUrl=jQuery(wym._options.srcSelector).val();if(sUrl.length>0){wym._exec(WYMeditor.INSERT_IMAGE,sStamp);jQuery("img[src$="+sStamp+"]",wym._doc.body).attr(WYMeditor.SRC,sUrl).attr(WYMeditor.TITLE,jQuery(wym._options.titleSelector).val()).attr(WYMeditor.ALT,jQuery(wym._options.altSelector).val())}window.close()});jQuery(wym._options.dialogTableSelector+" "+wym._options.submitSelector).click(function(){var iRows=jQuery(wym._options.rowsSelector).val();var iCols=jQuery(wym._options.colsSelector).val();if(iRows>0&&iCols>0){var table=wym._doc.createElement(WYMeditor.TABLE);var newRow=null;var newCol=null;var sCaption=jQuery(wym._options.captionSelector).val();var newCaption=table.createCaption();newCaption.innerHTML=sCaption;for(x=0;x<iRows;x++){newRow=table.insertRow(x);for(y=0;y<iCols;y++){newRow.insertCell(y)}}jQuery(table).attr("summary",jQuery(wym._options.summarySelector).val());var node=jQuery(wym.findUp(wym.container(),WYMeditor.MAIN_CONTAINERS)).get(0);if(!node||!node.parentNode){jQuery(wym._doc.body).append(table)}else{jQuery(node).after(table)}}window.close()});jQuery(wym._options.dialogPasteSelector+" "+wym._options.submitSelector).click(function(){var sText=jQuery(wym._options.textSelector).val();wym.paste(sText);window.close()});jQuery(wym._options.dialogPreviewSelector+" "+wym._options.previewSelector).html(wym.xhtml());jQuery(wym._options.cancelSelector).mousedown(function(){window.close()});if(jQuery.isFunction(wym._options.postInitDialog)){wym._options.postInitDialog(wym,window)}};WYMeditor.XmlHelper=function(){this._entitiesDiv=document.createElement("div");return this};WYMeditor.XmlHelper.prototype.tag=function(c,b,a){b=b||false;a=a||false;return"<"+c+(b?this.tagOptions(b):"")+(a?">":" />")};WYMeditor.XmlHelper.prototype.contentTag=function(b,c,a){a=a||false;return"<"+b+(a?this.tagOptions(a):"")+">"+c+"</"+b+">"};WYMeditor.XmlHelper.prototype.cdataSection=function(a){return"<![CDATA["+a+"]]>"};WYMeditor.XmlHelper.prototype.escapeOnce=function(a){return this._fixDoubleEscape(this.escapeEntities(a))};WYMeditor.XmlHelper.prototype._fixDoubleEscape=function(a){return a.replace(/&([a-z]+|(#\d+));/ig,"&$1;")};WYMeditor.XmlHelper.prototype.tagOptions=function(b){var a=this;a._formated_options="";for(var c in b){var d="";var e=b[c];if(typeof e!="function"&&e.length>0){if(parseInt(c)==c&&typeof e=="object"){c=e.shift();e=e.pop()}if(c!=""&&e!=""){a._formated_options+=" "+c+'="'+a.escapeOnce(e)+'"'}}}return a._formated_options};WYMeditor.XmlHelper.prototype.escapeEntities=function(c,b){this._entitiesDiv.innerHTML=c;this._entitiesDiv.textContent=c;var a=this._entitiesDiv.innerHTML;if(typeof b=="undefined"){if(b!=false){a=a.replace('"',""")}if(b==true){a=a.replace('"',"'")}}return a};WYMeditor.XmlHelper.prototype.parseAttributes=function(h){var a=[];var g=h.split(/((=\s*")(")("))|((=\s*\')(\')(\'))|((=\s*[^>\s]*))/g);if(g.toString()!=h){for(var d in g){var c=g[d];if(typeof c!="function"&&c.length!=0){var e=new RegExp("(\\w+)\\s*"+c);if(match=h.match(e)){var f=c.replace(/^[\s=]+/,"");var b=f.charAt(0);b=b=='"'?'"':(b=="'"?"'":"");if(b!=""){f=b=='"'?f.replace(/^"|"+$/g,""):f.replace(/^'|'+$/g,"")}h=h.replace(match[0],"");a.push([match[1],f])}}}}return 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|shortcut|icon)+$/i,"3":"type"},inside:"head"},map:{attributes:["id","name"],required:["id"]},meta:{attributes:{"0":"content","http-equiv":/^(content\-type|expires|refresh|set\-cookie)$/i,"1":"name","2":"scheme"},required:["content"]},"27":"noscript",object:{attributes:["archive","classid","codebase","codetype","data","declare","height","name","standby","type","usemap","width"]},"28":"ol",optgroup:{attributes:{"0":"label",disabled:/^(disabled)$/},required:["label"]},option:{attributes:{"0":"label",disabled:/^(disabled)$/,selected:/^(selected)$/,"1":"value"},inside:"select"},"29":"p",param:{attributes:{"0":"type",valuetype:/^(data|ref|object)$/,"1":"valuetype","2":"value"},required:["name"]},"30":"pre",q:{attributes:["cite"]},"31":"samp",script:{attributes:{type:/^(text\/ecmascript|text\/javascript|text\/jscript|text\/vbscript|text\/vbs|text\/xml)$/,"0":"charset",defer:/^(defer)$/,"1":"src"},required:["type"]},select:{attributes:{disabled:/^(disabled)$/,multiple:/^(multiple)$/,"0":"name","1":"size"},inside:"form"},"32":"small","33":"span","34":"strong",style:{attributes:{"0":"type",media:/^(screen|tty|tv|projection|handheld|print|braille|aural|all)$/},required:["type"]},"35":"sub","36":"sup",table:{attributes:{"0":"border","1":"cellpadding","2":"cellspacing",frame:/^(void|above|below|hsides|lhs|rhs|vsides|box|border)$/,rules:/^(none|groups|rows|cols|all)$/,"3":"summary","4":"width"}},tbody:{attributes:{align:/^(right|left|center|justify)$/,"0":"char","1":"charoff",valign:/^(top|middle|bottom|baseline)$/}},td:{attributes:{"0":"abbr",align:/^(left|right|center|justify|char)$/,"1":"axis","2":"char","3":"charoff",colspan:/^(\d)+$/,"4":"headers",rowspan:/^(\d)+$/,scope:/^(col|colgroup|row|rowgroup)$/,valign:/^(top|middle|bottom|baseline)$/}},textarea:{attributes:["cols","rows","disabled","name","readonly"],required:["cols","rows"],inside:"form"},tfoot:{attributes:{align:/^(right|left|center|justify)$/,"0":"char","1":"charoff",valign:/^(top|middle|bottom)$/,"2":"baseline"}},th:{attributes:{"0":"abbr",align:/^(left|right|center|justify|char)$/,"1":"axis","2":"char","3":"charoff",colspan:/^(\d)+$/,"4":"headers",rowspan:/^(\d)+$/,scope:/^(col|colgroup|row|rowgroup)$/,valign:/^(top|middle|bottom|baseline)$/}},thead:{attributes:{align:/^(right|left|center|justify)$/,"0":"char","1":"charoff",valign:/^(top|middle|bottom|baseline)$/}},"37":"title",tr:{attributes:{align:/^(right|left|center|justify|char)$/,"0":"char","1":"charoff",valign:/^(top|middle|bottom|baseline)$/}},"38":"tt","39":"ul","40":"var"},skiped_attributes:[],skiped_attribute_values:[],getValidTagAttributes:function(a,b){var c={};var g=this.getPossibleTagAttributes(a);for(var e in b){var f=b[e];var d=WYMeditor.Helper;if(!d.contains(this.skiped_attributes,e)&&!d.contains(this.skiped_attribute_values,f)){if(typeof f!="function"&&d.contains(g,e)){if(this.doesAttributeNeedsValidation(a,e)){if(this.validateAttribute(a,e,f)){c[e]=f}}else{c[e]=f}}}}return c},getUniqueAttributesAndEventsForTag:function(b){var a=[];if(this._tags[b]&&this._tags[b]["attributes"]){for(k in this._tags[b]["attributes"]){a.push(parseInt(k)==k?this._tags[b]["attributes"][k]:k)}}return a},getDefaultAttributesAndEventsForTags:function(){var a=[];for(var b in this._events){a.push(this._events[b])}for(var b in this._attributes){a.push(this._attributes[b])}return a},isValidTag:function(a){if(this._tags[a]){return true}for(var b in this._tags){if(this._tags[b]==a){return true}}return false},getDefaultAttributesAndEventsForTag:function(a){var i=[];if(this.isValidTag(a)){var g=this.getDefaultAttributesAndEventsForTags();for(var d in g){var f=g[d];if(typeof f=="object"){var e=WYMeditor.Helper;if((f.except&&e.contains(f.except,a))||(f.only&&!e.contains(f.only,a))){continue}var c=f.attributes?f.attributes:f.events;for(var b in c){i.push(typeof c[b]!="string"?b:c[b])}}}}return i},doesAttributeNeedsValidation:function(a,b){return this._tags[a]&&((this._tags[a]["attributes"]&&this._tags[a]["attributes"][b])||(this._tags[a]["required"]&&WYMeditor.Helper.contains(this._tags[a]["required"],b)))},validateAttribute:function(a,b,c){if(this._tags[a]&&(this._tags[a]["attributes"]&&this._tags[a]["attributes"][b]&&c.length>0&&!c.match(this._tags[a]["attributes"][b]))||(this._tags[a]&&this._tags[a]["required"]&&WYMeditor.Helper.contains(this._tags[a]["required"],b)&&c.length==0)){return false}return typeof this._tags[a]!="undefined"},getPossibleTagAttributes:function(a){if(!this._possible_tag_attributes){this._possible_tag_attributes={}}if(!this._possible_tag_attributes[a]){this._possible_tag_attributes[a]=this.getUniqueAttributesAndEventsForTag(a).concat(this.getDefaultAttributesAndEventsForTag(a))}return this._possible_tag_attributes[a]}};WYMeditor.ParallelRegex=function(a){this._case=a;this._patterns=[];this._labels=[];this._regex=null;return this};WYMeditor.ParallelRegex.prototype.addPattern=function(c,a){a=a||true;var b=this._patterns.length;this._patterns[b]=c;this._labels[b]=a;this._regex=null};WYMeditor.ParallelRegex.prototype.match=function(c){if(this._patterns.length==0){return[false,""]}var d=c.match(this._getCompoundedRegex());if(!d){return[false,""]}var a=d[0];for(var b=1;b<d.length;b++){if(d[b]){return[this._labels[b-1],a]}}return[true,d[0]]};WYMeditor.ParallelRegex.prototype._getCompoundedRegex=function(){if(this._regex==null){for(var a=0,b=this._patterns.length;a<b;a++){this._patterns[a]="("+this._untokenizeRegex(this._tokenizeRegex(this._patterns[a]).replace(/([\/])/g,"\\$1"))+")"}this._regex=new RegExp(this._patterns.join("|"),this._getPerlMatchingFlags())}return this._regex};WYMeditor.ParallelRegex.prototype._tokenizeRegex=function(a){return a.replace(/$\?(i|m|s|x|U)$/,"~~~~~~Tk1$1~~~~~~").replace(/$\?(\-[i|m|s|x|U])$/,"~~~~~~Tk2$1~~~~~~").replace(/$\?\=(.*)$/,"~~~~~~Tk3$1~~~~~~").replace(/$\?\!(.*)$/,"~~~~~~Tk4$1~~~~~~").replace(/$\?\<\=(.*)$/,"~~~~~~Tk5$1~~~~~~").replace(/$\?\<\!(.*)$/,"~~~~~~Tk6$1~~~~~~").replace(/$\?\:(.*)$/,"~~~~~~Tk7$1~~~~~~")};WYMeditor.ParallelRegex.prototype._untokenizeRegex=function(a){return a.replace(/~~~~~~Tk1(.{1})~~~~~~/,"(?$1)").replace(/~~~~~~Tk2(.{2})~~~~~~/,"(?$1)").replace(/~~~~~~Tk3(.*)~~~~~~/,"(?=$1)").replace(/~~~~~~Tk4(.*)~~~~~~/,"(?!$1)").replace(/~~~~~~Tk5(.*)~~~~~~/,"(?<=$1)").replace(/~~~~~~Tk6(.*)~~~~~~/,"(?<!$1)").replace(/~~~~~~Tk7(.*)~~~~~~/,"(?:$1)")};WYMeditor.ParallelRegex.prototype._getPerlMatchingFlags=function(){return(this._case?"m":"mi")};WYMeditor.StateStack=function(a){this._stack=[a];return this};WYMeditor.StateStack.prototype.getCurrent=function(){return this._stack[this._stack.length-1]};WYMeditor.StateStack.prototype.enter=function(a){this._stack.push(a)};WYMeditor.StateStack.prototype.leave=function(){if(this._stack.length==1){return false}this._stack.pop();return true};WYMeditor.LEXER_ENTER=1;WYMeditor.LEXER_MATCHED=2;WYMeditor.LEXER_UNMATCHED=3;WYMeditor.LEXER_EXIT=4;WYMeditor.LEXER_SPECIAL=5;WYMeditor.Lexer=function(c,b,a){b=b||"accept";this._case=a||false;this._regexes={};this._parser=c;this._mode=new WYMeditor.StateStack(b);this._mode_handlers={};this._mode_handlers[b]=b;return this};WYMeditor.Lexer.prototype.addPattern=function(a,b){var b=b||"accept";if(typeof this._regexes[b]=="undefined"){this._regexes[b]=new WYMeditor.ParallelRegex(this._case)}this._regexes[b].addPattern(a);if(typeof this._mode_handlers[b]=="undefined"){this._mode_handlers[b]=b}};WYMeditor.Lexer.prototype.addEntryPattern=function(b,c,a){if(typeof this._regexes[c]=="undefined"){this._regexes[c]=new WYMeditor.ParallelRegex(this._case)}this._regexes[c].addPattern(b,a);if(typeof this._mode_handlers[a]=="undefined"){this._mode_handlers[a]=a}};WYMeditor.Lexer.prototype.addExitPattern=function(a,b){if(typeof this._regexes[b]=="undefined"){this._regexes[b]=new WYMeditor.ParallelRegex(this._case)}this._regexes[b].addPattern(a,"__exit");if(typeof this._mode_handlers[b]=="undefined"){this._mode_handlers[b]=b}};WYMeditor.Lexer.prototype.addSpecialPattern=function(b,c,a){if(typeof this._regexes[c]=="undefined"){this._regexes[c]=new WYMeditor.ParallelRegex(this._case)}this._regexes[c].addPattern(b,"_"+a);if(typeof this._mode_handlers[a]=="undefined"){this._mode_handlers[a]=a}};WYMeditor.Lexer.prototype.mapHandler=function(b,a){this._mode_handlers[b]=a};WYMeditor.Lexer.prototype.parse=function(d){if(typeof this._parser=="undefined"){return false}var e=d.length;var c;while(typeof(c=this._reduce(d))=="object"){var d=c[0];var b=c[1];var a=c[2];var f=c[3];if(!this._dispatchTokens(b,a,f)){return false}if(d==""){return true}if(d.length==e){return false}e=d.length}if(!c){return false}return this._invokeParser(d,WYMeditor.LEXER_UNMATCHED)};WYMeditor.Lexer.prototype._dispatchTokens=function(b,a,c){c=c||false;if(!this._invokeParser(b,WYMeditor.LEXER_UNMATCHED)){return false}if(typeof c=="boolean"){return this._invokeParser(a,WYMeditor.LEXER_MATCHED)}if(this._isModeEnd(c)){if(!this._invokeParser(a,WYMeditor.LEXER_EXIT)){return false}return this._mode.leave()}if(this._isSpecialMode(c)){this._mode.enter(this._decodeSpecial(c));if(!this._invokeParser(a,WYMeditor.LEXER_SPECIAL)){return false}return this._mode.leave()}this._mode.enter(c);return this._invokeParser(a,WYMeditor.LEXER_ENTER)};WYMeditor.Lexer.prototype._isModeEnd=function(a){return(a==="__exit")};WYMeditor.Lexer.prototype._isSpecialMode=function(a){return(a.substring(0,1)=="_")};WYMeditor.Lexer.prototype._decodeSpecial=function(a){return a.substring(1)};WYMeditor.Lexer.prototype._invokeParser=function(content,is_match){if(!/ +/.test(content)&&((content==="")||(content==false))){return true}var current=this._mode.getCurrent();var handler=this._mode_handlers[current];var result;eval("result = this._parser."+handler+"(content, is_match);");return result};WYMeditor.Lexer.prototype._reduce=function(c){var a=this._regexes[this._mode.getCurrent()].match(c);var b=a[1];var e=a[0];if(e){var f=c.indexOf(b);var d=c.substr(0,f);c=c.substring(f+b.length);return[c,d,b,e]}return true};WYMeditor.XhtmlLexer=function(a){jQuery.extend(this,new WYMeditor.Lexer(a,"Text"));this.mapHandler("Text","Text");this.addTokens();this.init();return this};WYMeditor.XhtmlLexer.prototype.init=function(){};WYMeditor.XhtmlLexer.prototype.addTokens=function(){this.addCommentTokens("Text");this.addScriptTokens("Text");this.addCssTokens("Text");this.addTagTokens("Text")};WYMeditor.XhtmlLexer.prototype.addCommentTokens=function(a){this.addEntryPattern("","Comment")};WYMeditor.XhtmlLexer.prototype.addScriptTokens=function(a){this.addEntryPattern("<script",a,"Script");this.addExitPattern("<\/script>","Script")};WYMeditor.XhtmlLexer.prototype.addCssTokens=function(a){this.addEntryPattern("<style",a,"Css");this.addExitPattern("</style>","Css")};WYMeditor.XhtmlLexer.prototype.addTagTokens=function(a){this.addSpecialPattern("<\\s*[a-z0-9:-]+\\s*>",a,"OpeningTag");this.addEntryPattern("<[a-z0-9:-]+[\\/ \\>]+",a,"OpeningTag");this.addInTagDeclarationTokens("OpeningTag");this.addSpecialPattern("</\\s*[a-z0-9:-]+\\s*>",a,"ClosingTag")};WYMeditor.XhtmlLexer.prototype.addInTagDeclarationTokens=function(a){this.addSpecialPattern("\\s+",a,"Ignore");this.addAttributeTokens(a);this.addExitPattern("/>",a);this.addExitPattern(">",a)};WYMeditor.XhtmlLexer.prototype.addAttributeTokens=function(a){this.addSpecialPattern("\\s*[a-z-_0-9]*:?[a-z-_0-9]+\\s*(?==)\\s*",a,"TagAttributes");this.addEntryPattern('=\\s*"',a,"DoubleQuotedAttribute");this.addPattern('\\\\"',"DoubleQuotedAttribute");this.addExitPattern('"',"DoubleQuotedAttribute");this.addEntryPattern("=\\s*'",a,"SingleQuotedAttribute");this.addPattern("\\\\'","SingleQuotedAttribute");this.addExitPattern("'","SingleQuotedAttribute");this.addSpecialPattern("=\\s*[^>\\s]*",a,"UnquotedAttribute")};WYMeditor.XhtmlParser=function(a,b){var b=b||"Text";this._Lexer=new WYMeditor.XhtmlLexer(this);this._Listener=a;this._mode=b;this._matches=[];this._last_match="";this._current_match="";return this};WYMeditor.XhtmlParser.prototype.parse=function(a){this._Lexer.parse(this.beforeParsing(a));return this.afterParsing(this._Listener.getResult())};WYMeditor.XhtmlParser.prototype.beforeParsing=function(a){if(a.match(/class="MsoNormal"/)||a.match(/ns = "urn:schemas-microsoft-com/)){this._Listener.avoidStylingTagsAndAttributes()}return this._Listener.beforeParsing(a)};WYMeditor.XhtmlParser.prototype.afterParsing=function(a){if(this._Listener._avoiding_tags_implicitly){this._Listener.allowStylingTagsAndAttributes()}return this._Listener.afterParsing(a)};WYMeditor.XhtmlParser.prototype.Ignore=function(a,b){return true};WYMeditor.XhtmlParser.prototype.Text=function(a){this._Listener.addContent(a);return true};WYMeditor.XhtmlParser.prototype.Comment=function(b,a){return this._addNonTagBlock(b,a,"addComment")};WYMeditor.XhtmlParser.prototype.Script=function(b,a){return this._addNonTagBlock(b,a,"addScript")};WYMeditor.XhtmlParser.prototype.Css=function(b,a){return this._addNonTagBlock(b,a,"addCss")};WYMeditor.XhtmlParser.prototype._addNonTagBlock=function(a,c,b){switch(c){case WYMeditor.LEXER_ENTER:this._non_tag=a;break;case WYMeditor.LEXER_UNMATCHED:this._non_tag+=a;break;case WYMeditor.LEXER_EXIT:switch(b){case"addComment":this._Listener.addComment(this._non_tag+a);break;case"addScript":this._Listener.addScript(this._non_tag+a);break;case"addCss":this._Listener.addCss(this._non_tag+a);break}}return true};WYMeditor.XhtmlParser.prototype.OpeningTag=function(a,b){switch(b){case WYMeditor.LEXER_ENTER:this._tag=this.normalizeTag(a);this._tag_attributes={};break;case WYMeditor.LEXER_SPECIAL:this._callOpenTagListener(this.normalizeTag(a));break;case WYMeditor.LEXER_EXIT:this._callOpenTagListener(this._tag,this._tag_attributes)}return true};WYMeditor.XhtmlParser.prototype.ClosingTag=function(a,b){this._callCloseTagListener(this.normalizeTag(a));return true};WYMeditor.XhtmlParser.prototype._callOpenTagListener=function(a,b){var b=b||{};this.autoCloseUnclosedBeforeNewOpening(a);if(this._Listener.isBlockTag(a)){this._Listener._tag_stack.push(a);this._Listener.fixNestingBeforeOpeningBlockTag(a,b);this._Listener.openBlockTag(a,b);this._increaseOpenTagCounter(a)}else{if(this._Listener.isInlineTag(a)){this._Listener.inlineTag(a,b)}else{this._Listener.openUnknownTag(a,b);this._increaseOpenTagCounter(a)}}this._Listener.last_tag=a;this._Listener.last_tag_opened=true;this._Listener.last_tag_attributes=b};WYMeditor.XhtmlParser.prototype._callCloseTagListener=function(a){if(this._decreaseOpenTagCounter(a)){this.autoCloseUnclosedBeforeTagClosing(a);if(this._Listener.isBlockTag(a)){var b=this._Listener._tag_stack.pop();if(b==false){return}else{if(b!=a){a=b}}this._Listener.closeBlockTag(a)}else{this._Listener.closeUnknownTag(a)}}else{this._Listener.closeUnopenedTag(a)}this._Listener.last_tag=a;this._Listener.last_tag_opened=false};WYMeditor.XhtmlParser.prototype._increaseOpenTagCounter=function(a){this._Listener._open_tags[a]=this._Listener._open_tags[a]||0;this._Listener._open_tags[a]++};WYMeditor.XhtmlParser.prototype._decreaseOpenTagCounter=function(a){if(this._Listener._open_tags[a]){this._Listener._open_tags[a]--;if(this._Listener._open_tags[a]==0){this._Listener._open_tags[a]=undefined}return true}return false};WYMeditor.XhtmlParser.prototype.autoCloseUnclosedBeforeNewOpening=function(a){this._autoCloseUnclosed(a,false)};WYMeditor.XhtmlParser.prototype.autoCloseUnclosedBeforeTagClosing=function(a){this._autoCloseUnclosed(a,true)};WYMeditor.XhtmlParser.prototype._autoCloseUnclosed=function(c,d){var d=d||false;if(this._Listener._open_tags){for(var a in this._Listener._open_tags){var b=this._Listener._open_tags[a];if(b>0&&this._Listener.shouldCloseTagAutomatically(a,c,d)){this._callCloseTagListener(a,true)}}}};WYMeditor.XhtmlParser.prototype.getTagReplacements=function(){return this._Listener.getTagReplacements()};WYMeditor.XhtmlParser.prototype.normalizeTag=function(a){a=a.replace(/^([\s<\/>]*)|([\s<\/>]*)$/gm,"").toLowerCase();var b=this._Listener.getTagReplacements();if(b[a]){return b[a]}return a};WYMeditor.XhtmlParser.prototype.TagAttributes=function(a,b){if(WYMeditor.LEXER_SPECIAL==b){this._current_attribute=a}return true};WYMeditor.XhtmlParser.prototype.DoubleQuotedAttribute=function(a,b){if(WYMeditor.LEXER_UNMATCHED==b){this._tag_attributes[this._current_attribute]=a}return true};WYMeditor.XhtmlParser.prototype.SingleQuotedAttribute=function(a,b){if(WYMeditor.LEXER_UNMATCHED==b){this._tag_attributes[this._current_attribute]=a}return true};WYMeditor.XhtmlParser.prototype.UnquotedAttribute=function(a,b){this._tag_attributes[this._current_attribute]=a.replace(/^=/,"");return true};WYMeditor.XhtmlSaxListener=function(){this.output="";this.helper=new WYMeditor.XmlHelper();this._open_tags={};this.validator=WYMeditor.XhtmlValidator;this._tag_stack=[];this.avoided_tags=[];this.entities={" ":" ","¡":"¡","¢":"¢","£":"£","¤":"¤","¥":"¥","¦":"¦","§":"§","¨":"¨","©":"©","ª":"ª","«":"«","¬":"¬","":"","®":"®","¯":"¯","°":"°","±":"±","²":"²","³":"³","´":"´","µ":"µ","¶":"¶","·":"·","¸":"¸","¹":"¹","º":"º","»":"»","¼":"¼","½":"½","¾":"¾","¿":"¿","À":"À","Á":"Á","Â":"Â","Ã":"Ã","Ä":"Ä","Å":"Å","Æ":"Æ","Ç":"Ç","È":"È","É":"É","Ê":"Ê","Ë":"Ë","Ì":"Ì","Í":"Í","Î":"Î","Ï":"Ï","Ð":"Ð","Ñ":"Ñ","Ò":"Ò","Ó":"Ó","Ô":"Ô","Õ":"Õ","Ö":"Ö","×":"×","Ø":"Ø","Ù":"Ù","Ú":"Ú","Û":"Û","Ü":"Ü","Ý":"Ý","Þ":"Þ","ß":"ß","à":"à","á":"á","â":"â","ã":"ã","ä":"ä","å":"å","æ":"æ","ç":"ç","è":"è","é":"é","ê":"ê","ë":"ë","ì":"ì","í":"í","î":"î","ï":"ï","ð":"ð","ñ":"ñ","ò":"ò","ó":"ó","ô":"ô","õ":"õ","ö":"ö","÷":"÷","ø":"ø","ù":"ù","ú":"ú","û":"û","ü":"ü","ý":"ý","þ":"þ","ÿ":"ÿ","&OElig;":"Œ","&oelig;":"œ","&Scaron;":"Š","&scaron;":"š","&Yuml;":"Ÿ","&fnof;":"ƒ","&circ;":"ˆ","&tilde;":"˜","Α":"Α","Β":"Β","Γ":"Γ","Δ":"Δ","Ε":"Ε","Ζ":"Ζ","Η":"Η","Θ":"Θ","Ι":"Ι","Κ":"Κ","Λ":"Λ","Μ":"Μ","Ν":"Ν","Ξ":"Ξ","Ο":"Ο","Π":"Π","Ρ":"Ρ","Σ":"Σ","Τ":"Τ","Υ":"Υ","Φ":"Φ","Χ":"Χ","Ψ":"Ψ","Ω":"Ω","α":"α","β":"β","γ":"γ","δ":"δ","ε":"ε","ζ":"ζ","η":"η","θ":"θ","ι":"ι","κ":"κ","λ":"λ","μ":"μ","ν":"ν","ξ":"ξ","ο":"ο","π":"π","ρ":"ρ","&sigmaf;":"ς","σ":"σ","τ":"τ","υ":"υ","φ":"φ","χ":"χ","ψ":"ψ","ω":"ω","&thetasym;":"ϑ","&upsih;":"ϒ","ϖ":"ϖ","&ensp;":" ","&emsp;":" "," ":" ","&zwnj;":"‌","&zwj;":"‍","&lrm;":"‎","&rlm;":"‏","–":"–","—":"—","‘":"‘","’":"’","&sbquo;":"‚","“":"“","”":"”","&bdquo;":"„","&dagger;":"†","&Dagger;":"‡","•":"•","…":"…","&permil;":"‰","′":"′","″":"″","&lsaquo;":"‹","&rsaquo;":"›","&oline;":"‾","&frasl;":"⁄","€":"€","&image;":"ℑ","&weierp;":"℘","&real;":"ℜ","™":"™","&alefsym;":"ℵ","←":"←","↑":"↑","→":"→","↓":"↓","↔":"↔","&crarr;":"↵","⇐":"⇐","&uArr;":"⇑","⇒":"⇒","&dArr;":"⇓","⇔":"⇔","∀":"∀","∂":"∂","∃":"∃","∅":"∅","∇":"∇","∈":"∈","∉":"∉","&ni;":"∋","∏":"∏","∑":"∑","−":"−","&lowast;":"∗","√":"√","&prop;":"∝","∞":"∞","&ang;":"∠","&and;":"∧","&or;":"∨","∩":"∩","∪":"∪","∫":"∫","&there4;":"∴","&sim;":"∼","&cong;":"≅","≈":"≈","≠":"≠","&equiv;":"≡","≤":"≤","≥":"≥","⊂":"⊂","⊃":"⊃","&nsub;":"⊄","&sube;":"⊆","&supe;":"⊇","&oplus;":"⊕","&otimes;":"⊗","&perp;":"⊥","⋅":"⋅","&lceil;":"⌈","&rceil;":"⌉","&lfloor;":"⌊","&rfloor;":"⌋","&lang;":"〈","&rang;":"〉","&loz;":"◊","&spades;":"♠","&clubs;":"♣","&hearts;":"♥","&diams;":"♦"};this.block_tags=["a","abbr","acronym","address","area","b","base","bdo","big","blockquote","body","button","caption","cite","code","col","colgroup","dd","del","div","dfn","dl","dt","em","fieldset","form","head","h1","h2","h3","h4","h5","h6","html","i","ins","kbd","label","legend","li","map","noscript","object","ol","optgroup","option","p","param","pre","q","samp","script","select","small","span","strong","style","sub","sup","table","tbody","td","textarea","tfoot","th","thead","title","tr","tt","ul","var","extends"];this.inline_tags=["br","hr","img","input"];return this};WYMeditor.XhtmlSaxListener.prototype.shouldCloseTagAutomatically=function(a,c,b){var b=b||false;if(a=="td"){if((b&&c=="tr")||(!b&&c=="td")){return true}}if(a=="option"){if((b&&c=="select")||(!b&&c=="option")){return true}}return false};WYMeditor.XhtmlSaxListener.prototype.beforeParsing=function(a){this.output="";return a};WYMeditor.XhtmlSaxListener.prototype.afterParsing=function(a){a=this.replaceNamedEntities(a);a=this.joinRepeatedEntities(a);a=this.removeEmptyTags(a);a=this.removeBrInPre(a);return a};WYMeditor.XhtmlSaxListener.prototype.replaceNamedEntities=function(b){for(var a in this.entities){b=b.replace(new RegExp(a,"g"),this.entities[a])}return b};WYMeditor.XhtmlSaxListener.prototype.joinRepeatedEntities=function(b){var a="em|strong|sub|sup|acronym|pre|del|address";return b.replace(new RegExp("</("+a+")><\\1>",""),"").replace(new RegExp("(s*<("+a+")>s*){2}(.*)(s*</\\2>s*){2}",""),"<$2>$3<$2>")};WYMeditor.XhtmlSaxListener.prototype.removeEmptyTags=function(a){return a.replace(new RegExp("<("+this.block_tags.join("|").replace(/\|td/,"").replace(/\|th/,"")+")>(<br />| | |\\s)*</\\1>","g"),"")};WYMeditor.XhtmlSaxListener.prototype.removeBrInPre=function(c){var b=c.match(new RegExp("<pre[^>]*>(.*?)</pre>","gmi"));if(b){for(var a=0;a<b.length;a++){c=c.replace(b[a],b[a].replace(new RegExp("<br />","g"),String.fromCharCode(13,10)))}}return c};WYMeditor.XhtmlSaxListener.prototype.getResult=function(){return this.output};WYMeditor.XhtmlSaxListener.prototype.getTagReplacements=function(){return{b:"strong",i:"em"}};WYMeditor.XhtmlSaxListener.prototype.addContent=function(a){this.output+=a};WYMeditor.XhtmlSaxListener.prototype.addComment=function(a){if(this.remove_comments){this.output+=a}};WYMeditor.XhtmlSaxListener.prototype.addScript=function(a){if(!this.remove_scripts){this.output+=a}};WYMeditor.XhtmlSaxListener.prototype.addCss=function(a){if(!this.remove_embeded_styles){this.output+=a}};WYMeditor.XhtmlSaxListener.prototype.openBlockTag=function(a,b){this.output+=this.helper.tag(a,this.validator.getValidTagAttributes(a,b),true)};WYMeditor.XhtmlSaxListener.prototype.inlineTag=function(a,b){this.output+=this.helper.tag(a,this.validator.getValidTagAttributes(a,b))};WYMeditor.XhtmlSaxListener.prototype.openUnknownTag=function(a,b){};WYMeditor.XhtmlSaxListener.prototype.closeBlockTag=function(a){this.output=this.output.replace(/<br \/>$/,"")+this._getClosingTagContent("before",a)+"</"+a+">"+this._getClosingTagContent("after",a)};WYMeditor.XhtmlSaxListener.prototype.closeUnknownTag=function(a){};WYMeditor.XhtmlSaxListener.prototype.closeUnopenedTag=function(a){this.output+="</"+a+">"};WYMeditor.XhtmlSaxListener.prototype.avoidStylingTagsAndAttributes=function(){this.avoided_tags=["div","span"];this.validator.skiped_attributes=["style"];this.validator.skiped_attribute_values=["MsoNormal","main1"];this._avoiding_tags_implicitly=true};WYMeditor.XhtmlSaxListener.prototype.allowStylingTagsAndAttributes=function(){this.avoided_tags=[];this.validator.skiped_attributes=[];this.validator.skiped_attribute_values=[];this._avoiding_tags_implicitly=false};WYMeditor.XhtmlSaxListener.prototype.isBlockTag=function(a){return !WYMeditor.Helper.contains(this.avoided_tags,a)&&WYMeditor.Helper.contains(this.block_tags,a)};WYMeditor.XhtmlSaxListener.prototype.isInlineTag=function(a){return !WYMeditor.Helper.contains(this.avoided_tags,a)&&WYMeditor.Helper.contains(this.inline_tags,a)};WYMeditor.XhtmlSaxListener.prototype.insertContentAfterClosingTag=function(a,b){this._insertContentWhenClosingTag("after",a,b)};WYMeditor.XhtmlSaxListener.prototype.insertContentBeforeClosingTag=function(a,b){this._insertContentWhenClosingTag("before",a,b)};WYMeditor.XhtmlSaxListener.prototype.fixNestingBeforeOpeningBlockTag=function(a,b){if(a!="li"&&(a=="ul"||a=="ol")&&this.last_tag&&!this.last_tag_opened&&this.last_tag=="li"){this.output=this.output.replace(/<\/li>$/,"");this.insertContentAfterClosingTag(a,"</li>")}};WYMeditor.XhtmlSaxListener.prototype._insertContentWhenClosingTag=function(b,a,c){if(!this["_insert_"+b+"_closing"]){this["_insert_"+b+"_closing"]=[]}if(!this["_insert_"+b+"_closing"][a]){this["_insert_"+b+"_closing"][a]=[]}this["_insert_"+b+"_closing"][a].push(c)};WYMeditor.XhtmlSaxListener.prototype._getClosingTagContent=function(b,a){if(this["_insert_"+b+"_closing"]&&this["_insert_"+b+"_closing"][a]&&this["_insert_"+b+"_closing"][a].length>0){return this["_insert_"+b+"_closing"][a].pop()}return""};WYMeditor.WymCssLexer=function(b,a){var a=(typeof a=="undefined"?true:a);jQuery.extend(this,new WYMeditor.Lexer(b,(a?"Ignore":"WymCss")));this.mapHandler("WymCss","Ignore");if(a==true){this.addEntryPattern("/\\\x2a[<\\s]*WYMeditor[>\\s]*\\\x2a/","Ignore","WymCss");this.addExitPattern("/\\\x2a[</\\s]*WYMeditor[>\\s]*\\\x2a/","WymCss")}this.addSpecialPattern("[\\sa-z1-6]*\\\x2e[a-z-_0-9]+","WymCss","WymCssStyleDeclaration");this.addEntryPattern("/\\\x2a","WymCss","WymCssComment");this.addExitPattern("\\\x2a/","WymCssComment");this.addEntryPattern("\x7b","WymCss","WymCssStyle");this.addExitPattern("\x7d","WymCssStyle");this.addEntryPattern("/\\\x2a","WymCssStyle","WymCssFeedbackStyle");this.addExitPattern("\\\x2a/","WymCssFeedbackStyle");return this};WYMeditor.WymCssParser=function(){this._in_style=false;this._has_title=false;this.only_wym_blocks=true;this.css_settings={classesItems:[],editorStyles:[],dialogStyles:[]};return this};WYMeditor.WymCssParser.prototype.parse=function(a,b){var b=(typeof b=="undefined"?this.only_wym_blocks:b);this._Lexer=new WYMeditor.WymCssLexer(this,b);this._Lexer.parse(a)};WYMeditor.WymCssParser.prototype.Ignore=function(a,b){return true};WYMeditor.WymCssParser.prototype.WymCssComment=function(b,a){if(b.match(/end[a-z0-9\s]*wym[a-z0-9\s]*/mi)){return false}if(a==WYMeditor.LEXER_UNMATCHED){if(!this._in_style){this._has_title=true;this._current_item={title:WYMeditor.Helper.trim(b)}}else{if(this._current_item[this._current_element]){if(!this._current_item[this._current_element].expressions){this._current_item[this._current_element].expressions=[b]}else{this._current_item[this._current_element].expressions.push(b)}}}this._in_style=true}return true};WYMeditor.WymCssParser.prototype.WymCssStyle=function(b,a){if(a==WYMeditor.LEXER_UNMATCHED){b=WYMeditor.Helper.trim(b);if(b!=""){this._current_item[this._current_element].style=b}}else{if(a==WYMeditor.LEXER_EXIT){this._in_style=false;this._has_title=false;this.addStyleSetting(this._current_item)}}return true};WYMeditor.WymCssParser.prototype.WymCssFeedbackStyle=function(b,a){if(a==WYMeditor.LEXER_UNMATCHED){this._current_item[this._current_element].feedback_style=b.replace(/^([\s\/\*]*)|([\s\/\*]*)$/gm,"")}return true};WYMeditor.WymCssParser.prototype.WymCssStyleDeclaration=function(b){b=b.replace(/^([\s\.]*)|([\s\.*]*)$/gm,"");var a="";if(b.indexOf(".")>0){var c=b.split(".");this._current_element=c[1];var a=c[0]}else{this._current_element=b}if(!this._has_title){this._current_item={title:(!a?"":a.toUpperCase()+": ")+this._current_element};this._has_title=true}if(!this._current_item[this._current_element]){this._current_item[this._current_element]={name:this._current_element}}if(a){if(!this._current_item[this._current_element].tags){this._current_item[this._current_element].tags=[a]}else{this._current_item[this._current_element].tags.push(a)}}return true};WYMeditor.WymCssParser.prototype.addStyleSetting=function(a){for(var b in a){var c=a[b];if(typeof c=="object"&&b!="title"){this.css_settings.classesItems.push({name:WYMeditor.Helper.trim(c.name),title:a.title,expr:WYMeditor.Helper.trim((c.expressions||c.tags).join(", "))});if(c.feedback_style){this.css_settings.editorStyles.push({name:"."+WYMeditor.Helper.trim(c.name),css:c.feedback_style})}if(c.style){this.css_settings.dialogStyles.push({name:"."+WYMeditor.Helper.trim(c.name),css:c.style})}}}};jQuery.fn.isPhantomNode=function(){if(this[0].nodeType==3){return !(/[^\t\n\r ]/.test(this[0].data))}return false};WYMeditor.isPhantomNode=function(a){if(a.nodeType==3){return !(/[^\t\n\r ]/.test(a.data))}return false};WYMeditor.isPhantomString=function(a){return !(/[^\t\n\r ]/.test(a))};jQuery.fn.parentsOrSelf=function(b){var a=this;if(a[0].nodeType==3){a=a.parents().slice(0,1)}if(a.filter(b).size()==1){return a}else{return a.parents(b).slice(0,1)}};WYMeditor.Helper={replaceAll:function(d,a,c){var b=new RegExp(a,"g");return(d.replace(b,c))},insertAt:function(b,a,c){return(b.substr(0,c)+a+b.substring(c))},trim:function(a){return a.replace(/^(\s*)|(\s*)$/gm,"")},contains:function(a,c){for(var b=0;b<a.length;b++){if(a[b]===c){return true}}return false},indexOf:function(a,d){var b=-1;for(var c=0;c<a.length;c++){if(a[c]==d){b=c;break}}return(b)},findByName:function(a,b){for(var c=0;c<a.length;c++){var d=a[c];if(d.name==b){return(d)}}return(null)}};WYMeditor.WymClassExplorer=function(a){this._wym=a;this._class="className";this._newLine="\r\n"};WYMeditor.WymClassExplorer.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentWindow.document;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);jQuery(this._doc.body).html(this._wym._html);var wym=this;this._doc.body.onfocus=function(){wym._doc.designMode="on";wym._doc=iframe.contentWindow.document};this._doc.onbeforedeactivate=function(){wym.saveCaret()};this._doc.onkeyup=function(){wym.saveCaret();wym.keyup()};this._doc.onclick=function(){wym.saveCaret()};this._doc.body.onbeforepaste=function(){wym._iframe.contentWindow.event.returnValue=false};this._doc.body.onpaste=function(){wym._iframe.contentWindow.event.returnValue=false;wym.paste(window.clipboardData.getData("Text"))};if(this._initialized){if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()}this._initialized=true;this._doc.designMode="on";try{this._doc=iframe.contentWindow.document}catch(e){}};WYMeditor.WymClassExplorer.prototype._exec=function(c,d){switch(c){case WYMeditor.INDENT:case WYMeditor.OUTDENT:var a=this.findUp(this.container(),WYMeditor.LI);if(a){var b=a.parentNode.parentNode;if(a.parentNode.childNodes.length>1||b.tagName.toLowerCase()==WYMeditor.OL||b.tagName.toLowerCase()==WYMeditor.UL){this._doc.execCommand(c)}}break;default:if(d){this._doc.execCommand(c,false,d)}else{this._doc.execCommand(c)}break}this.listen()};WYMeditor.WymClassExplorer.prototype.selected=function(){var a=this._iframe.contentWindow.document.caretPos;if(a!=null){if(a.parentElement!=undefined){return(a.parentElement())}}};WYMeditor.WymClassExplorer.prototype.saveCaret=function(){this._doc.caretPos=this._doc.selection.createRange()};WYMeditor.WymClassExplorer.prototype.addCssRule=function(a,b){a.addRule(b.name,b.css)};WYMeditor.WymClassExplorer.prototype.insert=function(b){var a=this._doc.selection.createRange();if(jQuery(a.parentElement()).parents(this._options.iframeBodySelector).is("*")){try{a.pasteHTML(b)}catch(c){}}else{this.paste(b)}};WYMeditor.WymClassExplorer.prototype.wrap=function(d,b){var a=this._doc.selection.createRange();if(jQuery(a.parentElement()).parents(this._options.iframeBodySelector).is("*")){try{a.pasteHTML(d+a.text+b)}catch(c){}}};WYMeditor.WymClassExplorer.prototype.unwrap=function(){var a=this._doc.selection.createRange();if(jQuery(a.parentElement()).parents(this._options.iframeBodySelector).is("*")){try{var c=a.text;this._exec("Cut");a.pasteHTML(c)}catch(b){}}};WYMeditor.WymClassExplorer.prototype.keyup=function(){this._selected_image=null};WYMeditor.WymClassExplorer.prototype.setFocusToNode=function(b){var a=this._doc.selection.createRange();a.moveToElementText(b);a.collapse(false);a.move("character",-1);a.select();b.focus()};WYMeditor.WymClassMozilla=function(a){this._wym=a;this._class="class";this._newLine="\n"};WYMeditor.WymClassMozilla.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentDocument;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);this.html(this._wym._html);this.enableDesignMode();if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();jQuery(this._doc).bind("keydown",this.keydown);jQuery(this._doc).bind("keyup",this.keyup);jQuery(this._doc).bind("focus",this.enableDesignMode);if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()};WYMeditor.WymClassMozilla.prototype.html=function(a){if(typeof a==="string"){try{this._doc.designMode="off"}catch(b){}a=a.replace(/<em(\b[^>]*)>/gi,"<i$1>").replace(/<\/em>/gi,"</i>").replace(/<strong(\b[^>]*)>/gi,"<b$1>").replace(/<\/strong>/gi,"</b>");jQuery(this._doc.body).html(a);this.enableDesignMode()}else{return(jQuery(this._doc.body).html())}};WYMeditor.WymClassMozilla.prototype._exec=function(e,g){if(!this.selected()){return(false)}switch(e){case WYMeditor.INDENT:case WYMeditor.OUTDENT:var f=this.selected();var d=this._iframe.contentWindow.getSelection();var b=d.anchorNode;if(b.nodeName=="#text"){b=b.parentNode}f=this.findUp(f,WYMeditor.BLOCKS);b=this.findUp(b,WYMeditor.BLOCKS);if(f&&f==b&&f.tagName.toLowerCase()==WYMeditor.LI){var c=f.parentNode.parentNode;if(f.parentNode.childNodes.length>1||c.tagName.toLowerCase()==WYMeditor.OL||c.tagName.toLowerCase()==WYMeditor.UL){this._doc.execCommand(e,"",null)}}break;default:if(g){this._doc.execCommand(e,"",g)}else{this._doc.execCommand(e,"",null)}}var a=this.selected();if(a.tagName.toLowerCase()==WYMeditor.BODY){this._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}this.listen()};WYMeditor.WymClassMozilla.prototype.selected=function(){var b=this._iframe.contentWindow.getSelection();var a=b.focusNode;if(a){if(a.nodeName=="#text"){return(a.parentNode)}else{return(a)}}else{return(null)}};WYMeditor.WymClassMozilla.prototype.addCssRule=function(a,b){a.insertRule(b.name+" {"+b.css+"}",a.cssRules.length)};WYMeditor.WymClassMozilla.prototype.keydown=function(b){var c=WYMeditor.INSTANCES[this.title];var a=null;if(b.ctrlKey){if(b.keyCode==66){c._exec(WYMeditor.BOLD);return false}if(b.keyCode==73){c._exec(WYMeditor.ITALIC);return false}}else{if(b.keyCode==13){if(!b.shiftKey){a=c.selected();if(a&&a.tagName.toLowerCase()==WYMeditor.PRE){b.preventDefault();c.insert("<p></p>")}}}}};WYMeditor.WymClassMozilla.prototype.keyup=function(b){var d=WYMeditor.INSTANCES[this.title];d._selected_image=null;var a=null;if(b.keyCode==13&&!b.shiftKey){jQuery(d._doc.body).children(WYMeditor.BR).remove()}else{if(b.keyCode!=8&&b.keyCode!=17&&b.keyCode!=46&&b.keyCode!=224&&!b.metaKey&&!b.ctrlKey){a=d.selected();var c=a.tagName.toLowerCase();if(c=="strong"||c=="b"||c=="em"||c=="i"||c=="sub"||c=="sup"||c=="a"){c=a.parentNode.tagName.toLowerCase()}if(c==WYMeditor.BODY){d._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}}}};WYMeditor.WymClassMozilla.prototype.enableDesignMode=function(){if(this.designMode=="off"){try{this.designMode="on";this.execCommand("styleWithCSS","",false)}catch(a){}}};WYMeditor.WymClassMozilla.prototype.setFocusToNode=function(c){var a=document.createRange();a.selectNode(c);var b=this._iframe.contentWindow.getSelection();b.addRange(a);b.collapse(c,c.childNodes.length);this._iframe.contentWindow.focus()};WYMeditor.WymClassMozilla.prototype.openBlockTag=function(a,c){var c=this.validator.getValidTagAttributes(a,c);if(a=="span"&&c.style){var b=this.getTagForStyle(c.style);if(b){this._tag_stack.pop();var a=b;this._tag_stack.push(b);c.style=""}else{return}}this.output+=this.helper.tag(a,c,true)};WYMeditor.WymClassMozilla.prototype.getTagForStyle=function(a){if(/bold/.test(a)){return"strong"}if(/italic/.test(a)){return"em"}if(/sub/.test(a)){return"sub"}if(/sub/.test(a)){return"super"}return false};WYMeditor.WymClassOpera=function(a){this._wym=a;this._class="class";this._newLine="\r\n"};WYMeditor.WymClassOpera.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentWindow.document;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);this._doc.designMode="on";this.html(this._wym._html);if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();jQuery(this._doc).bind("keydown",this.keydown);jQuery(this._doc).bind("keyup",this.keyup);if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()};WYMeditor.WymClassOpera.prototype._exec=function(a,b){if(b){this._doc.execCommand(a,false,b)}else{this._doc.execCommand(a)}this.listen()};WYMeditor.WymClassOpera.prototype.selected=function(){var b=this._iframe.contentWindow.getSelection();var a=b.focusNode;if(a){if(a.nodeName=="#text"){return(a.parentNode)}else{return(a)}}else{return(null)}};WYMeditor.WymClassOpera.prototype.addCssRule=function(a,b){a.insertRule(b.name+" {"+b.css+"}",a.cssRules.length)};WYMeditor.WymClassOpera.prototype.keydown=function(a){var c=WYMeditor.INSTANCES[this.title];var b=c._iframe.contentWindow.getSelection();startNode=b.getRangeAt(0).startContainer;if(!jQuery(startNode).parentsOrSelf(WYMeditor.MAIN_CONTAINERS.join(","))[0]&&!jQuery(startNode).parentsOrSelf("li")&&a.keyCode!=WYMeditor.KEY.ENTER&&a.keyCode!=WYMeditor.KEY.LEFT&&a.keyCode!=WYMeditor.KEY.UP&&a.keyCode!=WYMeditor.KEY.RIGHT&&a.keyCode!=WYMeditor.KEY.DOWN&&a.keyCode!=WYMeditor.KEY.BACKSPACE&&a.keyCode!=WYMeditor.KEY.DELETE){c._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}};WYMeditor.WymClassOpera.prototype.keyup=function(a){var b=WYMeditor.INSTANCES[this.title];b._selected_image=null};WYMeditor.WymClassOpera.prototype.setFocusToNode=function(a){};WYMeditor.WymClassSafari=function(a){this._wym=a;this._class="class";this._newLine="\n"};WYMeditor.WymClassSafari.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentDocument;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);this._doc.designMode="on";this.html(this._wym._html);if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();jQuery(this._doc).bind("keydown",this.keydown);jQuery(this._doc).bind("keyup",this.keyup);if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()};WYMeditor.WymClassSafari.prototype._exec=function(e,g){if(!this.selected()){return(false)}switch(e){case WYMeditor.INDENT:case WYMeditor.OUTDENT:var f=this.selected();var d=this._iframe.contentWindow.getSelection();var b=d.anchorNode;if(b.nodeName=="#text"){b=b.parentNode}f=this.findUp(f,WYMeditor.BLOCKS);b=this.findUp(b,WYMeditor.BLOCKS);if(f&&f==b&&f.tagName.toLowerCase()==WYMeditor.LI){var c=f.parentNode.parentNode;if(f.parentNode.childNodes.length>1||c.tagName.toLowerCase()==WYMeditor.OL||c.tagName.toLowerCase()==WYMeditor.UL){this._doc.execCommand(e,"",null)}}break;case WYMeditor.INSERT_ORDEREDLIST:case WYMeditor.INSERT_UNORDEREDLIST:this._doc.execCommand(e,"",null);var f=this.selected();var a=this.findUp(f,WYMeditor.MAIN_CONTAINERS);if(a){jQuery(a).replaceWith(jQuery(a).html())}break;default:if(g){this._doc.execCommand(e,"",g)}else{this._doc.execCommand(e,"",null)}}var a=this.selected();if(a&&a.tagName.toLowerCase()==WYMeditor.BODY){this._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}this.listen()};WYMeditor.WymClassSafari.prototype.selected=function(){var b=this._iframe.contentWindow.getSelection();var a=b.focusNode;if(a){if(a.nodeName=="#text"){return(a.parentNode)}else{return(a)}}else{return(null)}};WYMeditor.WymClassSafari.prototype.addCssRule=function(a,b){a.insertRule(b.name+" {"+b.css+"}",a.cssRules.length)};WYMeditor.WymClassSafari.prototype.keydown=function(a){var b=WYMeditor.INSTANCES[this.title];if(a.ctrlKey){if(a.keyCode==66){b._exec(WYMeditor.BOLD);return false}if(a.keyCode==73){b._exec(WYMeditor.ITALIC);return false}}};WYMeditor.WymClassSafari.prototype.keyup=function(b){var d=WYMeditor.INSTANCES[this.title];d._selected_image=null;var a=null;if(b.keyCode==13&&!b.shiftKey){jQuery(d._doc.body).children(WYMeditor.BR).remove();a=d.selected();if(a&&a.tagName.toLowerCase()==WYMeditor.PRE){d._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}}if(b.keyCode==13&&b.shiftKey){d._exec("InsertLineBreak")}if(b.keyCode!=8&&b.keyCode!=17&&b.keyCode!=46&&b.keyCode!=224&&!b.metaKey&&!b.ctrlKey){a=d.selected();var c=a.tagName.toLowerCase();if(c=="strong"||c=="b"||c=="em"||c=="i"||c=="sub"||c=="sup"||c=="a"||c=="span"){c=a.parentNode.tagName.toLowerCase()}if(c==WYMeditor.BODY||c==WYMeditor.DIV){d._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}}};WYMeditor.WymClassSafari.prototype.setFocusToNode=function(c){var a=this._iframe.contentDocument.createRange();a.selectNode(c);var b=this._iframe.contentWindow.getSelection();b.addRange(a);b.collapse(c,c.childNodes.length);this._iframe.contentWindow.focus()};WYMeditor.WymClassSafari.prototype.openBlockTag=function(a,c){var c=this.validator.getValidTagAttributes(a,c);if(a=="span"&&c.style){var b=this.getTagForStyle(c.style);if(b){this._tag_stack.pop();var a=b;this._tag_stack.push(b);c.style="";if(typeof c["class"]=="string"){c["class"]=c["class"].replace(/apple-style-span/gi,"")}}else{return}}this.output+=this.helper.tag(a,c,true)};WYMeditor.WymClassSafari.prototype.getTagForStyle=function(a){if(/bold/.test(a)){return"strong"}if(/italic/.test(a)){return"em"}if(/sub/.test(a)){return"sub"}if(/super/.test(a)){return"sup"}return false}; \ No newline at end of file +if(!WYMeditor){var WYMeditor={}}(function(){if(!window.console||!console.firebug){var b=["log","debug","info","warn","error","assert","dir","dirxml","group","groupEnd","time","timeEnd","count","trace","profile","profileEnd"];WYMeditor.console={};for(var a=0;a<b.length;++a){WYMeditor.console[b[a]]=function(){}}}else{WYMeditor.console=window.console}})();jQuery.extend(WYMeditor,{VERSION:"0.5-rc1",INSTANCES:[],STRINGS:[],SKINS:[],NAME:"name",INDEX:"{Wym_Index}",WYM_INDEX:"wym_index",BASE_PATH:"{Wym_Base_Path}",CSS_PATH:"{Wym_Css_Path}",WYM_PATH:"{Wym_Wym_Path}",SKINS_DEFAULT_PATH:"skins/",SKINS_DEFAULT_CSS:"skin.css",SKINS_DEFAULT_JS:"skin.js",LANG_DEFAULT_PATH:"lang/",IFRAME_BASE_PATH:"{Wym_Iframe_Base_Path}",IFRAME_DEFAULT:"iframe/default/",JQUERY_PATH:"{Wym_Jquery_Path}",DIRECTION:"{Wym_Direction}",LOGO:"{Wym_Logo}",TOOLS:"{Wym_Tools}",TOOLS_ITEMS:"{Wym_Tools_Items}",TOOL_NAME:"{Wym_Tool_Name}",TOOL_TITLE:"{Wym_Tool_Title}",TOOL_CLASS:"{Wym_Tool_Class}",CLASSES:"{Wym_Classes}",CLASSES_ITEMS:"{Wym_Classes_Items}",CLASS_NAME:"{Wym_Class_Name}",CLASS_TITLE:"{Wym_Class_Title}",CONTAINERS:"{Wym_Containers}",CONTAINERS_ITEMS:"{Wym_Containers_Items}",CONTAINER_NAME:"{Wym_Container_Name}",CONTAINER_TITLE:"{Wym_Containers_Title}",CONTAINER_CLASS:"{Wym_Container_Class}",HTML:"{Wym_Html}",IFRAME:"{Wym_Iframe}",STATUS:"{Wym_Status}",DIALOG_TITLE:"{Wym_Dialog_Title}",DIALOG_BODY:"{Wym_Dialog_Body}",STRING:"string",BODY:"body",DIV:"div",P:"p",H1:"h1",H2:"h2",H3:"h3",H4:"h4",H5:"h5",H6:"h6",PRE:"pre",BLOCKQUOTE:"blockquote",A:"a",BR:"br",IMG:"img",TABLE:"table",TD:"td",TH:"th",UL:"ul",OL:"ol",LI:"li",CLASS:"class",HREF:"href",SRC:"src",TITLE:"title",ALT:"alt",DIALOG_LINK:"Link",DIALOG_IMAGE:"Image",DIALOG_TABLE:"Table",DIALOG_PASTE:"Paste_From_Word",BOLD:"Bold",ITALIC:"Italic",CREATE_LINK:"CreateLink",INSERT_IMAGE:"InsertImage",INSERT_TABLE:"InsertTable",INSERT_HTML:"InsertHTML",PASTE:"Paste",INDENT:"Indent",OUTDENT:"Outdent",TOGGLE_HTML:"ToggleHtml",FORMAT_BLOCK:"FormatBlock",PREVIEW:"Preview",UNLINK:"Unlink",INSERT_UNORDEREDLIST:"InsertUnorderedList",INSERT_ORDEREDLIST:"InsertOrderedList",MAIN_CONTAINERS:new Array("p","h1","h2","h3","h4","h5","h6","pre","blockquote"),BLOCKS:new Array("address","blockquote","div","dl","fieldset","form","h1","h2","h3","h4","h5","h6","hr","noscript","ol","p","pre","table","ul","dd","dt","li","tbody","td","tfoot","th","thead","tr"),KEY:{BACKSPACE:8,ENTER:13,END:35,HOME:36,LEFT:37,UP:38,RIGHT:39,DOWN:40,CURSOR:new Array(37,38,39,40),DELETE:46},NODE:{ELEMENT:1,ATTRIBUTE:2,TEXT:3},editor:function(b,a){this._index=WYMeditor.INSTANCES.push(this)-1;this._element=b;this._options=a;this._html=jQuery(b).val();if(this._options.html){this._html=this._options.html}this._options.basePath=this._options.basePath||this.computeBasePath();this._options.skinPath=this._options.skinPath||this._options.basePath+WYMeditor.SKINS_DEFAULT_PATH+this._options.skin+"/";this._options.wymPath=this._options.wymPath||this.computeWymPath();this._options.langPath=this._options.langPath||this._options.basePath+WYMeditor.LANG_DEFAULT_PATH;this._options.iframeBasePath=this._options.iframeBasePath||this._options.basePath+WYMeditor.IFRAME_DEFAULT;this._options.jQueryPath=this._options.jQueryPath||this.computeJqueryPath();this.init()}});jQuery.fn.wymeditor=function(a){a=jQuery.extend({html:"",basePath:false,skinPath:false,wymPath:false,iframeBasePath:false,jQueryPath:false,styles:false,stylesheet:false,skin:"default",initSkin:true,loadSkin:true,lang:"en",direction:"ltr",boxHtml:"<div class='wym_box'><div class='wym_area_top'>"+WYMeditor.TOOLS+"</div><div class='wym_area_left'></div><div class='wym_area_right'>"+WYMeditor.CONTAINERS+WYMeditor.CLASSES+"</div><div class='wym_area_main'>"+WYMeditor.HTML+WYMeditor.IFRAME+WYMeditor.STATUS+"</div><div class='wym_area_bottom'>"+WYMeditor.LOGO+"</div></div>",logoHtml:"<a class='wym_wymeditor_link' href='http://www.wymeditor.org/'>WYMeditor</a>",iframeHtml:"<div class='wym_iframe wym_section'><iframe src='/page/get_editor_iframe' onload='this.contentWindow.parent.WYMeditor.INSTANCES["+WYMeditor.INDEX+"].initIframe(this)'></iframe></div>",editorStyles:[],toolsHtml:"<div class='wym_tools wym_section'><h2>{Tools}</h2><ul>"+WYMeditor.TOOLS_ITEMS+"</ul></div>",toolsItemHtml:"<li class='"+WYMeditor.TOOL_CLASS+"'><a href='#' name='"+WYMeditor.TOOL_NAME+"' title='"+WYMeditor.TOOL_TITLE+"'>"+WYMeditor.TOOL_TITLE+"</a></li>",toolsItems:[{name:"Bold",title:"Strong",css:"wym_tools_strong"},{name:"Italic",title:"Emphasis",css:"wym_tools_emphasis"},{name:"Superscript",title:"Superscript",css:"wym_tools_superscript"},{name:"Subscript",title:"Subscript",css:"wym_tools_subscript"},{name:"InsertOrderedList",title:"Ordered_List",css:"wym_tools_ordered_list"},{name:"InsertUnorderedList",title:"Unordered_List",css:"wym_tools_unordered_list"},{name:"Indent",title:"Indent",css:"wym_tools_indent"},{name:"Outdent",title:"Outdent",css:"wym_tools_outdent"},{name:"Undo",title:"Undo",css:"wym_tools_undo"},{name:"Redo",title:"Redo",css:"wym_tools_redo"},{name:"CreateLink",title:"Link",css:"wym_tools_link"},{name:"Unlink",title:"Unlink",css:"wym_tools_unlink"},{name:"InsertImage",title:"Image",css:"wym_tools_image"},{name:"InsertTable",title:"Table",css:"wym_tools_table"},{name:"Paste",title:"Paste_From_Word",css:"wym_tools_paste"},{name:"ToggleHtml",title:"HTML",css:"wym_tools_html"},{name:"Preview",title:"Preview",css:"wym_tools_preview"}],containersHtml:"<div class='wym_containers wym_section'><h2>{Containers}</h2><ul>"+WYMeditor.CONTAINERS_ITEMS+"</ul></div>",containersItemHtml:"<li class='"+WYMeditor.CONTAINER_CLASS+"'><a href='#' name='"+WYMeditor.CONTAINER_NAME+"'>"+WYMeditor.CONTAINER_TITLE+"</a></li>",containersItems:[{name:"P",title:"Paragraph",css:"wym_containers_p"},{name:"H1",title:"Heading_1",css:"wym_containers_h1"},{name:"H2",title:"Heading_2",css:"wym_containers_h2"},{name:"H3",title:"Heading_3",css:"wym_containers_h3"},{name:"H4",title:"Heading_4",css:"wym_containers_h4"},{name:"H5",title:"Heading_5",css:"wym_containers_h5"},{name:"H6",title:"Heading_6",css:"wym_containers_h6"},{name:"PRE",title:"Preformatted",css:"wym_containers_pre"},{name:"BLOCKQUOTE",title:"Blockquote",css:"wym_containers_blockquote"},{name:"TH",title:"Table_Header",css:"wym_containers_th"}],classesHtml:"<div class='wym_classes wym_section'><h2>{Classes}</h2><ul>"+WYMeditor.CLASSES_ITEMS+"</ul></div>",classesItemHtml:"<li><a href='#' name='"+WYMeditor.CLASS_NAME+"'>"+WYMeditor.CLASS_TITLE+"</a></li>",classesItems:[],statusHtml:"<div class='wym_status wym_section'><h2>{Status}</h2></div>",htmlHtml:"<div class='wym_html wym_section'><h2>{Source_Code}</h2><textarea class='wym_html_val'></textarea></div>",boxSelector:".wym_box",toolsSelector:".wym_tools",toolsListSelector:" ul",containersSelector:".wym_containers",classesSelector:".wym_classes",htmlSelector:".wym_html",iframeSelector:".wym_iframe iframe",iframeBodySelector:".wym_iframe",statusSelector:".wym_status",toolSelector:".wym_tools a",containerSelector:".wym_containers a",classSelector:".wym_classes a",htmlValSelector:".wym_html_val",hrefSelector:".wym_href",srcSelector:".wym_src",titleSelector:".wym_title",altSelector:".wym_alt",textSelector:".wym_text",rowsSelector:".wym_rows",colsSelector:".wym_cols",captionSelector:".wym_caption",summarySelector:".wym_summary",submitSelector:".wym_submit",cancelSelector:".wym_cancel",previewSelector:"",dialogTypeSelector:".wym_dialog_type",dialogLinkSelector:".wym_dialog_link",dialogImageSelector:".wym_dialog_image",dialogTableSelector:".wym_dialog_table",dialogPasteSelector:".wym_dialog_paste",dialogPreviewSelector:".wym_dialog_preview",updateSelector:".wymupdate",updateEvent:"click",dialogFeatures:"menubar=no,titlebar=no,toolbar=no,resizable=no,width=560,height=300,top=0,left=0",dialogFeaturesPreview:"menubar=no,titlebar=no,toolbar=no,resizable=no,scrollbars=yes,width=560,height=300,top=0,left=0",dialogHtml:"<!DOCTYPE html PUBLIC '-//W3C//DTD XHTML 1.0 Strict//EN' 'http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd'><html dir='"+WYMeditor.DIRECTION+"'><head><link rel='stylesheet' type='text/css' media='screen' href='"+WYMeditor.CSS_PATH+"' /><title>"+WYMeditor.DIALOG_TITLE+"</title><script type='text/javascript' src='"+WYMeditor.JQUERY_PATH+"'><\/script><script type='text/javascript' src='"+WYMeditor.WYM_PATH+"'><\/script></head>"+WYMeditor.DIALOG_BODY+"</html>",dialogLinkHtml:"<body class='wym_dialog wym_dialog_link' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><fieldset><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_LINK+"' /><legend>{Link}</legend><div class='row'><label>{URL}</label><input type='text' class='wym_href' value='' size='40' /></div><div class='row'><label>{Title}</label><input type='text' class='wym_title' value='' size='40' /></div><div class='row row-indent'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogImageHtml:"<body class='wym_dialog wym_dialog_image' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><fieldset><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_IMAGE+"' /><legend>{Image}</legend><div class='row'><label>{URL}</label><input type='text' class='wym_src' value='' size='40' /></div><div class='row'><label>{Alternative_Text}</label><input type='text' class='wym_alt' value='' size='40' /></div><div class='row'><label>{Title}</label><input type='text' class='wym_title' value='' size='40' /></div><div class='row row-indent'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogTableHtml:"<body class='wym_dialog wym_dialog_table' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><fieldset><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_TABLE+"' /><legend>{Table}</legend><div class='row'><label>{Caption}</label><input type='text' class='wym_caption' value='' size='40' /></div><div class='row'><label>{Summary}</label><input type='text' class='wym_summary' value='' size='40' /></div><div class='row'><label>{Number_Of_Rows}</label><input type='text' class='wym_rows' value='3' size='3' /></div><div class='row'><label>{Number_Of_Cols}</label><input type='text' class='wym_cols' value='2' size='3' /></div><div class='row row-indent'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogPasteHtml:"<body class='wym_dialog wym_dialog_paste' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'><form><input type='hidden' class='wym_dialog_type' value='"+WYMeditor.DIALOG_PASTE+"' /><fieldset><legend>{Paste_From_Word}</legend><div class='row'><textarea class='wym_text' rows='10' cols='50'></textarea></div><div class='row'><input class='wym_submit' type='button' value='{Submit}' /><input class='wym_cancel' type='button'value='{Cancel}' /></div></fieldset></form></body>",dialogPreviewHtml:"<body class='wym_dialog wym_dialog_preview' onload='WYMeditor.INIT_DIALOG("+WYMeditor.INDEX+")'></body>",dialogStyles:[],stringDelimiterLeft:"{",stringDelimiterRight:"}",preInit:null,preBind:null,postInit:null,preInitDialog:null,postInitDialog:null},a);return this.each(function(){new WYMeditor.editor(jQuery(this),a)})};jQuery.extend({wymeditors:function(a){return(WYMeditor.INSTANCES[a])}});WYMeditor.editor.prototype.init=function(){if(jQuery.browser.msie){var WymClass=new WYMeditor.WymClassExplorer(this)}else{if(jQuery.browser.mozilla){var WymClass=new WYMeditor.WymClassMozilla(this)}else{if(jQuery.browser.opera){var WymClass=new WYMeditor.WymClassOpera(this)}else{if(jQuery.browser.safari||jQuery.browser.chrome){var WymClass=new WYMeditor.WymClassSafari(this)}}}}if(WymClass){if(jQuery.isFunction(this._options.preInit)){this._options.preInit(this)}var SaxListener=new WYMeditor.XhtmlSaxListener();jQuery.extend(SaxListener,WymClass);this.parser=new WYMeditor.XhtmlParser(SaxListener);if(this._options.styles||this._options.stylesheet){this.configureEditorUsingRawCss()}this.helper=new WYMeditor.XmlHelper();for(var prop in WymClass){this[prop]=WymClass[prop]}this._box=jQuery(this._element).hide().after(this._options.boxHtml).next().addClass("wym_box_"+this._index);if(jQuery.isFunction(jQuery.fn.data)){jQuery.data(this._box.get(0),WYMeditor.WYM_INDEX,this._index);jQuery.data(this._element.get(0),WYMeditor.WYM_INDEX,this._index)}var h=WYMeditor.Helper;var iframeHtml=this._options.iframeHtml;iframeHtml=h.replaceAll(iframeHtml,WYMeditor.INDEX,this._index);iframeHtml=h.replaceAll(iframeHtml,WYMeditor.IFRAME_BASE_PATH,this._options.iframeBasePath);var boxHtml=jQuery(this._box).html();boxHtml=h.replaceAll(boxHtml,WYMeditor.LOGO,this._options.logoHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.TOOLS,this._options.toolsHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.CONTAINERS,this._options.containersHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.CLASSES,this._options.classesHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.HTML,this._options.htmlHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.IFRAME,iframeHtml);boxHtml=h.replaceAll(boxHtml,WYMeditor.STATUS,this._options.statusHtml);var aTools=eval(this._options.toolsItems);var sTools="";for(var i=0;i<aTools.length;i++){var oTool=aTools[i];if(oTool.name&&oTool.title){var sTool=this._options.toolsItemHtml}var sTool=h.replaceAll(sTool,WYMeditor.TOOL_NAME,oTool.name);sTool=h.replaceAll(sTool,WYMeditor.TOOL_TITLE,this._options.stringDelimiterLeft+oTool.title+this._options.stringDelimiterRight);sTool=h.replaceAll(sTool,WYMeditor.TOOL_CLASS,oTool.css);sTools+=sTool}boxHtml=h.replaceAll(boxHtml,WYMeditor.TOOLS_ITEMS,sTools);var aClasses=eval(this._options.classesItems);var sClasses="";for(var i=0;i<aClasses.length;i++){var oClass=aClasses[i];if(oClass.name&&oClass.title){var sClass=this._options.classesItemHtml}sClass=h.replaceAll(sClass,WYMeditor.CLASS_NAME,oClass.name);sClass=h.replaceAll(sClass,WYMeditor.CLASS_TITLE,oClass.title);sClasses+=sClass}boxHtml=h.replaceAll(boxHtml,WYMeditor.CLASSES_ITEMS,sClasses);var aContainers=eval(this._options.containersItems);var sContainers="";for(var i=0;i<aContainers.length;i++){var oContainer=aContainers[i];if(oContainer.name&&oContainer.title){var sContainer=this._options.containersItemHtml}sContainer=h.replaceAll(sContainer,WYMeditor.CONTAINER_NAME,oContainer.name);sContainer=h.replaceAll(sContainer,WYMeditor.CONTAINER_TITLE,this._options.stringDelimiterLeft+oContainer.title+this._options.stringDelimiterRight);sContainer=h.replaceAll(sContainer,WYMeditor.CONTAINER_CLASS,oContainer.css);sContainers+=sContainer}boxHtml=h.replaceAll(boxHtml,WYMeditor.CONTAINERS_ITEMS,sContainers);boxHtml=this.replaceStrings(boxHtml);jQuery(this._box).html(boxHtml);jQuery(this._box).find(this._options.htmlSelector).hide();this.loadSkin()}};WYMeditor.editor.prototype.bindEvents=function(){var wym=this;jQuery(this._box).find(this._options.toolSelector).click(function(){wym._iframe.contentWindow.focus();wym.exec(jQuery(this).attr(WYMeditor.NAME));return(false)});jQuery(this._box).find(this._options.containerSelector).click(function(){wym.container(jQuery(this).attr(WYMeditor.NAME));return(false)});jQuery(this._box).find(this._options.htmlValSelector).keyup(function(){jQuery(wym._doc.body).html(jQuery(this).val())}).focus(function(){jQuery(this).toggleClass("hasfocus")}).blur(function(){jQuery(this).toggleClass("hasfocus")});jQuery(this._box).find(this._options.classSelector).click(function(){var aClasses=eval(wym._options.classesItems);var sName=jQuery(this).attr(WYMeditor.NAME);var oClass=WYMeditor.Helper.findByName(aClasses,sName);if(oClass){var jqexpr=oClass.expr;wym.toggleClass(sName,jqexpr)}wym._iframe.contentWindow.focus();return(false)});jQuery(this._options.updateSelector).bind(this._options.updateEvent,function(){wym.update()})};WYMeditor.editor.prototype.ready=function(){return(this._doc!=null)};WYMeditor.editor.prototype.box=function(){return(this._box)};WYMeditor.editor.prototype.html=function(a){if(typeof a==="string"){jQuery(this._doc.body).html(a)}else{return(jQuery(this._doc.body).html())}};WYMeditor.editor.prototype.xhtml=function(){return this.parser.parse(this.html())};WYMeditor.editor.prototype.exec=function(b){switch(b){case WYMeditor.CREATE_LINK:var a=this.container();if(a||this._selected_image){this.dialog(WYMeditor.DIALOG_LINK)}break;case WYMeditor.INSERT_IMAGE:this.dialog(WYMeditor.DIALOG_IMAGE);break;case WYMeditor.INSERT_TABLE:this.dialog(WYMeditor.DIALOG_TABLE);break;case WYMeditor.PASTE:this.dialog(WYMeditor.DIALOG_PASTE);break;case WYMeditor.TOGGLE_HTML:this.update();this.toggleHtml();if(!jQuery(this._box).find(this._options.htmlSelector).is(":visible")){this.listen()}break;case WYMeditor.PREVIEW:this.dialog(WYMeditor.PREVIEW,this._options.dialogFeaturesPreview);break;default:this._exec(b);break}};WYMeditor.editor.prototype.container=function(a){if(a){var d=null;if(a.toLowerCase()==WYMeditor.TH){d=this.container();switch(d.tagName.toLowerCase()){case WYMeditor.TD:case WYMeditor.TH:break;default:var e=new Array(WYMeditor.TD,WYMeditor.TH);d=this.findUp(this.container(),e);break}if(d!=null){a=(d.tagName.toLowerCase()==WYMeditor.TD)?WYMeditor.TH:WYMeditor.TD;this.switchTo(d,a);this.update()}}else{var e=new Array(WYMeditor.P,WYMeditor.H1,WYMeditor.H2,WYMeditor.H3,WYMeditor.H4,WYMeditor.H5,WYMeditor.H6,WYMeditor.PRE,WYMeditor.BLOCKQUOTE);d=this.findUp(this.container(),e);if(d){var i=null;if(a.toLowerCase()==WYMeditor.BLOCKQUOTE){var f=this.findUp(this.container(),WYMeditor.BLOCKQUOTE);if(f==null){i=this._doc.createElement(a);d.parentNode.insertBefore(i,d);i.appendChild(d);this.setFocusToNode(i.firstChild)}else{var c=f.childNodes;var g=c.length;var b=null;if(g>0){b=c.item(0)}for(var h=0;h<g;h++){f.parentNode.insertBefore(c.item(0),f)}f.parentNode.removeChild(f);if(b){this.setFocusToNode(b)}}}else{this.switchTo(d,a)}this.update()}}}else{return(this.selected())}};WYMeditor.editor.prototype.toggleClass=function(c,b){var a=(this._selected_image?this._selected_image:jQuery(this.selected()));a=jQuery(a).parentsOrSelf(b);jQuery(a).toggleClass(c);if(!jQuery(a).attr(WYMeditor.CLASS)){jQuery(a).removeAttr(this._class)}};WYMeditor.editor.prototype.findUp=function(d,c){if(d){var e=d.tagName.toLowerCase();if(typeof(c)==WYMeditor.STRING){while(e!=c&&e!=WYMeditor.BODY){d=d.parentNode;e=d.tagName.toLowerCase()}}else{var b=false;while(!b&&e!=WYMeditor.BODY){for(var a=0;a<c.length;a++){if(e==c[a]){b=true;break}}if(!b){d=d.parentNode;e=d.tagName.toLowerCase()}}}if(e!=WYMeditor.BODY){return(d)}else{return(null)}}else{return(null)}};WYMeditor.editor.prototype.switchTo=function(c,d){var b=this._doc.createElement(d);var a=jQuery(c).html();c.parentNode.replaceChild(b,c);jQuery(b).html(a);this.setFocusToNode(b)};WYMeditor.editor.prototype.replaceStrings=function(sVal){if(!WYMeditor.STRINGS[this._options.lang]){try{eval(jQuery.ajax({url:this._options.langPath+this._options.lang+".js",async:false}).responseText)}catch(e){WYMeditor.console.error("WYMeditor: error while parsing language file.");return sVal}}for(var key in WYMeditor.STRINGS[this._options.lang]){sVal=WYMeditor.Helper.replaceAll(sVal,this._options.stringDelimiterLeft+key+this._options.stringDelimiterRight,WYMeditor.STRINGS[this._options.lang][key])}return(sVal)};WYMeditor.editor.prototype.encloseString=function(a){return(this._options.stringDelimiterLeft+a+this._options.stringDelimiterRight)};WYMeditor.editor.prototype.status=function(a){jQuery(this._box).find(this._options.statusSelector).html(a)};WYMeditor.editor.prototype.update=function(){var a=this.xhtml();jQuery(this._element).val(a);jQuery(this._box).find(this._options.htmlValSelector).not(".hasfocus").val(a)};WYMeditor.editor.prototype.dialog=function(j,c,f){var a=c||this._wym._options.dialogFeatures;var d=window.open("","dialog",a);if(d){var b="";switch(j){case (WYMeditor.DIALOG_LINK):b=this._options.dialogLinkHtml;break;case (WYMeditor.DIALOG_IMAGE):b=this._options.dialogImageHtml;break;case (WYMeditor.DIALOG_TABLE):b=this._options.dialogTableHtml;break;case (WYMeditor.DIALOG_PASTE):b=this._options.dialogPasteHtml;break;case (WYMeditor.PREVIEW):b=this._options.dialogPreviewHtml;break;default:b=f}var e=WYMeditor.Helper;var g=this._options.dialogHtml;g=e.replaceAll(g,WYMeditor.BASE_PATH,this._options.basePath);g=e.replaceAll(g,WYMeditor.DIRECTION,this._options.direction);g=e.replaceAll(g,WYMeditor.CSS_PATH,this._options.skinPath+WYMeditor.SKINS_DEFAULT_CSS);g=e.replaceAll(g,WYMeditor.WYM_PATH,this._options.wymPath);g=e.replaceAll(g,WYMeditor.JQUERY_PATH,this._options.jQueryPath);g=e.replaceAll(g,WYMeditor.DIALOG_TITLE,this.encloseString(j));g=e.replaceAll(g,WYMeditor.DIALOG_BODY,b);g=e.replaceAll(g,WYMeditor.INDEX,this._index);g=this.replaceStrings(g);var i=d.document;i.write(g);i.close()}};WYMeditor.editor.prototype.toggleHtml=function(){jQuery(this._box).find(this._options.htmlSelector).toggle()};WYMeditor.editor.prototype.uniqueStamp=function(){var a=new Date();return("wym-"+a.getTime())};WYMeditor.editor.prototype.paste=function(b){var e;var a=this.selected();var c=b.split(this._newLine+this._newLine);var d=new RegExp(this._newLine,"g");if(a&&a.tagName.toLowerCase()!=WYMeditor.BODY){for(x=c.length-1;x>=0;x--){e=c[x];e=e.replace(d,"<br />");jQuery(a).after("<p>"+e+"</p>")}}else{for(x=0;x<c.length;x++){e=c[x];e=e.replace(d,"<br />");jQuery(this._doc.body).append("<p>"+e+"</p>")}}};WYMeditor.editor.prototype.insert=function(a){if(this._iframe.contentWindow.getSelection().focusNode!=null){this._exec(WYMeditor.INSERT_HTML,a)}else{this.paste(a)}};WYMeditor.editor.prototype.wrap=function(b,a){if(this._iframe.contentWindow.getSelection().focusNode!=null){this._exec(WYMeditor.INSERT_HTML,b+this._iframe.contentWindow.getSelection().toString()+a)}};WYMeditor.editor.prototype.unwrap=function(){if(this._iframe.contentWindow.getSelection().focusNode!=null){this._exec(WYMeditor.INSERT_HTML,this._iframe.contentWindow.getSelection().toString())}};WYMeditor.editor.prototype.addCssRules=function(e,c){var b=e.styleSheets[0];if(b){for(var a=0;a<c.length;a++){var d=c[a];if(d.name&&d.css){this.addCssRule(b,d)}}}};WYMeditor.editor.prototype.computeBasePath=function(){return jQuery(jQuery.grep(jQuery("script"),function(a){return(a.src&&a.src.match(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/))})).attr("src").replace(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/,"")};WYMeditor.editor.prototype.computeWymPath=function(){return jQuery(jQuery.grep(jQuery("script"),function(a){return(a.src&&a.src.match(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/))})).attr("src")};WYMeditor.editor.prototype.computeJqueryPath=function(){return jQuery(jQuery.grep(jQuery("script"),function(a){return(a.src&&a.src.match(/jquery(-(.*)){0,1}(\.pack|\.min|\.packed)?\.js(\?.*)?$/))})).attr("src")};WYMeditor.editor.prototype.computeCssPath=function(){return jQuery(jQuery.grep(jQuery("link"),function(a){return(a.href&&a.href.match(/wymeditor\/skins\/(.*)screen\.css(\?.*)?$/))})).attr("href")};WYMeditor.editor.prototype.configureEditorUsingRawCss=function(){var a=new WYMeditor.WymCssParser();if(this._options.stylesheet){a.parse(jQuery.ajax({url:this._options.stylesheet,async:false}).responseText)}else{a.parse(this._options.styles,false)}if(this._options.classesItems.length==0){this._options.classesItems=a.css_settings.classesItems}if(this._options.editorStyles.length==0){this._options.editorStyles=a.css_settings.editorStyles}if(this._options.dialogStyles.length==0){this._options.dialogStyles=a.css_settings.dialogStyles}};WYMeditor.editor.prototype.listen=function(){jQuery(this._doc.body).bind("mousedown",this.mousedown);var a=this._doc.body.getElementsByTagName("img");for(var b=0;b<a.length;b++){jQuery(a[b]).bind("mousedown",this.mousedown)}};WYMeditor.editor.prototype.mousedown=function(a){var b=WYMeditor.INSTANCES[this.ownerDocument.title];b._selected_image=(this.tagName.toLowerCase()==WYMeditor.IMG)?this:null;a.stopPropagation()};WYMeditor.loadCss=function(a){var c=document.createElement("link");c.rel="stylesheet";c.href=a;var b=jQuery("head").get(0);b.appendChild(c)};WYMeditor.editor.prototype.loadSkin=function(){if(this._options.loadSkin&&!WYMeditor.SKINS[this._options.skin]){var found=false;var rExp=new RegExp(this._options.skin+"/"+WYMeditor.SKINS_DEFAULT_CSS+"$");jQuery("link").each(function(){if(this.href.match(rExp)){found=true}});if(!found){WYMeditor.loadCss(this._options.skinPath+WYMeditor.SKINS_DEFAULT_CSS)}}jQuery(this._box).addClass("wym_skin_"+this._options.skin);if(this._options.initSkin&&!WYMeditor.SKINS[this._options.skin]){eval(jQuery.ajax({url:this._options.skinPath+WYMeditor.SKINS_DEFAULT_JS,async:false}).responseText)}if(WYMeditor.SKINS[this._options.skin]&&WYMeditor.SKINS[this._options.skin].init){WYMeditor.SKINS[this._options.skin].init(this)}};WYMeditor.INIT_DIALOG=function(index){var wym=window.opener.WYMeditor.INSTANCES[index];var doc=window.document;var selected=wym.selected();var dialogType=jQuery(wym._options.dialogTypeSelector).val();var sStamp=wym.uniqueStamp();switch(dialogType){case WYMeditor.DIALOG_LINK:if(selected&&selected.tagName&&selected.tagName.toLowerCase!=WYMeditor.A){selected=jQuery(selected).parentsOrSelf(WYMeditor.A)}if(!selected&&wym._selected_image){selected=jQuery(wym._selected_image).parentsOrSelf(WYMeditor.A)}break}if(jQuery.isFunction(wym._options.preInitDialog)){wym._options.preInitDialog(wym,window)}var styles=doc.styleSheets[0];var aCss=eval(wym._options.dialogStyles);wym.addCssRules(doc,aCss);if(selected){jQuery(wym._options.hrefSelector).val(jQuery(selected).attr(WYMeditor.HREF));jQuery(wym._options.srcSelector).val(jQuery(selected).attr(WYMeditor.SRC));jQuery(wym._options.titleSelector).val(jQuery(selected).attr(WYMeditor.TITLE));jQuery(wym._options.altSelector).val(jQuery(selected).attr(WYMeditor.ALT))}if(wym._selected_image){jQuery(wym._options.dialogImageSelector+" "+wym._options.srcSelector).val(jQuery(wym._selected_image).attr(WYMeditor.SRC));jQuery(wym._options.dialogImageSelector+" "+wym._options.titleSelector).val(jQuery(wym._selected_image).attr(WYMeditor.TITLE));jQuery(wym._options.dialogImageSelector+" "+wym._options.altSelector).val(jQuery(wym._selected_image).attr(WYMeditor.ALT))}jQuery(wym._options.dialogLinkSelector+" "+wym._options.submitSelector).click(function(){var sUrl=jQuery(wym._options.hrefSelector).val();if(sUrl.length>0){wym._exec(WYMeditor.CREATE_LINK,sStamp);jQuery("a[href="+sStamp+"]",wym._doc.body).attr(WYMeditor.HREF,sUrl).attr(WYMeditor.TITLE,jQuery(wym._options.titleSelector).val())}window.close()});jQuery(wym._options.dialogImageSelector+" "+wym._options.submitSelector).click(function(){var sUrl=jQuery(wym._options.srcSelector).val();if(sUrl.length>0){wym._exec(WYMeditor.INSERT_IMAGE,sStamp);jQuery("img[src$="+sStamp+"]",wym._doc.body).attr(WYMeditor.SRC,sUrl).attr(WYMeditor.TITLE,jQuery(wym._options.titleSelector).val()).attr(WYMeditor.ALT,jQuery(wym._options.altSelector).val())}window.close()});jQuery(wym._options.dialogTableSelector+" "+wym._options.submitSelector).click(function(){var iRows=jQuery(wym._options.rowsSelector).val();var iCols=jQuery(wym._options.colsSelector).val();if(iRows>0&&iCols>0){var table=wym._doc.createElement(WYMeditor.TABLE);var newRow=null;var newCol=null;var sCaption=jQuery(wym._options.captionSelector).val();var newCaption=table.createCaption();newCaption.innerHTML=sCaption;for(x=0;x<iRows;x++){newRow=table.insertRow(x);for(y=0;y<iCols;y++){newRow.insertCell(y)}}jQuery(table).attr("summary",jQuery(wym._options.summarySelector).val());var node=jQuery(wym.findUp(wym.container(),WYMeditor.MAIN_CONTAINERS)).get(0);if(!node||!node.parentNode){jQuery(wym._doc.body).append(table)}else{jQuery(node).after(table)}}window.close()});jQuery(wym._options.dialogPasteSelector+" "+wym._options.submitSelector).click(function(){var sText=jQuery(wym._options.textSelector).val();wym.paste(sText);window.close()});jQuery(wym._options.dialogPreviewSelector+" "+wym._options.previewSelector).html(wym.xhtml());jQuery(wym._options.cancelSelector).mousedown(function(){window.close()});if(jQuery.isFunction(wym._options.postInitDialog)){wym._options.postInitDialog(wym,window)}};WYMeditor.XmlHelper=function(){this._entitiesDiv=document.createElement("div");return this};WYMeditor.XmlHelper.prototype.tag=function(c,b,a){b=b||false;a=a||false;return"<"+c+(b?this.tagOptions(b):"")+(a?">":" />")};WYMeditor.XmlHelper.prototype.contentTag=function(b,c,a){a=a||false;return"<"+b+(a?this.tagOptions(a):"")+">"+c+"</"+b+">"};WYMeditor.XmlHelper.prototype.cdataSection=function(a){return"<![CDATA["+a+"]]>"};WYMeditor.XmlHelper.prototype.escapeOnce=function(a){return this._fixDoubleEscape(this.escapeEntities(a))};WYMeditor.XmlHelper.prototype._fixDoubleEscape=function(a){return a.replace(/&([a-z]+|(#\d+));/ig,"&$1;")};WYMeditor.XmlHelper.prototype.tagOptions=function(b){var a=this;a._formated_options="";for(var c in b){var d="";var e=b[c];if(typeof e!="function"&&e.length>0){if(parseInt(c)==c&&typeof e=="object"){c=e.shift();e=e.pop()}if(c!=""&&e!=""){a._formated_options+=" "+c+'="'+a.escapeOnce(e)+'"'}}}return a._formated_options};WYMeditor.XmlHelper.prototype.escapeEntities=function(c,b){this._entitiesDiv.innerHTML=c;this._entitiesDiv.textContent=c;var a=this._entitiesDiv.innerHTML;if(typeof b=="undefined"){if(b!=false){a=a.replace('"',""")}if(b==true){a=a.replace('"',"'")}}return a};WYMeditor.XmlHelper.prototype.parseAttributes=function(h){var a=[];var g=h.split(/((=\s*")(")("))|((=\s*\')(\')(\'))|((=\s*[^>\s]*))/g);if(g.toString()!=h){for(var d in g){var c=g[d];if(typeof c!="function"&&c.length!=0){var e=new RegExp("(\\w+)\\s*"+c);if(match=h.match(e)){var f=c.replace(/^[\s=]+/,"");var b=f.charAt(0);b=b=='"'?'"':(b=="'"?"'":"");if(b!=""){f=b=='"'?f.replace(/^"|"+$/g,""):f.replace(/^'|'+$/g,"")}h=h.replace(match[0],"");a.push([match[1],f])}}}}return a};WYMeditor.XhtmlValidator={_attributes:{core:{except:["base","head","html","meta","param","script","style","title"],attributes:["class","id","style","title","accesskey","tabindex"]},language:{except:["base","br","hr","iframe","param","script"],attributes:{dir:["ltr","rtl"],"0":"lang","1":"xml:lang"}},keyboard:{attributes:{accesskey:/^(\w){1}$/,tabindex:/^(\d)+$/}}},_events:{window:{only:["body"],attributes:["onload","onunload"]},form:{only:["form","input","textarea","select","a","label","button"],attributes:["onchange","onsubmit","onreset","onselect","onblur","onfocus"]},keyboard:{except:["base","bdo","br","frame","frameset","head","html","iframe","meta","param","script","style","title"],attributes:["onkeydown","onkeypress","onkeyup"]},mouse:{except:["base","bdo","br","head","html","meta","param","script","style","title"],attributes:["onclick","ondblclick","onmousedown","onmousemove","onmouseover","onmouseout","onmouseup"]}},_tags:{a:{attributes:{"0":"charset","1":"coords","2":"href","3":"hreflang","4":"name",rel:/^(alternate|designates|stylesheet|start|next|prev|contents|index|glossary|copyright|chapter|section|subsection|appendix|help|bookmark| |shortcut|icon)+$/,rev:/^(alternate|designates|stylesheet|start|next|prev|contents|index|glossary|copyright|chapter|section|subsection|appendix|help|bookmark| 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true};WYMeditor.XhtmlLexer=function(a){jQuery.extend(this,new WYMeditor.Lexer(a,"Text"));this.mapHandler("Text","Text");this.addTokens();this.init();return this};WYMeditor.XhtmlLexer.prototype.init=function(){};WYMeditor.XhtmlLexer.prototype.addTokens=function(){this.addCommentTokens("Text");this.addScriptTokens("Text");this.addCssTokens("Text");this.addTagTokens("Text")};WYMeditor.XhtmlLexer.prototype.addCommentTokens=function(a){this.addEntryPattern("","Comment")};WYMeditor.XhtmlLexer.prototype.addScriptTokens=function(a){this.addEntryPattern("<script",a,"Script");this.addExitPattern("<\/script>","Script")};WYMeditor.XhtmlLexer.prototype.addCssTokens=function(a){this.addEntryPattern("<style",a,"Css");this.addExitPattern("</style>","Css")};WYMeditor.XhtmlLexer.prototype.addTagTokens=function(a){this.addSpecialPattern("<\\s*[a-z0-9:-]+\\s*>",a,"OpeningTag");this.addEntryPattern("<[a-z0-9:-]+[\\/ 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WYMeditor.XhtmlLexer(this);this._Listener=a;this._mode=b;this._matches=[];this._last_match="";this._current_match="";return this};WYMeditor.XhtmlParser.prototype.parse=function(a){this._Lexer.parse(this.beforeParsing(a));return this.afterParsing(this._Listener.getResult())};WYMeditor.XhtmlParser.prototype.beforeParsing=function(a){if(a.match(/class="MsoNormal"/)||a.match(/ns = "urn:schemas-microsoft-com/)){this._Listener.avoidStylingTagsAndAttributes()}return this._Listener.beforeParsing(a)};WYMeditor.XhtmlParser.prototype.afterParsing=function(a){if(this._Listener._avoiding_tags_implicitly){this._Listener.allowStylingTagsAndAttributes()}return this._Listener.afterParsing(a)};WYMeditor.XhtmlParser.prototype.Ignore=function(a,b){return true};WYMeditor.XhtmlParser.prototype.Text=function(a){this._Listener.addContent(a);return true};WYMeditor.XhtmlParser.prototype.Comment=function(b,a){return this._addNonTagBlock(b,a,"addComment")};WYMeditor.XhtmlParser.prototype.Script=function(b,a){return this._addNonTagBlock(b,a,"addScript")};WYMeditor.XhtmlParser.prototype.Css=function(b,a){return this._addNonTagBlock(b,a,"addCss")};WYMeditor.XhtmlParser.prototype._addNonTagBlock=function(a,c,b){switch(c){case WYMeditor.LEXER_ENTER:this._non_tag=a;break;case WYMeditor.LEXER_UNMATCHED:this._non_tag+=a;break;case WYMeditor.LEXER_EXIT:switch(b){case"addComment":this._Listener.addComment(this._non_tag+a);break;case"addScript":this._Listener.addScript(this._non_tag+a);break;case"addCss":this._Listener.addCss(this._non_tag+a);break}}return true};WYMeditor.XhtmlParser.prototype.OpeningTag=function(a,b){switch(b){case WYMeditor.LEXER_ENTER:this._tag=this.normalizeTag(a);this._tag_attributes={};break;case WYMeditor.LEXER_SPECIAL:this._callOpenTagListener(this.normalizeTag(a));break;case WYMeditor.LEXER_EXIT:this._callOpenTagListener(this._tag,this._tag_attributes)}return true};WYMeditor.XhtmlParser.prototype.ClosingTag=function(a,b){this._callCloseTagListener(this.normalizeTag(a));return true};WYMeditor.XhtmlParser.prototype._callOpenTagListener=function(a,b){var b=b||{};this.autoCloseUnclosedBeforeNewOpening(a);if(this._Listener.isBlockTag(a)){this._Listener._tag_stack.push(a);this._Listener.fixNestingBeforeOpeningBlockTag(a,b);this._Listener.openBlockTag(a,b);this._increaseOpenTagCounter(a)}else{if(this._Listener.isInlineTag(a)){this._Listener.inlineTag(a,b)}else{this._Listener.openUnknownTag(a,b);this._increaseOpenTagCounter(a)}}this._Listener.last_tag=a;this._Listener.last_tag_opened=true;this._Listener.last_tag_attributes=b};WYMeditor.XhtmlParser.prototype._callCloseTagListener=function(a){if(this._decreaseOpenTagCounter(a)){this.autoCloseUnclosedBeforeTagClosing(a);if(this._Listener.isBlockTag(a)){var 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this._Listener._open_tags){var b=this._Listener._open_tags[a];if(b>0&&this._Listener.shouldCloseTagAutomatically(a,c,d)){this._callCloseTagListener(a,true)}}}};WYMeditor.XhtmlParser.prototype.getTagReplacements=function(){return this._Listener.getTagReplacements()};WYMeditor.XhtmlParser.prototype.normalizeTag=function(a){a=a.replace(/^([\s<\/>]*)|([\s<\/>]*)$/gm,"").toLowerCase();var b=this._Listener.getTagReplacements();if(b[a]){return b[a]}return a};WYMeditor.XhtmlParser.prototype.TagAttributes=function(a,b){if(WYMeditor.LEXER_SPECIAL==b){this._current_attribute=a}return true};WYMeditor.XhtmlParser.prototype.DoubleQuotedAttribute=function(a,b){if(WYMeditor.LEXER_UNMATCHED==b){this._tag_attributes[this._current_attribute]=a}return true};WYMeditor.XhtmlParser.prototype.SingleQuotedAttribute=function(a,b){if(WYMeditor.LEXER_UNMATCHED==b){this._tag_attributes[this._current_attribute]=a}return true};WYMeditor.XhtmlParser.prototype.UnquotedAttribute=function(a,b){this._tag_attributes[this._current_attribute]=a.replace(/^=/,"");return true};WYMeditor.XhtmlSaxListener=function(){this.output="";this.helper=new WYMeditor.XmlHelper();this._open_tags={};this.validator=WYMeditor.XhtmlValidator;this._tag_stack=[];this.avoided_tags=[];this.entities={" ":" ","¡":"¡","¢":"¢","£":"£","¤":"¤","¥":"¥","¦":"¦","§":"§","¨":"¨","©":"©","ª":"ª","«":"«","¬":"¬","":"","®":"®","¯":"¯","°":"°","±":"±","²":"²","³":"³","´":"´","µ":"µ","¶":"¶","·":"·","¸":"¸","¹":"¹","º":"º","»":"»","¼":"¼","½":"½","¾":"¾","¿":"¿","À":"À","Á":"Á","Â":"Â","Ã":"Ã","Ä":"Ä","Å":"Å","Æ":"Æ","Ç":"Ç","È":"È","É":"É","Ê":"Ê","Ë":"Ë","Ì":"Ì","Í":"Í","Î":"Î","Ï":"Ï","Ð":"Ð","Ñ":"Ñ","Ò":"Ò","Ó":"Ó","Ô":"Ô","Õ":"Õ","Ö":"Ö","×":"×","Ø":"Ø","Ù":"Ù","Ú":"Ú","Û":"Û","Ü":"Ü","Ý":"Ý","Þ":"Þ","ß":"ß","à":"à","á":"á","â":"â","ã":"ã","ä":"ä","å":"å","æ":"æ","ç":"ç","è":"è","é":"é","ê":"ê","ë":"ë","ì":"ì","í":"í","î":"î","ï":"ï","ð":"ð","ñ":"ñ","ò":"ò","ó":"ó","ô":"ô","õ":"õ","ö":"ö","÷":"÷","ø":"ø","ù":"ù","ú":"ú","û":"û","ü":"ü","ý":"ý","þ":"þ","ÿ":"ÿ","&OElig;":"Œ","&oelig;":"œ","&Scaron;":"Š","&scaron;":"š","&Yuml;":"Ÿ","&fnof;":"ƒ","&circ;":"ˆ","&tilde;":"˜","Α":"Α","Β":"Β","Γ":"Γ","Δ":"Δ","Ε":"Ε","Ζ":"Ζ","Η":"Η","Θ":"Θ","Ι":"Ι","Κ":"Κ","Λ":"Λ","Μ":"Μ","Ν":"Ν","Ξ":"Ξ","Ο":"Ο","Π":"Π","Ρ":"Ρ","Σ":"Σ","Τ":"Τ","Υ":"Υ","Φ":"Φ","Χ":"Χ","Ψ":"Ψ","Ω":"Ω","α":"α","β":"β","γ":"γ","δ":"δ","ε":"ε","ζ":"ζ","η":"η","θ":"θ","ι":"ι","κ":"κ","λ":"λ","μ":"μ","ν":"ν","ξ":"ξ","ο":"ο","π":"π","ρ":"ρ","&sigmaf;":"ς","σ":"σ","τ":"τ","υ":"υ","φ":"φ","χ":"χ","ψ":"ψ","ω":"ω","&thetasym;":"ϑ","&upsih;":"ϒ","ϖ":"ϖ","&ensp;":" ","&emsp;":" "," ":" ","&zwnj;":"‌","&zwj;":"‍","&lrm;":"‎","&rlm;":"‏","–":"–","—":"—","‘":"‘","’":"’","&sbquo;":"‚","“":"“","”":"”","&bdquo;":"„","&dagger;":"†","&Dagger;":"‡","•":"•","…":"…","&permil;":"‰","′":"′","″":"″","&lsaquo;":"‹","&rsaquo;":"›","&oline;":"‾","&frasl;":"⁄","€":"€","&image;":"ℑ","&weierp;":"℘","&real;":"ℜ","™":"™","&alefsym;":"ℵ","←":"←","↑":"↑","→":"→","↓":"↓","↔":"↔","&crarr;":"↵","⇐":"⇐","&uArr;":"⇑","⇒":"⇒","&dArr;":"⇓","⇔":"⇔","∀":"∀","∂":"∂","∃":"∃","∅":"∅","∇":"∇","∈":"∈","∉":"∉","&ni;":"∋","∏":"∏","∑":"∑","−":"−","&lowast;":"∗","√":"√","&prop;":"∝","∞":"∞","&ang;":"∠","&and;":"∧","&or;":"∨","∩":"∩","∪":"∪","∫":"∫","&there4;":"∴","&sim;":"∼","&cong;":"≅","≈":"≈","≠":"≠","&equiv;":"≡","≤":"≤","≥":"≥","⊂":"⊂","⊃":"⊃","&nsub;":"⊄","&sube;":"⊆","&supe;":"⊇","&oplus;":"⊕","&otimes;":"⊗","&perp;":"⊥","⋅":"⋅","&lceil;":"⌈","&rceil;":"⌉","&lfloor;":"⌊","&rfloor;":"⌋","&lang;":"〈","&rang;":"〉","&loz;":"◊","&spades;":"♠","&clubs;":"♣","&hearts;":"♥","&diams;":"♦"};this.block_tags=["a","abbr","acronym","address","area","b","base","bdo","big","blockquote","body","button","caption","cite","code","col","colgroup","dd","del","div","dfn","dl","dt","em","fieldset","form","head","h1","h2","h3","h4","h5","h6","html","i","ins","kbd","label","legend","li","map","noscript","object","ol","optgroup","option","p","param","pre","q","samp","script","select","small","span","strong","style","sub","sup","table","tbody","td","textarea","tfoot","th","thead","title","tr","tt","ul","var","extends"];this.inline_tags=["br","hr","img","input"];return this};WYMeditor.XhtmlSaxListener.prototype.shouldCloseTagAutomatically=function(a,c,b){var b=b||false;if(a=="td"){if((b&&c=="tr")||(!b&&c=="td")){return true}}if(a=="option"){if((b&&c=="select")||(!b&&c=="option")){return true}}return false};WYMeditor.XhtmlSaxListener.prototype.beforeParsing=function(a){this.output="";return a};WYMeditor.XhtmlSaxListener.prototype.afterParsing=function(a){a=this.replaceNamedEntities(a);a=this.joinRepeatedEntities(a);a=this.removeEmptyTags(a);a=this.removeBrInPre(a);return a};WYMeditor.XhtmlSaxListener.prototype.replaceNamedEntities=function(b){for(var a in this.entities){b=b.replace(new RegExp(a,"g"),this.entities[a])}return b};WYMeditor.XhtmlSaxListener.prototype.joinRepeatedEntities=function(b){var a="em|strong|sub|sup|acronym|pre|del|address";return b.replace(new RegExp("</("+a+")><\\1>",""),"").replace(new RegExp("(s*<("+a+")>s*){2}(.*)(s*</\\2>s*){2}",""),"<$2>$3<$2>")};WYMeditor.XhtmlSaxListener.prototype.removeEmptyTags=function(a){return a.replace(new RegExp("<("+this.block_tags.join("|").replace(/\|td/,"").replace(/\|p/,"").replace(/\|th/,"")+")>(<br />| | |\\s)*</\\1>","g"),"")};WYMeditor.XhtmlSaxListener.prototype.removeBrInPre=function(c){var b=c.match(new RegExp("<pre[^>]*>(.*?)</pre>","gmi"));if(b){for(var a=0;a<b.length;a++){c=c.replace(b[a],b[a].replace(new RegExp("<br />","g"),String.fromCharCode(13,10)))}}return c};WYMeditor.XhtmlSaxListener.prototype.getResult=function(){return this.output};WYMeditor.XhtmlSaxListener.prototype.getTagReplacements=function(){return{b:"strong",i:"em"}};WYMeditor.XhtmlSaxListener.prototype.addContent=function(a){this.output+=a};WYMeditor.XhtmlSaxListener.prototype.addComment=function(a){if(this.remove_comments){this.output+=a}};WYMeditor.XhtmlSaxListener.prototype.addScript=function(a){if(!this.remove_scripts){this.output+=a}};WYMeditor.XhtmlSaxListener.prototype.addCss=function(a){if(!this.remove_embeded_styles){this.output+=a}};WYMeditor.XhtmlSaxListener.prototype.openBlockTag=function(a,b){this.output+=this.helper.tag(a,this.validator.getValidTagAttributes(a,b),true)};WYMeditor.XhtmlSaxListener.prototype.inlineTag=function(a,b){this.output+=this.helper.tag(a,this.validator.getValidTagAttributes(a,b))};WYMeditor.XhtmlSaxListener.prototype.openUnknownTag=function(a,b){};WYMeditor.XhtmlSaxListener.prototype.closeBlockTag=function(a){this.output=this.output.replace(/<br \/>$/,"")+this._getClosingTagContent("before",a)+"</"+a+">"+this._getClosingTagContent("after",a)};WYMeditor.XhtmlSaxListener.prototype.closeUnknownTag=function(a){};WYMeditor.XhtmlSaxListener.prototype.closeUnopenedTag=function(a){this.output+="</"+a+">"};WYMeditor.XhtmlSaxListener.prototype.avoidStylingTagsAndAttributes=function(){this.avoided_tags=["div","span"];this.validator.skiped_attributes=["style"];this.validator.skiped_attribute_values=["MsoNormal","main1"];this._avoiding_tags_implicitly=true};WYMeditor.XhtmlSaxListener.prototype.allowStylingTagsAndAttributes=function(){this.avoided_tags=[];this.validator.skiped_attributes=[];this.validator.skiped_attribute_values=[];this._avoiding_tags_implicitly=false};WYMeditor.XhtmlSaxListener.prototype.isBlockTag=function(a){return !WYMeditor.Helper.contains(this.avoided_tags,a)&&WYMeditor.Helper.contains(this.block_tags,a)};WYMeditor.XhtmlSaxListener.prototype.isInlineTag=function(a){return !WYMeditor.Helper.contains(this.avoided_tags,a)&&WYMeditor.Helper.contains(this.inline_tags,a)};WYMeditor.XhtmlSaxListener.prototype.insertContentAfterClosingTag=function(a,b){this._insertContentWhenClosingTag("after",a,b)};WYMeditor.XhtmlSaxListener.prototype.insertContentBeforeClosingTag=function(a,b){this._insertContentWhenClosingTag("before",a,b)};WYMeditor.XhtmlSaxListener.prototype.fixNestingBeforeOpeningBlockTag=function(a,b){if(a!="li"&&(a=="ul"||a=="ol")&&this.last_tag&&!this.last_tag_opened&&this.last_tag=="li"){this.output=this.output.replace(/<\/li>$/,"");this.insertContentAfterClosingTag(a,"</li>")}};WYMeditor.XhtmlSaxListener.prototype._insertContentWhenClosingTag=function(b,a,c){if(!this["_insert_"+b+"_closing"]){this["_insert_"+b+"_closing"]=[]}if(!this["_insert_"+b+"_closing"][a]){this["_insert_"+b+"_closing"][a]=[]}this["_insert_"+b+"_closing"][a].push(c)};WYMeditor.XhtmlSaxListener.prototype._getClosingTagContent=function(b,a){if(this["_insert_"+b+"_closing"]&&this["_insert_"+b+"_closing"][a]&&this["_insert_"+b+"_closing"][a].length>0){return this["_insert_"+b+"_closing"][a].pop()}return""};WYMeditor.WymCssLexer=function(b,a){var a=(typeof a=="undefined"?true:a);jQuery.extend(this,new WYMeditor.Lexer(b,(a?"Ignore":"WymCss")));this.mapHandler("WymCss","Ignore");if(a==true){this.addEntryPattern("/\\\x2a[<\\s]*WYMeditor[>\\s]*\\\x2a/","Ignore","WymCss");this.addExitPattern("/\\\x2a[</\\s]*WYMeditor[>\\s]*\\\x2a/","WymCss")}this.addSpecialPattern("[\\sa-z1-6]*\\\x2e[a-z-_0-9]+","WymCss","WymCssStyleDeclaration");this.addEntryPattern("/\\\x2a","WymCss","WymCssComment");this.addExitPattern("\\\x2a/","WymCssComment");this.addEntryPattern("\x7b","WymCss","WymCssStyle");this.addExitPattern("\x7d","WymCssStyle");this.addEntryPattern("/\\\x2a","WymCssStyle","WymCssFeedbackStyle");this.addExitPattern("\\\x2a/","WymCssFeedbackStyle");return this};WYMeditor.WymCssParser=function(){this._in_style=false;this._has_title=false;this.only_wym_blocks=true;this.css_settings={classesItems:[],editorStyles:[],dialogStyles:[]};return this};WYMeditor.WymCssParser.prototype.parse=function(a,b){var b=(typeof b=="undefined"?this.only_wym_blocks:b);this._Lexer=new WYMeditor.WymCssLexer(this,b);this._Lexer.parse(a)};WYMeditor.WymCssParser.prototype.Ignore=function(a,b){return true};WYMeditor.WymCssParser.prototype.WymCssComment=function(b,a){if(b.match(/end[a-z0-9\s]*wym[a-z0-9\s]*/mi)){return false}if(a==WYMeditor.LEXER_UNMATCHED){if(!this._in_style){this._has_title=true;this._current_item={title:WYMeditor.Helper.trim(b)}}else{if(this._current_item[this._current_element]){if(!this._current_item[this._current_element].expressions){this._current_item[this._current_element].expressions=[b]}else{this._current_item[this._current_element].expressions.push(b)}}}this._in_style=true}return true};WYMeditor.WymCssParser.prototype.WymCssStyle=function(b,a){if(a==WYMeditor.LEXER_UNMATCHED){b=WYMeditor.Helper.trim(b);if(b!=""){this._current_item[this._current_element].style=b}}else{if(a==WYMeditor.LEXER_EXIT){this._in_style=false;this._has_title=false;this.addStyleSetting(this._current_item)}}return true};WYMeditor.WymCssParser.prototype.WymCssFeedbackStyle=function(b,a){if(a==WYMeditor.LEXER_UNMATCHED){this._current_item[this._current_element].feedback_style=b.replace(/^([\s\/\*]*)|([\s\/\*]*)$/gm,"")}return true};WYMeditor.WymCssParser.prototype.WymCssStyleDeclaration=function(b){b=b.replace(/^([\s\.]*)|([\s\.*]*)$/gm,"");var a="";if(b.indexOf(".")>0){var c=b.split(".");this._current_element=c[1];var a=c[0]}else{this._current_element=b}if(!this._has_title){this._current_item={title:(!a?"":a.toUpperCase()+": ")+this._current_element};this._has_title=true}if(!this._current_item[this._current_element]){this._current_item[this._current_element]={name:this._current_element}}if(a){if(!this._current_item[this._current_element].tags){this._current_item[this._current_element].tags=[a]}else{this._current_item[this._current_element].tags.push(a)}}return true};WYMeditor.WymCssParser.prototype.addStyleSetting=function(a){for(var b in a){var c=a[b];if(typeof c=="object"&&b!="title"){this.css_settings.classesItems.push({name:WYMeditor.Helper.trim(c.name),title:a.title,expr:WYMeditor.Helper.trim((c.expressions||c.tags).join(", "))});if(c.feedback_style){this.css_settings.editorStyles.push({name:"."+WYMeditor.Helper.trim(c.name),css:c.feedback_style})}if(c.style){this.css_settings.dialogStyles.push({name:"."+WYMeditor.Helper.trim(c.name),css:c.style})}}}};jQuery.fn.isPhantomNode=function(){if(this[0].nodeType==3){return !(/[^\t\n\r ]/.test(this[0].data))}return false};WYMeditor.isPhantomNode=function(a){if(a.nodeType==3){return !(/[^\t\n\r ]/.test(a.data))}return false};WYMeditor.isPhantomString=function(a){return !(/[^\t\n\r ]/.test(a))};jQuery.fn.parentsOrSelf=function(b){var a=this;if(a[0].nodeType==3){a=a.parents().slice(0,1)}if(a.filter(b).size()==1){return a}else{return a.parents(b).slice(0,1)}};WYMeditor.Helper={replaceAll:function(d,a,c){var b=new RegExp(a,"g");return(d.replace(b,c))},insertAt:function(b,a,c){return(b.substr(0,c)+a+b.substring(c))},trim:function(a){return a.replace(/^(\s*)|(\s*)$/gm,"")},contains:function(a,c){for(var b=0;b<a.length;b++){if(a[b]===c){return true}}return false},indexOf:function(a,d){var b=-1;for(var c=0;c<a.length;c++){if(a[c]==d){b=c;break}}return(b)},findByName:function(a,b){for(var c=0;c<a.length;c++){var d=a[c];if(d.name==b){return(d)}}return(null)}};WYMeditor.WymClassExplorer=function(a){this._wym=a;this._class="className";this._newLine="\r\n"};WYMeditor.WymClassExplorer.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentWindow.document;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);jQuery(this._doc.body).html(this._wym._html);var wym=this;this._doc.body.onfocus=function(){wym._doc.designMode="on";wym._doc=iframe.contentWindow.document};this._doc.onbeforedeactivate=function(){wym.saveCaret()};this._doc.onkeyup=function(){wym.saveCaret();wym.keyup()};this._doc.onclick=function(){wym.saveCaret()};this._doc.body.onbeforepaste=function(){wym._iframe.contentWindow.event.returnValue=false};this._doc.body.onpaste=function(){wym._iframe.contentWindow.event.returnValue=false;wym.paste(window.clipboardData.getData("Text"))};if(this._initialized){if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()}this._initialized=true;this._doc.designMode="on";try{this._doc=iframe.contentWindow.document}catch(e){}};WYMeditor.WymClassExplorer.prototype._exec=function(c,d){switch(c){case WYMeditor.INDENT:case WYMeditor.OUTDENT:var a=this.findUp(this.container(),WYMeditor.LI);if(a){var b=a.parentNode.parentNode;if(a.parentNode.childNodes.length>1||b.tagName.toLowerCase()==WYMeditor.OL||b.tagName.toLowerCase()==WYMeditor.UL){this._doc.execCommand(c)}}break;default:if(d){this._doc.execCommand(c,false,d)}else{this._doc.execCommand(c)}break}this.listen()};WYMeditor.WymClassExplorer.prototype.selected=function(){var a=this._iframe.contentWindow.document.caretPos;if(a!=null){if(a.parentElement!=undefined){return(a.parentElement())}}};WYMeditor.WymClassExplorer.prototype.saveCaret=function(){this._doc.caretPos=this._doc.selection.createRange()};WYMeditor.WymClassExplorer.prototype.addCssRule=function(a,b){a.addRule(b.name,b.css)};WYMeditor.WymClassExplorer.prototype.insert=function(b){var a=this._doc.selection.createRange();if(jQuery(a.parentElement()).parents(this._options.iframeBodySelector).is("*")){try{a.pasteHTML(b)}catch(c){}}else{this.paste(b)}};WYMeditor.WymClassExplorer.prototype.wrap=function(d,b){var a=this._doc.selection.createRange();if(jQuery(a.parentElement()).parents(this._options.iframeBodySelector).is("*")){try{a.pasteHTML(d+a.text+b)}catch(c){}}};WYMeditor.WymClassExplorer.prototype.unwrap=function(){var a=this._doc.selection.createRange();if(jQuery(a.parentElement()).parents(this._options.iframeBodySelector).is("*")){try{var c=a.text;this._exec("Cut");a.pasteHTML(c)}catch(b){}}};WYMeditor.WymClassExplorer.prototype.keyup=function(){this._selected_image=null};WYMeditor.WymClassExplorer.prototype.setFocusToNode=function(b){var a=this._doc.selection.createRange();a.moveToElementText(b);a.collapse(false);a.move("character",-1);a.select();b.focus()};WYMeditor.WymClassMozilla=function(a){this._wym=a;this._class="class";this._newLine="\n"};WYMeditor.WymClassMozilla.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentDocument;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);this.html(this._wym._html);this.enableDesignMode();if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();jQuery(this._doc).bind("keydown",this.keydown);jQuery(this._doc).bind("keyup",this.keyup);jQuery(this._doc).bind("focus",this.enableDesignMode);if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()};WYMeditor.WymClassMozilla.prototype.html=function(a){if(typeof a==="string"){try{this._doc.designMode="off"}catch(b){}a=a.replace(/<em(\b[^>]*)>/gi,"<i$1>").replace(/<\/em>/gi,"</i>").replace(/<strong(\b[^>]*)>/gi,"<b$1>").replace(/<\/strong>/gi,"</b>");jQuery(this._doc.body).html(a);this.enableDesignMode()}else{return(jQuery(this._doc.body).html())}};WYMeditor.WymClassMozilla.prototype._exec=function(e,g){if(!this.selected()){return(false)}switch(e){case WYMeditor.INDENT:case WYMeditor.OUTDENT:var f=this.selected();var d=this._iframe.contentWindow.getSelection();var b=d.anchorNode;if(b.nodeName=="#text"){b=b.parentNode}f=this.findUp(f,WYMeditor.BLOCKS);b=this.findUp(b,WYMeditor.BLOCKS);if(f&&f==b&&f.tagName.toLowerCase()==WYMeditor.LI){var c=f.parentNode.parentNode;if(f.parentNode.childNodes.length>1||c.tagName.toLowerCase()==WYMeditor.OL||c.tagName.toLowerCase()==WYMeditor.UL){this._doc.execCommand(e,"",null)}}break;default:if(g){this._doc.execCommand(e,"",g)}else{this._doc.execCommand(e,"",null)}}var a=this.selected();if(a.tagName.toLowerCase()==WYMeditor.BODY){this._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}this.listen()};WYMeditor.WymClassMozilla.prototype.selected=function(){var b=this._iframe.contentWindow.getSelection();var a=b.focusNode;if(a){if(a.nodeName=="#text"){return(a.parentNode)}else{return(a)}}else{return(null)}};WYMeditor.WymClassMozilla.prototype.addCssRule=function(a,b){a.insertRule(b.name+" {"+b.css+"}",a.cssRules.length)};WYMeditor.WymClassMozilla.prototype.keydown=function(b){var f=WYMeditor.INSTANCES[this.title];var a=null;if(b.keyCode===WYMeditor.KEY.ENTER){a=f.selected();if(a){var g=$(a),e=g.parent(),d=g.parents(".embedded-item");if(d.size()){var c=$("<p/>");if(g.hasClass("title")){d.before(c)}else{if(g.hasClass("content")){d.after(c)}}f.setFocusToNode(c.get(0));return false}}}if(b.ctrlKey){if(b.keyCode==66){f._exec(WYMeditor.BOLD);return false}if(b.keyCode==73){f._exec(WYMeditor.ITALIC);return false}}else{if(b.keyCode==13){if(!b.shiftKey){a=f.selected();if(a&&a.tagName.toLowerCase()==WYMeditor.PRE){b.preventDefault();f.insert("<p></p>")}}}}};WYMeditor.WymClassMozilla.prototype.keyup=function(b){var d=WYMeditor.INSTANCES[this.title];d._selected_image=null;var a=null;if(b.keyCode==13&&!b.shiftKey){jQuery(d._doc.body).children(WYMeditor.BR).remove()}else{if(b.keyCode!=8&&b.keyCode!=17&&b.keyCode!=46&&b.keyCode!=224&&!b.metaKey&&!b.ctrlKey){a=d.selected();var c=a.tagName.toLowerCase();if(c=="strong"||c=="b"||c=="em"||c=="i"||c=="sub"||c=="sup"||c=="a"){c=a.parentNode.tagName.toLowerCase()}if(c==WYMeditor.BODY){d._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}}}};WYMeditor.WymClassMozilla.prototype.enableDesignMode=function(){if(this.designMode=="off"){try{this.designMode="on";this.execCommand("styleWithCSS","",false)}catch(a){}}};WYMeditor.WymClassMozilla.prototype.setFocusToNode=function(c){var a=document.createRange();a.selectNode(c);var b=this._iframe.contentWindow.getSelection();b.addRange(a);b.collapse(c,c.childNodes.length);this._iframe.contentWindow.focus()};WYMeditor.WymClassMozilla.prototype.openBlockTag=function(a,c){var c=this.validator.getValidTagAttributes(a,c);if(a=="span"&&c.style){var b=this.getTagForStyle(c.style);if(b){this._tag_stack.pop();var a=b;this._tag_stack.push(b);c.style=""}else{return}}this.output+=this.helper.tag(a,c,true)};WYMeditor.WymClassMozilla.prototype.getTagForStyle=function(a){if(/bold/.test(a)){return"strong"}if(/italic/.test(a)){return"em"}if(/sub/.test(a)){return"sub"}if(/sub/.test(a)){return"super"}return false};WYMeditor.WymClassOpera=function(a){this._wym=a;this._class="class";this._newLine="\r\n"};WYMeditor.WymClassOpera.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentWindow.document;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);this._doc.designMode="on";this.html(this._wym._html);if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();jQuery(this._doc).bind("keydown",this.keydown);jQuery(this._doc).bind("keyup",this.keyup);if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()};WYMeditor.WymClassOpera.prototype._exec=function(a,b){if(b){this._doc.execCommand(a,false,b)}else{this._doc.execCommand(a)}this.listen()};WYMeditor.WymClassOpera.prototype.selected=function(){var b=this._iframe.contentWindow.getSelection();var a=b.focusNode;if(a){if(a.nodeName=="#text"){return(a.parentNode)}else{return(a)}}else{return(null)}};WYMeditor.WymClassOpera.prototype.addCssRule=function(a,b){a.insertRule(b.name+" {"+b.css+"}",a.cssRules.length)};WYMeditor.WymClassOpera.prototype.keydown=function(a){var c=WYMeditor.INSTANCES[this.title];var b=c._iframe.contentWindow.getSelection();startNode=b.getRangeAt(0).startContainer;if(!jQuery(startNode).parentsOrSelf(WYMeditor.MAIN_CONTAINERS.join(","))[0]&&!jQuery(startNode).parentsOrSelf("li")&&a.keyCode!=WYMeditor.KEY.ENTER&&a.keyCode!=WYMeditor.KEY.LEFT&&a.keyCode!=WYMeditor.KEY.UP&&a.keyCode!=WYMeditor.KEY.RIGHT&&a.keyCode!=WYMeditor.KEY.DOWN&&a.keyCode!=WYMeditor.KEY.BACKSPACE&&a.keyCode!=WYMeditor.KEY.DELETE){c._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}};WYMeditor.WymClassOpera.prototype.keyup=function(a){var b=WYMeditor.INSTANCES[this.title];b._selected_image=null};WYMeditor.WymClassOpera.prototype.setFocusToNode=function(a){};WYMeditor.WymClassSafari=function(a){this._wym=a;this._class="class";this._newLine="\n"};WYMeditor.WymClassSafari.prototype.initIframe=function(iframe){this._iframe=iframe;this._doc=iframe.contentDocument;var styles=this._doc.styleSheets[0];var aCss=eval(this._options.editorStyles);this.addCssRules(this._doc,aCss);this._doc.title=this._wym._index;jQuery("html",this._doc).attr("dir",this._options.direction);this._doc.designMode="on";this.html(this._wym._html);if(jQuery.isFunction(this._options.preBind)){this._options.preBind(this)}this._wym.bindEvents();jQuery(this._doc).bind("keydown",this.keydown);jQuery(this._doc).bind("keyup",this.keyup);if(jQuery.isFunction(this._options.postInit)){this._options.postInit(this)}this.listen()};WYMeditor.WymClassSafari.prototype._exec=function(e,g){if(!this.selected()){return(false)}switch(e){case WYMeditor.INDENT:case WYMeditor.OUTDENT:var f=this.selected();var d=this._iframe.contentWindow.getSelection();var b=d.anchorNode;if(b.nodeName=="#text"){b=b.parentNode}f=this.findUp(f,WYMeditor.BLOCKS);b=this.findUp(b,WYMeditor.BLOCKS);if(f&&f==b&&f.tagName.toLowerCase()==WYMeditor.LI){var c=f.parentNode.parentNode;if(f.parentNode.childNodes.length>1||c.tagName.toLowerCase()==WYMeditor.OL||c.tagName.toLowerCase()==WYMeditor.UL){this._doc.execCommand(e,"",null)}}break;case WYMeditor.INSERT_ORDEREDLIST:case WYMeditor.INSERT_UNORDEREDLIST:this._doc.execCommand(e,"",null);var f=this.selected();var a=this.findUp(f,WYMeditor.MAIN_CONTAINERS);if(a){jQuery(a).replaceWith(jQuery(a).html())}break;default:if(g){this._doc.execCommand(e,"",g)}else{this._doc.execCommand(e,"",null)}}var a=this.selected();if(a&&a.tagName.toLowerCase()==WYMeditor.BODY){this._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}this.listen()};WYMeditor.WymClassSafari.prototype.selected=function(){var b=this._iframe.contentWindow.getSelection();var a=b.focusNode;if(a){if(a.nodeName=="#text"){return(a.parentNode)}else{return(a)}}else{return(null)}};WYMeditor.WymClassSafari.prototype.addCssRule=function(a,b){a.insertRule(b.name+" {"+b.css+"}",a.cssRules.length)};WYMeditor.WymClassSafari.prototype.keydown=function(b){var f=WYMeditor.INSTANCES[this.title];if(b.keyCode===WYMeditor.KEY.ENTER){var a=f.selected();if(a){var g=$(a),e=g.parent(),d=g.parents(".embedded-item");if(d.size()){var c=$("<p/>");if(g.hasClass("title")){d.before(c)}else{if(g.hasClass("content")){d.after(c)}}f.setFocusToNode(c.get(0));return false}}}if(b.ctrlKey){if(b.keyCode==66){f._exec(WYMeditor.BOLD);return false}if(b.keyCode==73){f._exec(WYMeditor.ITALIC);return false}}};WYMeditor.WymClassSafari.prototype.keyup=function(b){var d=WYMeditor.INSTANCES[this.title];d._selected_image=null;var a=null;if(b.keyCode==13&&!b.shiftKey){jQuery(d._doc.body).children(WYMeditor.BR).remove();a=d.selected();if(a&&a.tagName.toLowerCase()==WYMeditor.PRE){d._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}}if(b.keyCode==13&&b.shiftKey){d._exec("InsertLineBreak")}if(b.keyCode!=8&&b.keyCode!=17&&b.keyCode!=46&&b.keyCode!=224&&!b.metaKey&&!b.ctrlKey){a=d.selected();var c=a.tagName.toLowerCase();if(c=="strong"||c=="b"||c=="em"||c=="i"||c=="sub"||c=="sup"||c=="a"||c=="span"){c=a.parentNode.tagName.toLowerCase()}if(c==WYMeditor.BODY||c==WYMeditor.DIV){d._exec(WYMeditor.FORMAT_BLOCK,WYMeditor.P)}}};WYMeditor.WymClassSafari.prototype.setFocusToNode=function(c){var a=this._iframe.contentDocument.createRange();a.selectNode(c);var b=this._iframe.contentWindow.getSelection();b.addRange(a);b.collapse(c,c.childNodes.length);this._iframe.contentWindow.focus()};WYMeditor.WymClassSafari.prototype.openBlockTag=function(a,c){var c=this.validator.getValidTagAttributes(a,c);if(a=="span"&&c.style){var b=this.getTagForStyle(c.style);if(b){this._tag_stack.pop();var a=b;this._tag_stack.push(b);c.style="";if(typeof c["class"]=="string"){c["class"]=c["class"].replace(/apple-style-span/gi,"")}}else{return}}this.output+=this.helper.tag(a,c,true)};WYMeditor.WymClassSafari.prototype.getTagForStyle=function(a){if(/bold/.test(a)){return"strong"}if(/italic/.test(a)){return"em"}if(/sub/.test(a)){return"sub"}if(/super/.test(a)){return"sup"}return false}; \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Feb '14

26 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/61ea14f9a8b6/ Changeset: 61ea14f9a8b6 User: davebgx Date: 2014-02-26 16:19:48 Summary: Fix missing parenthesis. Affected #: 1 file diff -r 070086f7eb7f71ec4324eb9892a56a6028eb3628 -r 61ea14f9a8b62bc891c638329e91b4aee347db0d lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -350,7 +350,7 @@ tool_dependency_type='package' ) if not can_install_tool_dependency: log.debug( "Tool dependency %s version %s cannot be installed (it was probably previously installed), so returning it." % \ - ( str( tool_dependency.name, str( tool_dependency.version ) ) ) ) + ( str( tool_dependency.name ), str( tool_dependency.version ) ) ) return tool_dependency else: can_install_tool_dependency = True https://bitbucket.org/galaxy/galaxy-central/commits/a24050956e78/ Changeset: a24050956e78 User: davebgx Date: 2014-02-26 16:20:44 Summary: Use log instead of print for tool dependency installation processes' stdout and stderr, since twill redirects those streams to a StringIO object. Affected #: 1 file diff -r 61ea14f9a8b62bc891c638329e91b4aee347db0d -r a24050956e787690b7a37564a932fdfb194cdb6a lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -162,14 +162,16 @@ is printed and saved to that thread's queue. The calling thread can then retrieve the data using thread.stdout and thread.stderr. """ + stdout_logger = logging.getLogger( 'fabric_util.STDOUT' ) + stderr_logger = logging.getLogger( 'fabric_util.STDERR' ) for line in iter( stdout.readline, '' ): output = line.rstrip() - print output + stdout_logger.debug( output ) stdout_queue.put( output ) stdout_queue.put( None ) for line in iter( stderr.readline, '' ): output = line.rstrip() - print output + stderr_logger.debug( output ) stderr_queue.put( output ) stderr_queue.put( None ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Fix for uninstalling a ToolShed tool repository revision with a tool with multiple versions installed not properly replacing with the still existing tool version in the tool panel.
by commits-noreply＠bitbucket.org 25 Feb '14

25 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/070086f7eb7f/ Changeset: 070086f7eb7f User: dan Date: 2014-02-25 23:36:59 Summary: Fix for uninstalling a ToolShed tool repository revision with a tool with multiple versions installed not properly replacing with the still existing tool version in the tool panel. Affected #: 1 file diff -r db5c4a4c9699f304ee1e18854a7f402b790353e6 -r 070086f7eb7f71ec4324eb9892a56a6028eb3628 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -1017,7 +1017,8 @@ replacement_tool_version = None # Since we are going to remove the tool from the section, replace it with the newest loaded version of the tool. for available_tool_version in available_tool_versions: - if available_tool_version.id in tool_section.elems.keys(): + available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() + if available_tool_version.id in tool_section.elems.keys() or section_key == available_tool_section_id: replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) replacement_tool_version = available_tool_version break @@ -1057,7 +1058,8 @@ replacement_tool_version = None # Since we are going to remove the tool from the section, replace it with the newest loaded version of the tool. for available_tool_version in available_tool_versions: - if available_tool_version.id in trans.app.toolbox.tool_panel.keys(): + available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() + if available_tool_version.id in trans.app.toolbox.tool_panel.keys() or not available_tool_section_id: replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) replacement_tool_version = available_tool_version break Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 25 Feb '14

25 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cf7ff18cb357/ Changeset: cf7ff18cb357 Branch: stable User: jeremy goecks Date: 2014-02-25 22:43:18 Summary: Trackster bug fixes: (a) ignore arrow keys in location textbox; (b) set title for location textbox; and (c) test low and high correctly when changing location. Pack scripts. Affected #: 4 files diff -r c1bd56cbe034548518eb87463e1524b45fc6b52a -r cf7ff18cb3573c42c4bd77459112b40298df0ff6 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ad,af,ae){af=".group";n[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=n[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=n[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}n[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);n[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));n[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){R.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:ad.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=(ae.type==="color"&&!ae.default_value?l.get_random_color():ae.default_value)});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input/>").attr({id:am,name:am}).val(ax).addClass("color-input").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.prefs.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.prefs.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(o);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ad,af,ae){af=".group";n[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=n[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=n[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}n[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);n[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));n[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){R.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:ad.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=(ae.type==="color"&&!ae.default_value?l.get_random_color():ae.default_value)});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input/>").attr({id:am,name:am}).val(ax).addClass("color-input").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.prefs.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.prefs.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(o);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file diff -r c1bd56cbe034548518eb87463e1524b45fc6b52a -r cf7ff18cb3573c42c4bd77459112b40298df0ff6 static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.prefs.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.prefs.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].prefs.name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.prefs.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.prefs.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].prefs.name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keyup(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file diff -r c1bd56cbe034548518eb87463e1524b45fc6b52a -r cf7ff18cb3573c42c4bd77459112b40298df0ff6 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -972,9 +972,12 @@ view.location_span.show(); view.chrom_select.show(); } + + // Suppress key presses so that they do impact viz. + e.stopPropagation(); }; this.nav_input = $("<input/>").addClass("nav-input").hide().bind("keyup focusout", submit_nav).appendTo(this.nav_controls); - this.location_span = $("<span/>").addClass("location").attr('original-title', 'Click to change location').tooltip( { placement: 'bottom' } ).appendTo(this.nav_controls); + this.location_span = $("<span/>").addClass("location").attr('title', 'Click to change location').tooltip( { placement: 'bottom' } ).appendTo(this.nav_controls); this.location_span.click(function() { view.location_span.hide(); view.chrom_select.hide(); @@ -1299,7 +1302,7 @@ view.reference_track.init(); } } - if (low && high) { + if (low !== undefined && high !== undefined) { view.low = Math.max(low, 0); view.high = Math.min(high, view.max_high); } diff -r c1bd56cbe034548518eb87463e1524b45fc6b52a -r cf7ff18cb3573c42c4bd77459112b40298df0ff6 static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -292,7 +292,7 @@ */ init_keyboard_nav: function(view) { // Keyboard navigation. Scroll ~7% of height when scrolling up/down. - $(document).keydown(function(e) { + $(document).keyup(function(e) { // Do not navigate if arrow keys used in input element. if ($(e.srcElement).is(':input')) { return; https://bitbucket.org/galaxy/galaxy-central/commits/db5c4a4c9699/ Changeset: db5c4a4c9699 User: jeremy goecks Date: 2014-02-25 22:43:51 Summary: Automated merge of stable to default. Affected #: 4 files diff -r 43dfc8ccc72ea49314c25dce9248d66d279dfe01 -r db5c4a4c9699f304ee1e18854a7f402b790353e6 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ad,af,ae){af=".group";n[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=n[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=n[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}n[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);n[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));n[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){R.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:ad.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=(ae.type==="color"&&!ae.default_value?l.get_random_color():ae.default_value)});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input/>").attr({id:am,name:am}).val(ax).addClass("color-input").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.prefs.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.prefs.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(o);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ad,af,ae){af=".group";n[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=n[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=n[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}n[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);n[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));n[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){R.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:ad.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=(ae.type==="color"&&!ae.default_value?l.get_random_color():ae.default_value)});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input/>").attr({id:am,name:am}).val(ax).addClass("color-input").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.prefs.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.prefs.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(o);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file diff -r 43dfc8ccc72ea49314c25dce9248d66d279dfe01 -r db5c4a4c9699f304ee1e18854a7f402b790353e6 static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.prefs.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.prefs.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].prefs.name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.prefs.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.prefs.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].prefs.name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keyup(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file diff -r 43dfc8ccc72ea49314c25dce9248d66d279dfe01 -r db5c4a4c9699f304ee1e18854a7f402b790353e6 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -972,9 +972,12 @@ view.location_span.show(); view.chrom_select.show(); } + + // Suppress key presses so that they do impact viz. + e.stopPropagation(); }; this.nav_input = $("<input/>").addClass("nav-input").hide().bind("keyup focusout", submit_nav).appendTo(this.nav_controls); - this.location_span = $("<span/>").addClass("location").attr('original-title', 'Click to change location').tooltip( { placement: 'bottom' } ).appendTo(this.nav_controls); + this.location_span = $("<span/>").addClass("location").attr('title', 'Click to change location').tooltip( { placement: 'bottom' } ).appendTo(this.nav_controls); this.location_span.click(function() { view.location_span.hide(); view.chrom_select.hide(); @@ -1299,7 +1302,7 @@ view.reference_track.init(); } } - if (low && high) { + if (low !== undefined && high !== undefined) { view.low = Math.max(low, 0); view.high = Math.min(high, view.max_high); } diff -r 43dfc8ccc72ea49314c25dce9248d66d279dfe01 -r db5c4a4c9699f304ee1e18854a7f402b790353e6 static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -292,7 +292,7 @@ */ init_keyboard_nav: function(view) { // Keyboard navigation. Scroll ~7% of height when scrolling up/down. - $(document).keydown(function(e) { + $(document).keyup(function(e) { // Do not navigate if arrow keys used in input element. if ($(e.srcElement).is(':input')) { return; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: More fixes for fabric.local elimination when installing tool dependencies.
by commits-noreply＠bitbucket.org 25 Feb '14

25 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/43dfc8ccc72e/ Changeset: 43dfc8ccc72e User: greg Date: 2014-02-25 21:04:08 Summary: More fixes for fabric.local elimination when installing tool dependencies. Affected #: 1 file diff -r 1edc3c13a7a272102a2a9c178440466ba7ab5525 -r 43dfc8ccc72ea49314c25dce9248d66d279dfe01 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -15,6 +15,7 @@ from contextlib import contextmanager from galaxy.util import DATABASE_MAX_STRING_SIZE +from galaxy.util import DATABASE_MAX_STRING_SIZE_PRETTY from galaxy.util import shrink_string_by_size from galaxy.util import unicodify from galaxy.util.template import fill_template @@ -227,12 +228,10 @@ stdout = output.stdout stderr = output.stderr if len( stdout ) > DATABASE_MAX_STRING_SIZE: - print "Process id %s stdout > %s, so only a portion will be saved in the database." % \ - ( str( pid ), str( DATABASE_MAX_STRING_SIZE_PRETTY ) ) + print "Length of stdout > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) stdout = shrink_string_by_size( stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) if len( stderr ) > DATABASE_MAX_STRING_SIZE: - print "Process id %s stderr > %s, so only a portion will be saved in the database." % \ - ( str( pid ), str( DATABASE_MAX_STRING_SIZE_PRETTY ) ) + print "Length of stderr > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) stderr = shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) if output.return_code not in [ 0 ]: tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: A bit of cleanup and some important fixes in re-engineered code for eliminating fabric.local when installing tool dependencies along with repositories from the tool shed.
by commits-noreply＠bitbucket.org 25 Feb '14

25 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1edc3c13a7a2/ Changeset: 1edc3c13a7a2 User: greg Date: 2014-02-25 20:37:44 Summary: A bit of cleanup and some important fixes in re-engineered code for eliminating fabric.local when installing tool dependencies along with repositories from the tool shed. Affected #: 1 file diff -r 451b411b4b19ca34ed154352b07b3f49983d1197 -r 1edc3c13a7a272102a2a9c178440466ba7ab5525 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -14,6 +14,8 @@ import shlex from contextlib import contextmanager +from galaxy.util import DATABASE_MAX_STRING_SIZE +from galaxy.util import shrink_string_by_size from galaxy.util import unicodify from galaxy.util.template import fill_template from galaxy import eggs @@ -34,7 +36,7 @@ log = logging.getLogger( __name__ ) INSTALLATION_LOG = 'INSTALLATION.log' -NO_CMD_OUTPUT_TIMEOUT = 600 +NO_CMD_OUTPUT_TIMEOUT = 600.0 VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz' @@ -159,12 +161,12 @@ is printed and saved to that thread's queue. The calling thread can then retrieve the data using thread.stdout and thread.stderr. """ - for line in iter( stdout.readline, b'' ): + for line in iter( stdout.readline, '' ): output = line.rstrip() print output stdout_queue.put( output ) stdout_queue.put( None ) - for line in iter( stderr.readline, b'' ): + for line in iter( stderr.readline, '' ): output = line.rstrip() print output stderr_queue.put( output ) @@ -222,14 +224,26 @@ context = app.install_model.context output = run_local_command( cmd ) log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) - if output.return_code not in [ None, env.ok_ret_codes ]: + stdout = output.stdout + stderr = output.stderr + if len( stdout ) > DATABASE_MAX_STRING_SIZE: + print "Process id %s stdout > %s, so only a portion will be saved in the database." % \ + ( str( pid ), str( DATABASE_MAX_STRING_SIZE_PRETTY ) ) + stdout = shrink_string_by_size( stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) + if len( stderr ) > DATABASE_MAX_STRING_SIZE: + print "Process id %s stderr > %s, so only a portion will be saved in the database." % \ + ( str( pid ), str( DATABASE_MAX_STRING_SIZE_PRETTY ) ) + stderr = shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) + if output.return_code not in [ 0 ]: tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR - if output.stderr: - tool_dependency.error_message = unicodify( str( output.stderr )[ :32768 ] ) - elif output.stdout: - tool_dependency.error_message = unicodify( str( output.stdout )[ :32768 ] ) + if stderr: + tool_dependency.error_message = unicodify( stderr ) + elif stdout: + tool_dependency.error_message = unicodify( stdout ) else: - tool_dependency.error_message = "Unknown error occurred executing shell command %s, return_code: %s" % ( str( cmd ), str( output.return_code ) ) + # We have a problem if there was no stdout and no stderr. + tool_dependency.error_message = "Unknown error occurred executing shell command %s, return_code: %s" % \ + ( str( cmd ), str( output.return_code ) ) context.add( tool_dependency ) context.flush() if return_output: @@ -833,7 +847,6 @@ stdout_queue, process_handle.stderr, stderr_queue ) ) - stdio_thread.daemon = True stdio_thread.start() # Check the queues for output until there is nothing more to get. start_timer = time.time() @@ -884,9 +897,11 @@ current_wait_time = time.time() - start_timer if stdout_queue.empty() and stderr_queue.empty() and current_wait_time < NO_CMD_OUTPUT_TIMEOUT: break - # Let's be tidy and join the threads we've started. - stdout_reader.join() - stderr_reader.join() + # Wait until each of the threads we've started terminate. The following calls will block each thread + # until it terminates either normally, through an unhandled exception, or until the timeout occurs. + stdio_thread.join( NO_CMD_OUTPUT_TIMEOUT ) + stdout_reader.join( NO_CMD_OUTPUT_TIMEOUT ) + stderr_reader.join( NO_CMD_OUTPUT_TIMEOUT ) # Close subprocess' file descriptors. process_handle.stdout.close() process_handle.stderr.close() @@ -895,6 +910,7 @@ # Handle error condition (deal with stdout being None, too) output = _AttributeString( stdout.strip() if stdout else "" ) errors = _AttributeString( stderr.strip() if stderr else "" ) + process_handle.poll() output.return_code = process_handle.returncode output.stderr = errors return output Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Make sure shlex receives a string when installing tool dependencies along with repositories intstalled from the tool shed.
by commits-noreply＠bitbucket.org 25 Feb '14

25 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/451b411b4b19/ Changeset: 451b411b4b19 User: greg Date: 2014-02-25 18:09:36 Summary: Make sure shlex receives a string when installing tool dependencies along with repositories intstalled from the tool shed. Affected #: 1 file diff -r d15e1876ba0affc36e73945e587a35e5ff243063 -r 451b411b4b19ca34ed154352b07b3f49983d1197 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -810,7 +810,7 @@ be captured and logged in nearly real time. This is similar to fabric.local, but allows us to retain control over the process. """ - wrapped_command = shlex.split( "/bin/sh -c '%s'" % command ) + wrapped_command = shlex.split( "/bin/sh -c '%s'" % str( command ) ) # Launch the command as subprocess. A bufsize of 1 means line buffered. process_handle = subprocess.Popen( wrapped_command, stdout=subprocess.PIPE, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Rework the code allowing us to eliminate fabric.local when installing tool dependency packages.
by commits-noreply＠bitbucket.org 25 Feb '14

25 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d15e1876ba0a/ Changeset: d15e1876ba0a User: greg Date: 2014-02-25 17:35:12 Summary: Rework the code allowing us to eliminate fabric.local when installing tool dependency packages. Affected #: 1 file diff -r cab3db6e1d592fe04fbce998eeee0061e6cf3e5b -r d15e1876ba0affc36e73945e587a35e5ff243063 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -3,15 +3,16 @@ import logging import os +import Queue import shutil +import subprocess import sys import tempfile import td_common_util +import threading import time import shlex -from subprocess import PIPE, Popen -from threading import Thread from contextlib import contextmanager from galaxy.util import unicodify from galaxy.util.template import fill_template @@ -37,6 +38,30 @@ VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz' +class AsynchronousReader( threading.Thread ): + """ + A helper class to implement asynchronous reading of a stream in a separate thread. Read lines are pushed + onto a queue to be consumed in another thread. + """ + + def __init__( self, fd, queue ): + threading.Thread.__init__( self ) + self._fd = fd + self._queue = queue + self.lines = [] + + def run( self ): + """Read lines and put them on the queue.""" + for line in iter( self._fd.readline, '' ): + stripped_line = line.rstrip() + self.lines.append( stripped_line ) + self._queue.put( stripped_line ) + + def installation_complete( self ): + """Make sure there is more installation and compilation logging content expected.""" + return not self.is_alive() and self._queue.empty() + + class EnvFileBuilder( object ): def __init__( self, install_dir ): @@ -129,35 +154,28 @@ raise NotImplementedError( "Install Fabric version 1.0 or later." ) def enqueue_output( stdout, stdout_queue, stderr, stderr_queue ): - ''' - This method places streamed stdout and stderr into a threaded IPC queue target, defined as follows: - - stdio_thread = Thread( target=enqueue_output, args=( process_handle.stdout, stdout_queue, process_handle.stderr, stderr_queue ) ) - - When input is received, it logs that input to the defined logger, and saves it to that thread's queue. The calling thread - can then retrieve that data using thread.stdout and thread.stderr. - ''' - stdout_logger = logging.getLogger( 'fabric_util.STDOUT' ) - stderr_logger = logging.getLogger( 'fabric_util.STDERR' ) + """ + This method places streamed stdout and stderr into a threaded IPC queue target. Received data + is printed and saved to that thread's queue. The calling thread can then retrieve the data using + thread.stdout and thread.stderr. + """ for line in iter( stdout.readline, b'' ): output = line.rstrip() - stdout_logger.debug( output ) + print output stdout_queue.put( output ) - stdout.close() stdout_queue.put( None ) for line in iter( stderr.readline, b'' ): output = line.rstrip() - stderr_logger.debug( output ) + print output stderr_queue.put( output ) - stderr.close() stderr_queue.put( None ) def file_append( text, file_path, skip_if_contained=True, make_executable=True ): - ''' + """ Append a line to a file unless skip_if_contained is True and the line already exists in the file. This method creates the file if it doesn't exist. If make_executable is True, the permissions on the file are set to executable by the owner. This method is similar to a local version of fabric.contrib.files.append. - ''' + """ if not os.path.exists( file_path ): local( 'touch %s' % file_path ) if make_executable: @@ -202,10 +220,9 @@ def handle_command( app, tool_dependency, install_dir, cmd, return_output=False ): context = app.install_model.context - with settings( warn_only=True ): - output = local( cmd, capture=True ) + output = run_local_command( cmd ) log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) - if output.return_code: + if output.return_code not in [ None, env.ok_ret_codes ]: tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR if output.stderr: tool_dependency.error_message = unicodify( str( output.stderr )[ :32768 ] ) @@ -787,31 +804,100 @@ if os.path.exists( work_dir ): local( 'rm -rf %s' % work_dir ) -def run_local_command( command, capture_output=True, stream_output=True ): - # TODO: Overhaul this method. - import Queue +def run_local_command( command ): + """ + Wrap subprocess.Popen in such a way that the stderr and stdout from running a shell command will + be captured and logged in nearly real time. This is similar to fabric.local, but allows us to + retain control over the process. + """ wrapped_command = shlex.split( "/bin/sh -c '%s'" % command ) - stdout_queue = Queue() - stderr_queue = Queue() - process_handle = Popen( wrapped_command, stdout=PIPE, stderr=PIPE, bufsize=1, close_fds=False, cwd=state.env[ 'lcwd' ] ) - stdio_thread = Thread( target=enqueue_output, args=( process_handle.stdout, stdout_queue, process_handle.stderr, stderr_queue ) ) + # Launch the command as subprocess. A bufsize of 1 means line buffered. + process_handle = subprocess.Popen( wrapped_command, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + bufsize=1, + close_fds=False, + cwd=state.env[ 'lcwd' ] ) + pid = process_handle.pid + # Launch the asynchronous readers of the process' stdout and stderr. + stdout_queue = Queue.Queue() + stdout_reader = AsynchronousReader( process_handle.stdout, stdout_queue ) + stdout_reader.start() + stderr_queue = Queue.Queue() + stderr_reader = AsynchronousReader( process_handle.stderr, stderr_queue ) + stderr_reader.start() + # Place streamed stdout and stderr into a threaded IPC queue target so it can + # be printed and stored for later retrieval when generating the INSTALLATION.log. + stdio_thread = threading.Thread( target=enqueue_output, + args=( process_handle.stdout, + stdout_queue, + process_handle.stderr, + stderr_queue ) ) stdio_thread.daemon = True stdio_thread.start() - stdout, stderr = wait_for_process( process_handle, stream_output, stdout_queue, stderr_queue ) + # Check the queues for output until there is nothing more to get. + start_timer = time.time() + while not stdout_reader.installation_complete() or not stderr_reader.installation_complete(): + # Show what we received from standard output. + while not stdout_queue.empty(): + try: + line = stdout_queue.get() + except Queue.Empty: + err_msg = "\nShutting down process id %s because it generated no stdout for the defined timout period of %d seconds.\n" % \ + ( pid, NO_CMD_OUTPUT_TIMEOUT ) + print err_msg + stdout_reader.lines.append( err_msg ) + # Close subprocess' file descriptors. + process_handle.stdout.close() + process_handle.stderr.close() + process_handle.kill() + line = None + break + if line: + print line + start_timer = time.time() + else: + break + # Show what we received from standard error. + while not stderr_queue.empty(): + try: + line = stderr_queue.get() + except Queue.Empty: + err_msg = "\nShutting down process id %s because it generated no stderr for the defined timout period of %d seconds.\n" % \ + ( pid, NO_CMD_OUTPUT_TIMEOUT ) + print err_msg + stderr_reader.lines.append( err_msg ) + # Close subprocess' file descriptor. + process_handle.stdout.close() + process_handle.stderr.close() + process_handle.kill() + line = None + break + if line: + print line + start_timer = time.time() + else: + stderr_queue.task_done() + break + # Sleep a bit before asking the readers again. + time.sleep( .1 ) + current_wait_time = time.time() - start_timer + if stdout_queue.empty() and stderr_queue.empty() and current_wait_time < NO_CMD_OUTPUT_TIMEOUT: + break + # Let's be tidy and join the threads we've started. + stdout_reader.join() + stderr_reader.join() + # Close subprocess' file descriptors. + process_handle.stdout.close() + process_handle.stderr.close() + stdout = '\n'.join( stdout_reader.lines ) + stderr = '\n'.join( stderr_reader.lines ) # Handle error condition (deal with stdout being None, too) output = _AttributeString( stdout.strip() if stdout else "" ) errors = _AttributeString( stderr.strip() if stderr else "" ) - output.failed = False output.return_code = process_handle.returncode output.stderr = errors - if process_handle.returncode not in env.ok_ret_codes: - output.failed = True - message = "Encountered an error (return code %s) while executing '%s'" % ( process_handle.returncode, command ) - log.error( message ) - output.succeeded = not output.failed - # If we were capturing, this will be a string; otherwise it will be None. - if capture_output: - return output + return output def set_galaxy_environment( galaxy_user, tool_dependency_dir, host='localhost', shell='/bin/bash -l -c' ): """General Galaxy environment configuration. This method is not currently used.""" @@ -822,50 +908,3 @@ env.use_sudo = False env.safe_cmd = local return env - -def wait_for_process( process_handle, stream_output, stdout_queue, stderr_queue ): - # TODO: Overhaul this method. - import Queue - pid = process_handle.pid - standard_out = [] - standard_err = [] - process_handle.wait() - # Generate stdout. - while True: - try: - line = stdout_queue.get( timeout=NO_CMD_OUTPUT_TIMEOUT ) - except Queue.Empty: - err_msg = "\nShutting down process id %s because it generated no stdout for the defined timout period of %d seconds.\n" % \ - ( pid, NO_CMD_OUTPUT_TIMEOUT ) - print err_msg - standard_out.append( err_msg ) - stdout_queue.task_done() - process_handle.kill() - break - else: - if line: - standard_out.append( line ) - else: - stdout_queue.task_done() - break - # Generate stderr. - while True: - try: - line = stderr_queue.get( timeout=NO_CMD_OUTPUT_TIMEOUT ) - except Queue.Empty: - err_msg = "\nShutting down process id %s because it generated no stderr for the defined timout period of %d seconds.\n" % \ - ( pid, NO_CMD_OUTPUT_TIMEOUT ) - print err_msg - standard_err.append( err_msg ) - stderr_queue.task_done() - process_handle.kill() - break - else: - if line: - standard_err.append( line ) - else: - stderr_queue.task_done() - break - stdout = '\n'.join( standard_out ) - stderr = '\n'.join( standard_err ) - return stdout, stderr Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 25 Feb '14

25 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c1bd56cbe034/ Changeset: c1bd56cbe034 Branch: stable User: carlfeberhard Date: 2014-02-25 16:33:34 Summary: Fix to file_ext rendering in download button url (https://trello.com/c/Y0K7C7ay, https://trello.com/c/CsFihudx) Affected #: 2 files diff -r c809477959724304e2342ed5fbdba9d4b412b347 -r c1bd56cbe034548518eb87463e1524b45fc6b52a static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -466,6 +466,8 @@ // fetch first if no details in the model if( this.model.inReadyState() && !this.model.hasDetails() ){ this.model.fetch({ silent: true }).always( function( model ){ + // re-render urls based on new hda data + hdaView.urls = hdaView.model.urls(); _renderBodyAndExpand(); }); } else { diff -r c809477959724304e2342ed5fbdba9d4b412b347 -r c1bd56cbe034548518eb87463e1524b45fc6b52a static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=this._buildNewRender();if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_buildNewRender:function(){var c=$(a.templates.skeleton(this.model.toJSON()));c.find(".dataset-primary-actions").append(this._render_titleButtons());c.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(c);return c},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect",},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=this._buildNewRender();if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_buildNewRender:function(){var c=$(a.templates.skeleton(this.model.toJSON()));c.find(".dataset-primary-actions").append(this._render_titleButtons());c.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(c);return c},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect",},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){c.urls=c.model.urls();d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/cab3db6e1d59/ Changeset: cab3db6e1d59 User: carlfeberhard Date: 2014-02-25 16:36:31 Summary: merge stable Affected #: 2 files diff -r bc1173309bd5a503af402d1cc69dd992127ace0b -r cab3db6e1d592fe04fbce998eeee0061e6cf3e5b static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -471,6 +471,8 @@ // fetch first if no details in the model if( this.model.inReadyState() && !this.model.hasDetails() ){ this.model.fetch({ silent: true }).always( function( model ){ + // re-render urls based on new hda data + hdaView.urls = hdaView.model.urls(); _renderBodyAndExpand(); }); } else { diff -r bc1173309bd5a503af402d1cc69dd992127ace0b -r cab3db6e1d592fe04fbce998eeee0061e6cf3e5b static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=this._buildNewRender();if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_buildNewRender:function(){var c=$(a.templates.skeleton(this.model.toJSON()));c.find(".dataset-primary-actions").append(this._render_titleButtons());c.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(c);return c},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=this._buildNewRender();if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_buildNewRender:function(){var c=$(a.templates.skeleton(this.model.toJSON()));c.find(".dataset-primary-actions").append(this._render_titleButtons());c.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(c);return c},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){c.urls=c.model.urls();d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Variable name fix for the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 25 Feb '14

25 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bc1173309bd5/ Changeset: bc1173309bd5 User: greg Date: 2014-02-25 14:52:11 Summary: Variable name fix for the tool shed's install and test framework. Affected #: 1 file diff -r 1c91163d6c768452d106bdc8d843406fd7696ac7 -r bc1173309bd5a503af402d1cc69dd992127ace0b test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -172,6 +172,6 @@ # This timeout currently defaults to 10 minutes. if timeout_counter > repository_installation_timeout: raise AssertionError( 'Repository installation timed out after %d seconds, repository state is %s.' % \ - ( timeout_counter, repository.status ) ) + ( timeout_counter, galaxy_repository.status ) ) break time.sleep( 1 ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Use fabric for installation of tool dependencies.
by commits-noreply＠bitbucket.org 24 Feb '14

24 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1c91163d6c76/ Changeset: 1c91163d6c76 User: davebgx Date: 2014-02-24 19:50:26 Summary: Use fabric for installation of tool dependencies. Affected #: 1 file diff -r 2e8917d8f6d97a984c8b984363a56e15ec4a81fa -r 1c91163d6c768452d106bdc8d843406fd7696ac7 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -30,11 +30,6 @@ from fabric.api import prefix from fabric.operations import _AttributeString -try: - from Queue import Queue, Empty -except ImportError: - from queue import Queue, Empty - log = logging.getLogger( __name__ ) INSTALLATION_LOG = 'INSTALLATION.log' @@ -205,13 +200,10 @@ for shell_file_path in shell_file_paths: env_file_builder.append_line( action="source", value=shell_file_path ) -def handle_command( app, tool_dependency, install_dir, cmd, return_output=False, use_fabric=False ): +def handle_command( app, tool_dependency, install_dir, cmd, return_output=False ): context = app.install_model.context - if use_fabric: - with settings( warn_only=True ): - output = local( cmd, capture=True ) - else: - output = run_local_command( cmd, capture_output=True, stream_output=True ) + with settings( warn_only=True ): + output = local( cmd, capture=True ) log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) if output.return_code: tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR @@ -303,7 +295,7 @@ set_prior_environment_commands.append( 'echo "%s: $%s"' % ( inherited_env_var_name, inherited_env_var_name ) ) command = ' ; '.join( set_prior_environment_commands ) # Run the command and capture the output. - command_return = handle_command( app, tool_dependency, install_dir, command, return_output=True, use_fabric=True ) + command_return = handle_command( app, tool_dependency, install_dir, command, return_output=True ) # And extract anything labeled with the name of the environment variable we're populating here. if '%s: ' % inherited_env_var_name in command_return: environment_variable_value = command_return.split( '\n' ) @@ -685,7 +677,7 @@ elif action_type == 'shell_command': with settings( warn_only=True ): cmd = install_environment.build_command( action_dict[ 'command' ] ) - return_code = handle_command( app, tool_dependency, install_dir, cmd, use_fabric=False ) + return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return tool_dependency elif action_type == 'template_command': @@ -796,6 +788,8 @@ local( 'rm -rf %s' % work_dir ) def run_local_command( command, capture_output=True, stream_output=True ): + # TODO: Overhaul this method. + import Queue wrapped_command = shlex.split( "/bin/sh -c '%s'" % command ) stdout_queue = Queue() stderr_queue = Queue() @@ -830,6 +824,8 @@ return env def wait_for_process( process_handle, stream_output, stdout_queue, stderr_queue ): + # TODO: Overhaul this method. + import Queue pid = process_handle.pid standard_out = [] standard_err = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Keep track of the time taken to install and test each repository in the Tool Shed's install and test framework.
by commits-noreply＠bitbucket.org 24 Feb '14

24 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2e8917d8f6d9/ Changeset: 2e8917d8f6d9 User: greg Date: 2014-02-24 17:58:58 Summary: Keep track of the time taken to install and test each repository in the Tool Shed's install and test framework. Affected #: 2 files diff -r ef5f750810f791d39d5fe37f256b2526fa9916ae -r 2e8917d8f6d97a984c8b984363a56e15ec4a81fa test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -212,6 +212,7 @@ repository = install_and_test_base_util.get_repository( name, owner, changeset_revision ) if repository is None: # The repository was not previously installed, so install it now. + start_time = time.time() tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_dict ) repository, error_message = install_and_test_base_util.install_repository( app, repository_dict ) install_and_test_statistics_dict[ 'total_repositories_processed' ] += 1 @@ -340,6 +341,8 @@ repository_dict, params, can_update_tool_shed ) + print '\nAttempting to install revision %s of repository %s owned by %s took %s seconds.\n' % \ + ( changeset_revision, name, owner, str( time.time() - start_time ) ) else: remove_tests( app, repository ) print 'Skipped attempt to install revision %s of repository %s owned by %s because ' % \ diff -r ef5f750810f791d39d5fe37f256b2526fa9916ae -r 2e8917d8f6d97a984c8b984363a56e15ec4a81fa test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -143,6 +143,7 @@ repository = install_and_test_base_util.get_repository( name, owner, changeset_revision ) if repository is None: # The repository was not previously installed, so install it now. + start_time = time.time() tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_dict ) repository, error_message = install_and_test_base_util.install_repository( app, repository_dict ) install_and_test_statistics_dict[ 'total_repositories_processed' ] += 1 @@ -192,6 +193,8 @@ encoded_repository_metadata_id, install_and_test_statistics_dict, can_update_tool_shed ) + print '\nAttempting to install revision %s of repository %s owned by %s took %s seconds.\n' % \ + ( changeset_revision, name, owner, str( time.time() - start_time ) ) else: print 'Skipped attempt to install revision %s of repository %s owned by %s because ' % \ ( changeset_revision, name, owner ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Enhance the Tool Shed fabric_util.wait_for_process method to timeout after a reasonable period of waiting for stderr or stdout during tool dependency package compilation.
by commits-noreply＠bitbucket.org 24 Feb '14

24 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ef5f750810f7/ Changeset: ef5f750810f7 User: greg Date: 2014-02-24 16:20:14 Summary: Enhance the Tool Shed fabric_util.wait_for_process method to timeout after a reasonable period of waiting for stderr or stdout during tool dependency package compilation. Affected #: 1 file diff -r f573461f3667e8f120dc05bbd11a019d5fae1960 -r ef5f750810f791d39d5fe37f256b2526fa9916ae lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -38,6 +38,7 @@ log = logging.getLogger( __name__ ) INSTALLATION_LOG = 'INSTALLATION.log' +NO_CMD_OUTPUT_TIMEOUT = 600 VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz' @@ -829,19 +830,46 @@ return env def wait_for_process( process_handle, stream_output, stdout_queue, stderr_queue ): + pid = process_handle.pid standard_out = [] standard_err = [] process_handle.wait() + # Generate stdout. while True: - line = stdout_queue.get() - if line is None: + try: + line = stdout_queue.get( timeout=NO_CMD_OUTPUT_TIMEOUT ) + except Queue.Empty: + err_msg = "\nShutting down process id %s because it generated no stdout for the defined timout period of %d seconds.\n" % \ + ( pid, NO_CMD_OUTPUT_TIMEOUT ) + print err_msg + standard_out.append( err_msg ) + stdout_queue.task_done() + process_handle.kill() break - standard_out.append(line) + else: + if line: + standard_out.append( line ) + else: + stdout_queue.task_done() + break + # Generate stderr. while True: - line = stderr_queue.get() - if line is None: + try: + line = stderr_queue.get( timeout=NO_CMD_OUTPUT_TIMEOUT ) + except Queue.Empty: + err_msg = "\nShutting down process id %s because it generated no stderr for the defined timout period of %d seconds.\n" % \ + ( pid, NO_CMD_OUTPUT_TIMEOUT ) + print err_msg + standard_err.append( err_msg ) + stderr_queue.task_done() + process_handle.kill() break - standard_err.append(line) + else: + if line: + standard_err.append( line ) + else: + stderr_queue.task_done() + break stdout = '\n'.join( standard_out ) stderr = '\n'.join( standard_err ) return stdout, stderr Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Charts: Remove message box
by commits-noreply＠bitbucket.org 24 Feb '14

24 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f573461f3667/ Changeset: f573461f3667 User: guerler Date: 2014-02-24 08:47:45 Summary: Charts: Remove message box Affected #: 2 files diff -r dc448888a8651b5555f54e838532ab09e0248cbd -r f573461f3667e8f120dc05bbd11a019d5fae1960 config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -79,7 +79,11 @@ // refresh title _refreshTitle: function() { - this.portlet.title('Charts - ' + this.config.get('title')); + var title = this.config.get('title'); + if (title) { + title = ' - ' + title; + } + this.portlet.title('Charts' + title); }, // current view diff -r dc448888a8651b5555f54e838532ab09e0248cbd -r f573461f3667e8f120dc05bbd11a019d5fae1960 config/plugins/visualizations/charts/static/views/chart.js --- a/config/plugins/visualizations/charts/static/views/chart.js +++ b/config/plugins/visualizations/charts/static/views/chart.js @@ -253,7 +253,7 @@ this.chart.set('id', Utils.uuid()); this.chart.set('dataset_id', this.app.options.dataset.id); this.chart.set('type', 'bardiagram'); - this.chart.set('title', 'Chart title'); + this.chart.set('title', 'New Chart'); }, // create chart @@ -266,22 +266,6 @@ date : Utils.time() }); - // validate - if (!this.chart.get('title')) { - this.message.update({message : 'Please enter a title for your chart.'}); - return; - } - - if (!this.chart.get('type')) { - this.message.update({message : 'Please select a chart type.'}); - return; - } - - if (this.chart.groups.length == 0) { - this.message.update({message : 'Please configure at least one data source.'}); - return; - } - // create/get chart var current = this.app.charts.get(this.chart.id); if (!current) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Ui: Fix title function in portlets
by commits-noreply＠bitbucket.org 24 Feb '14

24 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dc448888a865/ Changeset: dc448888a865 User: guerler Date: 2014-02-24 08:17:36 Summary: Ui: Fix title function in portlets Affected #: 7 files diff -r 33b8fa988ad0cf58277553f1cc569a581cfd652d -r dc448888a8651b5555f54e838532ab09e0248cbd config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -40,7 +40,7 @@ // create portlet if (!this.options.config.widget) { - this.portlet = new Portlet.View({icon : 'fa-bar-chart-o', title : 'Charts'}); + this.portlet = new Portlet.View({icon : 'fa-bar-chart-o'}); } else { this.portlet = $('<div></div>'); } @@ -64,6 +64,22 @@ this.config.on('change:current_view', function() { self._showCurrent(); }); + this.config.on('change:title', function() { + self._refreshTitle(); + }); + + // render + this.render(); + }, + + // render + render: function() { + this._refreshTitle(); + }, + + // refresh title + _refreshTitle: function() { + this.portlet.title('Charts - ' + this.config.get('title')); }, // current view diff -r 33b8fa988ad0cf58277553f1cc569a581cfd652d -r dc448888a8651b5555f54e838532ab09e0248cbd config/plugins/visualizations/charts/static/models/config.js --- a/config/plugins/visualizations/charts/static/models/config.js +++ b/config/plugins/visualizations/charts/static/models/config.js @@ -9,7 +9,8 @@ defaults : { query_limit : 20, query_pace : 1000, - query_max : 5 + query_max : 5, + title : 'Create a new chart' } }); diff -r 33b8fa988ad0cf58277553f1cc569a581cfd652d -r dc448888a8651b5555f54e838532ab09e0248cbd config/plugins/visualizations/charts/static/views/chart.js --- a/config/plugins/visualizations/charts/static/views/chart.js +++ b/config/plugins/visualizations/charts/static/views/chart.js @@ -23,11 +23,6 @@ // configure options this.options = Utils.merge(options, this.optionsDefault); - // main elements - this.message = new Ui.Message(); - this.title = new Ui.Input({placeholder: 'Chart title'}); - this.dataset = new Ui.Input({value : app.options.dataset.id, disabled: true, visible: false}); - // // table with chart types // @@ -115,9 +110,21 @@ } }); - // construct element + // + // main/default tab + // + + // construct elements + this.title = new Ui.Input({ + placeholder: 'Chart title', + onchange: function() { + self.app.config.set('title', self.title.value()); + } + }); + this.dataset = new Ui.Input({value : app.options.dataset.id, disabled: true, visible: false}); + + // append element var $settings = $('<div/>'); - $settings.append(Utils.wrap(this.message.$el)); $settings.append(Utils.wrap((new Ui.Label({ title : 'Provide a chart title:'})).$el)); $settings.append(Utils.wrap(this.title.$el)); $settings.append(Utils.wrap((new Ui.Label({ title : 'Select a chart type:'})).$el)); @@ -140,6 +147,7 @@ var self = this; this.chart.on('change:title', function(chart) { self.title.value(chart.get('title')); + self.app.config.set('title', chart.get('title')); }); this.chart.on('change:type', function(chart) { self.table.value(chart.get('type')); diff -r 33b8fa988ad0cf58277553f1cc569a581cfd652d -r dc448888a8651b5555f54e838532ab09e0248cbd config/plugins/visualizations/charts/static/views/charts.js --- a/config/plugins/visualizations/charts/static/views/charts.js +++ b/config/plugins/visualizations/charts/static/views/charts.js @@ -25,6 +25,13 @@ self.app.chart_view.$el.show(); }, onchange : function(chart_id) { + // get chart + var chart = self.app.charts.get(chart_id); + + // update main title + self.app.config.set('title', chart.get('title')); + + // show viewport self.app.viewport_view.show(chart_id); } }); diff -r 33b8fa988ad0cf58277553f1cc569a581cfd652d -r dc448888a8651b5555f54e838532ab09e0248cbd config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -25,8 +25,7 @@ // add table to portlet this.portlet = new Portlet.View({ - title : '', - icon : 'fa-signal', + title : 'title', height : this.options.height, overflow : 'hidden', operations : { diff -r 33b8fa988ad0cf58277553f1cc569a581cfd652d -r dc448888a8651b5555f54e838532ab09e0248cbd static/scripts/mvc/ui/ui-portlet.js --- a/static/scripts/mvc/ui/ui-portlet.js +++ b/static/scripts/mvc/ui/ui-portlet.js @@ -10,7 +10,7 @@ // defaults options optionsDefault: { title : '', - icon : 'fa-tasks', + icon : '', buttons : null, body : null, height : null, @@ -20,6 +20,7 @@ }, // elements + $title : null, $content : null, $buttons : null, $operations : null, @@ -35,6 +36,9 @@ // link content this.$content = this.$el.find('#content'); + // link title + this.$title = this.$el.find('#title-text'); + // set content height if (this.options.height) { this.$el.find('#body').css('height', this.options.height); @@ -128,7 +132,7 @@ // title title: function(new_title) { - var $el = this.$el.find('#title'); + var $el = this.$title; if (new_title) { $el.html(new_title); } @@ -147,7 +151,7 @@ if (options.icon) tmpl += '<i style="padding-top: 3px; float: left; font-size: 1.2em" class="icon fa ' + options.icon + '"> </i>'; - tmpl += '<div id="title" style="padding-top: 2px; float: left;">' + options.title + '</div>'; + tmpl += '<div id="title-text" style="padding-top: 2px; float: left;">' + options.title + '</div>'; tmpl += '</div>' + '</div>'; diff -r 33b8fa988ad0cf58277553f1cc569a581cfd652d -r dc448888a8651b5555f54e838532ab09e0248cbd static/scripts/packed/mvc/ui/ui-portlet.js --- a/static/scripts/packed/mvc/ui/ui-portlet.js +++ b/static/scripts/packed/mvc/ui/ui-portlet.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,optionsDefault:{title:"",icon:"fa-tasks",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$content:null,$buttons:null,$operations:null,initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$content=this.$el.find("#content");if(this.options.height){this.$el.find("#body").css("height",this.options.height);this.$el.find("#content").css("overflow",this.options.overflow)}this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var c=this;$.each(this.options.buttons,function(e,f){f.$el.prop("id",e);c.$buttons.append(f.$el)})}else{this.$buttons.remove()}this.$operations=$(this.el).find("#operations");if(this.options.operations){var c=this;$.each(this.options.operations,function(e,f){f.$el.prop("id",e);c.$operations.append(f.$el)})}if(this.options.body){this.append(this.options.body)}},append:function(c){this.$content.append(a.wrap(c))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast");this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},enableButton:function(c){this.$buttons.find("#"+c).prop("disabled",false)},disableButton:function(c){this.$buttons.find("#"+c).prop("disabled",true)},hideOperation:function(c){this.$operations.find("#"+c).hide()},showOperation:function(c){this.$operations.find("#"+c).show()},setOperation:function(e,d){var c=this.$operations.find("#"+e);c.off("click");c.on("click",d)},title:function(d){var c=this.$el.find("#title");if(d){c.html(d)}return c.html()},_template:function(d){var c='<div class="toolForm">';if(d.title||d.icon){c+='<div id="title" class="toolFormTitle" style="overflow:hidden;"><div id="operations" style="float: right;"></div><div style="overflow: hidden">';if(d.icon){c+='<i style="padding-top: 3px; float: left; font-size: 1.2em" class="icon fa '+d.icon+'"> </i>'}c+='<div id="title" style="padding-top: 2px; float: left;">'+d.title+"</div>";c+="</div></div>"}c+='<div id="body" class="toolFormBody">';if(d.placement=="top"){c+='<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'}c+='<div id="content" class="content" style="height: inherit; padding: 10px;"></div>';if(d.placement=="bottom"){c+='<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'}c+="</div></div>";return c}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$content=this.$el.find("#content");this.$title=this.$el.find("#title-text");if(this.options.height){this.$el.find("#body").css("height",this.options.height);this.$el.find("#content").css("overflow",this.options.overflow)}this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var c=this;$.each(this.options.buttons,function(e,f){f.$el.prop("id",e);c.$buttons.append(f.$el)})}else{this.$buttons.remove()}this.$operations=$(this.el).find("#operations");if(this.options.operations){var c=this;$.each(this.options.operations,function(e,f){f.$el.prop("id",e);c.$operations.append(f.$el)})}if(this.options.body){this.append(this.options.body)}},append:function(c){this.$content.append(a.wrap(c))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast");this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},enableButton:function(c){this.$buttons.find("#"+c).prop("disabled",false)},disableButton:function(c){this.$buttons.find("#"+c).prop("disabled",true)},hideOperation:function(c){this.$operations.find("#"+c).hide()},showOperation:function(c){this.$operations.find("#"+c).show()},setOperation:function(e,d){var c=this.$operations.find("#"+e);c.off("click");c.on("click",d)},title:function(d){var c=this.$title;if(d){c.html(d)}return c.html()},_template:function(d){var c='<div class="toolForm">';if(d.title||d.icon){c+='<div id="title" class="toolFormTitle" style="overflow:hidden;"><div id="operations" style="float: right;"></div><div style="overflow: hidden">';if(d.icon){c+='<i style="padding-top: 3px; float: left; font-size: 1.2em" class="icon fa '+d.icon+'"> </i>'}c+='<div id="title-text" style="padding-top: 2px; float: left;">'+d.title+"</div>";c+="</div></div>"}c+='<div id="body" class="toolFormBody">';if(d.placement=="top"){c+='<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'}c+='<div id="content" class="content" style="height: inherit; padding: 10px;"></div>';if(d.placement=="bottom"){c+='<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'}c+="</div></div>";return c}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Charts: Load tab titles from model
by commits-noreply＠bitbucket.org 24 Feb '14

24 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/33b8fa988ad0/ Changeset: 33b8fa988ad0 User: guerler Date: 2014-02-24 07:14:42 Summary: Charts: Load tab titles from model Affected #: 1 file diff -r 462a28f96c2172113d1cad657e271e792493b49e -r 33b8fa988ad0cf58277553f1cc569a581cfd652d config/plugins/visualizations/charts/static/views/chart.js --- a/config/plugins/visualizations/charts/static/views/chart.js +++ b/config/plugins/visualizations/charts/static/views/chart.js @@ -10,7 +10,7 @@ header : true, content : 'No content available.' }, - + // initialize initialize: function(app, options) { @@ -85,7 +85,8 @@ this.tabs = new Tabs.View({ title_new : 'Add Data', onnew : function() { - self._addGroupModel(); + var group = self._addGroupModel(); + self.tabs.show(group.id); }, operations : { 'save' : new Ui.ButtonIcon({ @@ -95,8 +96,7 @@ onclick : function() { // ensure that data group is available if (self.chart.groups.length == 0) { - var group = self._addGroupModel(); - self.tabs.show(group.id); + self._addGroupModel(); } // save chart @@ -171,11 +171,27 @@ this.app.chart.groups.on('reset', function(group) { self._removeAllGroups(); }); - + this.app.chart.groups.on('change:label', function(group) { + self._refreshLabels(); + }); + // reset this._resetChart(); }, + // update + _refreshLabels: function() { + var self = this; + var counter = 0; + this.chart.groups.each(function(group) { + var title = group.get('label', ''); + if (title == '') { + title = 'Chart data'; + } + self.tabs.title(group.id, ++counter + ': ' + title); + }); + }, + // new group _addGroupModel: function() { var group = new Group({ @@ -199,18 +215,23 @@ // add new tab this.tabs.add({ - title : count + ': Chart Data', id : group.id, $el : group_view.$el, ondel : function() { self.chart.groups.remove(group.id); } }); + + // update titles + this._refreshLabels() }, // remove group _removeGroup: function(group) { this.tabs.del(group.id); + + // update titles + this._refreshLabels() }, // remove group Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Ui/Charts: Enable user to add/remove tabs and include that in Charts
by commits-noreply＠bitbucket.org 24 Feb '14

24 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/462a28f96c21/ Changeset: 462a28f96c21 User: guerler Date: 2014-02-24 06:44:07 Summary: Ui/Charts: Enable user to add/remove tabs and include that in Charts Affected #: 12 files diff -r fac578cca75887d811e67993a655fed20c0d8713 -r 462a28f96c2172113d1cad657e271e792493b49e config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -1,10 +1,10 @@ // dependencies define(['mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils', - 'plugin/views/charts', 'plugin/views/viewport', 'plugin/views/chart', 'plugin/views/group', - 'plugin/models/config', 'plugin/models/datasets', 'plugin/models/chart', 'plugin/models/charts', 'plugin/models/group', 'plugin/models/types'], + 'plugin/views/charts', 'plugin/views/viewport', 'plugin/views/chart', + 'plugin/models/config', 'plugin/models/datasets', 'plugin/models/chart', 'plugin/models/charts', 'plugin/models/types'], function( Portlet, Ui, Utils, - ChartsView, ViewportView, ChartView, GroupView, - Config, Datasets, Chart, Charts, Group, Types + ChartsView, ViewportView, ChartView, + Config, Datasets, Chart, Charts, Types ) { // widget @@ -26,14 +26,12 @@ this.types = new Types(); this.chart = new Chart(); this.charts = new Charts(); - this.group = new Group(); // create dataset handler this.datasets = new Datasets(this); // create views this.charts_view = new ChartsView(this); - this.group_view = new GroupView(this); this.chart_view = new ChartView(this); this.viewport_view = new ViewportView(this); @@ -49,9 +47,8 @@ // append views this.portlet.append(this.charts_view.$el); - this.portlet.append(this.group_view.$el); this.portlet.append(this.chart_view.$el); - + // set element if (!this.options.config.widget) { this.setElement(this.portlet.$el); @@ -60,7 +57,6 @@ } // hide views - this.group_view.$el.hide(); this.charts_view.$el.hide(); // events diff -r fac578cca75887d811e67993a655fed20c0d8713 -r 462a28f96c2172113d1cad657e271e792493b49e config/plugins/visualizations/charts/static/library/table.js --- a/config/plugins/visualizations/charts/static/library/table.js +++ b/config/plugins/visualizations/charts/static/library/table.js @@ -20,8 +20,8 @@ // events events : { - 'click' : 'onclick', - 'dblclick' : 'ondblclick' + 'click' : '_onclick', + 'dblclick' : '_ondblclick' }, // first @@ -33,7 +33,7 @@ this.options = Utils.merge(options, this.optionsDefault); // create new element - this.setElement(this.template(options)); + this.setElement(this._template(options)); // initialize row this.row = $('<tr></tr>'); @@ -64,46 +64,26 @@ // append append: function(id) { - this.commit(id); + this._commit(id); }, // prepend prepend: function(id) { - this.commit(id, true); - }, - - // commit - commit: function(id, prepend) { - // add - this.row.attr('id', id); - - // add row - if (prepend) { - $(this.el).find('tbody').prepend(this.row); - } else { - $(this.el).find('tbody').append(this.row); - } - - // row - this.row = $('<tr></tr>'); - - // row count - this.row_count++; - this.refresh(); + this._commit(id, true); }, // remove remove: function(id) { $(this.el).find('#' + id).remove(); this.row_count--; - this.refresh(); + this._refresh(); }, // remove removeAll: function() { $(this.el).find('tbody').html(''); this.row_count = 0; - this.refresh(); + this._refresh(); }, // value @@ -134,13 +114,28 @@ } }, - // confirm new value - confirm: function(new_value) { - this.value(new_value); + // commit + _commit: function(id, prepend) { + // add + this.row.attr('id', id); + + // add row + if (prepend) { + $(this.el).find('tbody').prepend(this.row); + } else { + $(this.el).find('tbody').append(this.row); + } + + // row + this.row = $('<tr></tr>'); + + // row count + this.row_count++; + this._refresh(); }, // onclick - onclick: function(e) { + _onclick: function(e) { // get values var old_value = this.value(); var new_value = $(e.target).closest('tr').attr('id'); @@ -150,13 +145,13 @@ if (this.options.onconfirm) { this.options.onconfirm(new_value); } else { - this.confirm(new_value); + this.value(new_value); } } }, - // onclick - ondblclick: function(e) { + // ondblclick + _ondblclick: function(e) { var value = this.value(); if (value && this.options.ondblclick) { this.options.ondblclick(value); @@ -164,7 +159,7 @@ }, // refresh - refresh: function() { + _refresh: function() { if (this.row_count == 0) { this.$el.find('tmessage').show(); } else { @@ -173,7 +168,7 @@ }, // load html template - template: function(options) + _template: function(options) { return '<div>' + '<table class="grid">' + diff -r fac578cca75887d811e67993a655fed20c0d8713 -r 462a28f96c2172113d1cad657e271e792493b49e config/plugins/visualizations/charts/static/library/ui.js --- a/config/plugins/visualizations/charts/static/library/ui.js +++ b/config/plugins/visualizations/charts/static/library/ui.js @@ -6,7 +6,7 @@ { // options optionsDefault: { - label : '' + title : '' }, // initialize @@ -15,17 +15,17 @@ this.options = Utils.merge(options, this.optionsDefault); // create new element - this.setElement(this.template(this.options)); + this.setElement(this._template(this.options)); }, // template - template: function(options) { - return '<label><b>' + options.label + '</b></label>'; + _template: function(options) { + return '<label><b>' + options.title + '</b></label>'; }, // value value: function() { - return options.label; + return options.title; } }); @@ -35,10 +35,9 @@ // options optionsDefault: { id : null, - label : '', + title : '', float : 'right', cls : 'btn-default', - type : 'submit', icon : '' }, @@ -52,43 +51,99 @@ // add event $(this.el).on('click', options.onclick); + + // add tooltip + $(this.el).tooltip({title: options.tooltip, placement: 'bottom'}); + }, + + // element + _template: function(options) { + var str = '<button id="' + options.id + '" type="submit" style="margin-right: 5px; float: ' + options.float + ';" type="button" class="btn ' + options.cls + '">'; + if (options.icon) { + str += '<i class="icon fa ' + options.icon + '"></i> ' ; + } + str += options.title + + '</button>'; + return str; + } +}); + +// plugin +var ButtonIcon = Backbone.View.extend( +{ + // options + optionsDefault: { + title : '', + id : null, + float : 'right', + cls : 'icon-btn', + icon : '', + tooltip : '' + }, + + // initialize + initialize : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // add event + $(this.el).on('click', options.onclick); + + // add tooltip + $(this.el).tooltip({title: options.tooltip, placement: 'bottom'}); + }, + + // element + _template: function(options) { + // width + var width = ''; + if (options.title) { + width = 'width: auto;'; + } + + // string + var str = '<div id="' + options.id + '" style="margin-right: 5px; float: ' + options.float + '; ' + width + '" class="' + options.cls + '">'; + + // title + if (options.title) { + str += '<div style="margin-right: 5px; margin-left: 5px;">' + + '<i class="icon fa ' + options.icon + '"/> ' + + '<span style="position: relative; font-size: 0.8em; top: -1px;">' + options.title + '</span>' + + '</div>'; + } else { + str += '<i class="icon fa ' + options.icon + '"/>'; + } + str += '</div>'; + return str; + } +}); + +// plugin +var Anchor = Backbone.View.extend( +{ + // options + optionsDefault: { + title : '' + }, + + // initialize + initialize : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // add event + $(this.el).on('click', options.onclick); }, // element _template: function(options) { - var str = '<button id="' + options.id + '" type="' + options.type + '" style="margin-right: 5px; float: ' + options.float + ';" type="button" class="btn ' + options.cls + '">'; - if (options.icon) { - str += '<i class="icon fa ' + options.icon + '"></i> ' ; - } - str += options.label + - '</button>'; - return str; - } -}); - -// plugin -var Anchor = Backbone.View.extend( -{ - // options - optionsDefault: { - label : '' - }, - - // initialize - initialize : function(options) { - // get options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this._template(this.options)); - - // add event - $(this.el).on('click', options.onclick); - }, - - // element - _template: function(options) { - return '<div><a href="javascript:void(0)">' + options.label + '</a></div>'; + return '<div><a href="javascript:void(0)">' + options.title + '</a></div>'; } }); @@ -118,7 +173,7 @@ // show message if (options.message != '') { - this.$el.html(this.template(this.options)); + this.$el.html(this._template(this.options)); this.$el.fadeIn(); // check if message is persistent @@ -139,7 +194,7 @@ }, // element - template: function(options) { + _template: function(options) { return '<div class="alert alert-' + options.status + '" style="padding: 2px 2px 2px 10px;">' + options.message + '</div>'; } }); @@ -159,7 +214,7 @@ this.options = Utils.merge(options, this.optionsDefault); // create new element - this.setElement(this.template(this.options)); + this.setElement(this._template(this.options)); // add click event var self = this; @@ -172,7 +227,7 @@ }, // element - template: function(options) { + _template: function(options) { return '<div class="search">' + '<form onsubmit="return false;">' + '<input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="' + options.searchword + '">' + @@ -189,7 +244,7 @@ { // options optionsDefault: { - label : 'Unlabeled', + title : 'Unlabeled', body : null }, @@ -199,7 +254,7 @@ this.options = Utils.merge(options, this.optionsDefault); // create new element - this.setElement(this.template(this.options)); + this.setElement(this._template(this.options)); if (this.options.body) { this.$el.find('.body').append(this.options.body); @@ -207,9 +262,9 @@ }, // element - template: function(options) { + _template: function(options) { return '<div id="title" class="title">' + - options.label + ':' + + options.title + ':' + '</div>'; } }); @@ -370,48 +425,6 @@ }); // plugin -var ButtonIcon = Backbone.View.extend( -{ - // options - optionsDefault: { - id : null, - label : '', - float : 'right', - cls : 'icon-btn', - type : 'submit', - icon : '', - tooltip : '' - }, - - // initialize - initialize : function(options) { - // get options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this.template(this.options)); - - // add event - $(this.el).on('click', options.onclick); - - // add tooltip - $(this.el).tooltip({title: options.tooltip, placement: 'bottom'}); - }, - - // element - template: function(options) { - var str = '<a id="' + options.id + '" style="margin-right: 5px; float: ' + options.float + ';" class="' + options.cls + '">'; - if (options.icon) { - str += '<i class="icon fa ' + options.icon + '"></i>'; - } - str += options.label + - '</a>'; - return str; - } -}); - - -// plugin var Input = Backbone.View.extend( { // options @@ -429,7 +442,7 @@ this.options = Utils.merge(options, this.optionsDefault); // create new element - this.setElement(this.template(this.options)); + this.setElement(this._template(this.options)); // disable input field if (this.options.disabled) { @@ -440,6 +453,14 @@ if (!this.options.visible) { this.$el.hide(); } + + // onchange event handler + var self = this; + if (this.options.onchange) { + this.$el.on('input', function() { + self.options.onchange(); + }); + } }, // value @@ -451,7 +472,7 @@ }, // element - template: function(options) { + _template: function(options) { return '<input id="' + options.id + '" type="' + options.type + '" value="' + options.value + '" placeholder="' + options.placeholder + '" class="form-control">'; } }); diff -r fac578cca75887d811e67993a655fed20c0d8713 -r 462a28f96c2172113d1cad657e271e792493b49e config/plugins/visualizations/charts/static/library/ui.select.js --- a/config/plugins/visualizations/charts/static/library/ui.select.js +++ b/config/plugins/visualizations/charts/static/library/ui.select.js @@ -19,6 +19,11 @@ // create new element this.setElement(this._template(this.options)); + // initial value + if (this.options.value) { + this.$el.val(this.options.value); + } + // add change event var self = this; if (this.options.onchange) { diff -r fac578cca75887d811e67993a655fed20c0d8713 -r 462a28f96c2172113d1cad657e271e792493b49e config/plugins/visualizations/charts/static/models/group.js --- a/config/plugins/visualizations/charts/static/models/group.js +++ b/config/plugins/visualizations/charts/static/models/group.js @@ -4,6 +4,12 @@ // model return Backbone.Model.extend( { + // options + defaults : { + label : 'Data label', + date : '' + }, + // reset reset: function() { diff -r fac578cca75887d811e67993a655fed20c0d8713 -r 462a28f96c2172113d1cad657e271e792493b49e config/plugins/visualizations/charts/static/views/chart.js --- a/config/plugins/visualizations/charts/static/views/chart.js +++ b/config/plugins/visualizations/charts/static/views/chart.js @@ -1,6 +1,6 @@ // dependencies -define(['mvc/ui/ui-tabs', 'plugin/library/table', 'plugin/library/ui', 'utils/utils', 'plugin/models/chart', 'plugin/views/groups'], - function(Tabs, Table, Ui, Utils, Chart, GroupsView) { +define(['mvc/ui/ui-tabs', 'plugin/library/table', 'plugin/library/ui', 'utils/utils', 'plugin/models/chart', 'plugin/models/group', 'plugin/views/group'], + function(Tabs, Table, Ui, Utils, Chart, Group, GroupView) { // widget return Backbone.View.extend( @@ -28,10 +28,9 @@ this.title = new Ui.Input({placeholder: 'Chart title'}); this.dataset = new Ui.Input({value : app.options.dataset.id, disabled: true, visible: false}); - // configure dataset - this.groups_view = new GroupsView(this.app); - - // table + // + // table with chart types + // var self = this; this.table = new Table({ header : false, @@ -40,7 +39,7 @@ // show modal self.app.modal.show({ title : 'Switching the chart type?', - body : 'You configured data sources. If you switch chart types your configurations will be removed.', + body : 'If you continue your data selections will cleared.', buttons : { 'Cancel' : function() { // hide modal @@ -51,13 +50,13 @@ self.app.modal.hide(); // confirm - self.table.confirm(type); + self.table.value(type); } } }); } else { // confirm - self.table.confirm(type); + self.table.value(type); } }, onchange : function(type) { @@ -70,7 +69,7 @@ content: 'No chart types available' }); - // add types + // load chart types into table var types_n = 0; var types = app.types.attributes; for (var id in types){ @@ -80,47 +79,55 @@ this.table.append(id); } + // + // tabs + // + this.tabs = new Tabs.View({ + title_new : 'Add Data', + onnew : function() { + self._addGroupModel(); + }, + operations : { + 'save' : new Ui.ButtonIcon({ + icon : 'fa-save', + tooltip : 'Draw Chart', + title : 'Draw', + onclick : function() { + // ensure that data group is available + if (self.chart.groups.length == 0) { + var group = self._addGroupModel(); + self.tabs.show(group.id); + } + + // save chart + self._saveChart(); + } + }), + 'back' : new Ui.ButtonIcon({ + icon : 'fa-caret-left', + tooltip : 'Return to Viewer', + title : 'Return', + onclick : function() { + self.$el.hide(); + self.app.charts_view.$el.show(); + } + }) + } + }); + // construct element var $settings = $('<div/>'); $settings.append(Utils.wrap(this.message.$el)); - $settings.append(Utils.wrap((new Ui.Label({ label : 'Provide a chart title:'})).$el)); + $settings.append(Utils.wrap((new Ui.Label({ title : 'Provide a chart title:'})).$el)); $settings.append(Utils.wrap(this.title.$el)); - $settings.append(Utils.wrap((new Ui.Label({ label : 'Select a chart type:'})).$el)); + $settings.append(Utils.wrap((new Ui.Label({ title : 'Select a chart type:'})).$el)); $settings.append(Utils.wrap(this.table.$el)); - - // tabs - this.tabs = new Tabs.View({ - operations : { - 'save' : new Ui.ButtonIcon({ - icon : 'fa-save', - tooltip : 'Save Chart', - onclick : function() { - self._saveChart(); - } - }), - 'back' : new Ui.ButtonIcon({ - icon : 'fa-caret-left', - tooltip : 'Return', - onclick : function() { - self.$el.hide(); - self.app.charts_view.$el.show(); - } - }) - } - }); // add tab this.tabs.add({ - $el: $settings, - title: 'Start', - id: 'settings' - }); - - // add tab - this.tabs.add({ - $el: this.groups_view.$el, - title: 'Chart Groups', - id: 'groups' + id : 'settings', + title : 'Start', + $el : $settings }); // elements @@ -129,7 +136,7 @@ // hide back button on startup this.tabs.hideOperation('back'); - // model events + // chart events var self = this; this.chart.on('change:title', function(chart) { self.title.value(chart.get('title')); @@ -141,7 +148,7 @@ self._resetChart(); }); - // collection events + // charts events this.app.charts.on('add', function(chart) { self.tabs.showOperation('back'); }); @@ -154,12 +161,66 @@ self.tabs.hideOperation('back'); }); + // groups events + this.app.chart.groups.on('add', function(group) { + self._addGroup(group); + }); + this.app.chart.groups.on('remove', function(group) { + self._removeGroup(group); + }); + this.app.chart.groups.on('reset', function(group) { + self._removeAllGroups(); + }); + // reset this._resetChart(); }, + // new group + _addGroupModel: function() { + var group = new Group({ + id : Utils.uuid(), + dataset_id : this.chart.get('dataset_id') + }); + this.chart.groups.add(group); + return group; + }, + + // add group + _addGroup: function(group) { + // link this + var self = this; + + // create view + var group_view = new GroupView(this.app, {group: group}); + + // number of groups + var count = self.chart.groups.length; + + // add new tab + this.tabs.add({ + title : count + ': Chart Data', + id : group.id, + $el : group_view.$el, + ondel : function() { + self.chart.groups.remove(group.id); + } + }); + }, + + // remove group + _removeGroup: function(group) { + this.tabs.del(group.id); + }, + + // remove group + _removeAllGroups: function(group) { + this.tabs.delRemovable(); + }, + // reset _resetChart: function() { + // reset chart details this.chart.set('id', Utils.uuid()); this.chart.set('dataset_id', this.app.options.dataset.id); this.chart.set('type', 'bardiagram'); diff -r fac578cca75887d811e67993a655fed20c0d8713 -r 462a28f96c2172113d1cad657e271e792493b49e config/plugins/visualizations/charts/static/views/charts.js --- a/config/plugins/visualizations/charts/static/views/charts.js +++ b/config/plugins/visualizations/charts/static/views/charts.js @@ -1,5 +1,5 @@ // dependencies -define(['mvc/ui/ui-portlet', 'plugin/library/table', 'plugin/library/ui', 'utils/utils'], function(Portlet, Table, Ui, Utils) { +define(['mvc/ui/ui-portlet', 'plugin/library/table', 'plugin/library/ui', 'utils/utils', 'plugin/models/group'], function(Portlet, Table, Ui, Utils, Group) { // widget return Backbone.View.extend( @@ -17,11 +17,11 @@ // get chart var chart = self.app.charts.get(chart_id); self.app.chart.copy(chart); - - // show edit + + // hide this element self.$el.hide(); - // update model and show create + // show chart view self.app.chart_view.$el.show(); }, onchange : function(chart_id) { diff -r fac578cca75887d811e67993a655fed20c0d8713 -r 462a28f96c2172113d1cad657e271e792493b49e config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -12,46 +12,34 @@ initialize: function(app, options) { // link app this.app = app; - + + // link this + var self = this; + // get current chart object this.chart = this.app.chart; - this.group = this.app.group; + + // access group + this.group = options.group; // ui elements - this.message = new Ui.Message(); - this.label = new Ui.Input({placeholder: 'Group label'}); + this.label = new Ui.Input({ + placeholder: 'Data label', + onchange: function() { + self.group.set('label', self.label.value()); + } + }); this.table = new Table({content: 'No data column.'}); // add table to portlet - var self = this; - this.portlet = new Portlet.View({ - icon : 'fa-edit', - title : 'Define group properties:', - operations : { - 'save' : new Ui.ButtonIcon({ - icon : 'fa-save', - tooltip : 'Save', - onclick : function() { - // save/add group - self._saveGroup(); - } - }), - 'back' : new Ui.ButtonIcon({ - icon : 'fa-caret-left', - tooltip : 'Return', - onclick : function() { - self.$el.hide(); - self.app.chart_view.$el.show(); - } - }) - } - }); - this.portlet.append(this.message.$el); - this.portlet.append(this.label.$el); - this.portlet.append(this.table.$el); + var $view = $('<div/>'); + $view.append(Utils.wrap((new Ui.Label({title: 'Provide a label:'})).$el)); + $view.append(Utils.wrap(this.label.$el)); + $view.append(Utils.wrap((new Ui.Label({title: 'Select columns:'})).$el)); + $view.append(Utils.wrap(this.table.$el)); // add element - this.setElement(this.portlet.$el); + this.setElement($view); // change var self = this; @@ -67,20 +55,17 @@ this.group.on('change', function() { self._refreshGroup(); }); - this.group.on('reset', function() { - self._resetGroup(); - }); + + // refresh + this._refresh(); }, - // show - show: function() { - this.$el.show(); - }, - - // reset - _resetGroup: function() { - this.group.set('id', Utils.uuid()); - this.group.set('label', 'Group label'); + // render + _refresh: function() { + this._refreshDataset(); + this._refreshType(); + this._refreshLabel(); + this._refreshGroup(); }, // update dataset @@ -98,7 +83,7 @@ // check if (!dataset) { - this.app.log('Config::render()', 'Failed to retrieve dataset.'); + this.app.log('Group::_refreshDataset()', 'Failed to retrieve dataset.'); return; } @@ -138,9 +123,13 @@ data : this.columns, onchange : function(value) { self.group.set(this.gid, value); - } + }, + value : this.group.get(id) }); + // set model value + this.group.set(id, select.value()); + // add row to table this.table.add(data_def.title); this.table.add(select.$el); @@ -154,14 +143,7 @@ // update _refreshGroup: function() { - // update select fields - for (var id in this.list) { - var col = this.group.get(id); - if (col === undefined) { - col = 0; - } - this.list[id].value(col); - } + this.group.set('date', Utils.time()); }, // update label @@ -171,48 +153,6 @@ label_text = ''; } this.label.value(label_text); - }, - - // create group - _saveGroup: function() { - // get current chart - var chart = this.chart; - - // update group object - var group = this.group; - for (var key in this.list) { - group.set(key, this.list[key].value()); - } - - // add label - group.set({ - dataset_id : this.chart.get('dataset_id'), - label : this.label.value(), - date : Utils.time() - }); - - // validate - if (!group.get('label')) { - this.message.update({message : 'Please enter a label for your group.'}); - return; - } - - // get groups of current chart - var groups = this.chart.groups; - - // create/update group - var group_update = groups.get(group.id); - if (group_update) { - group_update.set(group.attributes); - } else { - groups.add(group.clone()); - } - - // hide - this.$el.hide(); - - // update main - this.app.chart_view.$el.show(); } }); diff -r fac578cca75887d811e67993a655fed20c0d8713 -r 462a28f96c2172113d1cad657e271e792493b49e config/plugins/visualizations/charts/static/views/groups.js --- a/config/plugins/visualizations/charts/static/views/groups.js +++ /dev/null @@ -1,154 +0,0 @@ -// dependencies -define(['mvc/ui/ui-portlet', 'plugin/library/table', 'plugin/library/ui', 'utils/utils'], function(Portlet, Table, Ui, Utils) { - -// chart config -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - // link app - this.app = app; - - // get current chart object - this.chart = this.app.chart; - - // table - this.table = new Table({ - content : 'Add data columns to this table.', - ondblclick : function(group_id) { - // get group - var group = self.app.chart.groups.get(group_id); - - // show edit - self.app.chart_view.$el.hide(); - self.app.group_view.show(); - self.app.group_view.group.set(group.attributes); - } - }); - - // add table to portlet - var self = this; - this.portlet = new Portlet.View({ - icon : '', - title : 'Select data columns:', - height : 100, - operations : { - 'new' : new Ui.ButtonIcon({ - icon : 'fa-plus', - tooltip: 'Create', - onclick: function() { - self.app.group.reset(); - self.app.chart_view.$el.hide(); - self.app.group_view.show(); - } - }), - 'edit' : new Ui.ButtonIcon({ - icon : 'fa-pencil', - tooltip: 'Edit', - onclick: function() { - // check if element has been selected - var group_id = self.table.value(); - if (!group_id) { - return; - } - - // get group - var group = self.app.chart.groups.get(group_id); - - // show edit - self.app.chart_view.$el.hide(); - self.app.group_view.show(); - self.app.group_view.group.set(group.attributes); - } - }), - 'delete' : new Ui.ButtonIcon({ - icon : 'fa-minus', - tooltip: 'Delete', - onclick: function() { - // check if element has been selected - var id = self.table.value(); - if (!id) { - return; - } - // remove group from chart - self.chart.groups.remove(id); - } - }) - } - }); - this.portlet.append(this.table.$el); - - // add element - this.setElement(this.portlet.$el); - - // change - var self = this; - this.chart.on('change', function() { - self._refresh(); - }); - this.chart.on('reset', function() { - self._removeGroupAll(); - }); - this.chart.on('change:type', function() { - self.app.group_view.trigger('change'); - }); - this.chart.groups.on('add', function(group) { - self._addGroup(group); - }); - this.chart.groups.on('remove', function(group) { - self._removeGroup(group); - }); - this.chart.groups.on('reset', function(group) { - self._removeGroupAll(); - }); - this.chart.groups.on('change', function(group) { - self._removeGroup(group); - self._addGroup(group); - }); - }, - - // refresh - _refresh: function() { - this._removeGroupAll(); - var self = this; - var groups = this.chart.groups; - if (groups) { - groups.each(function(group) { self._addGroup(group); }); - } - }, - - // add - _addGroup: function(group) { - // make custom info string - var info = '['; - var chart_type = this.chart.get('type'); - if (chart_type) { - var chart_settings = this.app.types.get(chart_type); - for (var key in chart_settings.data) { - info += key + '=' + group.get(key) + ', ' - } - } - info = info.substring(0, info.length - 2) + ']'; - - // add to table - this.table.add(group.get('label')); - this.table.add(info); - this.table.add('Last changed: ' + group.get('date')); - this.table.prepend(group.id); - this.table.value(group.id); - }, - - // remove - _removeGroup: function(group) { - // remove from to table - this.table.remove(group.id); - }, - - // data config reset - _removeGroupAll: function() { - // reset options table - this.table.removeAll(); - } -}); - -}); \ No newline at end of file diff -r fac578cca75887d811e67993a655fed20c0d8713 -r 462a28f96c2172113d1cad657e271e792493b49e static/scripts/mvc/ui/ui-portlet.js --- a/static/scripts/mvc/ui/ui-portlet.js +++ b/static/scripts/mvc/ui/ui-portlet.js @@ -109,12 +109,12 @@ this.$buttons.find('#' + id).prop('disabled', true); }, - // enable operation + // hide operation hideOperation: function(id) { this.$operations.find('#' + id).hide(); }, - // disable operation + // show operation showOperation: function(id) { this.$operations.find('#' + id).show(); }, diff -r fac578cca75887d811e67993a655fed20c0d8713 -r 462a28f96c2172113d1cad657e271e792493b49e static/scripts/mvc/ui/ui-tabs.js --- a/static/scripts/mvc/ui/ui-tabs.js +++ b/static/scripts/mvc/ui/ui-tabs.js @@ -12,9 +12,14 @@ $nav: null, $content: null, + // first + first_tab: null, + // defaults options optionsDefault: { - operations: null, + title_new : '', + operations : null, + onnew : null }, // initialize @@ -22,10 +27,12 @@ // configure options this.options = Utils.merge(options, this.optionsDefault); - // create element + // create tabs var $tabs = $(this._template(this.options)); - this.$nav = $tabs.find('.tab-navigation'); - this.$content = $tabs.find('.tab-content'); + + // link elements + this.$nav = $tabs.find('.tab-navigation'); + this.$content = $tabs.find('.tab-content'); // create new element this.setElement($tabs); @@ -38,42 +45,111 @@ self.$nav.append(item.$el); }); } + + // add built-in add-new-tab tab + if (this.options.onnew) { + // create tab object + var $tab_new = $(this._template_tab_new(this.options)); + + // append to navbar + this.$nav.append($tab_new); + + // add tooltip + $tab_new.tooltip({title: 'Add a new tab', placement: 'bottom'}); + + // link click event + $tab_new.on('click', function(e) { + $tab_new.tooltip('hide'); + self.options.onnew(); + }); + } }, // append add: function(options) { - // collect parameters - var $el = options.$el; - var title = options.title; + // get tab id var id = options.id; // create tab object var tab = { - $title : $(this._template_tab(options)), - $content : $(this._template_tab_content(options)) + $title : $(this._template_tab(options)), + $content : $(this._template_tab_content(options)), + removable : options.ondel ? true : false } - // add nav element - this.$nav.append(tab.$title); - - // add content - tab.$content.append($el); - this.$content.append(tab.$content); - // add to list this.list[id] = tab; - // check list size + // add a new tab either before the add-new-tab tab or behind the last tab + if (this.options.onnew) { + this.$nav.find('#new-tab').before(tab.$title); + } else { + this.$nav.append(tab.$title); + } + + // add content + tab.$content.append(options.$el); + this.$content.append(tab.$content); + + // activate this tab if this is the first tab if (_.size(this.list) == 1) { tab.$title.addClass('active'); tab.$content.addClass('active'); + this.first_tab = id; + } + + // add click event to remove tab + if (options.ondel) { + var $del_icon = tab.$title.find('#delete'); + $del_icon.tooltip({title: 'Delete this tab', placement: 'bottom'}); + $del_icon.on('click', function(e) { + $del_icon.tooltip('destroy'); + options.ondel(); + return false; + }); + } + }, + + // delete tab + del: function(id) { + // delete tab from list/dom + var tab = this.list[id]; + tab.$title.remove(); + tab.$content.remove(); + delete tab; + + // check if first tab has been deleted + if (this.first_tab == id) { + this.first_tab = null; + } + + // show first tab + if (this.first_tab != null) { + this.show(this.first_tab); + } + }, + + // delete tab + delRemovable: function() { + // delete tab from list/dom + for (var id in this.list) { + var tab = this.list[id]; + if (tab.removable) { + this.del(id); + } } }, // show - show: function(){ + show: function(id){ + // show tab view this.$el.fadeIn('fast'); this.visible = true; + + // show selected tab + if (id) { + this.list[id].$title.find('a').tab('show'); + } }, // hide @@ -82,12 +158,12 @@ this.visible = false; }, - // enable operation + // hide operation hideOperation: function(id) { this.$nav.find('#' + id).hide(); }, - // disable operation + // show operation showOperation: function(id) { this.$nav.find('#' + id).show(); }, @@ -100,8 +176,8 @@ }, // title - title: function(id, new_label) { - var $el = this.$el.find('#title-' + id + ' a'); + title: function(id, new_title) { + var $el = this.list[id].$title.find('#text'); if (new_title) { $el.html(new_title); } @@ -117,10 +193,29 @@ }, // fill template tab + _template_tab_new: function(options) { + return '<li id="new-tab">' + + '<a href="javascript:void(0);">' + + '<i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>' + + options.title_new + + '</a>' + + '</li>'; + }, + + // fill template tab _template_tab: function(options) { - return '<li id="title-' + options.id + '">' + - '<a title="" href="#tab-' + options.id + '" data-toggle="tab" data-original-title="">' + options.title + '</a>' + - '</li>'; + var tmpl = '<li id="title-' + options.id + '">' + + '<a title="" href="#tab-' + options.id + '" data-toggle="tab" data-original-title="">' + + '<span id="text">' + options.title + '</span>'; + + if (options.ondel) { + tmpl += '<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'; + } + + tmpl += '</a>' + + '</li>'; + + return tmpl; }, // fill template tab content diff -r fac578cca75887d811e67993a655fed20c0d8713 -r 462a28f96c2172113d1cad657e271e792493b49e static/scripts/packed/mvc/ui/ui-tabs.js --- a/static/scripts/packed/mvc/ui/ui-tabs.js +++ b/static/scripts/packed/mvc/ui/ui-tabs.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,list:{},$nav:null,$content:null,optionsDefault:{operations:null,},initialize:function(e){this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);if(this.options.operations){var d=this;$.each(this.options.operations,function(f,g){g.$el.prop("id",f);d.$nav.append(g.$el)})}},add:function(c){var d=c.$el;var f=c.title;var g=c.id;var e={$title:$(this._template_tab(c)),$content:$(this._template_tab_content(c))};this.$nav.append(e.$title);e.$content.append(d);this.$content.append(e.$content);this.list[g]=e;if(_.size(this.list)==1){e.$title.addClass("active");e.$content.addClass("active")}},show:function(){this.$el.fadeIn("fast");this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,c){var d=this.$el.find("#title-"+e+" a");if(new_title){d.html(new_title)}return d.html()},_template:function(c){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"/><div class="tab-content"/></div>'},_template_tab:function(c){return'<li id="title-'+c.id+'"><a title="" href="#tab-'+c.id+'" data-toggle="tab" data-original-title="">'+c.title+"</a></li>"},_template_tab_content:function(c){return'<div id="tab-'+c.id+'" class="tab-pane"/>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(e){this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);if(this.options.operations){var d=this;$.each(this.options.operations,function(g,h){h.$el.prop("id",g);d.$nav.append(h.$el)})}if(this.options.onnew){var f=$(this._template_tab_new(this.options));this.$nav.append(f);f.tooltip({title:"Add a new tab",placement:"bottom"});f.on("click",function(g){f.tooltip("hide");d.options.onnew()})}},add:function(d){var f=d.id;var e={$title:$(this._template_tab(d)),$content:$(this._template_tab_content(d)),removable:d.ondel?true:false};this.list[f]=e;if(this.options.onnew){this.$nav.find("#new-tab").before(e.$title)}else{this.$nav.append(e.$title)}e.$content.append(d.$el);this.$content.append(e.$content);if(_.size(this.list)==1){e.$title.addClass("active");e.$content.addClass("active");this.first_tab=f}if(d.ondel){var c=e.$title.find("#delete");c.tooltip({title:"Delete this tab",placement:"bottom"});c.on("click",function(g){c.tooltip("destroy");d.ondel();return false})}},del:function(d){var c=this.list[d];c.$title.remove();c.$content.remove();delete c;if(this.first_tab==d){this.first_tab=null}if(this.first_tab!=null){this.show(this.first_tab)}},delRemovable:function(){for(var d in this.list){var c=this.list[d];if(c.removable){this.del(d)}}},show:function(c){this.$el.fadeIn("fast");this.visible=true;if(c){this.list[c].$title.find("a").tab("show")}},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,d){var c=this.list[e].$title.find("#text");if(d){c.html(d)}return c.html()},_template:function(c){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"/><div class="tab-content"/></div>'},_template_tab_new:function(c){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+c.title_new+"</a></li>"},_template_tab:function(d){var c='<li id="title-'+d.id+'"><a title="" href="#tab-'+d.id+'" data-toggle="tab" data-original-title=""><span id="text">'+d.title+"</span>";if(d.ondel){c+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'}c+="</a></li>";return c},_template_tab_content:function(c){return'<div id="tab-'+c.id+'" class="tab-pane"/>'}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 21 Feb '14

21 Feb '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/767d9f567b6f/ Changeset: 767d9f567b6f User: jmchilton Date: 2014-02-22 05:09:57 Summary: Unit tests for various data tool parameter handling. Test optional datasets can be used in tool evaluation (in test_evaluation.py). Add test_data_parameters.py which test many random DataToolParameter behaviors. Test various paths to DataToolParameter.to_python - including recently enhanced ability to use optional dataset with 'multiple=True' data parameters. Test filtering on datatypes, implicit conversion options (both existing conversions and new ones) both when building HTML forms and picking intial values for workflows. Test special handling of hidden datasets. Tests picking intial datasets when optional and without repeats when used in subsequent calls. Affected #: 2 files diff -r 2403d6f67500ec35b16ce604142d98766286b65a -r 767d9f567b6fa5f6554ec2180b4f1249587f1473 test/unit/tools/test_data_parameters.py --- /dev/null +++ b/test/unit/tools/test_data_parameters.py @@ -0,0 +1,223 @@ +from unittest import TestCase + +from galaxy import model +from galaxy.util import bunch +from galaxy.tools.parameters import basic + +from elementtree.ElementTree import XML + +import tools_support + + +class DataToolParameterTestCase( TestCase, tools_support.UsesApp ): + + def test_to_python_none_values( self ): + assert None is self.param.to_python( None, self.app ) + assert 'None' == self.param.to_python( 'None', self.app ) + assert '' == self.param.to_python( '', self.app ) + + def test_to_python_hda( self ): + hda = self._new_hda() + as_python = self.param.to_python( hda.id, self.app ) + assert hda == as_python + + def test_to_python_multi_hdas( self ): + hda1 = self._new_hda() + hda2 = self._new_hda() + as_python = self.param.to_python( "%s,%s" % ( hda1.id, hda2.id ), self.app ) + assert as_python == [ hda1, hda2 ] + + def test_to_python_multi_none( self ): + self.multiple = True + hda = self._new_hda() + # Selection is Optional. may be selected with other stuff, + # not sure the UI should really allow this but easy enough + # to just filter it out. + assert [hda] == self.param.to_python( '%s,None' % hda.id, self.app ) + + def test_field_filter_on_types( self ): + hda1 = MockHistoryDatasetAssociation( name="hda1", id=1 ) + hda2 = MockHistoryDatasetAssociation( name="hda2", id=2 ) + self.stub_active_datasets( hda1, hda2 ) + field = self.param.get_html_field( trans=self.trans ) + assert len( field.options ) == 2 + assert field.options[ 0 ][ 0 ] == "1: hda1" + assert field.options[ 1 ][ 0 ] == "2: hda2" + + assert field.options[ 1 ][ 2 ] # Last one selected + assert not field.options[ 0 ][ 2 ] # Others not selected + + hda2.datatype_matches = False + field = self.param.get_html_field( trans=self.trans ) + assert len( field.options ) == 1 + assert field.options[ 0 ][ 2 ] is True # Last one selected + + def test_field_display_hidden_hdas_only_if_selected( self ): + hda1 = MockHistoryDatasetAssociation( name="hda1", id=1 ) + hda2 = MockHistoryDatasetAssociation( name="hda2", id=2 ) + self.stub_active_datasets( hda1, hda2 ) + hda1.visible = False + hda2.visible = False + field = self.param.get_html_field( trans=self.trans, value=hda2 ) + assert len( field.options ) == 1 # hda1 not an option, not visible or selected + assert field.options[ 0 ][ 0 ] == "2: (hidden) hda2" + + def test_field_implicit_conversion_new( self ): + hda1 = MockHistoryDatasetAssociation( name="hda1", id=1 ) + hda1.datatype_matches = False + hda1.conversion_destination = ( "tabular", None ) + self.stub_active_datasets( hda1 ) + field = self.param.get_html_field( trans=self.trans ) + assert len( field.options ) == 1 + assert field.options[ 0 ][ 0 ] == "1: (as tabular) hda1" + assert field.options[ 0 ][ 1 ] == 1 + + def test_field_implicit_conversion_existing( self ): + hda1 = MockHistoryDatasetAssociation( name="hda1", id=1 ) + hda1.datatype_matches = False + hda1.conversion_destination = ( "tabular", MockHistoryDatasetAssociation( name="hda1converted", id=2 ) ) + self.stub_active_datasets( hda1 ) + field = self.param.get_html_field( trans=self.trans ) + assert len( field.options ) == 1 + assert field.options[ 0 ][ 0 ] == "1: (as tabular) hda1" + # This is difference with previous test, value is existing + # hda id not new one. + assert field.options[ 0 ][ 1 ] == 2 + + def test_field_multiple( self ): + self.multiple = True + field = self.param.get_html_field( trans=self.trans ) + assert field.multiple + + def test_field_empty_selection( self ): + field = self.param.get_html_field( trans=self.trans ) + assert len( field.options ) == 0 + + def test_field_empty_selection_optional( self ): + self.optional = True + field = self.param.get_html_field( trans=self.trans ) + assert len( field.options ) == 1 + option = field.options[ 0 ] + assert option[ 0 ] == "Selection is Optional" + assert option[ 1 ] == "None" + assert option[ 2 ] is True + + def test_get_initial_value_prevents_repeats( self ): + hda1 = MockHistoryDatasetAssociation( name="hda1", id=1 ) + hda2 = MockHistoryDatasetAssociation( name="hda2", id=2 ) + self.stub_active_datasets( hda1, hda2 ) + already_used = [] + assert hda2 == self.param.get_initial_value_from_history_prevent_repeats( self.trans, {}, already_used ) + assert hda1 == self.param.get_initial_value_from_history_prevent_repeats( self.trans, {}, already_used ) + + def test_get_initial_value_is_empty_string_if_no_match( self ): + hda1 = MockHistoryDatasetAssociation( name="hda1", id=1 ) + hda1.visible = False + hda2 = MockHistoryDatasetAssociation( name="hda2", id=2 ) + hda2.visible = False + self.stub_active_datasets( hda1, hda2 ) + assert '' == self.param.get_initial_value( self.trans, {} ) + + def test_get_initial_none_when_optional( self ): + self.optional = True + hda1 = MockHistoryDatasetAssociation( name="hda1", id=1 ) + hda2 = MockHistoryDatasetAssociation( name="hda2", id=2 ) + self.stub_active_datasets( hda1, hda2 ) + assert self.param.get_initial_value( self.trans, {} ) is None + + def test_get_initial_with_previously_converted_data( self ): + hda1 = MockHistoryDatasetAssociation( name="hda1", id=1 ) + hda1.datatype_matches = False + converted = MockHistoryDatasetAssociation( name="hda1converted", id=2 ) + hda1.conversion_destination = ( "tabular", converted ) + self.stub_active_datasets( hda1 ) + assert converted == self.param.get_initial_value( self.trans, {} ) + + def test_get_initial_with_to_be_converted_data( self ): + hda1 = MockHistoryDatasetAssociation( name="hda1", id=1 ) + hda1.datatype_matches = False + hda1.conversion_destination = ( "tabular", None ) + self.stub_active_datasets( hda1 ) + assert hda1 == self.param.get_initial_value( self.trans, {} ) + + def _new_hda( self ): + hda = model.HistoryDatasetAssociation() + hda.visible = True + hda.dataset = model.Dataset() + self.app.model.context.add( hda ) + self.app.model.context.flush( ) + return hda + + def setUp( self ): + self.setup_app( mock_model=False ) + self.mock_tool = bunch.Bunch( + app=self.app, + tool_type="default", + ) + self.test_history = model.History() + self.app.model.context.add( self.test_history ) + self.app.model.context.flush() + self.trans = bunch.Bunch( + app=self.app, + get_history=lambda: self.test_history, + get_current_user_roles=lambda: [], + workflow_building_mode=False, + webapp=bunch.Bunch( name="galaxy" ), + ) + self.multiple = False + self.optional = False + self._param = None + + def stub_active_datasets( self, *hdas ): + self.test_history._active_datasets_children_and_roles = hdas + + @property + def param( self ): + if not self._param: + multi_text = "" + if self.multiple: + multi_text = 'multiple="True"' + optional_text = "" + if self.optional: + optional_text = 'optional="True"' + template_xml = '''<param name="data2" type="data" ext="txt" %s %s></param>''' + self.param_xml = XML( template_xml % ( multi_text, optional_text ) ) + self._param = basic.DataToolParameter( self.mock_tool, self.param_xml ) + + return self._param + + +class MockHistoryDatasetAssociation( object ): + """ Fake HistoryDatasetAssociation stubbed out for testing matching and + stuff like that. + """ + + def __init__( self, test_dataset=None, name="Test Dataset", id=1 ): + if not test_dataset: + test_dataset = model.Dataset() + self.states = model.HistoryDatasetAssociation.states + self.deleted = False + self.dataset = test_dataset + self.visible = True + self.datatype_matches = True + self.conversion_destination = ( None, None ) + self.datatype = bunch.Bunch( + matches_any=lambda formats: self.datatype_matches, + ) + self.dbkey = "hg19" + self.implicitly_converted_parent_datasets = False + + self.name = name + self.hid = id + self.id = id + self.children = [] + + @property + def state( self ): + return self.dataset.state + + def get_dbkey( self ): + return self.dbkey + + def find_conversion_destination( self, formats ): + return self.conversion_destination diff -r 2403d6f67500ec35b16ce604142d98766286b65a -r 767d9f567b6fa5f6554ec2180b4f1249587f1473 test/unit/tools/test_evaluation.py --- a/test/unit/tools/test_evaluation.py +++ b/test/unit/tools/test_evaluation.py @@ -20,6 +20,7 @@ from galaxy.tools.parameters.grouping import ConditionalWhen from galaxy.tools.parameters.basic import IntegerToolParameter from galaxy.tools.parameters.basic import SelectToolParameter +from galaxy.tools.parameters.basic import DataToolParameter from elementtree.ElementTree import XML # Import after model, to ensure elementtree @@ -78,6 +79,18 @@ command_line, extra_filenames = self.evaluator.build( ) self.assertEquals( command_line, "prog1 --thresh=4 --test_param=true" ) + def test_evaluation_of_optional_datasets( self ): + # Make sure optional dataset don't cause evaluation to break and + # evaluate in cheetah templates as 'None'. + select_xml = XML('''<param name="input1" type="data" optional="true"></param>''') + parameter = DataToolParameter( self.tool, select_xml ) + self.job.parameters = [ JobParameter( name="input1", value=u'null' ) ] + self.tool.set_params( { "input1": parameter } ) + self.tool._command_line = "prog1 --opt_input='${input1}'" + self._set_compute_environment() + command_line, extra_filenames = self.evaluator.build( ) + self.assertEquals( command_line, "prog1 --opt_input='None'" ) + def test_evaluation_with_path_rewrites_wrapped( self ): self.tool.check_values = True self.__test_evaluation_with_path_rewrites() https://bitbucket.org/galaxy/galaxy-central/commits/9051ceb43593/ Changeset: 9051ceb43593 User: jmchilton Date: 2014-02-22 05:09:57 Summary: Rearrange unit tests. Move tests that were in tests/unit but could logically be placed into tests/unit/tools or tests/unit/jobs into these directory. Affected #: 8 files diff -r 767d9f567b6fa5f6554ec2180b4f1249587f1473 -r 9051ceb435937348e6417fb96eb9611474496828 test/unit/jobs/test_command_factory.py --- /dev/null +++ b/test/unit/jobs/test_command_factory.py @@ -0,0 +1,156 @@ +from os import getcwd +from unittest import TestCase + +from galaxy.jobs.command_factory import build_command +from galaxy.util.bunch import Bunch + +MOCK_COMMAND_LINE = "/opt/galaxy/tools/bowtie /mnt/galaxyData/files/000/input000.dat" +TEST_METADATA_LINE = "set_metadata_and_stuff.sh" +TEST_FILES_PATH = "file_path" + + +class TestCommandFactory(TestCase): + + def setUp(self): + self.job_wrapper = MockJobWrapper() + self.workdir_outputs = [] + + def workdir_outputs(job_wrapper, **kwds): + assert job_wrapper == self.job_wrapper + return self.workdir_outputs + + self.runner = Bunch(app=Bunch(model=Bunch(Dataset=Bunch(file_path=TEST_FILES_PATH))), get_work_dir_outputs=workdir_outputs) + self.include_metadata = False + self.include_work_dir_outputs = True + + def test_simplest_command(self): + self.include_work_dir_outputs = False + self.__assert_command_is( MOCK_COMMAND_LINE ) + + def test_shell_commands(self): + self.include_work_dir_outputs = False + dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"] + self.job_wrapper.dependency_shell_commands = dep_commands + self.__assert_command_is( "%s; %s" % (dep_commands[0], MOCK_COMMAND_LINE) ) + + def test_remote_dependency_resolution(self): + self.include_work_dir_outputs = False + dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"] + self.job_wrapper.dependency_shell_commands = dep_commands + self.__assert_command_is(MOCK_COMMAND_LINE, remote_command_params=dict(dependency_resolution="remote")) + + def test_explicit_local_dependency_resolution(self): + self.include_work_dir_outputs = False + dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"] + self.job_wrapper.dependency_shell_commands = dep_commands + self.__assert_command_is("%s; %s" % (dep_commands[0], MOCK_COMMAND_LINE), + remote_command_params=dict(dependency_resolution="local")) + + def test_task_prepare_inputs(self): + self.include_work_dir_outputs = False + self.job_wrapper.prepare_input_files_cmds = ["/opt/split1", "/opt/split2"] + self.__assert_command_is( "/opt/split1; /opt/split2; %s" % MOCK_COMMAND_LINE ) + + def test_workdir_outputs(self): + self.include_work_dir_outputs = True + self.workdir_outputs = [("foo", "bar")] + self.__assert_command_is( '%s; return_code=$?; if [ -f foo ] ; then cp foo bar ; fi; sh -c "exit $return_code"' % MOCK_COMMAND_LINE ) + + def test_set_metadata_skipped_if_unneeded(self): + self.include_metadata = True + self.include_work_dir_outputs = False + self.__assert_command_is( MOCK_COMMAND_LINE ) + + def test_set_metadata(self): + self._test_set_metadata() + + def test_strips_trailing_semicolons(self): + self.job_wrapper.command_line = "%s;" % MOCK_COMMAND_LINE + self._test_set_metadata() + + def _test_set_metadata(self): + self.include_metadata = True + self.include_work_dir_outputs = False + self.job_wrapper.metadata_line = TEST_METADATA_LINE + expected_command = '%s; return_code=$?; cd %s; %s; sh -c "exit $return_code"' % (MOCK_COMMAND_LINE, getcwd(), TEST_METADATA_LINE) + self.__assert_command_is( expected_command ) + + def test_empty_metadata(self): + """ + As produced by TaskWrapper. + """ + self.include_metadata = True + self.include_work_dir_outputs = False + self.job_wrapper.metadata_line = ' ' + # Empty metadata command do not touch command line. + expected_command = '%s' % (MOCK_COMMAND_LINE) + self.__assert_command_is( expected_command ) + + def test_metadata_kwd_defaults(self): + configured_kwds = self.__set_metadata_with_kwds() + assert configured_kwds['exec_dir'] == getcwd() + assert configured_kwds['tmp_dir'] == self.job_wrapper.working_directory + assert configured_kwds['dataset_files_path'] == TEST_FILES_PATH + assert configured_kwds['output_fnames'] == ['output1'] + + def test_metadata_kwds_overrride(self): + configured_kwds = self.__set_metadata_with_kwds( + exec_dir="/path/to/remote/galaxy", + tmp_dir="/path/to/remote/staging/directory/job1", + dataset_files_path="/path/to/remote/datasets/", + output_fnames=['/path/to/remote_output1'], + ) + assert configured_kwds['exec_dir'] == "/path/to/remote/galaxy" + assert configured_kwds['tmp_dir'] == "/path/to/remote/staging/directory/job1" + assert configured_kwds['dataset_files_path'] == "/path/to/remote/datasets/" + assert configured_kwds['output_fnames'] == ['/path/to/remote_output1'] + + def __set_metadata_with_kwds(self, **kwds): + self.include_metadata = True + self.include_work_dir_outputs = False + self.job_wrapper.metadata_line = TEST_METADATA_LINE + if kwds: + self.__command(remote_command_params=dict(metadata_kwds=kwds)) + else: + self.__command() + return self.job_wrapper.configured_external_metadata_kwds + + def __assert_command_is(self, expected_command, **command_kwds): + command = self.__command(**command_kwds) + self.assertEqual(command, expected_command) + + def __command(self, **extra_kwds): + kwds = dict( + runner=self.runner, + job_wrapper=self.job_wrapper, + include_metadata=self.include_metadata, + include_work_dir_outputs=self.include_work_dir_outputs, + **extra_kwds + ) + return build_command(**kwds) + + +class MockJobWrapper(object): + + def __init__(self): + self.write_version_cmd = None + self.command_line = MOCK_COMMAND_LINE + self.dependency_shell_commands = [] + self.metadata_line = None + self.configured_external_metadata_kwds = None + self.working_directory = "job1" + self.prepare_input_files_cmds = None + + def get_command_line(self): + return self.command_line + + @property + def requires_setting_metadata(self): + return self.metadata_line is not None + + def setup_external_metadata(self, *args, **kwds): + self.configured_external_metadata_kwds = kwds + return self.metadata_line + + def get_output_fnames(self): + return ["output1"] diff -r 767d9f567b6fa5f6554ec2180b4f1249587f1473 -r 9051ceb435937348e6417fb96eb9611474496828 test/unit/jobs/test_job_output_checker.py --- /dev/null +++ b/test/unit/jobs/test_job_output_checker.py @@ -0,0 +1,62 @@ +from unittest import TestCase +from galaxy.util.bunch import Bunch +from galaxy.jobs.output_checker import check_output +from galaxy.jobs.error_level import StdioErrorLevel + + +class OutputCheckerTestCase( TestCase ): + + def setUp( self ): + self.tool = Bunch( + stdio_regexes=[], + stdio_exit_codes=[], + ) + self.job = Bunch( + stdout=None, + stderr=None, + get_id_tag=lambda: "test_id", + ) + self.stdout = '' + self.stderr = '' + self.tool_exit_code = None + + def test_default_no_stderr_success( self ): + self.__assertSuccessful() + + def test_default_stderr_failure( self ): + self.stderr = 'foo' + self.__assertNotSuccessful() + + def test_exit_code_error( self ): + mock_exit_code = Bunch( range_start=1, range_end=1, error_level=StdioErrorLevel.FATAL, desc=None ) + self.tool.stdio_exit_codes.append( mock_exit_code ) + self.tool_exit_code = 1 + self.__assertNotSuccessful() + + def test_exit_code_success( self ): + mock_exit_code = Bunch( range_start=1, range_end=1, error_level=StdioErrorLevel.FATAL, desc=None ) + self.tool.stdio_exit_codes.append( mock_exit_code ) + self.tool_exit_code = 0 + self.__assertSuccessful() + + def test_problematic_strings( self ): + problematic_str = '\x80abc' + regex_rule = Bunch( match=r'.abc', stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None ) + self.tool.stdio_regexes = [ regex_rule ] + self.stderr = problematic_str + self.__assertNotSuccessful() + + problematic_str = '\x80abc' + regex_rule = Bunch( match=r'.abcd', stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None ) + self.tool.stdio_regexes = [ regex_rule ] + self.stderr = problematic_str + self.__assertSuccessful() + + def __assertSuccessful( self ): + self.assertTrue( self.__check_output() ) + + def __assertNotSuccessful( self ): + self.assertFalse( self.__check_output() ) + + def __check_output( self ): + return check_output( self.tool, self.stdout, self.stderr, self.tool_exit_code, self.job ) diff -r 767d9f567b6fa5f6554ec2180b4f1249587f1473 -r 9051ceb435937348e6417fb96eb9611474496828 test/unit/test_command_factory.py --- a/test/unit/test_command_factory.py +++ /dev/null @@ -1,156 +0,0 @@ -from os import getcwd -from unittest import TestCase - -from galaxy.jobs.command_factory import build_command -from galaxy.util.bunch import Bunch - -MOCK_COMMAND_LINE = "/opt/galaxy/tools/bowtie /mnt/galaxyData/files/000/input000.dat" -TEST_METADATA_LINE = "set_metadata_and_stuff.sh" -TEST_FILES_PATH = "file_path" - - -class TestCommandFactory(TestCase): - - def setUp(self): - self.job_wrapper = MockJobWrapper() - self.workdir_outputs = [] - - def workdir_outputs(job_wrapper, **kwds): - assert job_wrapper == self.job_wrapper - return self.workdir_outputs - - self.runner = Bunch(app=Bunch(model=Bunch(Dataset=Bunch(file_path=TEST_FILES_PATH))), get_work_dir_outputs=workdir_outputs) - self.include_metadata = False - self.include_work_dir_outputs = True - - def test_simplest_command(self): - self.include_work_dir_outputs = False - self.__assert_command_is( MOCK_COMMAND_LINE ) - - def test_shell_commands(self): - self.include_work_dir_outputs = False - dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"] - self.job_wrapper.dependency_shell_commands = dep_commands - self.__assert_command_is( "%s; %s" % (dep_commands[0], MOCK_COMMAND_LINE) ) - - def test_remote_dependency_resolution(self): - self.include_work_dir_outputs = False - dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"] - self.job_wrapper.dependency_shell_commands = dep_commands - self.__assert_command_is(MOCK_COMMAND_LINE, remote_command_params=dict(dependency_resolution="remote")) - - def test_explicit_local_dependency_resolution(self): - self.include_work_dir_outputs = False - dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"] - self.job_wrapper.dependency_shell_commands = dep_commands - self.__assert_command_is("%s; %s" % (dep_commands[0], MOCK_COMMAND_LINE), - remote_command_params=dict(dependency_resolution="local")) - - def test_task_prepare_inputs(self): - self.include_work_dir_outputs = False - self.job_wrapper.prepare_input_files_cmds = ["/opt/split1", "/opt/split2"] - self.__assert_command_is( "/opt/split1; /opt/split2; %s" % MOCK_COMMAND_LINE ) - - def test_workdir_outputs(self): - self.include_work_dir_outputs = True - self.workdir_outputs = [("foo", "bar")] - self.__assert_command_is( '%s; return_code=$?; if [ -f foo ] ; then cp foo bar ; fi; sh -c "exit $return_code"' % MOCK_COMMAND_LINE ) - - def test_set_metadata_skipped_if_unneeded(self): - self.include_metadata = True - self.include_work_dir_outputs = False - self.__assert_command_is( MOCK_COMMAND_LINE ) - - def test_set_metadata(self): - self._test_set_metadata() - - def test_strips_trailing_semicolons(self): - self.job_wrapper.command_line = "%s;" % MOCK_COMMAND_LINE - self._test_set_metadata() - - def _test_set_metadata(self): - self.include_metadata = True - self.include_work_dir_outputs = False - self.job_wrapper.metadata_line = TEST_METADATA_LINE - expected_command = '%s; return_code=$?; cd %s; %s; sh -c "exit $return_code"' % (MOCK_COMMAND_LINE, getcwd(), TEST_METADATA_LINE) - self.__assert_command_is( expected_command ) - - def test_empty_metadata(self): - """ - As produced by TaskWrapper. - """ - self.include_metadata = True - self.include_work_dir_outputs = False - self.job_wrapper.metadata_line = ' ' - # Empty metadata command do not touch command line. - expected_command = '%s' % (MOCK_COMMAND_LINE) - self.__assert_command_is( expected_command ) - - def test_metadata_kwd_defaults(self): - configured_kwds = self.__set_metadata_with_kwds() - assert configured_kwds['exec_dir'] == getcwd() - assert configured_kwds['tmp_dir'] == self.job_wrapper.working_directory - assert configured_kwds['dataset_files_path'] == TEST_FILES_PATH - assert configured_kwds['output_fnames'] == ['output1'] - - def test_metadata_kwds_overrride(self): - configured_kwds = self.__set_metadata_with_kwds( - exec_dir="/path/to/remote/galaxy", - tmp_dir="/path/to/remote/staging/directory/job1", - dataset_files_path="/path/to/remote/datasets/", - output_fnames=['/path/to/remote_output1'], - ) - assert configured_kwds['exec_dir'] == "/path/to/remote/galaxy" - assert configured_kwds['tmp_dir'] == "/path/to/remote/staging/directory/job1" - assert configured_kwds['dataset_files_path'] == "/path/to/remote/datasets/" - assert configured_kwds['output_fnames'] == ['/path/to/remote_output1'] - - def __set_metadata_with_kwds(self, **kwds): - self.include_metadata = True - self.include_work_dir_outputs = False - self.job_wrapper.metadata_line = TEST_METADATA_LINE - if kwds: - self.__command(remote_command_params=dict(metadata_kwds=kwds)) - else: - self.__command() - return self.job_wrapper.configured_external_metadata_kwds - - def __assert_command_is(self, expected_command, **command_kwds): - command = self.__command(**command_kwds) - self.assertEqual(command, expected_command) - - def __command(self, **extra_kwds): - kwds = dict( - runner=self.runner, - job_wrapper=self.job_wrapper, - include_metadata=self.include_metadata, - include_work_dir_outputs=self.include_work_dir_outputs, - **extra_kwds - ) - return build_command(**kwds) - - -class MockJobWrapper(object): - - def __init__(self): - self.write_version_cmd = None - self.command_line = MOCK_COMMAND_LINE - self.dependency_shell_commands = [] - self.metadata_line = None - self.configured_external_metadata_kwds = None - self.working_directory = "job1" - self.prepare_input_files_cmds = None - - def get_command_line(self): - return self.command_line - - @property - def requires_setting_metadata(self): - return self.metadata_line is not None - - def setup_external_metadata(self, *args, **kwds): - self.configured_external_metadata_kwds = kwds - return self.metadata_line - - def get_output_fnames(self): - return ["output1"] diff -r 767d9f567b6fa5f6554ec2180b4f1249587f1473 -r 9051ceb435937348e6417fb96eb9611474496828 test/unit/test_job_output_checker.py --- a/test/unit/test_job_output_checker.py +++ /dev/null @@ -1,62 +0,0 @@ -from unittest import TestCase -from galaxy.util.bunch import Bunch -from galaxy.jobs.output_checker import check_output -from galaxy.jobs.error_level import StdioErrorLevel - - -class OutputCheckerTestCase( TestCase ): - - def setUp( self ): - self.tool = Bunch( - stdio_regexes=[], - stdio_exit_codes=[], - ) - self.job = Bunch( - stdout=None, - stderr=None, - get_id_tag=lambda: "test_id", - ) - self.stdout = '' - self.stderr = '' - self.tool_exit_code = None - - def test_default_no_stderr_success( self ): - self.__assertSuccessful() - - def test_default_stderr_failure( self ): - self.stderr = 'foo' - self.__assertNotSuccessful() - - def test_exit_code_error( self ): - mock_exit_code = Bunch( range_start=1, range_end=1, error_level=StdioErrorLevel.FATAL, desc=None ) - self.tool.stdio_exit_codes.append( mock_exit_code ) - self.tool_exit_code = 1 - self.__assertNotSuccessful() - - def test_exit_code_success( self ): - mock_exit_code = Bunch( range_start=1, range_end=1, error_level=StdioErrorLevel.FATAL, desc=None ) - self.tool.stdio_exit_codes.append( mock_exit_code ) - self.tool_exit_code = 0 - self.__assertSuccessful() - - def test_problematic_strings( self ): - problematic_str = '\x80abc' - regex_rule = Bunch( match=r'.abc', stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None ) - self.tool.stdio_regexes = [ regex_rule ] - self.stderr = problematic_str - self.__assertNotSuccessful() - - problematic_str = '\x80abc' - regex_rule = Bunch( match=r'.abcd', stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None ) - self.tool.stdio_regexes = [ regex_rule ] - self.stderr = problematic_str - self.__assertSuccessful() - - def __assertSuccessful( self ): - self.assertTrue( self.__check_output() ) - - def __assertNotSuccessful( self ): - self.assertFalse( self.__check_output() ) - - def __check_output( self ): - return check_output( self.tool, self.stdout, self.stderr, self.tool_exit_code, self.job ) diff -r 767d9f567b6fa5f6554ec2180b4f1249587f1473 -r 9051ceb435937348e6417fb96eb9611474496828 test/unit/test_tool_deps.py --- a/test/unit/test_tool_deps.py +++ /dev/null @@ -1,378 +0,0 @@ -import tempfile -import os.path -from stat import S_IXUSR -from os import makedirs, stat, symlink, chmod, environ -from shutil import rmtree -from galaxy.tools.deps import DependencyManager, INDETERMINATE_DEPENDENCY -from galaxy.tools.deps.resolvers.galaxy_packages import GalaxyPackageDependency -from galaxy.tools.deps.resolvers.modules import ModuleDependencyResolver, ModuleDependency -from galaxy.util.bunch import Bunch -from contextlib import contextmanager -from subprocess import Popen, PIPE - - -def test_tool_dependencies(): - # Setup directories - - with __test_base_path() as base_path: - for name, version, sub in [ ( "dep1", "1.0", "env.sh" ), ( "dep1", "2.0", "bin" ), ( "dep2", "1.0", None ) ]: - if sub == "bin": - p = os.path.join( base_path, name, version, "bin" ) - else: - p = os.path.join( base_path, name, version ) - try: - makedirs( p ) - except: - pass - if sub == "env.sh": - __touch( os.path.join( p, "env.sh" ) ) - - dm = DependencyManager( default_base_path=base_path ) - dependency = dm.find_dep( "dep1", "1.0" ) - assert dependency.script == os.path.join( base_path, 'dep1', '1.0', 'env.sh' ) - assert dependency.path == os.path.join( base_path, 'dep1', '1.0' ) - assert dependency.version == "1.0" - dependency = dm.find_dep( "dep1", "2.0" ) - assert dependency.script == None - assert dependency.path == os.path.join( base_path, 'dep1', '2.0' ) - assert dependency.version == "2.0" - - ## Test default versions - symlink( os.path.join( base_path, 'dep1', '2.0'), os.path.join( base_path, 'dep1', 'default' ) ) - dependency = dm.find_dep( "dep1", None ) - assert dependency.version == "2.0" - - ## Test default resolve will be fall back on default package dependency - ## when using the default resolver. - dependency = dm.find_dep( "dep1", "2.1" ) - assert dependency.version == "2.0" # 2.0 is defined as default_version - - -TEST_REPO_USER = "devteam" -TEST_REPO_NAME = "bwa" -TEST_REPO_CHANGESET = "12abcd41223da" -TEST_VERSION = "0.5.9" - - -def test_toolshed_set_enviornment_requiremetns(): - with __test_base_path() as base_path: - test_repo = __build_test_repo('set_environment') - dm = DependencyManager( default_base_path=base_path ) - env_settings_dir = os.path.join(base_path, "environment_settings", TEST_REPO_NAME, TEST_REPO_USER, TEST_REPO_NAME, TEST_REPO_CHANGESET) - os.makedirs(env_settings_dir) - dependency = dm.find_dep( TEST_REPO_NAME, version=None, type='set_environment', installed_tool_dependencies=[test_repo] ) - assert dependency.version == None - assert dependency.script == os.path.join(env_settings_dir, "env.sh") - - -def test_toolshed_package_requirements(): - with __test_base_path() as base_path: - test_repo = __build_test_repo('package', version=TEST_VERSION) - dm = DependencyManager( default_base_path=base_path ) - package_dir = __build_ts_test_package(base_path) - dependency = dm.find_dep( TEST_REPO_NAME, version=TEST_VERSION, type='package', installed_tool_dependencies=[test_repo] ) - assert dependency.version == TEST_VERSION - assert dependency.script == os.path.join(package_dir, "env.sh") - - -def test_toolshed_tools_fallback_on_manual_dependencies(): - with __test_base_path() as base_path: - dm = DependencyManager( default_base_path=base_path ) - test_repo = __build_test_repo('package', version=TEST_VERSION) - env_path = __setup_galaxy_package_dep(base_path, "dep1", "1.0") - dependency = dm.find_dep( "dep1", version="1.0", type='package', installed_tool_dependencies=[test_repo] ) - assert dependency.version == "1.0" - assert dependency.script == env_path - - -def test_toolshed_greater_precendence(): - with __test_base_path() as base_path: - dm = DependencyManager( default_base_path=base_path ) - test_repo = __build_test_repo('package', version=TEST_VERSION) - ts_package_dir = __build_ts_test_package(base_path) - gx_env_path = __setup_galaxy_package_dep(base_path, TEST_REPO_NAME, TEST_VERSION) - ts_env_path = os.path.join(ts_package_dir, "env.sh") - dependency = dm.find_dep( TEST_REPO_NAME, version=TEST_VERSION, type='package', installed_tool_dependencies=[test_repo] ) - assert dependency.script != gx_env_path # Not the galaxy path, it should be the tool shed path used. - assert dependency.script == ts_env_path - - -def __build_ts_test_package(base_path, script_contents=''): - package_dir = os.path.join(base_path, TEST_REPO_NAME, TEST_VERSION, TEST_REPO_USER, TEST_REPO_NAME, TEST_REPO_CHANGESET) - __touch(os.path.join(package_dir, 'env.sh'), script_contents) - return package_dir - - -def test_module_dependency_resolver(): - with __test_base_path() as temp_directory: - module_script = os.path.join(temp_directory, "modulecmd") - __write_script(module_script, '''#!/bin/sh -cat %s/example_output 1>&2; -''' % temp_directory) - with open(os.path.join(temp_directory, "example_output"), "w") as f: - # Subset of module avail from MSI cluster. - f.write(''' --------------------------- /soft/modules/modulefiles --------------------------- -JAGS/3.2.0-gcc45 -JAGS/3.3.0-gcc4.7.2 -ProbABEL/0.1-3 -ProbABEL/0.1-9e -R/2.12.2 -R/2.13.1 -R/2.14.1 -R/2.15.0 -R/2.15.1 -R/3.0.1(default) -abokia-blast/2.0.2-130524/ompi_intel -abokia-blast/2.0.2-130630/ompi_intel - ---------------------------- /soft/intel/modulefiles ---------------------------- -advisor/2013/update1 intel/11.1.075 mkl/10.2.1.017 -advisor/2013/update2 intel/11.1.080 mkl/10.2.5.035 -advisor/2013/update3 intel/12.0 mkl/10.2.7.041 -''') - resolver = ModuleDependencyResolver(None, modulecmd=module_script) - module = resolver.resolve( name="R", version=None, type="package" ) - assert module.module_name == "R" - assert module.module_version == None - - module = resolver.resolve( name="R", version="3.0.1", type="package" ) - assert module.module_name == "R" - assert module.module_version == "3.0.1" - - module = resolver.resolve( name="R", version="3.0.4", type="package" ) - assert module == INDETERMINATE_DEPENDENCY - - -def test_module_dependency(): - with __test_base_path() as temp_directory: - ## Create mock modulecmd script that just exports a variable - ## the way modulecmd sh load would, but also validate correct - ## module name and version are coming through. - mock_modulecmd = os.path.join(temp_directory, 'modulecmd') - __write_script(mock_modulecmd, '''#!/bin/sh -if [ $3 != "foomodule/1.0" ]; -then - exit 1 -fi -echo 'FOO="bar"' -''') - resolver = Bunch(modulecmd=mock_modulecmd) - dependency = ModuleDependency(resolver, "foomodule", "1.0") - __assert_foo_exported( dependency.shell_commands( Bunch( type="package" ) ) ) - - -def __write_script(path, contents): - with open(path, 'w') as f: - f.write(contents) - st = stat(path) - chmod(path, st.st_mode | S_IXUSR) - - -def test_galaxy_dependency_object_script(): - with __test_base_path() as base_path: - ## Create env.sh file that just exports variable FOO and verify it - ## shell_commands export it correctly. - env_path = __setup_galaxy_package_dep(base_path, TEST_REPO_NAME, TEST_VERSION, "export FOO=\"bar\"") - dependency = GalaxyPackageDependency(env_path, os.path.dirname(env_path), TEST_VERSION) - __assert_foo_exported( dependency.shell_commands( Bunch( type="package" ) ) ) - - -def test_shell_commands_built(): - ## Test that dependency manager builds valid shell commands for a list of - ## requirements. - with __test_base_path() as base_path: - dm = DependencyManager( default_base_path=base_path ) - __setup_galaxy_package_dep( base_path, TEST_REPO_NAME, TEST_VERSION, contents="export FOO=\"bar\"" ) - mock_requirements = [ Bunch(type="package", version=TEST_VERSION, name=TEST_REPO_NAME ) ] - commands = dm.dependency_shell_commands( mock_requirements ) - __assert_foo_exported( commands ) - - -def __assert_foo_exported( commands ): - command = ["bash", "-c", "%s; echo \"$FOO\"" % "".join(commands)] - process = Popen(command, stdout=PIPE) - output = process.communicate()[0].strip() - assert output == 'bar', "Command %s exports FOO as %s, not bar" % (command, output) - - -def __setup_galaxy_package_dep(base_path, name, version, contents=""): - dep_directory = os.path.join( base_path, name, version ) - env_path = os.path.join( dep_directory, "env.sh" ) - __touch( env_path, contents ) - return env_path - - -def __touch( fname, data=None ): - dirname = os.path.dirname( fname ) - if not os.path.exists( dirname ): - makedirs( dirname ) - f = open( fname, 'w' ) - try: - if data: - f.write( data ) - finally: - f.close() - - -def __build_test_repo(type, version=None): - return Bunch( - owner=TEST_REPO_USER, - name=TEST_REPO_NAME, - type=type, - version=version, - tool_shed_repository=Bunch( - owner=TEST_REPO_USER, - name=TEST_REPO_NAME, - installed_changeset_revision=TEST_REPO_CHANGESET - ) - ) - - -@contextmanager -def __test_base_path(): - base_path = tempfile.mkdtemp() - try: - yield base_path - finally: - rmtree(base_path) - - -def test_parse(): - with __parse_resolvers('''<dependency_resolvers> - <tool_shed_packages /> - <galaxy_packages /> -</dependency_resolvers> -''') as dependency_resolvers: - assert 'ToolShed' in dependency_resolvers[0].__class__.__name__ - assert 'Galaxy' in dependency_resolvers[1].__class__.__name__ - - with __parse_resolvers('''<dependency_resolvers> - <galaxy_packages /> - <tool_shed_packages /> -</dependency_resolvers> -''') as dependency_resolvers: - assert 'Galaxy' in dependency_resolvers[0].__class__.__name__ - assert 'ToolShed' in dependency_resolvers[1].__class__.__name__ - - with __parse_resolvers('''<dependency_resolvers> - <galaxy_packages /> - <tool_shed_packages /> - <galaxy_packages versionless="true" /> -</dependency_resolvers> -''') as dependency_resolvers: - assert not dependency_resolvers[0].versionless - assert dependency_resolvers[2].versionless - - with __parse_resolvers('''<dependency_resolvers> - <galaxy_packages /> - <tool_shed_packages /> - <galaxy_packages base_path="/opt/galaxy/legacy/"/> -</dependency_resolvers> -''') as dependency_resolvers: - # Unspecified base_paths are both default_base_paths - assert dependency_resolvers[0].base_path == dependency_resolvers[1].base_path - # Can specify custom base path... - assert dependency_resolvers[2].base_path == "/opt/galaxy/legacy" - # ... that is different from the default. - assert dependency_resolvers[0].base_path != dependency_resolvers[2].base_path - - -def test_uses_tool_shed_dependencies(): - with __dependency_manager('''<dependency_resolvers> - <galaxy_packages /> -</dependency_resolvers> -''') as dm: - assert not dm.uses_tool_shed_dependencies() - - with __dependency_manager('''<dependency_resolvers> - <tool_shed_packages /> -</dependency_resolvers> -''') as dm: - assert dm.uses_tool_shed_dependencies() - - -def test_config_module_defaults(): - with __parse_resolvers('''<dependency_resolvers> - <modules prefetch="false" /> -</dependency_resolvers> -''') as dependency_resolvers: - module_resolver = dependency_resolvers[0] - assert module_resolver.module_checker.__class__.__name__ == "AvailModuleChecker" - - -def test_config_modulepath(): - # Test reads and splits MODULEPATH if modulepath is not specified. - with __parse_resolvers('''<dependency_resolvers> - <modules find_by="directory" modulepath="/opt/modules/modulefiles:/usr/local/modules/modulefiles" /> -</dependency_resolvers> -''') as dependency_resolvers: - assert dependency_resolvers[0].module_checker.directories == ["/opt/modules/modulefiles", "/usr/local/modules/modulefiles"] - - -def test_config_MODULEPATH(): - # Test reads and splits MODULEPATH if modulepath is not specified. - with __environ({"MODULEPATH": "/opt/modules/modulefiles:/usr/local/modules/modulefiles"}): - with __parse_resolvers('''<dependency_resolvers> - <modules find_by="directory" /> -</dependency_resolvers> -''') as dependency_resolvers: - assert dependency_resolvers[0].module_checker.directories == ["/opt/modules/modulefiles", "/usr/local/modules/modulefiles"] - - -def test_config_MODULESHOME(): - # Test fallbacks to read MODULESHOME if modulepath is not specified and - # neither is MODULEPATH. - with __environ({"MODULESHOME": "/opt/modules"}, remove="MODULEPATH"): - with __parse_resolvers('''<dependency_resolvers> - <modules find_by="directory" /> -</dependency_resolvers> -''') as dependency_resolvers: - assert dependency_resolvers[0].module_checker.directories == ["/opt/modules/modulefiles"] - - -def test_config_module_directory_searcher(): - with __parse_resolvers('''<dependency_resolvers> - <modules find_by="directory" modulepath="/opt/Modules/modulefiles" /> -</dependency_resolvers> -''') as dependency_resolvers: - module_resolver = dependency_resolvers[0] - assert module_resolver.module_checker.directories == ["/opt/Modules/modulefiles"] - - -@contextmanager -def __environ(values, remove=[]): - """ - Modify the environment for a test, adding/updating values in dict `values` and - removing any environment variables mentioned in list `remove`. - """ - new_keys = set(environ.keys()) - set(values.keys()) - old_environ = environ.copy() - try: - environ.update(values) - for to_remove in remove: - try: - del environ[remove] - except KeyError: - pass - yield - finally: - environ.update(old_environ) - for key in new_keys: - del environ[key] - - -@contextmanager -def __parse_resolvers(xml_content): - with __dependency_manager(xml_content) as dm: - yield dm.dependency_resolvers - - -@contextmanager -def __dependency_manager(xml_content): - with __test_base_path() as base_path: - f = tempfile.NamedTemporaryFile() - f.write(xml_content) - f.flush() - dm = DependencyManager( default_base_path=base_path, conf_file=f.name ) - yield dm diff -r 767d9f567b6fa5f6554ec2180b4f1249587f1473 -r 9051ceb435937348e6417fb96eb9611474496828 test/unit/test_tool_loader.py --- a/test/unit/test_tool_loader.py +++ /dev/null @@ -1,191 +0,0 @@ -from tempfile import mkdtemp -from shutil import rmtree -import os - -from galaxy.util import parse_xml -from galaxy.tools.loader import template_macro_params, load_tool - -def test_loader(): - - class TestToolDirectory(object): - def __init__(self): - self.temp_directory = mkdtemp() - - def __enter__(self): - return self - - def __exit__(self, type, value, tb): - rmtree(self.temp_directory) - - def write(self, contents, name="tool.xml"): - open(os.path.join(self.temp_directory, name), "w").write(contents) - - def load(self, name="tool.xml", preprocess=True): - if preprocess: - loader = load_tool - else: - loader = parse_xml - return loader(os.path.join(self.temp_directory, name)) - - ## Test simple macro replacement. - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs" /> - <macros> - <macro name="inputs"> - <inputs /> - </macro> - </macros> -</tool>''') - xml = tool_dir.load(preprocess=False) - assert xml.find("inputs") is None - xml = tool_dir.load(preprocess=True) - assert xml.find("inputs") is not None - - # Test importing macros from external files - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs" /> - <macros> - <import>external.xml</import> - </macros> -</tool>''') - - tool_dir.write(''' -<macros> - <macro name="inputs"> - <inputs /> - </macro> -</macros>''', name="external.xml") - xml = tool_dir.load(preprocess=False) - assert xml.find("inputs") is None - xml = tool_dir.load(preprocess=True) - assert xml.find("inputs") is not None - - # Test macros with unnamed yield statements. - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs"> - <input name="first_input" /> - </expand> - <macros> - <macro name="inputs"> - <inputs> - <yield /> - </inputs> - </macro> - </macros> -</tool>''') - xml = tool_dir.load() - assert xml.find("inputs").find("input").get("name") == "first_input" - - # Test recursive macro applications. - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs"> - <input name="first_input" /> - <expand macro="second" /> - </expand> - <macros> - <macro name="inputs"> - <inputs> - <yield /> - </inputs> - </macro> - <macro name="second"> - <input name="second_input" /> - </macro> - </macros> -</tool>''') - xml = tool_dir.load() - assert xml.find("inputs").findall("input")[1].get("name") == "second_input" - - # Test recursive macro applications. - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs"> - <input name="first_input" /> - <expand macro="second" /> - </expand> - <macros> - <macro name="inputs"> - <inputs> - <yield /> - </inputs> - </macro> - <macro name="second"> - <expand macro="second_delegate" /> - </macro> - <macro name="second_delegate"> - <input name="second_input" /> - </macro> - </macros> -</tool>''') - xml = tool_dir.load() - assert xml.find("inputs").findall("input")[1].get("name") == "second_input" - - # Test <xml> is shortcut for macro type="xml" - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs" /> - <macros> - <xml name="inputs"> - <inputs /> - </xml> - </macros> -</tool>''') - xml = tool_dir.load() - assert xml.find("inputs") is not None - - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <command interpreter="python">tool_wrapper.py - #include source=$tool_params - </command> - <macros> - <template name="tool_params">-a 1 -b 2</template> - </macros> -</tool> -''') - xml = tool_dir.load() - params_dict = template_macro_params(xml.getroot()) - assert params_dict['tool_params'] == "-a 1 -b 2" - - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <macros> - <token name="@CITATION@">The citation.</token> - </macros> - <help>@CITATION@</help> - <another> - <tag /> - </another> -</tool> -''') - xml = tool_dir.load() - help_el = xml.find("help") - assert help_el.text == "The citation.", help_el.text - - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <macros> - <token name="@TAG_VAL@">The value.</token> - </macros> - <another> - <tag value="@TAG_VAL@" /> - </another> -</tool> -''') - xml = tool_dir.load() - tag_el = xml.find("another").find("tag") - value = tag_el.get('value') - assert value == "The value.", value diff -r 767d9f567b6fa5f6554ec2180b4f1249587f1473 -r 9051ceb435937348e6417fb96eb9611474496828 test/unit/tools/test_tool_deps.py --- /dev/null +++ b/test/unit/tools/test_tool_deps.py @@ -0,0 +1,378 @@ +import tempfile +import os.path +from stat import S_IXUSR +from os import makedirs, stat, symlink, chmod, environ +from shutil import rmtree +from galaxy.tools.deps import DependencyManager, INDETERMINATE_DEPENDENCY +from galaxy.tools.deps.resolvers.galaxy_packages import GalaxyPackageDependency +from galaxy.tools.deps.resolvers.modules import ModuleDependencyResolver, ModuleDependency +from galaxy.util.bunch import Bunch +from contextlib import contextmanager +from subprocess import Popen, PIPE + + +def test_tool_dependencies(): + # Setup directories + + with __test_base_path() as base_path: + for name, version, sub in [ ( "dep1", "1.0", "env.sh" ), ( "dep1", "2.0", "bin" ), ( "dep2", "1.0", None ) ]: + if sub == "bin": + p = os.path.join( base_path, name, version, "bin" ) + else: + p = os.path.join( base_path, name, version ) + try: + makedirs( p ) + except: + pass + if sub == "env.sh": + __touch( os.path.join( p, "env.sh" ) ) + + dm = DependencyManager( default_base_path=base_path ) + dependency = dm.find_dep( "dep1", "1.0" ) + assert dependency.script == os.path.join( base_path, 'dep1', '1.0', 'env.sh' ) + assert dependency.path == os.path.join( base_path, 'dep1', '1.0' ) + assert dependency.version == "1.0" + dependency = dm.find_dep( "dep1", "2.0" ) + assert dependency.script == None + assert dependency.path == os.path.join( base_path, 'dep1', '2.0' ) + assert dependency.version == "2.0" + + ## Test default versions + symlink( os.path.join( base_path, 'dep1', '2.0'), os.path.join( base_path, 'dep1', 'default' ) ) + dependency = dm.find_dep( "dep1", None ) + assert dependency.version == "2.0" + + ## Test default resolve will be fall back on default package dependency + ## when using the default resolver. + dependency = dm.find_dep( "dep1", "2.1" ) + assert dependency.version == "2.0" # 2.0 is defined as default_version + + +TEST_REPO_USER = "devteam" +TEST_REPO_NAME = "bwa" +TEST_REPO_CHANGESET = "12abcd41223da" +TEST_VERSION = "0.5.9" + + +def test_toolshed_set_enviornment_requiremetns(): + with __test_base_path() as base_path: + test_repo = __build_test_repo('set_environment') + dm = DependencyManager( default_base_path=base_path ) + env_settings_dir = os.path.join(base_path, "environment_settings", TEST_REPO_NAME, TEST_REPO_USER, TEST_REPO_NAME, TEST_REPO_CHANGESET) + os.makedirs(env_settings_dir) + dependency = dm.find_dep( TEST_REPO_NAME, version=None, type='set_environment', installed_tool_dependencies=[test_repo] ) + assert dependency.version == None + assert dependency.script == os.path.join(env_settings_dir, "env.sh") + + +def test_toolshed_package_requirements(): + with __test_base_path() as base_path: + test_repo = __build_test_repo('package', version=TEST_VERSION) + dm = DependencyManager( default_base_path=base_path ) + package_dir = __build_ts_test_package(base_path) + dependency = dm.find_dep( TEST_REPO_NAME, version=TEST_VERSION, type='package', installed_tool_dependencies=[test_repo] ) + assert dependency.version == TEST_VERSION + assert dependency.script == os.path.join(package_dir, "env.sh") + + +def test_toolshed_tools_fallback_on_manual_dependencies(): + with __test_base_path() as base_path: + dm = DependencyManager( default_base_path=base_path ) + test_repo = __build_test_repo('package', version=TEST_VERSION) + env_path = __setup_galaxy_package_dep(base_path, "dep1", "1.0") + dependency = dm.find_dep( "dep1", version="1.0", type='package', installed_tool_dependencies=[test_repo] ) + assert dependency.version == "1.0" + assert dependency.script == env_path + + +def test_toolshed_greater_precendence(): + with __test_base_path() as base_path: + dm = DependencyManager( default_base_path=base_path ) + test_repo = __build_test_repo('package', version=TEST_VERSION) + ts_package_dir = __build_ts_test_package(base_path) + gx_env_path = __setup_galaxy_package_dep(base_path, TEST_REPO_NAME, TEST_VERSION) + ts_env_path = os.path.join(ts_package_dir, "env.sh") + dependency = dm.find_dep( TEST_REPO_NAME, version=TEST_VERSION, type='package', installed_tool_dependencies=[test_repo] ) + assert dependency.script != gx_env_path # Not the galaxy path, it should be the tool shed path used. + assert dependency.script == ts_env_path + + +def __build_ts_test_package(base_path, script_contents=''): + package_dir = os.path.join(base_path, TEST_REPO_NAME, TEST_VERSION, TEST_REPO_USER, TEST_REPO_NAME, TEST_REPO_CHANGESET) + __touch(os.path.join(package_dir, 'env.sh'), script_contents) + return package_dir + + +def test_module_dependency_resolver(): + with __test_base_path() as temp_directory: + module_script = os.path.join(temp_directory, "modulecmd") + __write_script(module_script, '''#!/bin/sh +cat %s/example_output 1>&2; +''' % temp_directory) + with open(os.path.join(temp_directory, "example_output"), "w") as f: + # Subset of module avail from MSI cluster. + f.write(''' +-------------------------- /soft/modules/modulefiles --------------------------- +JAGS/3.2.0-gcc45 +JAGS/3.3.0-gcc4.7.2 +ProbABEL/0.1-3 +ProbABEL/0.1-9e +R/2.12.2 +R/2.13.1 +R/2.14.1 +R/2.15.0 +R/2.15.1 +R/3.0.1(default) +abokia-blast/2.0.2-130524/ompi_intel +abokia-blast/2.0.2-130630/ompi_intel + +--------------------------- /soft/intel/modulefiles ---------------------------- +advisor/2013/update1 intel/11.1.075 mkl/10.2.1.017 +advisor/2013/update2 intel/11.1.080 mkl/10.2.5.035 +advisor/2013/update3 intel/12.0 mkl/10.2.7.041 +''') + resolver = ModuleDependencyResolver(None, modulecmd=module_script) + module = resolver.resolve( name="R", version=None, type="package" ) + assert module.module_name == "R" + assert module.module_version == None + + module = resolver.resolve( name="R", version="3.0.1", type="package" ) + assert module.module_name == "R" + assert module.module_version == "3.0.1" + + module = resolver.resolve( name="R", version="3.0.4", type="package" ) + assert module == INDETERMINATE_DEPENDENCY + + +def test_module_dependency(): + with __test_base_path() as temp_directory: + ## Create mock modulecmd script that just exports a variable + ## the way modulecmd sh load would, but also validate correct + ## module name and version are coming through. + mock_modulecmd = os.path.join(temp_directory, 'modulecmd') + __write_script(mock_modulecmd, '''#!/bin/sh +if [ $3 != "foomodule/1.0" ]; +then + exit 1 +fi +echo 'FOO="bar"' +''') + resolver = Bunch(modulecmd=mock_modulecmd) + dependency = ModuleDependency(resolver, "foomodule", "1.0") + __assert_foo_exported( dependency.shell_commands( Bunch( type="package" ) ) ) + + +def __write_script(path, contents): + with open(path, 'w') as f: + f.write(contents) + st = stat(path) + chmod(path, st.st_mode | S_IXUSR) + + +def test_galaxy_dependency_object_script(): + with __test_base_path() as base_path: + ## Create env.sh file that just exports variable FOO and verify it + ## shell_commands export it correctly. + env_path = __setup_galaxy_package_dep(base_path, TEST_REPO_NAME, TEST_VERSION, "export FOO=\"bar\"") + dependency = GalaxyPackageDependency(env_path, os.path.dirname(env_path), TEST_VERSION) + __assert_foo_exported( dependency.shell_commands( Bunch( type="package" ) ) ) + + +def test_shell_commands_built(): + ## Test that dependency manager builds valid shell commands for a list of + ## requirements. + with __test_base_path() as base_path: + dm = DependencyManager( default_base_path=base_path ) + __setup_galaxy_package_dep( base_path, TEST_REPO_NAME, TEST_VERSION, contents="export FOO=\"bar\"" ) + mock_requirements = [ Bunch(type="package", version=TEST_VERSION, name=TEST_REPO_NAME ) ] + commands = dm.dependency_shell_commands( mock_requirements ) + __assert_foo_exported( commands ) + + +def __assert_foo_exported( commands ): + command = ["bash", "-c", "%s; echo \"$FOO\"" % "".join(commands)] + process = Popen(command, stdout=PIPE) + output = process.communicate()[0].strip() + assert output == 'bar', "Command %s exports FOO as %s, not bar" % (command, output) + + +def __setup_galaxy_package_dep(base_path, name, version, contents=""): + dep_directory = os.path.join( base_path, name, version ) + env_path = os.path.join( dep_directory, "env.sh" ) + __touch( env_path, contents ) + return env_path + + +def __touch( fname, data=None ): + dirname = os.path.dirname( fname ) + if not os.path.exists( dirname ): + makedirs( dirname ) + f = open( fname, 'w' ) + try: + if data: + f.write( data ) + finally: + f.close() + + +def __build_test_repo(type, version=None): + return Bunch( + owner=TEST_REPO_USER, + name=TEST_REPO_NAME, + type=type, + version=version, + tool_shed_repository=Bunch( + owner=TEST_REPO_USER, + name=TEST_REPO_NAME, + installed_changeset_revision=TEST_REPO_CHANGESET + ) + ) + + +@contextmanager +def __test_base_path(): + base_path = tempfile.mkdtemp() + try: + yield base_path + finally: + rmtree(base_path) + + +def test_parse(): + with __parse_resolvers('''<dependency_resolvers> + <tool_shed_packages /> + <galaxy_packages /> +</dependency_resolvers> +''') as dependency_resolvers: + assert 'ToolShed' in dependency_resolvers[0].__class__.__name__ + assert 'Galaxy' in dependency_resolvers[1].__class__.__name__ + + with __parse_resolvers('''<dependency_resolvers> + <galaxy_packages /> + <tool_shed_packages /> +</dependency_resolvers> +''') as dependency_resolvers: + assert 'Galaxy' in dependency_resolvers[0].__class__.__name__ + assert 'ToolShed' in dependency_resolvers[1].__class__.__name__ + + with __parse_resolvers('''<dependency_resolvers> + <galaxy_packages /> + <tool_shed_packages /> + <galaxy_packages versionless="true" /> +</dependency_resolvers> +''') as dependency_resolvers: + assert not dependency_resolvers[0].versionless + assert dependency_resolvers[2].versionless + + with __parse_resolvers('''<dependency_resolvers> + <galaxy_packages /> + <tool_shed_packages /> + <galaxy_packages base_path="/opt/galaxy/legacy/"/> +</dependency_resolvers> +''') as dependency_resolvers: + # Unspecified base_paths are both default_base_paths + assert dependency_resolvers[0].base_path == dependency_resolvers[1].base_path + # Can specify custom base path... + assert dependency_resolvers[2].base_path == "/opt/galaxy/legacy" + # ... that is different from the default. + assert dependency_resolvers[0].base_path != dependency_resolvers[2].base_path + + +def test_uses_tool_shed_dependencies(): + with __dependency_manager('''<dependency_resolvers> + <galaxy_packages /> +</dependency_resolvers> +''') as dm: + assert not dm.uses_tool_shed_dependencies() + + with __dependency_manager('''<dependency_resolvers> + <tool_shed_packages /> +</dependency_resolvers> +''') as dm: + assert dm.uses_tool_shed_dependencies() + + +def test_config_module_defaults(): + with __parse_resolvers('''<dependency_resolvers> + <modules prefetch="false" /> +</dependency_resolvers> +''') as dependency_resolvers: + module_resolver = dependency_resolvers[0] + assert module_resolver.module_checker.__class__.__name__ == "AvailModuleChecker" + + +def test_config_modulepath(): + # Test reads and splits MODULEPATH if modulepath is not specified. + with __parse_resolvers('''<dependency_resolvers> + <modules find_by="directory" modulepath="/opt/modules/modulefiles:/usr/local/modules/modulefiles" /> +</dependency_resolvers> +''') as dependency_resolvers: + assert dependency_resolvers[0].module_checker.directories == ["/opt/modules/modulefiles", "/usr/local/modules/modulefiles"] + + +def test_config_MODULEPATH(): + # Test reads and splits MODULEPATH if modulepath is not specified. + with __environ({"MODULEPATH": "/opt/modules/modulefiles:/usr/local/modules/modulefiles"}): + with __parse_resolvers('''<dependency_resolvers> + <modules find_by="directory" /> +</dependency_resolvers> +''') as dependency_resolvers: + assert dependency_resolvers[0].module_checker.directories == ["/opt/modules/modulefiles", "/usr/local/modules/modulefiles"] + + +def test_config_MODULESHOME(): + # Test fallbacks to read MODULESHOME if modulepath is not specified and + # neither is MODULEPATH. + with __environ({"MODULESHOME": "/opt/modules"}, remove="MODULEPATH"): + with __parse_resolvers('''<dependency_resolvers> + <modules find_by="directory" /> +</dependency_resolvers> +''') as dependency_resolvers: + assert dependency_resolvers[0].module_checker.directories == ["/opt/modules/modulefiles"] + + +def test_config_module_directory_searcher(): + with __parse_resolvers('''<dependency_resolvers> + <modules find_by="directory" modulepath="/opt/Modules/modulefiles" /> +</dependency_resolvers> +''') as dependency_resolvers: + module_resolver = dependency_resolvers[0] + assert module_resolver.module_checker.directories == ["/opt/Modules/modulefiles"] + + +@contextmanager +def __environ(values, remove=[]): + """ + Modify the environment for a test, adding/updating values in dict `values` and + removing any environment variables mentioned in list `remove`. + """ + new_keys = set(environ.keys()) - set(values.keys()) + old_environ = environ.copy() + try: + environ.update(values) + for to_remove in remove: + try: + del environ[remove] + except KeyError: + pass + yield + finally: + environ.update(old_environ) + for key in new_keys: + del environ[key] + + +@contextmanager +def __parse_resolvers(xml_content): + with __dependency_manager(xml_content) as dm: + yield dm.dependency_resolvers + + +@contextmanager +def __dependency_manager(xml_content): + with __test_base_path() as base_path: + f = tempfile.NamedTemporaryFile() + f.write(xml_content) + f.flush() + dm = DependencyManager( default_base_path=base_path, conf_file=f.name ) + yield dm diff -r 767d9f567b6fa5f6554ec2180b4f1249587f1473 -r 9051ceb435937348e6417fb96eb9611474496828 test/unit/tools/test_tool_loader.py --- /dev/null +++ b/test/unit/tools/test_tool_loader.py @@ -0,0 +1,191 @@ +from tempfile import mkdtemp +from shutil import rmtree +import os + +from galaxy.util import parse_xml +from galaxy.tools.loader import template_macro_params, load_tool + +def test_loader(): + + class TestToolDirectory(object): + def __init__(self): + self.temp_directory = mkdtemp() + + def __enter__(self): + return self + + def __exit__(self, type, value, tb): + rmtree(self.temp_directory) + + def write(self, contents, name="tool.xml"): + open(os.path.join(self.temp_directory, name), "w").write(contents) + + def load(self, name="tool.xml", preprocess=True): + if preprocess: + loader = load_tool + else: + loader = parse_xml + return loader(os.path.join(self.temp_directory, name)) + + ## Test simple macro replacement. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs" /> + <macros> + <macro name="inputs"> + <inputs /> + </macro> + </macros> +</tool>''') + xml = tool_dir.load(preprocess=False) + assert xml.find("inputs") is None + xml = tool_dir.load(preprocess=True) + assert xml.find("inputs") is not None + + # Test importing macros from external files + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs" /> + <macros> + <import>external.xml</import> + </macros> +</tool>''') + + tool_dir.write(''' +<macros> + <macro name="inputs"> + <inputs /> + </macro> +</macros>''', name="external.xml") + xml = tool_dir.load(preprocess=False) + assert xml.find("inputs") is None + xml = tool_dir.load(preprocess=True) + assert xml.find("inputs") is not None + + # Test macros with unnamed yield statements. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs"> + <input name="first_input" /> + </expand> + <macros> + <macro name="inputs"> + <inputs> + <yield /> + </inputs> + </macro> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs").find("input").get("name") == "first_input" + + # Test recursive macro applications. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs"> + <input name="first_input" /> + <expand macro="second" /> + </expand> + <macros> + <macro name="inputs"> + <inputs> + <yield /> + </inputs> + </macro> + <macro name="second"> + <input name="second_input" /> + </macro> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs").findall("input")[1].get("name") == "second_input" + + # Test recursive macro applications. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs"> + <input name="first_input" /> + <expand macro="second" /> + </expand> + <macros> + <macro name="inputs"> + <inputs> + <yield /> + </inputs> + </macro> + <macro name="second"> + <expand macro="second_delegate" /> + </macro> + <macro name="second_delegate"> + <input name="second_input" /> + </macro> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs").findall("input")[1].get("name") == "second_input" + + # Test <xml> is shortcut for macro type="xml" + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs" /> + <macros> + <xml name="inputs"> + <inputs /> + </xml> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs") is not None + + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <command interpreter="python">tool_wrapper.py + #include source=$tool_params + </command> + <macros> + <template name="tool_params">-a 1 -b 2</template> + </macros> +</tool> +''') + xml = tool_dir.load() + params_dict = template_macro_params(xml.getroot()) + assert params_dict['tool_params'] == "-a 1 -b 2" + + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <macros> + <token name="@CITATION@">The citation.</token> + </macros> + <help>@CITATION@</help> + <another> + <tag /> + </another> +</tool> +''') + xml = tool_dir.load() + help_el = xml.find("help") + assert help_el.text == "The citation.", help_el.text + + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <macros> + <token name="@TAG_VAL@">The value.</token> + </macros> + <another> + <tag value="@TAG_VAL@" /> + </another> +</tool> +''') + xml = tool_dir.load() + tag_el = xml.find("another").find("tag") + value = tag_el.get('value') + assert value == "The value.", value https://bitbucket.org/galaxy/galaxy-central/commits/fac578cca758/ Changeset: fac578cca758 User: jmchilton Date: 2014-02-22 05:09:57 Summary: Introduce DatasetMatcher to simplify DatasetToolParameter... This reduces code duplication related dataset_collectors now and abstracts out important functionality I reuse further to collect dataset collections downstream. Was originally added in 28d43f4 as DatasetParamContext and backed out of right away. I have reworked it so that it no longer breaks implicit conversion, the relevant classes and methods have less generic names, and it has a healthy set of test cases. In addition to basic tests on matching datasets to parameters, selections, and implicit conversions - these tests include testing of dataset security inconjuction with data_destination tools as well as filtering data parameters on other data parameters. Affected #: 3 files diff -r 9051ceb435937348e6417fb96eb9611474496828 -r fac578cca75887d811e67993a655fed20c0d8713 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -16,6 +16,7 @@ from sanitize import ToolParameterSanitizer import validation import dynamic_options +from .dataset_matcher import DatasetMatcher # For BaseURLToolParameter from galaxy.web import url_for from galaxy.model.item_attrs import Dictifiable @@ -1610,52 +1611,36 @@ self.conversions.append( ( name, conv_extensions, conv_types ) ) def get_html_field( self, trans=None, value=None, other_values={} ): - filter_value = None - if self.options: - try: - filter_value = self.options.get_options( trans, other_values )[0][0] - except IndexError: - pass # no valid options history = self._get_history( trans ) if value is not None: if type( value ) != list: value = [ value ] + dataset_matcher = DatasetMatcher( trans, self, value, other_values ) field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) # CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field() def dataset_collector( hdas, parent_hid ): - current_user_roles = trans.get_current_user_roles() for i, hda in enumerate( hdas ): hda_name = hda.name if parent_hid is not None: hid = "%s.%d" % ( parent_hid, i + 1 ) else: hid = str( hda.hid ) - if not hda.dataset.state in [galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED] and \ - ( hda.visible or ( value and hda in value and not hda.implicitly_converted_parent_datasets ) ) and \ - trans.app.security_agent.can_access_dataset( current_user_roles, hda.dataset ): - # If we are sending data to an external application, then we need to make sure there are no roles - # associated with the dataset that restrict it's access from "public". - if self.tool and self.tool.tool_type == 'data_destination' and not trans.app.security_agent.dataset_is_public( hda.dataset ): - continue - if self.options and self._options_filter_attribute( hda ) != filter_value: - continue - if hda.datatype.matches_any( self.formats ): - selected = ( value and ( hda in value ) ) - if hda.visible: - hidden_text = "" - else: - hidden_text = " (hidden)" - field.add_option( "%s:%s %s" % ( hid, hidden_text, hda_name ), hda.id, selected ) + hda_match = dataset_matcher.hda_match( hda ) + if not hda_match: + continue + if not hda_match.implicit_conversion: + selected = dataset_matcher.selected( hda ) + if hda.visible: + hidden_text = "" else: - target_ext, converted_dataset = hda.find_conversion_destination( self.formats ) - if target_ext: - if converted_dataset: - hda = converted_dataset - if not trans.app.security_agent.can_access_dataset( current_user_roles, hda.dataset ): - continue - selected = ( value and ( hda in value ) ) - field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected ) + hidden_text = " (hidden)" + field.add_option( "%s:%s %s" % ( hid, hidden_text, hda_name ), hda.id, selected ) + else: + hda = hda_match.hda # Get converted dataset + target_ext = hda_match.target_ext + selected = dataset_matcher.selected( hda ) + field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected ) # Also collect children via association object dataset_collector( hda.children, hid ) dataset_collector( history.active_datasets_children_and_roles, None ) @@ -1685,30 +1670,18 @@ if trans is None or trans.workflow_building_mode or trans.webapp.name == 'tool_shed': return DummyDataset() history = self._get_history( trans, history ) + dataset_matcher = DatasetMatcher( trans, self, None, context ) if self.optional: return None most_recent_dataset = [] - filter_value = None - if self.options: - try: - filter_value = self.options.get_options( trans, context )[0][0] - except IndexError: - pass # no valid options def dataset_collector( datasets ): for i, data in enumerate( datasets ): - if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED]: - is_valid = False - if data.datatype.matches_any( self.formats ): - is_valid = True - else: - target_ext, converted_dataset = data.find_conversion_destination( self.formats ) - if target_ext: - is_valid = True - if converted_dataset: - data = converted_dataset - if not is_valid or ( self.options and self._options_filter_attribute( data ) != filter_value ): + if data.visible and dataset_matcher.hda_accessible( data, check_security=False ): + match = dataset_matcher.valid_hda_match( data, check_security=False ) + if not match or dataset_matcher.filter( match.hda ): continue + data = match.hda most_recent_dataset.append(data) # Also collect children via association object dataset_collector( data.children ) diff -r 9051ceb435937348e6417fb96eb9611474496828 -r fac578cca75887d811e67993a655fed20c0d8713 lib/galaxy/tools/parameters/dataset_matcher.py --- /dev/null +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -0,0 +1,126 @@ +import galaxy.model + +from logging import getLogger +log = getLogger( __name__ ) + +ROLES_UNSET = object() +INVALID_STATES = [ galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED ] + + +class DatasetMatcher( object ): + """ Utility class to aid DataToolParameter and similar classes in reasoning + about what HDAs could match or are selected for a parameter and value. + + Goal here is to both encapsulate and reuse logic related to filtering, + datatype matching, hiding errored dataset, finding implicit conversions, + and permission handling. + """ + + def __init__( self, trans, param, value, other_values ): + self.trans = trans + self.param = param + self.tool = param.tool + self.value = value + self.current_user_roles = ROLES_UNSET + filter_value = None + if param.options: + try: + filter_value = param.options.get_options( trans, other_values )[0][0] + except IndexError: + pass # no valid options + self.filter_value = filter_value + + def hda_accessible( self, hda, check_security=True ): + """ Does HDA correspond to dataset that is an a valid state and is + accessible to user. + """ + dataset = hda.dataset + state_valid = not dataset.state in INVALID_STATES + return state_valid and ( not check_security or self.__can_access_dataset( dataset ) ) + + def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ): + """ Return False of this parameter can not be matched to a the supplied + HDA, otherwise return a description of the match (either a + HdaDirectMatch describing a direct match or a HdaImplicitMatch + describing an implicit conversion.) + """ + if self.filter( hda ): + return False + formats = self.param.formats + if hda.datatype.matches_any( formats ): + return HdaDirectMatch( hda ) + if not check_implicit_conversions: + return False + target_ext, converted_dataset = hda.find_conversion_destination( formats ) + if target_ext: + if converted_dataset: + hda = converted_dataset + if check_security and not self.__can_access_dataset( hda.dataset ): + return False + return HdaImplicitMatch( hda, target_ext ) + return False + + def hda_match( self, hda, check_implicit_conversions=True ): + """ If HDA is accessible, return information about whether it could + match this parameter and if so how. See valid_hda_match for more + information. + """ + accessible = self.hda_accessible( hda ) + if accessible and ( hda.visible or ( self.selected( hda ) and not hda.implicitly_converted_parent_datasets ) ): + # If we are sending data to an external application, then we need to make sure there are no roles + # associated with the dataset that restrict it's access from "public". + require_public = self.tool and self.tool.tool_type == 'data_destination' + if require_public and not self.trans.app.security_agent.dataset_is_public( hda.dataset ): + return False + if self.filter( hda ): + return False + return self.valid_hda_match( hda, check_implicit_conversions=check_implicit_conversions ) + + def selected( self, hda ): + """ Given value for DataToolParameter, is this HDA "selected". + """ + value = self.value + return value and hda in value + + def filter( self, hda ): + """ Filter out this value based on other values for job (if + applicable). + """ + param = self.param + return param.options and param._options_filter_attribute( hda ) != self.filter_value + + def __can_access_dataset( self, dataset ): + # Lazily cache current_user_roles. + if self.current_user_roles is ROLES_UNSET: + self.current_user_roles = self.trans.get_current_user_roles() + return self.trans.app.security_agent.can_access_dataset( self.current_user_roles, dataset ) + + +class HdaDirectMatch( object ): + """ Supplied HDA was a valid option directly (did not need to find implicit + conversion). + """ + + def __init__( self, hda ): + self.hda = hda + + @property + def implicit_conversion( self ): + return False + + +class HdaImplicitMatch( object ): + """ Supplied HDA was a valid option directly (did not need to find implicit + conversion). + """ + + def __init__( self, hda, target_ext ): + self.hda = hda + self.target_ext = target_ext + + @property + def implicit_conversion( self ): + return True + + +__all__ = [ DatasetMatcher ] diff -r 9051ceb435937348e6417fb96eb9611474496828 -r fac578cca75887d811e67993a655fed20c0d8713 test/unit/tools/test_dataset_matcher.py --- /dev/null +++ b/test/unit/tools/test_dataset_matcher.py @@ -0,0 +1,167 @@ +from unittest import TestCase + +from galaxy import model +from galaxy.util import bunch +from galaxy.tools.parameters import basic +from galaxy.tools.parameters import dataset_matcher + +from elementtree.ElementTree import XML + +import tools_support +from .test_data_parameters import MockHistoryDatasetAssociation + + +class DatasetMatcherTestCase( TestCase, tools_support.UsesApp ): + + def test_hda_accessible( self ): + # Cannot access errored or discard datasets. + self.mock_hda.dataset.state = model.Dataset.states.ERROR + assert not self.test_context.hda_accessible( self.mock_hda ) + + self.mock_hda.dataset.state = model.Dataset.states.DISCARDED + assert not self.test_context.hda_accessible( self.mock_hda ) + + # Can access datasets in other states. + self.mock_hda.dataset.state = model.Dataset.states.OK + assert self.test_context.hda_accessible( self.mock_hda ) + + self.mock_hda.dataset.state = model.Dataset.states.QUEUED + assert self.test_context.hda_accessible( self.mock_hda ) + + # Cannot access dataset if security agent says no. + self.app.security_agent.can_access_dataset = lambda roles, dataset: False + assert not self.test_context.hda_accessible( self.mock_hda ) + + def test_selected( self ): + self.test_context.value = [] + assert not self.test_context.selected( self.mock_hda ) + + self.test_context.value = [ self.mock_hda ] + assert self.test_context.selected( self.mock_hda ) + + def test_hda_mismatches( self ): + # Datasets not visible are not "valid" for param. + self.mock_hda.visible = False + assert not self.test_context.hda_match( self.mock_hda ) + + # Datasets that don't match datatype are not valid. + self.mock_hda.visible = True + self.mock_hda.datatype_matches = False + assert not self.test_context.hda_match( self.mock_hda ) + + def test_valid_hda_direct_match( self ): + # Datasets that visible and matching are valid + self.mock_hda.visible = True + self.mock_hda.datatype_matches = True + hda_match = self.test_context.hda_match( self.mock_hda, check_implicit_conversions=False ) + assert hda_match + + # Match is not a conversion and so matching hda is the same hda + # supplied. + assert not hda_match.implicit_conversion + assert hda_match.hda == self.mock_hda + + def test_valid_hda_implicit_convered( self ): + # Find conversion returns an HDA to an already implicitly converted + # dataset. + self.mock_hda.datatype_matches = False + converted_hda = model.HistoryDatasetAssociation() + self.mock_hda.conversion_destination = ( "tabular", converted_hda ) + hda_match = self.test_context.hda_match( self.mock_hda ) + + assert hda_match + assert hda_match.implicit_conversion + assert hda_match.hda == converted_hda + assert hda_match.target_ext == "tabular" + + def test_hda_match_implicit_can_convert( self ): + # Find conversion returns a target extension to convert to, but not + # a previously implicitly converted dataset. + self.mock_hda.datatype_matches = False + self.mock_hda.conversion_destination = ( "tabular", None ) + hda_match = self.test_context.hda_match( self.mock_hda ) + + assert hda_match + assert hda_match.implicit_conversion + assert hda_match.hda == self.mock_hda + assert hda_match.target_ext == "tabular" + + def test_hda_match_properly_skips_conversion( self ): + self.mock_hda.datatype_matches = False + self.mock_hda.conversion_destination = ( "tabular", bunch.Bunch() ) + hda_match = self.test_context.hda_match( self.mock_hda, check_implicit_conversions=False ) + assert not hda_match + + def test_data_destination_tools_require_public( self ): + self.tool.tool_type = "data_destination" + + # Public datasets okay and valid + self.app.security_agent.dataset_is_public = lambda dataset: True + hda_match = self.test_context.hda_match( self.mock_hda ) + assert hda_match + + # Non-public datasets not valid + self.app.security_agent.dataset_is_public = lambda dataset: False + hda_match = self.test_context.hda_match( self.mock_hda ) + assert not hda_match + + def test_filtered_hda_matched_key( self ): + self.filtered_param = True + data1_val = model.HistoryDatasetAssociation() + data1_val.dbkey = "hg18" + self.other_values = { "data1": data1_val } + assert self.test_context.filter_value == "hg18" + + # mock_hda is hg19, other is hg18 so should not be "valid hda" + hda_match = self.test_context.hda_match( self.mock_hda ) + assert not hda_match + + def test_filtered_hda_unmatched_key( self ): + self.filtered_param = True + data1_val = model.HistoryDatasetAssociation() + data1_val.dbkey = "hg19" + self.other_values = { "data1": data1_val } + + # Other param value and this dataset both hg19, should be valid + hda_match = self.test_context.hda_match( self.mock_hda ) + assert hda_match + + def setUp( self ): + self.setup_app() + self.mock_hda = MockHistoryDatasetAssociation() + self.tool = bunch.Bunch( + app=self.app, + tool_type="default", + ) + self.current_user_roles = [] + self.other_values = {} + + # Reset lazily generated stuff + self.filtered_param = False + self._test_context = None + self.param = None + + @property + def test_context( self ): + if self._test_context is None: + option_xml = "" + if self.filtered_param: + option_xml = '''<options><filter type="data_meta" ref="data1" key="dbkey" /></options>''' + param_xml = XML( '''<param name="data2" type="data" ext="txt">%s</param>''' % option_xml ) + self.param = basic.DataToolParameter( + tool=self.tool, + elem=param_xml, + ) + + self._test_context = dataset_matcher.DatasetMatcher( + trans=bunch.Bunch( + app=self.app, + get_current_user_roles=lambda: self.current_user_roles, + workflow_building_mode=True, + ), + param=self.param, + value=[ ], + other_values=self.other_values + ) + + return self._test_context Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Embedded histories: refactor and clean up
by commits-noreply＠bitbucket.org 21 Feb '14

21 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2403d6f67500/ Changeset: 2403d6f67500 User: carlfeberhard Date: 2014-02-21 23:19:19 Summary: Embedded histories: refactor and clean up Affected #: 10 files diff -r 6b6c7de6bbe10721674f50ebb5e8a600d8586416 -r 2403d6f67500ec35b16ce604142d98766286b65a lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -753,21 +753,7 @@ history.annotation = self.get_item_annotation_str( trans.sa_session, history.user, history ) for dataset in datasets: dataset.annotation = self.get_item_annotation_str( trans.sa_session, history.user, dataset ) - - user_is_owner = trans.user == history.user - history.annotation = self.get_item_annotation_str( trans.sa_session, history.user, history ) - - hda_dicts = [] - datasets = self.get_history_datasets( trans, history ) - for hda in datasets: - hda_dict = self.get_hda_dict( trans, hda ) - hda_dict[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, history.user, hda ) - hda_dicts.append( hda_dict ) - history_dict = self.get_history_dict( trans, history, hda_dictionaries=hda_dicts ) - history_dict[ 'annotation' ] = history.annotation - - return trans.fill_template( "history/item_content.mako", item=history, item_data=datasets, - user_is_owner=user_is_owner, history_dict=history_dict, hda_dicts=hda_dicts ) + return trans.stream_template_mako( "/history/item_content.mako", item = history, item_data = datasets ) @web.expose def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): diff -r 6b6c7de6bbe10721674f50ebb5e8a600d8586416 -r 2403d6f67500ec35b16ce604142d98766286b65a lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -721,27 +721,52 @@ def get_item( self, trans, id ): return self.get_page( trans, id ) + def _get_embedded_history_html( self, trans, id ): + """ + Returns html suitable for embedding in another page. + """ + history = self.get_history( trans, id, False, True ) + if not history: + return None + + # create ownership flag for template, dictify models + # note: adding original annotation since this is published - get_dict returns user-based annos + user_is_owner = trans.user == history.user + history.annotation = self.get_item_annotation_str( trans.sa_session, history.user, history ) + + hda_dicts = [] + datasets = self.get_history_datasets( trans, history ) + for hda in datasets: + hda_dict = self.get_hda_dict( trans, hda ) + hda_dict[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, history.user, hda ) + hda_dicts.append( hda_dict ) + history_dict = self.get_history_dict( trans, history, hda_dictionaries=hda_dicts ) + history_dict[ 'annotation' ] = history.annotation + + filled = trans.fill_template( "history/embed.mako", item=history, item_data=datasets, + user_is_owner=user_is_owner, history_dict=history_dict, hda_dicts=hda_dicts ) + return filled + def _get_embed_html( self, trans, item_class, item_id ): """ Returns HTML for embedding an item in a page. """ item_class = self.get_class( item_class ) if item_class == model.History: - history = self.get_history( trans, item_id, False, True ) - history.annotation = self.get_item_annotation_str( trans.sa_session, history.user, history ) - if history: - datasets = self.get_history_datasets( trans, history ) - return trans.fill_template( "history/embed.mako", item=history, item_data=datasets ) + return self._get_embedded_history_html( trans, item_id ) + elif item_class == model.HistoryDatasetAssociation: dataset = self.get_dataset( trans, item_id, False, True ) dataset.annotation = self.get_item_annotation_str( trans.sa_session, dataset.history.user, dataset ) if dataset: data = self.get_data( dataset ) return trans.fill_template( "dataset/embed.mako", item=dataset, item_data=data ) + elif item_class == model.StoredWorkflow: workflow = self.get_stored_workflow( trans, item_id, False, True ) workflow.annotation = self.get_item_annotation_str( trans.sa_session, workflow.user, workflow ) if workflow: self.get_stored_workflow_steps( trans, workflow ) return trans.fill_template( "workflow/embed.mako", item=workflow, item_data=workflow.latest_workflow.steps ) + elif item_class == model.Visualization: visualization = self.get_visualization( trans, item_id, False, True ) visualization.annotation = self.get_item_annotation_str( trans.sa_session, visualization.user, visualization ) diff -r 6b6c7de6bbe10721674f50ebb5e8a600d8586416 -r 2403d6f67500ec35b16ce604142d98766286b65a static/scripts/mvc/history/readonly-history-panel.js --- a/static/scripts/mvc/history/readonly-history-panel.js +++ b/static/scripts/mvc/history/readonly-history-panel.js @@ -107,6 +107,9 @@ // ---- handle models passed on init if( this.model ){ + if( this.logger ){ + this.model.logger = this.logger; + } this._setUpWebStorage( attributes.initiallyExpanded, attributes.show_deleted, attributes.show_hidden ); this._setUpModelEventHandlers(); } @@ -302,6 +305,9 @@ newHistoryJSON.user = Galaxy.currUser.toJSON(); } this.model = new historyModel.History( newHistoryJSON, newHdaJSON, attributes ); + if( this.logger ){ + this.model.logger = this.logger; + } this._setUpWebStorage( attributes.initiallyExpanded, attributes.show_deleted, attributes.show_hidden ); this._setUpModelEventHandlers(); this.selectedHdaIds = []; diff -r 6b6c7de6bbe10721674f50ebb5e8a600d8586416 -r 2403d6f67500ec35b16ce604142d98766286b65a static/scripts/packed/mvc/history/readonly-history-panel.js --- a/static/scripts/packed/mvc/history/readonly-history-panel.js +++ b/static/scripts/packed/mvc/history/readonly-history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-base"],function(e,a){var d=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(f){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([f],[true])))},removeExpandedHda:function(f){this.save("expandedHdas",_.omit(this.get("expandedHdas"),f))},toString:function(){return"HistoryPrefs("+this.id+")"}});d.historyStorageKey=function c(f){if(!f){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+f)}return("history:"+f)};var b=Backbone.View.extend(LoggableMixin).extend({HDAViewClass:a.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",msgsSelector:".message-container",emptyMsgSelector:".empty-history-message",emptyMsg:_l("This history is empty"),noneFoundMsg:_l("No matching datasets found"),initialize:function(f){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.linkTarget=f.linkTarget||"_blank";this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.filters=[];this.searchFor="";this._setUpListeners();if(this.model){this._setUpWebStorage(f.initiallyExpanded,f.show_deleted,f.show_hidden);this._setUpModelEventHandlers()}if(f.onready){f.onready.call(this)}},_setUpListeners:function(){this.on("error",function(g,j,f,i,h){this.errorHandler(g,j,f,i,h)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this.hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}},errorHandler:function(h,k,g,j,i){var f=this._parseErrorMessage(h,k,g,j,i);if(k&&k.status===0&&k.readyState===0){}else{if(k&&k.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",f.message,f.details)})}else{this.displayMessage("error",f.message,f.details)}}}},_parseErrorMessage:function(i,m,h,l,k){var g=Galaxy.currUser,f={message:this._bePolite(l),details:{user:(g instanceof User)?(g.toJSON()):(g+""),source:(i instanceof Backbone.Model)?(i.toJSON()):(i+""),xhr:m,options:(m)?(_.omit(h,"xhr")):(h)}};_.extend(f.details,k||{});if(m&&_.isFunction(m.getAllResponseHeaders)){var j=m.getAllResponseHeaders();j=_.compact(j.split("\n"));j=_.map(j,function(n){return n.split(": ")});f.details.xhr.responseHeaders=_.object(j)}return f},_bePolite:function(f){f=f||_l("An error occurred while getting updates from the server");return f+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadHistoryWithHDADetails:function(i,h,g,k){var f=this,j=function(l){return f.getExpandedHdaIds(l.id)};return this.loadHistory(i,h,g,k,j)},loadHistory:function(i,h,g,l,j){this.trigger("loading-history",this);h=h||{};var f=this;var k=e.History.getHistoryData(i,{historyFn:g,hdaFn:l,hdaDetailIds:h.initiallyExpanded||j});return this._loadHistoryFromXHR(k,h).fail(function(o,m,n){f.trigger("error",f,o,h,_l("An error was encountered while "+m),{historyId:i,history:n||{}})}).always(function(){f.trigger("loading-done",f)})},_loadHistoryFromXHR:function(h,g){var f=this;h.then(function(i,j){f.setModel(i,j,g)});h.fail(function(j,i){f.render()});return h},setModel:function(h,f,g){g=g||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){h.user=Galaxy.currUser.toJSON()}this.model=new e.History(h,f,g);this._setUpWebStorage(g.initiallyExpanded,g.show_deleted,g.show_hidden);this._setUpModelEventHandlers();this.selectedHdaIds=[];this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(g,f,h){this.storage=new d({id:d.historyStorageKey(this.model.get("id"))});if(_.isObject(g)){this.storage.set("exandedHdas",g)}if(_.isBoolean(f)){this.storage.set("show_deleted",f)}if(_.isBoolean(h)){this.storage.set("show_hidden",h)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var f in sessionStorage){if(f.indexOf("history:")===0){sessionStorage.removeItem(f)}}},getStoredOptions:function(g){if(!g||g==="current"){return(this.storage)?(this.storage.get()):({})}var f=sessionStorage.getItem(d.historyStorageKey(g));return(f===null)?({}):(JSON.parse(f))},getExpandedHdaIds:function(f){var g=this.getStoredOptions(f).expandedHdas;return((_.isEmpty(g))?([]):(_.keys(g)))},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addHdaView,this);this.model.on("error error:hdas",function(g,i,f,h){this.errorHandler(g,i,f,h)},this)},render:function(h,i){h=(h===undefined)?(this.fxSpeed):(h);var f=this,g;if(this.model){g=this.renderModel()}else{g=this.renderWithoutModel()}$(f).queue("fx",[function(j){if(h&&f.$el.is(":visible")){f.$el.fadeOut(h,j)}else{j()}},function(j){f.$el.empty();if(g){f.$el.append(g.children())}j()},function(j){if(h&&!f.$el.is(":visible")){f.$el.fadeIn(h,j)}else{j()}},function(j){if(i){i.call(this)}f.trigger("rendered",this);j()}]);return this},renderWithoutModel:function(){var f=$("<div/>"),g=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return f.append(g)},renderModel:function(){var f=$("<div/>");f.append(b.templates.historyPanel(this.model.toJSON()));f.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(f);this.renderHdas(f);return f},_renderSearchButton:function(f){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(f){f=f||this.$el;f.find("[title]").tooltip({placement:"bottom"})},createHdaView:function(g){var f=g.get("id"),h=new this.HDAViewClass({model:g,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[f],hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(h);return h},_setUpHdaListeners:function(g){var f=this;g.on("body-expanded",function(h){f.storage.addExpandedHda(h)});g.on("body-collapsed",function(h){f.storage.removeExpandedHda(h)});g.on("error",function(i,k,h,j){f.errorHandler(i,k,h,j)})},renderHdas:function(g){g=g||this.$el;var f=this,i={},h=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);g.find(this.datasetsSelector).empty();if(h.length){h.each(function(k){var j=k.get("id"),l=f.createHdaView(k);i[j]=l;if(_.contains(f.selectedHdaIds,j)){l.selected=true}f.attachHdaView(l.render(),g)});g.find(this.emptyMsgSelector).hide()}else{g.find(this.emptyMsgSelector).text((this.model.hdas.length&&this.searchFor)?(this.noneFoundMsg):(this.emptyMsg)).show()}this.hdaViews=i;return this.hdaViews},attachHdaView:function(h,g){g=g||this.$el;var f=g.find(this.datasetsSelector);f.prepend(h.$el)},addHdaView:function(i){this.log("add."+this,i);var g=this;if(!i.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function h(k){var j=g.$el.find(g.emptyMsgSelector);if(j.is(":visible")){j.fadeOut(g.fxSpeed,k)}else{k()}},function f(k){g.scrollToTop();var j=g.$el.find(g.datasetsSelector),l=g.createHdaView(i);g.hdaViews[i.id]=l;l.render().$el.hide().prependTo(j).slideDown(g.fxSpeed)}])},refreshHdas:function(g,f){if(this.model){return this.model.refresh(g,f)}return $.when()},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(f){f.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},setUpSearchInput:function(g){var h=this,k=".history-search-input";function j(l){h.searchFor=l;h.filters=[function(m){return m.matchesAll(h.searchFor)}];h.trigger("search:searching",l,h);h.renderHdas()}function f(l){if(h.model.hdas.haveDetails()){j(l);return}h.$el.find(k).searchInput("toggle-loading");h.model.hdas.fetchAllDetails({silent:true}).always(function(){h.$el.find(k).searchInput("toggle-loading")}).done(function(){j(l)})}function i(){h.searchFor="";h.filters=[];h.trigger("search:clear",h);h.renderHdas()}g.searchInput({initialVal:h.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:f,onsearch:j,onclear:i});return g},showSearchControls:function(g){g=(g===undefined)?(this.fxSpeed):(g);var f=this.$el.find(".history-search-controls"),h=f.find(".history-search-input");if(!h.children().size()){this.setUpSearchInput(h)}f.slideDown(g,function(){$(this).find("input").focus()})},hideSearchControls:function(f){f=(f===undefined)?(this.fxSpeed):(f);this.$el.find(".history-search-controls").slideUp(f)},toggleSearchControls:function(f){speed=(jQuery.type(f)==="number")?(f):(this.fxSpeed);if(this.$el.find(".history-search-controls").is(":visible")){this.hideSearchControls(speed)}else{this.showSearchControls(speed)}},showLoadingIndicator:function(g,f,h){f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},hideLoadingIndicator:function(f,g){f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},displayMessage:function(k,l,j){var h=this;this.scrollToTop();var i=this.$el.find(this.msgsSelector),f=$("<div/>").addClass(k+"message").html(l);if(!_.isEmpty(j)){var g=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(h._messageToModalOptions(k,l,j));return false});f.append(" ",g)}return i.html(f)},_messageToModalOptions:function(j,l,i){var f=this,k=$("<div/>"),h={title:"Details"};function g(m){m=_.omit(m,_.functions(m));return["<table>",_.map(m,function(o,n){o=(_.isObject(o))?(g(o)):(o);return'<tr><td style="vertical-align: top; color: grey">'+n+'</td><td style="padding-left: 8px">'+o+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(i)){h.body=k.append(g(i))}else{h.body=k.html(i)}h.buttons={Ok:function(){Galaxy.modal.hide();f.clearMessages()}};return h},clearMessages:function(){var f=this.$el.find(this.msgsSelector);f.empty()},scrollPosition:function(){return this.$el.scrollTop()},scrollTo:function(f){this.$el.scrollTop(f);return this},scrollToTop:function(){this.$el.scrollTop(0);return this},scrollIntoView:function(k,g){if(g===undefined){this.scrollTo(k);return this}var f=window,j=this.$el.parent(),i=$(f).innerHeight(),h=(i/2)-(g/2);this.scrollTo(k-h);return this},scrollToId:function(g){if((!g)||(!this.hdaViews[g])){return this}var f=this.hdaViews[g].$el;this.scrollIntoView(f.offset().top,f.outerHeight());return this},scrollToHid:function(f){var g=this.model.hdas.getByHid(f);if(!g){return this}return this.scrollToId(g.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});b.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]};return{ReadOnlyHistoryPanel:b}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-base"],function(e,a){var d=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(f){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([f],[true])))},removeExpandedHda:function(f){this.save("expandedHdas",_.omit(this.get("expandedHdas"),f))},toString:function(){return"HistoryPrefs("+this.id+")"}});d.historyStorageKey=function c(f){if(!f){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+f)}return("history:"+f)};var b=Backbone.View.extend(LoggableMixin).extend({HDAViewClass:a.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",msgsSelector:".message-container",emptyMsgSelector:".empty-history-message",emptyMsg:_l("This history is empty"),noneFoundMsg:_l("No matching datasets found"),initialize:function(f){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.linkTarget=f.linkTarget||"_blank";this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.filters=[];this.searchFor="";this._setUpListeners();if(this.model){if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(f.initiallyExpanded,f.show_deleted,f.show_hidden);this._setUpModelEventHandlers()}if(f.onready){f.onready.call(this)}},_setUpListeners:function(){this.on("error",function(g,j,f,i,h){this.errorHandler(g,j,f,i,h)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this.hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}},errorHandler:function(h,k,g,j,i){var f=this._parseErrorMessage(h,k,g,j,i);if(k&&k.status===0&&k.readyState===0){}else{if(k&&k.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",f.message,f.details)})}else{this.displayMessage("error",f.message,f.details)}}}},_parseErrorMessage:function(i,m,h,l,k){var g=Galaxy.currUser,f={message:this._bePolite(l),details:{user:(g instanceof User)?(g.toJSON()):(g+""),source:(i instanceof Backbone.Model)?(i.toJSON()):(i+""),xhr:m,options:(m)?(_.omit(h,"xhr")):(h)}};_.extend(f.details,k||{});if(m&&_.isFunction(m.getAllResponseHeaders)){var j=m.getAllResponseHeaders();j=_.compact(j.split("\n"));j=_.map(j,function(n){return n.split(": ")});f.details.xhr.responseHeaders=_.object(j)}return f},_bePolite:function(f){f=f||_l("An error occurred while getting updates from the server");return f+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadHistoryWithHDADetails:function(i,h,g,k){var f=this,j=function(l){return f.getExpandedHdaIds(l.id)};return this.loadHistory(i,h,g,k,j)},loadHistory:function(i,h,g,l,j){this.trigger("loading-history",this);h=h||{};var f=this;var k=e.History.getHistoryData(i,{historyFn:g,hdaFn:l,hdaDetailIds:h.initiallyExpanded||j});return this._loadHistoryFromXHR(k,h).fail(function(o,m,n){f.trigger("error",f,o,h,_l("An error was encountered while "+m),{historyId:i,history:n||{}})}).always(function(){f.trigger("loading-done",f)})},_loadHistoryFromXHR:function(h,g){var f=this;h.then(function(i,j){f.setModel(i,j,g)});h.fail(function(j,i){f.render()});return h},setModel:function(h,f,g){g=g||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){h.user=Galaxy.currUser.toJSON()}this.model=new e.History(h,f,g);if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(g.initiallyExpanded,g.show_deleted,g.show_hidden);this._setUpModelEventHandlers();this.selectedHdaIds=[];this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(g,f,h){this.storage=new d({id:d.historyStorageKey(this.model.get("id"))});if(_.isObject(g)){this.storage.set("exandedHdas",g)}if(_.isBoolean(f)){this.storage.set("show_deleted",f)}if(_.isBoolean(h)){this.storage.set("show_hidden",h)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var f in sessionStorage){if(f.indexOf("history:")===0){sessionStorage.removeItem(f)}}},getStoredOptions:function(g){if(!g||g==="current"){return(this.storage)?(this.storage.get()):({})}var f=sessionStorage.getItem(d.historyStorageKey(g));return(f===null)?({}):(JSON.parse(f))},getExpandedHdaIds:function(f){var g=this.getStoredOptions(f).expandedHdas;return((_.isEmpty(g))?([]):(_.keys(g)))},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addHdaView,this);this.model.on("error error:hdas",function(g,i,f,h){this.errorHandler(g,i,f,h)},this)},render:function(h,i){h=(h===undefined)?(this.fxSpeed):(h);var f=this,g;if(this.model){g=this.renderModel()}else{g=this.renderWithoutModel()}$(f).queue("fx",[function(j){if(h&&f.$el.is(":visible")){f.$el.fadeOut(h,j)}else{j()}},function(j){f.$el.empty();if(g){f.$el.append(g.children())}j()},function(j){if(h&&!f.$el.is(":visible")){f.$el.fadeIn(h,j)}else{j()}},function(j){if(i){i.call(this)}f.trigger("rendered",this);j()}]);return this},renderWithoutModel:function(){var f=$("<div/>"),g=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return f.append(g)},renderModel:function(){var f=$("<div/>");f.append(b.templates.historyPanel(this.model.toJSON()));f.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(f);this.renderHdas(f);return f},_renderSearchButton:function(f){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(f){f=f||this.$el;f.find("[title]").tooltip({placement:"bottom"})},createHdaView:function(g){var f=g.get("id"),h=new this.HDAViewClass({model:g,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[f],hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(h);return h},_setUpHdaListeners:function(g){var f=this;g.on("body-expanded",function(h){f.storage.addExpandedHda(h)});g.on("body-collapsed",function(h){f.storage.removeExpandedHda(h)});g.on("error",function(i,k,h,j){f.errorHandler(i,k,h,j)})},renderHdas:function(g){g=g||this.$el;var f=this,i={},h=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);g.find(this.datasetsSelector).empty();if(h.length){h.each(function(k){var j=k.get("id"),l=f.createHdaView(k);i[j]=l;if(_.contains(f.selectedHdaIds,j)){l.selected=true}f.attachHdaView(l.render(),g)});g.find(this.emptyMsgSelector).hide()}else{g.find(this.emptyMsgSelector).text((this.model.hdas.length&&this.searchFor)?(this.noneFoundMsg):(this.emptyMsg)).show()}this.hdaViews=i;return this.hdaViews},attachHdaView:function(h,g){g=g||this.$el;var f=g.find(this.datasetsSelector);f.prepend(h.$el)},addHdaView:function(i){this.log("add."+this,i);var g=this;if(!i.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function h(k){var j=g.$el.find(g.emptyMsgSelector);if(j.is(":visible")){j.fadeOut(g.fxSpeed,k)}else{k()}},function f(k){g.scrollToTop();var j=g.$el.find(g.datasetsSelector),l=g.createHdaView(i);g.hdaViews[i.id]=l;l.render().$el.hide().prependTo(j).slideDown(g.fxSpeed)}])},refreshHdas:function(g,f){if(this.model){return this.model.refresh(g,f)}return $.when()},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(f){f.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},setUpSearchInput:function(g){var h=this,k=".history-search-input";function j(l){h.searchFor=l;h.filters=[function(m){return m.matchesAll(h.searchFor)}];h.trigger("search:searching",l,h);h.renderHdas()}function f(l){if(h.model.hdas.haveDetails()){j(l);return}h.$el.find(k).searchInput("toggle-loading");h.model.hdas.fetchAllDetails({silent:true}).always(function(){h.$el.find(k).searchInput("toggle-loading")}).done(function(){j(l)})}function i(){h.searchFor="";h.filters=[];h.trigger("search:clear",h);h.renderHdas()}g.searchInput({initialVal:h.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:f,onsearch:j,onclear:i});return g},showSearchControls:function(g){g=(g===undefined)?(this.fxSpeed):(g);var f=this.$el.find(".history-search-controls"),h=f.find(".history-search-input");if(!h.children().size()){this.setUpSearchInput(h)}f.slideDown(g,function(){$(this).find("input").focus()})},hideSearchControls:function(f){f=(f===undefined)?(this.fxSpeed):(f);this.$el.find(".history-search-controls").slideUp(f)},toggleSearchControls:function(f){speed=(jQuery.type(f)==="number")?(f):(this.fxSpeed);if(this.$el.find(".history-search-controls").is(":visible")){this.hideSearchControls(speed)}else{this.showSearchControls(speed)}},showLoadingIndicator:function(g,f,h){f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},hideLoadingIndicator:function(f,g){f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},displayMessage:function(k,l,j){var h=this;this.scrollToTop();var i=this.$el.find(this.msgsSelector),f=$("<div/>").addClass(k+"message").html(l);if(!_.isEmpty(j)){var g=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(h._messageToModalOptions(k,l,j));return false});f.append(" ",g)}return i.html(f)},_messageToModalOptions:function(j,l,i){var f=this,k=$("<div/>"),h={title:"Details"};function g(m){m=_.omit(m,_.functions(m));return["<table>",_.map(m,function(o,n){o=(_.isObject(o))?(g(o)):(o);return'<tr><td style="vertical-align: top; color: grey">'+n+'</td><td style="padding-left: 8px">'+o+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(i)){h.body=k.append(g(i))}else{h.body=k.html(i)}h.buttons={Ok:function(){Galaxy.modal.hide();f.clearMessages()}};return h},clearMessages:function(){var f=this.$el.find(this.msgsSelector);f.empty()},scrollPosition:function(){return this.$el.scrollTop()},scrollTo:function(f){this.$el.scrollTop(f);return this},scrollToTop:function(){this.$el.scrollTop(0);return this},scrollIntoView:function(k,g){if(g===undefined){this.scrollTo(k);return this}var f=window,j=this.$el.parent(),i=$(f).innerHeight(),h=(i/2)-(g/2);this.scrollTo(k-h);return this},scrollToId:function(g){if((!g)||(!this.hdaViews[g])){return this}var f=this.hdaViews[g].$el;this.scrollIntoView(f.offset().top,f.outerHeight());return this},scrollToHid:function(f){var g=this.model.hdas.getByHid(f);if(!g){return this}return this.scrollToId(g.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});b.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]};return{ReadOnlyHistoryPanel:b}}); \ No newline at end of file diff -r 6b6c7de6bbe10721674f50ebb5e8a600d8586416 -r 2403d6f67500ec35b16ce604142d98766286b65a static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1652,7 +1652,7 @@ .history-panel .message-container{cursor:pointer} .history-panel .message-container [class$=message]{margin:0px;margin-bottom:8px} .history-panel .history-controls{margin:10px;padding:0px}.history-panel .history-controls .history-search-controls{display:none;padding:0px 0px 8px 0px} -.history-panel .history-controls .history-title{margin-bottom:4px} +.history-panel .history-controls .history-title{margin-bottom:8px} .history-panel .history-controls .history-name{word-wrap:break-word;font-weight:bold} .history-panel .history-controls .history-title input{width:100%;margin:-2px 0 -2px -4px;font-weight:bold} .history-panel .history-controls .history-subtitle{margin-bottom:8px} @@ -1688,8 +1688,8 @@ .dataset.state-discarded{background:#eee}.dataset.state-discarded .state-icon:before{content:"\f014"} .dataset.state-noPermission{background:#eee;filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60}.dataset.state-noPermission .state-icon{font-size:20px}.dataset.state-noPermission .state-icon:before{content:"\f023"} .dataset.state-new{background:#eee}.dataset.state-new .state-icon:before{content:"\f06a"} -.annotated-history-panel{padding-top:10px}.annotated-history-panel [class$=messagesmall]{margin:8px 0px 8px 0px} -.annotated-history-panel .history-controls{margin:0px 0px 16px 4px;padding:0px}.annotated-history-panel .history-controls .history-name{font-size:150%} +.annotated-history-panel [class$=messagesmall]{margin:8px 0px 8px 0px} +.annotated-history-panel .history-controls{margin:0px 0px 16px 4px;padding:0px}.annotated-history-panel .history-controls .history-name{font-size:150%;margin-bottom:4px} .annotated-history-panel .history-controls .history-subtitle{margin:0px;padding:0px 0px 0px 4px;padding-left:4px} .annotated-history-panel .history-controls .history-annotation{border:1px solid lightgrey;border-width:1px 0px 0px 0px;padding:4px 0px 4px 0px;margin:4px;white-space:pre-wrap} .annotated-history-panel .history-controls .history-annotation:empty{display:none} diff -r 6b6c7de6bbe10721674f50ebb5e8a600d8586416 -r 2403d6f67500ec35b16ce604142d98766286b65a static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -411,7 +411,7 @@ } .history-title { - margin-bottom: 4px; + margin-bottom: 8px; } .history-name { word-wrap: break-word; @@ -692,7 +692,6 @@ .annotated-history-panel { //TODO: most of these styles are specific to history/display.mako and not to this type of panel in general //TODO: some of these styles are also overrides of history-panel - remove those from hpanel and revisit this - padding-top: 10px; [class$=messagesmall] { margin: 8px 0px 8px 0px; @@ -704,6 +703,7 @@ .history-name { font-size: 150%; + margin-bottom: 4px; } .history-subtitle { margin: 0px; diff -r 6b6c7de6bbe10721674f50ebb5e8a600d8586416 -r 2403d6f67500ec35b16ce604142d98766286b65a templates/display_base.mako --- a/templates/display_base.mako +++ b/templates/display_base.mako @@ -36,7 +36,8 @@ ${h.js( "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.rating", "galaxy.autocom_tagging" )} ${history_panel_javascripts()} - ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery-ui", "libs/require", "libs/farbtastic" )} + ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover", + "libs/jquery/jquery.mousewheel", "libs/jquery/jquery-ui", "libs/require", "libs/farbtastic" )} <script type="text/javascript"> @@ -152,18 +153,6 @@ border-right-style: solid; border-right-color: #66AA66; } - - .embedded-item.history .item-content { - padding: 8px; - background-color: white; - border-radius: 0px 0px 4px 4px; - } - .embedded-item.history hr { - margin-bottom: 2px; - } - .embedded-item.history .history-panel { - padding: 2px 0px 8px 0px; - } </style></%def> diff -r 6b6c7de6bbe10721674f50ebb5e8a600d8586416 -r 2403d6f67500ec35b16ce604142d98766286b65a templates/webapps/galaxy/history/display.mako --- a/templates/webapps/galaxy/history/display.mako +++ b/templates/webapps/galaxy/history/display.mako @@ -15,6 +15,9 @@ <%def name="stylesheets()"> ${parent.stylesheets()} <style type="text/css"> + .history-panel { + margin-top: 8px; + } </style></%def> @@ -48,7 +51,7 @@ historyJSON = ${h.to_json_string( history_dict )}, hdaJSON = ${h.to_json_string( hda_dicts )}; //window.historyJSON = historyJSON; - window.hdaJSON = hdaJSON; + //window.hdaJSON = hdaJSON; require.config({ baseUrl : "${h.url_for( '/static/scripts' )}" diff -r 6b6c7de6bbe10721674f50ebb5e8a600d8586416 -r 2403d6f67500ec35b16ce604142d98766286b65a templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -1,13 +1,73 @@ -<%inherit file="/embed_base.mako"/> -<%! - from galaxy.web.framework.helpers import iff +##<%inherit file="/embed_base.mako"/> +<%namespace file="/display_common.mako" import="*" /> + +## Some duplication with embed_base here, needed a way to override the main embedded-item html for histories +<% + encoded_history_id = trans.security.encode_id( item.id ) + import_href = h.url_for( controller='history', action='imp', id=encoded_history_id ) + display_href = h.url_for( controller='history', action='display_by_username_and_slug', + username=item.user.username, slug=item.slug ) %> +<div id="history-${encoded_history_id}" class='embedded-item display history'> + <div class='title'> + <div style="float: left"> + <a class="expand-content-btn icon-button toggle-expand" href="${display_href}" + title="Show or hide history contents"></a> + </div> + <div style="float: right;"> + <a title="Import history" class="icon-button import" href="${import_href}"></a> + <a title="View history" class="icon-button go-to-full-screen" href="${display_href}"></a> + </div> + <h4> + <a class="toggle-embed" href="${display_href}" title="Show or hide history contents"> + Galaxy History | ${get_item_name( item )} + </a> + </h4> + %if hasattr( item, "annotation") and item.annotation: + <div class="annotation">${item.annotation}</div> + %endif + </div> + <div class='summary-content'> + ## currently, no summary content for history + </div> + <div class='expanded-content'> + <div class='item-content'> + <div class='history-panel'></div> + </div> + </div> +</div> -<%def name="render_summary_content( history, datasets )"> +<script type="text/javascript"> -## <ul> -## <% num_datasets = len ( datasets ) %> -## <li>${num_datasets} dataset${iff( num_datasets != 1, "s", "" )} -## <li>Operations: ... -## </ul> -</%def> +require.config({ + baseUrl : "${h.url_for( '/static/scripts' )}" +}); +require([ 'mvc/history/annotated-history-panel' ], function( panelMod ){ + + function toggleExpanded( ev ){ + var $embeddedHistory = $( "#history-${encoded_history_id}" ); + $embeddedHistory.find( '.expand-content-btn' ).toggleClass( 'toggle-expand' ).toggleClass( 'toggle' ); + $embeddedHistory.find( ".summary-content" ).slideToggle( "fast" ); + $embeddedHistory.find( ".annotation" ).slideToggle( "fast" ); + $embeddedHistory.find( ".expanded-content" ).slideToggle( "fast" ); + ev.preventDefault(); + } + + $(function(){ + var debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false, + historyModel = require( 'mvc/history/history-model' ), + $embeddedHistory = $( "#history-${encoded_history_id}" ), + panel = new panelMod.AnnotatedHistoryPanel({ + el : $embeddedHistory.find( ".history-panel" ), + model : new historyModel.History( + ${h.to_json_string( history_dict )}, + ${h.to_json_string( hda_dicts )}, + { logger: ( debugging )?( console ):( null ) } + ) + }).render(); + + $embeddedHistory.find( '.expand-content-btn' ).click( toggleExpanded ); + $embeddedHistory.find( '.toggle-embed' ).click( toggleExpanded ); + }); +}); +</script> diff -r 6b6c7de6bbe10721674f50ebb5e8a600d8586416 -r 2403d6f67500ec35b16ce604142d98766286b65a templates/webapps/galaxy/page/display.mako --- a/templates/webapps/galaxy/page/display.mako +++ b/templates/webapps/galaxy/page/display.mako @@ -5,12 +5,12 @@ <script type="text/javascript"> $(function() { - // Setup embedded content: // (a) toggles for showing/hiding embedded content; // (b) ... $('.embedded-item').each( function() { var container = $(this); + if( container.hasClass( 'history' ) ){ return; } // Show embedded item. var show_embedded_item = function() { @@ -88,9 +88,12 @@ <%def name="stylesheets()"> ${parent.stylesheets()} - ${h.css( "base", "history", "autocomplete_tagging" )} + ${h.css( "base", "autocomplete_tagging" )} <style type="text/css"> .toggle { display: none; } + .embedded-item .title { + padding-top: 1px; + } .embedded-item h4 { margin: 0px; } @@ -119,6 +122,30 @@ .embedded-item .trackster-nav { position: inherit; } + + /* ---------------------------- histories */ + .embedded-item.history .toggle { + display: inline; + } + .embedded-item.history .expanded-content { + /* generates a fake wide border */ + padding: 4px; + } + /** wraps around the history */ + .embedded-item.history .item-content { + background-color: white; + padding: 8px; + border-radius: 0px 0px 4px 4px; + } + .embedded-item.history .history-panel .datasets-list { + margin-bottom: 8px; + } + .embedded-item.history .history-panel .errormessage { + margin-top: 8px; + } + .annotated-history-panel .history-controls { + margin: 0px 0px 16px 0px; + } </style></%def> @@ -131,4 +158,4 @@ <%def name="render_item( page, page_data=None )"> ${page_data} -</%def> \ No newline at end of file +</%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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