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September 2012

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commit/galaxy-central: greg: Enhance the way that multiple versions of the same tool simultaneously loaded into a Galaxy instance are displayed in the tool panel. Only one link will now be displayed in the tool panel for the tool versions, but the tool page will inlcude a select list allowing the user to select a specific version of the tool. Re-running a job for a specific version of a tool (from the history item) works the same as it did before this change set.
by Bitbucket 06 Sep '12

06 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b43eadc8cdb4/ changeset: b43eadc8cdb4 user: greg date: 2012-09-06 20:33:11 summary: Enhance the way that multiple versions of the same tool simultaneously loaded into a Galaxy instance are displayed in the tool panel. Only one link will now be displayed in the tool panel for the tool versions, but the tool page will inlcude a select list allowing the user to select a specific version of the tool. Re-running a job for a specific version of a tool (from the history item) works the same as it did before this change set. affected #: 4 files diff -r e6444e7a16851514d3efa3ef34acab8362356f8c -r b43eadc8cdb486b7bfa971ff89552ba04126ef0d lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -150,14 +150,39 @@ tool_path=tool_path, config_elems=config_elems ) self.shed_tool_confs.append( shed_tool_conf_dict ) + def __add_tool_to_tool_panel( self, tool_id, panel_component, section=False ): + # See if a version of this tool is already loaded into the tool panel. The value of panel_component + # will be a ToolSection (if the value of section=True) or self.tool_panel (if section=False). + tool = self.tools_by_id[ tool_id ] + if section: + panel_dict = panel_component.elems + else: + panel_dict = panel_component + already_loaded = False + for lineage_id in tool.lineage_ids: + if lineage_id in self.tools_by_id: + loaded_version_key = 'tool_%s' % lineage_id + if loaded_version_key in panel_dict: + already_loaded = True + break + if not already_loaded: + inserted = False + key = 'tool_%s' % tool.id + # The value of panel_component is the in-memory tool panel dictionary. + for index, integrated_panel_key in enumerate( self.integrated_tool_panel.keys() ): + if key == integrated_panel_key: + panel_dict.insert( index, key, tool ) + inserted = True + if not inserted: + # If the tool is not defined in integrated_tool_panel.xml, append it to the tool panel. + panel_dict[ key ] = tool + log.debug( "Loaded tool id: %s, version: %s." % ( tool.id, tool.version ) ) def load_tool_panel( self ): for key, val in self.integrated_tool_panel.items(): if key.startswith( 'tool_' ): tool_id = key.replace( 'tool_', '', 1 ) if tool_id in self.tools_by_id: - tool = self.tools_by_id[ tool_id ] - self.tool_panel[ key ] = tool - log.debug( "Loaded tool id: %s, version: %s." % ( tool.id, tool.version ) ) + self.__add_tool_to_tool_panel( tool_id, self.tool_panel, section=False ) elif key.startswith( 'workflow_' ): workflow_id = key.replace( 'workflow_', '', 1 ) if workflow_id in self.workflows_by_id: @@ -177,9 +202,7 @@ if section_key.startswith( 'tool_' ): tool_id = section_key.replace( 'tool_', '', 1 ) if tool_id in self.tools_by_id: - tool = self.tools_by_id[ tool_id ] - section.elems[ section_key ] = tool - log.debug( "Loaded tool id: %s, version: %s." % ( tool.id, tool.version ) ) + self.__add_tool_to_tool_panel( tool_id, section, section=True ) elif section_key.startswith( 'workflow_' ): workflow_id = section_key.replace( 'workflow_', '', 1 ) if workflow_id in self.workflows_by_id: @@ -297,6 +320,21 @@ else: return tool return None + def get_loaded_tools_by_lineage( self, tool_id ): + """Get all loaded tools associated by lineage to the tool whose id is tool_id.""" + tv = self.__get_tool_version( tool_id ) + if tv: + tool_version_ids = tv.get_version_ids( self.app ) + available_tool_versions = [] + for tool_version_id in tool_version_ids: + if tool_version_id in self.tools_by_id: + available_tool_versions.append( self.tools_by_id[ tool_version_id ] ) + return available_tool_versions + else: + if tool_id in self.tools_by_id: + tool = self.tools_by_id[ tool_id ] + return [ tool ] + return [] def __get_tool_version( self, tool_id ): """Return a ToolVersion if one exists for the tool_id""" return self.sa_session.query( self.app.model.ToolVersion ) \ @@ -334,7 +372,7 @@ # If there is not yet a tool_shed_repository record, we're in the process of installing # a new repository, so any included tools can be loaded into the tool panel. can_load_into_panel_dict = True - tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) + tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) key = 'tool_%s' % str( tool.id ) if can_load_into_panel_dict: if guid is not None: @@ -350,6 +388,8 @@ tool_version = self.app.model.ToolVersion( tool_id=tool.id, tool_shed_repository=tool_shed_repository ) self.sa_session.add( tool_version ) self.sa_session.flush() + # Load the tool's lineage ids. + tool.lineage_ids = tool.tool_version.get_version_ids( self.app ) if self.app.config.get_bool( 'enable_tool_tags', False ): tag_names = elem.get( "tags", "" ).split( "," ) for tag_name in tag_names: @@ -375,7 +415,7 @@ # Allow for the same tool to be loaded into multiple places in the tool panel. self.tools_by_id[ tool.id ] = tool if load_panel_dict: - panel_dict[ key ] = tool + self.__add_tool_to_tool_panel( tool.id, panel_dict, section=isinstance( panel_dict, galaxy.tools.ToolSection ) ) # Always load the tool into the integrated_panel_dict, or it will not be included in the integrated_tool_panel.xml file. if key in integrated_panel_dict or index is None: integrated_panel_dict[ key ] = tool @@ -789,6 +829,8 @@ self.guid = guid self.old_id = None self.version = None + # Enable easy access to this tool's version lineage. + self.lineage_ids = [] # Parse XML element containing configuration self.parse( root, guid=guid ) self.external_runJob_script = app.config.drmaa_external_runjob_script diff -r e6444e7a16851514d3efa3ef34acab8362356f8c -r b43eadc8cdb486b7bfa971ff89552ba04126ef0d lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1518,15 +1518,40 @@ if tool_elem.get( 'guid' ) in guids_to_remove: tool_elems_to_remove.append( tool_elem ) for tool_elem in tool_elems_to_remove: - # Remove the tool sub-element from the section element. - config_elem.remove( tool_elem ) + if tool_elem in config_elem: + # Remove the tool sub-element from the section element. + config_elem.remove( tool_elem ) # Remove the tool from the section in the in-memory tool panel. if section_key in trans.app.toolbox.tool_panel: tool_section = trans.app.toolbox.tool_panel[ section_key ] - tool_key = 'tool_%s' % str( tool_elem.get( 'guid' ) ) - # Remove empty sections only from the in-memory config_elems, but leave the in-memory tool panel alone. + guid = tool_elem.get( 'guid' ) + tool_key = 'tool_%s' % str( guid ) + # Get the list of versions of this tool that are currently available in the toolbox. + available_tool_versions = trans.app.toolbox.get_loaded_tools_by_lineage( guid ) if tool_key in tool_section.elems: - del tool_section.elems[ tool_key ] + if available_tool_versions: + available_tool_versions.reverse() + replacement_tool_key = None + 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(): + replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) + replacement_tool_version = available_tool_version + break + if replacement_tool_key and replacement_tool_version: + # Get the index of the tool_key in the tool_section. + for tool_section_elems_index, key in enumerate( tool_section.elems.keys() ): + if key == tool_key: + break + # Remove the tool from the tool section. + del tool_section.elems[ tool_key ] + # Add the replacement tool at the same location in the tool section. + tool_section.elems.insert( tool_section_elems_index, replacement_tool_key, replacement_tool_version ) + else: + del tool_section.elems[ tool_key ] + else: + del tool_section.elems[ tool_key ] if uninstall: # Remove the tool from the section in the in-memory integrated tool panel. if section_key in trans.app.toolbox.integrated_tool_panel: @@ -1538,10 +1563,35 @@ # Keep a list of all empty section elements so they can be removed. config_elems_to_remove.append( config_elem ) elif config_elem.tag == 'tool': - if config_elem.get( 'guid' ) in guids_to_remove: + guid = config_elem.get( 'guid' ) + if guid in guids_to_remove: tool_key = 'tool_%s' % str( config_elem.get( 'guid' ) ) + # Get the list of versions of this tool that are currently available in the toolbox. + available_tool_versions = trans.app.toolbox.get_loaded_tools_by_lineage( guid ) if tool_key in trans.app.toolbox.tool_panel: - del trans.app.toolbox.tool_panel[ tool_key ] + if available_tool_versions: + available_tool_versions.reverse() + replacement_tool_key = None + 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(): + replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) + replacement_tool_version = available_tool_version + break + if replacement_tool_key and replacement_tool_version: + # Get the index of the tool_key in the tool_section. + for tool_panel_index, key in enumerate( trans.app.toolbox.tool_panel.keys() ): + if key == tool_key: + break + # Remove the tool from the tool panel. + del trans.app.toolbox.tool_panel[ tool_key ] + # Add the replacement tool at the same location in the tool panel. + trans.app.toolbox.tool_panel.insert( tool_panel_index, replacement_tool_key, replacement_tool_version ) + else: + del trans.app.toolbox.tool_panel[ tool_key ] + else: + del trans.app.toolbox.tool_panel[ tool_key ] if uninstall: if tool_key in trans.app.toolbox.integrated_tool_panel: del trans.app.toolbox.integrated_tool_panel[ tool_key ] diff -r e6444e7a16851514d3efa3ef34acab8362356f8c -r b43eadc8cdb486b7bfa971ff89552ba04126ef0d lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py +++ b/lib/galaxy/web/controllers/tool_runner.py @@ -35,31 +35,57 @@ def default(self, trans, tool_id=None, **kwd): """Catches the tool id and redirects as needed""" return self.index(trans, tool_id=tool_id, **kwd) - + def __get_tool_components( self, tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=False ): + """ + Retrieve all loaded versions of a tool from the toolbox and return a select list enabling selection of a different version, the list of the tool's + loaded versions, and the specified tool. + """ + toolbox = self.get_toolbox() + tool_version_select_field = None + tools = [] + # Backwards compatibility for datasource tools that have default tool_id configured, but which are now using only GALAXY_URL. + tool_ids = util.listify( tool_id ) + for tool_id in tool_ids: + if get_loaded_tools_by_lineage: + tools = toolbox.get_loaded_tools_by_lineage( tool_id ) + else: + tools = toolbox.get_tool( tool_id, tool_version=tool_version, get_all_versions=True ) + if len( tools ) > 1: + tool_version_select_field = self.build_tool_version_select_field( tools, tool_id, set_selected ) + for tool in tools: + if tool.id == tool_id: + break + else: + tool = tools[ 0 ] + else: + tool = tools[ 0 ] + break + return tool_version_select_field, tools, tool @web.expose def index(self, trans, tool_id=None, from_noframe=None, **kwd): # No tool id passed, redirect to main page if tool_id is None: return trans.response.send_redirect( url_for( "/static/welcome.html" ) ) - # Load the tool - toolbox = self.get_toolbox() - #Backwards compatibility for datasource tools that have default tool_id configured, but which are now using only GALAXY_URL - if isinstance( tool_id, list ): - tool_ids = tool_id - else: - tool_ids = [ tool_id ] - for tool_id in tool_ids: - tool = toolbox.get_tool( tool_id ) - if tool: - break + set_selected = 'refresh' in kwd + tool_version_select_field, tools, tool = self.__get_tool_components( tool_id, + tool_version=None, + get_loaded_tools_by_lineage=True, + set_selected=set_selected ) # No tool matching the tool id, display an error (shouldn't happen) if not tool: - tool_id = ','.join( tool_ids ) log.error( "index called with tool id '%s' but no such tool exists", tool_id ) trans.log_event( "Tool id '%s' does not exist" % tool_id ) - return "Tool '%s' does not exist, kwd=%s " % (tool_id, kwd) + return "Tool '%s' does not exist, kwd=%s " % ( tool_id, kwd ) if tool.require_login and not trans.user: - return trans.response.send_redirect( url_for( controller='user', action='login', cntrller='user', message="You must be logged in to use this tool.", status="info", redirect=url_for( controller='/tool_runner', action='index', tool_id=tool_id, **kwd ) ) ) + message = "You must be logged in to use this tool." + status = "info" + redirect = url_for( controller='/tool_runner', action='index', tool_id=tool_id, **kwd ) + return trans.response.send_redirect( url_for( controller='user', + action='login', + cntrller='user', + message=message, + status=status, + redirect=redirect ) ) params = util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers #do param translation here, used by datasource tools if tool.input_translator: @@ -68,14 +94,21 @@ # so make sure to create a new history if we've never had one before. history = trans.get_history( create=True ) template, vars = tool.handle_input( trans, params.__dict__ ) - if len(params) > 0: - trans.log_event( "Tool params: %s" % (str(params)), tool_id=tool_id ) + if len( params ) > 0: + trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id ) add_frame = AddFrameData() add_frame.debug = trans.debug if from_noframe is not None: add_frame.wiki_url = trans.app.config.wiki_url add_frame.from_noframe = True - return trans.fill_template( template, history=history, toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars ) + return trans.fill_template( template, + history=history, + toolbox=self.get_toolbox(), + tool_version_select_field=tool_version_select_field, + tool=tool, + util=util, + add_frame=add_frame, + **vars ) @web.expose def rerun( self, trans, id=None, from_noframe=None, **kwd ): @@ -113,21 +146,10 @@ tool_id = job.tool_id tool_version = job.tool_version try: - # Load the tool - toolbox = self.get_toolbox() - tools = toolbox.get_tool( tool_id, tool_version=tool_version, get_all_versions=True ) - if len( tools ) > 1: - tool_id_select_field = self.build_tool_id_select_field( tools, tool_id ) - for tool in tools: - if tool.id == tool_id: - break - else: - tool = tools[ 0 ] - tool_id_version_message = 'This job was initially run with tool id "%s", version "%s", and multiple derivations ' % ( job.tool_id, job.tool_version ) - tool_id_version_message += 'of this tool are available. Rerun the job with the selected tool or choose another derivation of the tool.' - else: - tool_id_select_field = None - tool = tools[ 0 ] + tool_version_select_field, tools, tool = self.__get_tool_components( tool_id, + tool_version=tool_version, + get_loaded_tools_by_lineage=False, + set_selected=True ) if ( tool.id == job.tool_id or tool.old_id == job.tool_id ) and tool.version == job.tool_version: tool_id_version_message = '' elif tool.id == job.tool_id: @@ -199,27 +221,27 @@ add_frame.from_noframe = True return trans.fill_template( "tool_form.mako", history=history, - toolbox=toolbox, - tool_id_select_field=tool_id_select_field, + toolbox=self.get_toolbox(), + tool_version_select_field=tool_version_select_field, tool=tool, util=util, add_frame=add_frame, tool_id_version_message=tool_id_version_message, **vars ) - def build_tool_id_select_field( self, tools, selected_tool_id ): + def build_tool_version_select_field( self, tools, tool_id, set_selected ): """Build a SelectField whose options are the ids for the received list of tools.""" options = [] refresh_on_change_values = [] for tool in tools: - options.append( ( tool.id, tool.id ) ) + options.insert( 0, ( tool.version, tool.id ) ) refresh_on_change_values.append( tool.id ) select_field = SelectField( name='tool_id', refresh_on_change=True, refresh_on_change_values=refresh_on_change_values ) for option_tup in options: - selected = option_tup[0] == selected_tool_id + selected = set_selected and option_tup[1] == tool_id if selected: - select_field.add_option( option_tup[0], option_tup[1], selected=True ) + select_field.add_option( 'version %s' % option_tup[0], option_tup[1], selected=True ) else: - select_field.add_option( option_tup[0], option_tup[1] ) + select_field.add_option( 'version %s' % option_tup[0], option_tup[1] ) return select_field @web.expose def redirect( self, trans, redirect_url=None, **kwd ): diff -r e6444e7a16851514d3efa3ef34acab8362356f8c -r b43eadc8cdb486b7bfa971ff89552ba04126ef0d templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -287,25 +287,17 @@ %endif <div class="toolForm" id="${tool.id}"> - %if tool.has_multiple_pages: - <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div> - %else: - <div class="toolFormTitle">${tool.name} (version ${tool.version})</div> - %endif - <div class="toolFormBody"> - <form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> - %if tool_id_select_field: - <div class="form-row"> - <label>Tool id:</label> - ${tool_id_select_field.get_html()} - <div class="toolParamHelp" style="clear: both;"> - Select a different derivation of this tool to rerun the job. - </div> - </div> - <div style="clear: both"></div> - %else: - <input type="hidden" name="tool_id" value="${tool.id}"> - %endif + <form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> + %if tool.has_multiple_pages: + <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div> + %elif not tool_version_select_field: + <div class="toolFormTitle">${tool.name} (version ${tool.version})</div> + %else: + <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()}</div> + %endif + <div class="toolFormBody"> + <input type="hidden" name="refresh" value="refresh"> + <input type="hidden" name="tool_id" value="${tool.id}"><input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> %if tool.display_by_page[tool_state.page]: ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )} @@ -320,8 +312,8 @@ %endif </div> %endif - </form> - </div> + </div> + </form></div> %if tool.help: <div class="toolHelp"> 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: jgoecks: Pack scripts.
by Bitbucket 05 Sep '12

05 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e6444e7a1685/ changeset: e6444e7a1685 user: jgoecks date: 2012-09-06 04:28:32 summary: Pack scripts. affected #: 2 files diff -r d5626302446db334804820f0a29fc4d0c7d72a0e -r e6444e7a16851514d3efa3ef34acab8362356f8c static/scripts/packed/viz/trackster.js --- a/static/scripts/packed/viz/trackster.js +++ b/static/scripts/packed/viz/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var g=arguments[0];for(var f=1;f<arguments.length;f++){var d=arguments[f];for(var e in d){g[e]=d[e]}}return g};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tooltip().click(a)};var trackster_module=function(d,S){var o=d("class").extend,s=d("slotting"),I=d("painters");var m={};var k=function(Z,aa){m[Z.attr("id")]=aa};var l=function(Z,ab,ad,ac){ad=".group";var aa={};m[Z.attr("id")]=ac;Z.bind("drag",{handle:"."+ab,relative:true},function(al,am){var ak=$(this),ap=$(this).parent(),ah=ap.children(),aj=m[$(this).attr("id")],ag,af,an,ae,ai;af=$(this).parents(ad);if(af.length!==0){an=af.position().top;ae=an+af.outerHeight();if(am.offsetY<an){$(this).insertBefore(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable_before(aj,ao);return}else{if(am.offsetY>ae){$(this).insertAfter(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable(aj);return}}}af=null;for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));an=ag.position().top;ae=an+ag.outerHeight();if(ag.is(ad)&&this!==ag.get(0)&&am.offsetY>=an&&am.offsetY<=ae){if(am.offsetY-an<ae-am.offsetY){ag.find(".content-div").prepend(this)}else{ag.find(".content-div").append(this)}if(aj.container){aj.container.remove_drawable(aj)}m[ag.attr("id")].add_drawable(aj);return}}for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));if(am.offsetY<ag.position().top&&!(ag.hasClass("reference-track")||ag.hasClass("intro"))){break}}if(ai===ah.length){if(this!==ah.get(ai-1)){ap.append(this);m[ap.attr("id")].move_drawable(aj,ai)}}else{if(this!==ah.get(ai)){$(this).insertBefore(ah.get(ai));m[ap.attr("id")].move_drawable(aj,(am.deltaY>0?ai-1:ai))}}}).bind("dragstart",function(){aa["border-top"]=Z.css("border-top");aa["border-bottom"]=Z.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(aa)})};S.moveable=l;var Y=16,D=9,A=20,x=100,F=12000,P=400,H=5000,u=100,n="There was an error in indexing this dataset. 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If the visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",N=10,E=20;function U(aa,Z){if(!Z){Z=0}var ab=Math.pow(10,Z);return Math.round(aa*ab)/ab}var p=function(aa,Z,ac){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ac.name;this.view=aa;this.container=Z;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ac.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ac.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;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=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ad){ad.stopPropagation()});var ab=this;this.container_div.hover(function(){ab.icons_div.show()},function(){ab.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(Z){if(Z.content_visible){Z.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");Z.hide_contents();Z.content_visible=false}else{Z.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");Z.content_visible=true;Z.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(aa){var ac=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},Z=function(){aa.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(ad){if((ad.keyCode||ad.which)===27){ac()}else{if((ad.keyCode||ad.which)===13){Z()}}};$(window).bind("keypress.check_enter_esc",ab);show_modal("Configure",aa.config.build_form(),{Cancel:ac,OK:Z})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(Z){this.old_name=this.name;this.name=Z;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var Z=this.view;this.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(aa,af,ae,ad,Z,ac){var ab=this;this.action_icons[aa]=$("<a/>").attr("href","javascript:void(0);").attr("title",af).addClass("icon-button").addClass(ae).tooltip().click(function(){ad(ab)}).appendTo(this.icons_div);if(ac){this.action_icons[aa].hide()}},build_action_icons:function(Z){var ab;for(var aa=0;aa<Z.length;aa++){ab=Z[aa];this.add_action_icon(ab.name,ab.title,ab.css_class,ab.on_click_fn,ab.prepend,ab.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(aa,Z,ab){p.call(this,aa,Z,ab);this.obj_type=ab.obj_type;this.drawables=[]};o(w.prototype,p.prototype,{unpack_drawables:function(ab){this.drawables=[];var aa;for(var Z=0;Z<ab.length;Z++){aa=object_from_template(ab[Z],this.view,this);this.add_drawable(aa)}},init:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].init()}},_draw:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z]._draw()}},to_dict:function(){var aa=[];for(var Z=0;Z<this.drawables.length;Z++){aa.push(this.drawables[Z].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:aa}},add_drawable:function(Z){this.drawables.push(Z);Z.container=this;this.changed()},add_drawable_before:function(ab,Z){this.changed();var aa=this.drawables.indexOf(Z);if(aa!==-1){this.drawables.splice(aa,0,ab);return true}return false},replace_drawable:function(ab,Z,aa){var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables[ac]=Z;if(aa){ab.container_div.replaceWith(Z.container_div)}this.changed()}return ac},remove_drawable:function(aa){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);aa.container=null;this.changed();return true}return false},move_drawable:function(aa,ab){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);this.drawables.splice(ab,0,aa);this.changed();return true}return false}});var M=function(aa,Z,ac){o(ac,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,aa,Z,ac);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new V(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ac){this.unpack_drawables(ac.drawables)}if("filters" in ac){var ab=this.filters_manager;this.filters_manager=new V(this,ac.filters);ab.parent_div.replaceWith(this.filters_manager.parent_div);if(ac.filters.visible){this.setup_multitrack_filtering()}}};o(M.prototype,p.prototype,w.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters();Z._restore_filter_managers()}else{Z.setup_multitrack_filtering();Z.request_draw(true)}Z.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var Z=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(Z)}return Z},build_header_div:function(){var Z=$("<div/>").addClass("track-header");Z.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(Z);return Z},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ab=this.drawables.length;if(ab===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ab===1){if(this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ah,af,al=true,ad=this.drawables[0].get_type(),Z=0;for(ai=0;ai<ab;ai++){af=this.drawables[ai];if(af.get_type()!==ad){can_composite=false;break}if(af instanceof c){Z++}}if(al||Z===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(Z>1&&Z===this.drawables.length){var am={},aa;af=this.drawables[0];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];am[aa.name]=[aa]}for(ai=1;ai<this.drawables.length;ai++){af=this.drawables[ai];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];if(aa.name in am){am[aa.name].push(aa)}}}this.filters_manager.remove_all();var ac,ae,ag,aj;for(var ak in am){ac=am[ak];if(ac.length===Z){ae=new Q({name:ac[0].name,index:ac[0].index});this.filters_manager.add_filter(ae)}}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 Z=0;Z<this.drawables.length;Z++){this.drawables[Z].filters_manager=this.saved_filters_managers[Z]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var Z=0;Z<this.drawables.length;Z++){drawable=this.drawables[Z];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=[];for(var aa=0;aa<this.drawables.length;aa++){ad.push(this.drawables[aa].name)}var ab="Composite Track of "+this.drawables.length+" tracks ("+ad.join(", ")+")";var ac=new g(this.view,this.view,{name:ab,drawables:this.drawables});var Z=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);this.update_icons()},remove_drawable:function(Z){w.prototype.remove_drawable.call(this,Z);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var Z=o(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return Z},request_draw:function(Z,ab){for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].request_draw(Z,ab)}}});var X=function(Z){o(Z,{obj_type:"View"});w.call(this,"View",Z.container,Z);this.chrom=null;this.vis_id=Z.vis_id;this.dbkey=Z.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.init();this.canvas_manager=new CanvasManager(this.container.get(0).ownerDocument);this.reset()};_.extend(X.prototype,Backbone.Events);o(X.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ab=this.container,Z=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ab);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ab);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ab);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,Z);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ac=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_datasets(add_datasets_url,add_track_async_url,function(ad){_.each(ad,function(ae){Z.add_drawable(object_from_template(ae,Z,Z))})})});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("href","javascript:void(0);").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=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var aa=function(ad){if(ad.type==="focusout"||(ad.keyCode||ad.which)===13||(ad.keyCode||ad.which)===27){if((ad.keyCode||ad.which)!==27){Z.go_to($(this).val())}$(this).hide();$(this).val("");Z.location_span.show();Z.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",aa).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){Z.location_span.hide();Z.chrom_select.hide();Z.nav_input.val(Z.chrom+":"+Z.low+"-"+Z.high);Z.nav_input.css("display","inline-block");Z.nav_input.select();Z.nav_input.focus()});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(){Z.zoom_out();Z.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){Z.zoom_in();Z.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){Z.change_chrom(Z.chrom_select.val())});this.browser_content_div.click(function(ad){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ad){Z.zoom_in(ad.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ad,ae){this.current_x=ae.offsetX}).bind("drag",function(ad,af){var ag=af.offsetX-this.current_x;this.current_x=af.offsetX;var ae=Math.round(ag/Z.viewport_container.width()*(Z.max_high-Z.max_low));Z.move_delta(-ae)});this.overview_close.click(function(){Z.reset_overview()});this.viewport_container.bind("draginit",function(ad,ae){if(ad.clientX>Z.viewport_container.width()-16){return false}}).bind("dragstart",function(ad,ae){ae.original_low=Z.low;ae.current_height=ad.clientY;ae.current_x=ae.offsetX}).bind("drag",function(af,ah){var ad=$(this);var ai=ah.offsetX-ah.current_x;var ae=ad.scrollTop()-(af.clientY-ah.current_height);ad.scrollTop(ae);ah.current_height=af.clientY;ah.current_x=ah.offsetX;var ag=Math.round(ai/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}).bind("mousewheel",function(af,ah,ae,ad){if(ae){ae*=50;var ag=Math.round(-ae/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}});this.top_labeltrack.bind("dragstart",function(ad,ae){return $("<div />").css({height:Z.browser_content_div.height()+Z.top_labeltrack.height()+Z.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ah,ai){$(ai.proxy).css({left:Math.min(ah.pageX,ai.startX)-Z.container.offset().left,width:Math.abs(ah.pageX-ai.startX)});var ae=Math.min(ah.pageX,ai.startX)-Z.container.offset().left,ad=Math.max(ah.pageX,ai.startX)-Z.container.offset().left,ag=(Z.high-Z.low),af=Z.viewport_container.width();Z.update_location(Math.round(ae/af*ag)+Z.low,Math.round(ad/af*ag)+Z.low)}).bind("dragend",function(ai,aj){var ae=Math.min(ai.pageX,aj.startX),ad=Math.max(ai.pageX,aj.startX),ag=(Z.high-Z.low),af=Z.viewport_container.width(),ah=Z.low;Z.low=Math.round(ae/af*ag)+ah;Z.high=Math.round(ad/af*ag)+ah;$(aj.proxy).remove();Z.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}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){Z.resize_window()},500)});$(document).bind("redraw",function(){Z.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(aa,ac,Z,ad){if(this.timer){clearTimeout(this.timer)}if(ad){var ab=this;this.timer=setTimeout(function(){ab.trigger("navigate",aa+":"+ac+"-"+Z)},500)}else{view.trigger("navigate",aa+":"+ac+"-"+Z)}},update_location:function(Z,ab){this.location_span.text(commatize(Z)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(Z)+"-"+commatize(ab));var aa=view.chrom_select.val();if(aa!==""){this.trigger_navigate(aa,view.low,view.high,true)}},load_chroms:function(ab){ab.num=u;ab.dbkey=this.dbkey;var Z=this,aa=$.Deferred();$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ad){if(ad.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ad.reference){Z.add_label_track(new y(Z))}Z.chrom_data=ad.chrom_info;var ag='<option value="">Select Chrom/Contig</option>';for(var af=0,ac=Z.chrom_data.length;af<ac;af++){var ae=Z.chrom_data[af].chrom;ag+='<option value="'+ae+'">'+ae+"</option>"}if(ad.prev_chroms){ag+='<option value="previous">Previous '+u+"</option>"}if(ad.next_chroms){ag+='<option value="next">Next '+u+"</option>"}Z.chrom_select.html(ag);Z.chrom_start_index=ad.start_index;aa.resolve(ad)},error:function(){alert("Could not load chroms for this dbkey:",Z.dbkey)}});return aa},change_chrom:function(ae,aa,ag){var ab=this;if(!ab.chrom_data){ab.load_chroms_deferred.then(function(){ab.change_chrom(ae,aa,ag)});return}if(!ae||ae==="None"){return}if(ae==="previous"){ab.load_chroms({low:this.chrom_start_index-u});return}if(ae==="next"){ab.load_chroms({low:this.chrom_start_index+u});return}var af=$.grep(ab.chrom_data,function(ah,ai){return ah.chrom===ae})[0];if(af===undefined){ab.load_chroms({chrom:ae},function(){ab.change_chrom(ae,aa,ag)});return}else{if(ae!==ab.chrom){ab.chrom=ae;ab.chrom_select.val(ab.chrom);ab.max_high=af.len-1;ab.reset();ab.request_redraw(true);for(var ad=0,Z=ab.drawables.length;ad<Z;ad++){var ac=ab.drawables[ad];if(ac.init){ac.init()}}if(ab.reference_track){ab.reference_track.init()}}if(aa!==undefined&&ag!==undefined){ab.low=Math.max(aa,0);ab.high=Math.min(ag,ab.max_high)}else{ab.low=0;ab.high=ab.max_high}ab.reset_overview();ab.request_redraw()}},go_to:function(ad){ad=ad.replace(/ |,/g,"");var ah=this,Z,ac,aa=ad.split(":"),af=aa[0],ag=aa[1];if(ag!==undefined){try{var ae=ag.split("-");Z=parseInt(ae[0],10);ac=parseInt(ae[1],10)}catch(ab){return false}}ah.change_chrom(af,Z,ac)},move_fraction:function(ab){var Z=this;var aa=Z.high-Z.low;this.move_delta(ab*aa)},move_delta:function(ac){var Z=this;var ab=Z.high-Z.low;if(Z.low-ac<Z.max_low){Z.low=Z.max_low;Z.high=Z.max_low+ab}else{if(Z.high-ac>Z.max_high){Z.high=Z.max_high;Z.low=Z.max_high-ab}else{Z.high-=ac;Z.low-=ac}}Z.request_redraw();var aa=Z.chrom_select.val();this.trigger_navigate(aa,Z.low,Z.high,true)},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);Z.init();this.changed();this.update_intro_div()},add_label_track:function(Z){Z.view=this;Z.init();this.label_tracks.push(Z)},remove_drawable:function(ab,aa){w.prototype.remove_drawable.call(this,ab);if(aa){var Z=this;ab.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ah,Z,ag,ai){var af=this,ae=(ai?[ai]:af.drawables),ab;var aa;for(var ad=0;ad<ae.length;ad++){aa=ae[ad];ab=-1;for(var ac=0;ac<af.tracks_to_be_redrawn.length;ac++){if(af.tracks_to_be_redrawn[ac][0]===aa){ab=ac;break}}if(ab<0){af.tracks_to_be_redrawn.push([aa,Z,ag])}else{af.tracks_to_be_redrawn[ad][1]=Z;af.tracks_to_be_redrawn[ad][2]=ag}}if(!this.requested_redraw){requestAnimationFrame(function(){af._redraw(ah)});this.requested_redraw=true}},_redraw:function(aj){this.requested_redraw=false;var ag=this.low,ac=this.high;if(ag<this.max_low){ag=this.max_low}if(ac>this.max_high){ac=this.max_high}var ai=this.high-this.low;if(this.high!==0&&ai<this.min_separation){ac=ag+this.min_separation}this.low=Math.floor(ag);this.high=Math.ceil(ac);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var Z=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=13;this.overview_box.css({left:Z,width:Math.max(ak,af)}).show();if(af<ak){this.overview_box.css("left",Z-(ak-af)/2)}if(this.overview_highlight){this.overview_highlight.css({left:Z,width:af})}if(!aj){var ab,aa,ah;for(var ad=0,ae=this.tracks_to_be_redrawn.length;ad<ae;ad++){ab=this.tracks_to_be_redrawn[ad][0];aa=this.tracks_to_be_redrawn[ad][1];ah=this.tracks_to_be_redrawn[ad][2];if(ab){ab._draw(aa,ah)}}this.tracks_to_be_redrawn=[];for(ad=0,ae=this.label_tracks.length;ad<ae;ad++){this.label_tracks[ad]._draw()}}},zoom_in:function(aa,ab){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ac=this.high-this.low,ad=ac/2+this.low,Z=(ac/this.zoom_factor)/2;if(aa){ad=aa/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ad-Z);this.high=Math.round(ad+Z);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var aa=this.high-this.low,ab=aa/2+this.low,Z=(aa*this.zoom_factor)/2;this.low=Math.round(ab-Z);this.high=Math.round(ab+Z);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(ab){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ab.dataset_id){return}this.overview_viewport.find(".track").remove()}var aa=ab.copy({content_div:this.overview_viewport}),Z=this;aa.header_div.hide();aa.is_overview=true;Z.overview_drawable=aa;this.overview_drawable.postdraw_actions=function(){Z.overview_highlight.show().height(Z.overview_drawable.content_div.height());Z.overview_viewport.height(Z.overview_drawable.content_div.height()+Z.overview_box.outerHeight());Z.overview_close.show();Z.resize_window()};Z.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-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 q=function(ab,ag,ac){this.track=ab;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],aa=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params.push(new e(aa,am,ae,(aa in ac?ac[aa]:ao),ai.min,ai.max))}else{if(ak==="select"){this.params.push(new K(aa,am,ae,(aa in ac?ac[aa]:ao)))}else{console.log("WARNING: unrecognized tool parameter type:",aa,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).click(function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("param-input").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: both;'/>").appendTo(au)});this.parent_div.find("input").click(function(){$(this).select()});var ap=$("<div>").addClass("param-row").appendTo(this.parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ap);var Z=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ap);Z.click(function(){ah.run_on_region()});af.click(function(){ah.run_on_dataset()});if("visible" in ac&&ac.visible){this.parent_div.show()}};o(q.prototype,{update_params:function(){for(var Z=0;Z<this.params.length;Z++){this.params[Z].update_value()}},state_dict:function(){var aa={};for(var Z=0;Z<this.params.length;Z++){aa[this.params[Z].name]=this.params[Z].value}aa.visible=this.parent_div.is(":visible");return aa},get_param_values_dict:function(){var Z={};this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();Z[aa]=ab});return Z},get_param_values:function(){var Z=[];this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();if(aa){Z[Z.length]=ab}});return Z},run_on_dataset:function(){var Z=this;Z.run({target_dataset_id:this.track.original_dataset_id,tool_id:Z.name},null,function(aa){show_modal(Z.name+" is Running",Z.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ae=this.track,ab=aa.tool_id+ae.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),Z;if(ae.container===view){var ad=new M(view,view,{name:this.name});var ac=ae.container.replace_drawable(ae,ad,false);ad.container_div.insertBefore(ae.view.content_div.children()[ac]);ad.add_drawable(ae);ae.container_div.appendTo(ad.content_div);Z=ad}else{Z=ae.container}var af=new ae.constructor(view,Z,{name:ab,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ae.mode);af.set_filters_manager(ae.filters_manager.copy(af));af.update_icons();Z.add_drawable(af);af.tiles_div.text("Starting job.");this.update_params();this.run(aa,af,function(ag){af.set_dataset(new Dataset(ag));af.tiles_div.text("Running job.");af.init()})},run:function(Z,ab,ac){Z.inputs=this.get_param_values_dict();var aa=new ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(Z),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ad){return ad!=="pending"}});$.when(aa.go()).then(function(ad){if(ad==="no converter"){ab.container_div.addClass("error");ab.content_div.text(G)}else{if(ad.error){ab.container_div.addClass("error");ab.content_div.text(v+ad.message)}else{ac(ad)}}})}});var K=function(aa,Z,ab,ac){this.name=aa;this.label=Z;this.html=$(ab);this.value=ac};o(K.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ab,aa,ad,ae,ac,Z){K.call(this,ab,aa,ad,ae);this.min=ac;this.max=Z};o(e.prototype,K.prototype,{update_value:function(){K.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var f=function(Z){this.manager=null;this.name=Z.name;this.index=Z.index;this.tool_id=Z.tool_id;this.tool_exp_name=Z.tool_exp_name};o(f.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var Q=function(ah){f.call(this,ah);this.low=("low" in ah?ah.low:-Number.MAX_VALUE);this.high=("high" in ah?ah.high:Number.MAX_VALUE);this.min=("min" in ah?ah.min:Number.MAX_VALUE);this.max=("max" in ah?ah.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ad=function(ai,aj,ak){ai.click(function(){var ap=aj.text(),an=parseFloat(ak.slider("option","max")),am=(an<=1?4:an<=1000000?an.toString().length:6),ao=false,al=$(this).parents(".slider-row");al.addClass("input");if(ak.slider("option","values")){am=2*am+1;ao=true}aj.text("");$("<input type='text'/>").attr("size",am).attr("maxlength",am).attr("value",ap).appendTo(aj).focus().select().click(function(aq){aq.stopPropagation()}).blur(function(){$(this).remove();aj.text(ap);al.removeClass("input")}).keyup(function(av){if(av.keyCode===27){$(this).trigger("blur")}else{if(av.keyCode===13){var at=ak.slider("option","min"),aq=ak.slider("option","max"),au=function(aw){return(isNaN(aw)||aw>aq||aw<at)},ar=$(this).val();if(!ao){ar=parseFloat(ar);if(au(ar)){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}else{ar=ar.split("-");ar=[parseFloat(ar[0]),parseFloat(ar[1])];if(au(ar[0])||au(ar[1])){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}ak.slider((ao?"values":"value"),ar);al.removeClass("input")}}})})};var aa=this;aa.parent_div=$("<div/>").addClass("filter-row slider-row");var Z=$("<div/>").addClass("elt-label").appendTo(aa.parent_div),af=$("<span/>").addClass("slider-name").text(aa.name+" ").appendTo(Z),ab=$("<span/>").text(this.low+"-"+this.high),ac=$("<span/>").addClass("slider-value").appendTo(Z).append("[").append(ab).append("]");aa.values_span=ab;var ae=$("<div/>").addClass("slider").appendTo(aa.parent_div);aa.control_element=$("<div/>").attr("id",aa.name+"-filter-control").appendTo(ae);aa.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(ai,aj){aa.slide(ai,aj)},change:function(ai,aj){aa.control_element.slider("option","slide").call(aa.control_element,ai,aj)}});aa.slider=aa.control_element;aa.slider_label=ab;ad(ac,ab,aa.control_element);var ag=$("<div/>").addClass("display-controls").appendTo(aa.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(aa.manager.alpha_filter!==aa){aa.manager.alpha_filter=aa;aa.manager.parent_div.find(".layer-transparent").removeClass("active").hide();aa.transparency_icon.addClass("active").show()}else{aa.manager.alpha_filter=null;aa.transparency_icon.removeClass("active")}aa.manager.track.request_draw(true,true)}).appendTo(ag).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(aa.manager.height_filter!==aa){aa.manager.height_filter=aa;aa.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();aa.height_icon.addClass("active").show()}else{aa.manager.height_filter=null;aa.height_icon.removeClass("active")}aa.manager.track.request_draw(true,true)}).appendTo(ag).hide();aa.parent_div.hover(function(){aa.transparency_icon.show();aa.height_icon.show()},function(){if(aa.manager.alpha_filter!==aa){aa.transparency_icon.hide()}if(aa.manager.height_filter!==aa){aa.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(aa.parent_div)};o(Q.prototype,{to_dict:function(){var Z=f.prototype.to_dict.call(this);return o(Z,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new Q({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ab,Z){var aa=Z-ab;return(aa<=2?0.01:1)},slide:function(ab,ac){var aa=ac.values;this.values_span.text(aa[0]+"-"+aa[1]);this.low=aa[0];this.high=aa[1];var Z=this;setTimeout(function(){if(aa[0]===Z.low&&aa[1]===Z.high){Z.manager.track.request_draw(true,true)}},25)},applies_to:function(Z){if(Z.length>this.index){return true}return false},_keep_val:function(Z){return(isNaN(Z)||(Z>=this.low&&Z<=this.high))},keep:function(aa){if(!this.applies_to(aa)){return true}var ac=this;var ad=aa[this.index];if(ad instanceof Array){var ab=true;for(var Z=0;Z<ad.length;Z++){if(!this._keep_val(ad[Z])){ab=false;break}}return ab}else{return this._keep_val(aa[this.index])}},update_attrs:function(ac){var Z=false;if(!this.applies_to(ac)){return Z}var aa=ac[this.index];if(!(aa instanceof Array)){aa=[aa]}for(var ab=0;ab<aa.length;ab++){var ad=aa[ab];if(ad<this.min){this.min=Math.floor(ad);Z=true}if(ad>this.max){this.max=Math.ceil(ad);Z=true}}return Z},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var aa=this.slider.slider("option","min"),Z=this.slider.slider("option","max");if(this.min<aa||this.max>Z){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var V=function(ab,ah){this.track=ab;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aj){aj.stopPropagation()}).click(function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()}).bind("keydown",function(aj){aj.stopPropagation()});if(ah&&"filters" in ah){var Z=("alpha_filter" in ah?ah.alpha_filter:null),ac=("height_filter" in ah?ah.height_filter:null),ae=ah.filters,aa;for(var af=0;af<ae.length;af++){if(ae[af].type==="number"){aa=new Q(ae[af]);this.add_filter(aa);if(aa.name===Z){this.alpha_filter=aa;aa.transparency_icon.addClass("active").show()}if(aa.name===ac){this.height_filter=aa;aa.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ah&&ah.visible){this.parent_div.show()}}if(this.filters.length!==0){var ai=$("<div/>").addClass("param-row").appendTo(this.parent_div);var ag=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ai);var ad=this;ag.click(function(){ad.run_on_dataset()})}};o(V.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var ac={},ab=[],aa;for(var Z=0;Z<this.filters.length;Z++){aa=this.filters[Z];ab.push(aa.to_dict())}ac.filters=ab;ac.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);ac.height_filter=(this.height_filter?this.height_filter.name:null);ac.visible=this.parent_div.is(":visible");return ac},copy:function(aa){var ab=new V(aa);for(var Z=0;Z<this.filters.length;Z++){ab.add_filter(this.filters[Z].copy())}return ab},add_filter:function(Z){Z.manager=this;this.parent_div.append(Z.parent_div);this.filters.push(Z)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.update_ui_elt()}},clear_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.slider.slider("option","values",[aa.min,aa.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var af=function(aj,ah,ai){if(!(ah in aj)){aj[ah]=ai}return aj[ah]};var ae={},ag,Z;for(var ad=0;ad<this.filters.length;ad++){ag=this.filters[ad];if(ag.tool_id){if(ag.min!==ag.low){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" >= "+ag.low}if(ag.max!==ag.high){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" <= "+ag.high}}}var aa=[];for(var ac in ae){aa[aa.length]=[ac,ae[ac]]}(function ab(an,ak){var ai=ak[0],aj=ai[0],am=ai[1],al="("+am.join(") and (")+")",ah={cond:al,input:an,target_dataset_id:an,tool_id:aj},ak=ak.slice(1);$.getJSON(run_tool_url,ah,function(ao){if(ao.error){show_modal("Filter Dataset","Error running tool "+aj,{Close:hide_modal})}else{if(ak.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ab(ao.dataset_id,ak)}}})})(this.track.dataset_id,aa)}});var z=function(Z,aa){I.Scaler.call(this,aa);this.filter=Z};z.prototype.gen_val=function(Z){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(Z[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(Z){this.track=Z.track;this.params=Z.params;this.values={};this.restore_values((Z.saved_values?Z.saved_values:{}));this.onchange=Z.onchange};o(C.prototype,{restore_values:function(Z){var aa=this;$.each(this.params,function(ab,ac){if(Z[ac.key]!==undefined){aa.values[ac.key]=Z[ac.key]}else{aa.values[ac.key]=ac.default_value}})},build_form:function(){var ac=this;var Z=$("<div />");var ab;function aa(ah,ad){for(var al=0;al<ah.length;al++){ab=ah[al];if(ab.hidden){continue}var af="param_"+al;var ap=ac.values[ab.key];var ar=$("<div class='form-row' />").appendTo(ad);ar.append($("<label />").attr("for",af).text(ab.label+":"));if(ab.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",af).attr("name",af).attr("checked",ap))}else{if(ab.type==="text"){ar.append($('<input type="text"/>').attr("id",af).val(ap).click(function(){$(this).select()}))}else{if(ab.type==="select"){var an=$("<select />").attr("id",af);for(var aj=0;aj<ab.options.length;aj++){$("<option/>").text(ab.options[aj].label).attr("value",ab.options[aj].value).appendTo(an)}an.val(ap);ar.append(an)}else{if(ab.type==="color"){var aq=$("<div/>").appendTo(ar),am=$("<input />").attr("id",af).attr("name",af).val(ap).css("float","left").appendTo(aq).click(function(au){$(".bs-tooltip").removeClass("in");var at=$(this).siblings(".bs-tooltip").addClass("in");at.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(at).height()/2)+($(this).height()/2)}).show();at.click(function(av){av.stopPropagation()});$(document).bind("click.color-picker",function(){at.hide();$(document).unbind("click.color-picker")});au.stopPropagation()}),ak=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aq).attr("title","Set new random color").tooltip(),ao=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aq).hide(),ag=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ao),ae=$("<div class='tooltip-arrow'></div>").appendTo(ao),ai=$.farbtastic(ag,{width:100,height:100,callback:am,color:ap});aq.append($("<div/>").css("clear","both"));(function(at){ak.click(function(){at.setColor(get_random_color())})})(ai)}else{ar.append($("<input />").attr("id",af).attr("name",af).val(ap))}}}}if(ab.help){ar.append($("<div class='help'/>").text(ab.help))}}}aa(this.params,Z);return Z},update_from_form:function(Z){var ab=this;var aa=false;$.each(this.params,function(ac,ae){if(!ae.hidden){var af="param_"+ac;var ad=Z.find("#"+af).val();if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad)}else{if(ae.type==="bool"){ad=Z.find("#"+af).is(":checked")}}}if(ad!==ab.values[ae.key]){ab.values[ae.key]=ad;aa=true}}});if(aa){this.onchange();this.track.changed()}}});var b=function(Z,ad,ab,aa,ac){this.track=Z;this.region=ad;this.low=ad.get("start");this.high=ad.get("end");this.resolution=ab;this.html_elt=$("<div class='track-tile'/>").append(aa).height($(aa).attr("height"));this.data=ac;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(Z,ae,ab,aa,ac,ad){b.call(this,Z,ae,ab,aa,ac);this.max_val=ad};o(j.prototype,b.prototype);var L=function(ac,ak,ad,ab,af,am,ag,an,aa,aj){b.call(this,ac,ak,ad,ab,af);this.mode=ag;this.all_slotted=aa;this.feature_mapper=aj;this.has_icons=false;if(an){this.has_icons=true;var ah=this;ab=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ab.width}).prependTo(this.html_elt);var ai=new GenomeRegion({chrom:ac.view.chrom,start:this.low,end:this.high}),al=af.length,ae=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),Z=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ae.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()});Z.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()})}};o(L.prototype,b.prototype);L.prototype.predisplay_actions=function(){var aa=this,Z={};if(aa.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(al){if(!this.hovered){return}var ag=$(this).offset(),ak=al.pageX-ag.left,aj=al.pageY-ag.top,ap=aa.feature_mapper.get_feature_data(ak,aj),ah=(ap?ap[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ah||$(this).attr("id")!==ah.toString()){$(this).remove()}});if(ap){var ac=Z[ah];if(!ac){var ah=ap[0],am={name:ap[3],start:ap[1],end:ap[2],strand:ap[4]},af=aa.track.filters_manager.filters,ae;for(var ai=0;ai<af.length;ai++){ae=af[ai];am[ae.name]=ap[ae.index]}var ac=$("<div/>").attr("id",ah).addClass("feature-popup"),aq=$("<table/>"),ao,an,ar;for(ao in am){an=am[ao];ar=$("<tr/>").appendTo(aq);$("<th/>").appendTo(ar).text(ao);$("<td/>").attr("align","left").appendTo(ar).text(typeof(an)==="number"?U(an,2):an)}ac.append($("<div class='feature-popup-inner'>").append(aq));Z[ah]=ac}ac.appendTo($(this).parents(".track-content").children(".overlay"));var ad=ak+parseInt(aa.html_elt.css("left"))-ac.width()/2,ab=aj+parseInt(aa.html_elt.css("top"))+7;ac.css("left",ad+"px").css("top",ab+"px")}else{if(!al.isPropagationStopped()){al.stopPropagation();$(this).siblings().each(function(){$(this).trigger(al)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var h=function(ab,aa,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ab,aa,ad);this.data_url=("data_url" in ad?ad.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:H);this.dataset_check_url=("converted_datasets_state_url" in ad?ad.converted_datasets_state_url:converted_datasets_state_url);var Z=this,ac=new Dataset({id:ad.dataset_id,hda_ldda:ad.hda_ldda});this.data_manager=("data_manager" in ad?ad.data_manager:new GenomeDataManager({dataset:ac,data_url:Z.data_url,dataset_state_url:Z.dataset_check_url,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(h.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(Z){Z.view.set_overview(Z)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters()}else{Z.filters_manager.init_filters()}Z.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(Z){Z.dynamic_tool_div.toggle();if(Z.dynamic_tool_div.is(":visible")){Z.set_name(Z.name+Z.tool_region_and_parameters_str())}else{Z.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(Z){var ac='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ab=_.template(ac,{track:Z});var ae=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aa=function(){var ag=$('select[name="regions"] option:selected').val(),ai,af=new GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ah=_.map($(".bookmark"),function(aj){return new GenomeRegion({from_str:$(aj).children(".position").text()})});if(ag==="cur"){ai=[af]}else{if(ag==="bookmarks"){ai=ah}else{ai=[af].concat(ah)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:Z.dataset_id,hda_ldda:Z.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ai).toJSON())})},ad=function(af){if((af.keyCode||af.which)===27){ae()}else{if((af.keyCode||af.which)===13){aa()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ab,{No:ae,Yes:aa})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var Z=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(Z)}this.name_div=$("<div/>").addClass("track-name").appendTo(Z).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return Z},on_resize:function(){},add_resize_handle:function(){var Z=this;var ac=false;var ab=false;var aa=$("<div class='track-resize'>");$(Z.container_div).hover(function(){if(Z.content_visible){ac=true;aa.show()}},function(){ac=false;if(!ab){aa.hide()}});aa.hide().bind("dragstart",function(ad,ae){ab=true;ae.original_height=$(Z.content_div).height()}).bind("drag",function(ae,af){var ad=Math.min(Math.max(af.original_height+af.deltaY,Z.min_height_px),Z.max_height_px);$(Z.tiles_div).css("height",ad);Z.visible_height_px=(Z.max_height_px===ad?0:ad);Z.on_resize()}).bind("dragend",function(ad,ae){Z.tile_cache.clear();ab=false;if(!ac){aa.hide()}Z.config.values.height=Z.visible_height_px;Z.changed()}).appendTo(Z.container_div)},set_display_modes:function(ac,af){this.display_modes=ac;this.mode=(af?af:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var aa=this,ad={};for(var ab=0,Z=aa.display_modes.length;ab<Z;ab++){var ae=aa.display_modes[ab];ad[ae]=function(ag){return function(){aa.change_mode(ag);aa.icons_div.show();aa.container_div.mouseleave(function(){aa.icons_div.hide()})}}(ae)}make_popupmenu(this.action_icons.mode_icon,ad)},build_action_icons:function(){p.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 y){return"ReferenceTrack"}else{if(this instanceof i){return"LineTrack"}else{if(this instanceof R){return"ReadTrack"}else{if(this instanceof O){return"VcfTrack"}else{if(this instanceof g){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.content_div.css("height","auto");aa.tiles_div.children().remove();aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}var Z=$.Deferred();$.getJSON(this.dataset_check_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.tiles_div.text(n);if(ab.message){var ac=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.tiles_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.tiles_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.tiles_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.tiles_div.html(t);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab==="data"||ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.update_icons()}aa.tiles_div.text(T);if(aa.view.chrom){aa.tiles_div.text("");aa.tiles_div.css("height",aa.visible_height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){Z.resolve();aa.container_div.removeClass("nodata error pending");aa.request_draw()})}else{Z.resolve()}}}}}}});this.update_icons();return Z},predraw_init:function(){}});var J=function(ab,aa,ac){h.call(this,ab,aa,ac);var Z=this;l(Z.container_div,Z.drag_handle_class,".group",Z);this.filters_manager=new V(this,("filters" in ac?ac.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ac&&ac.tool?new q(this,ac.tool,ac.tool_state):null);this.tile_cache=new Cache(N);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ac.mode){this.change_mode(ac.mode)}};o(J.prototype,p.prototype,h.prototype,{action_icons_def:h.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(Z){$(".bs-tooltip").remove();Z.slotters[Z.view.resolution_px_b].max_rows*=2;Z.request_draw(true)},hide:true}]),copy:function(Z){var aa=this.to_dict();o(aa,{data_manager:this.data_manager});var ab=new this.constructor(this.view,Z,aa);ab.change_mode(this.mode);ab.enabled=this.enabled;return ab},set_filters_manager:function(Z){this.filters_manager=Z;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(aa){var Z=this;Z.mode=aa;Z.config.values.mode=aa;Z.tile_cache.clear();Z.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+Z.mode+")");return Z},update_icons:function(){var Z=this;if(Z.filters_available){Z.action_icons.filters_icon.show()}else{Z.action_icons.filters_icon.hide()}if(Z.tool){Z.action_icons.tools_icon.show();Z.action_icons.param_space_viz_icon.show()}else{Z.action_icons.tools_icon.hide();Z.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(aa,ab,Z){return aa+"_"+ab+"_"+Z},request_draw:function(aa,Z){this.view.request_redraw(false,aa,Z,this)},before_draw:function(){},_draw:function(aa,ak){if(!this.can_draw()){return}var ai=this.view.low,ae=this.view.high,ag=ae-ai,ab=this.view.container.width(),am=this.view.resolution_px_b,ad=this.view.resolution_b_px;if(this.is_overview){ai=this.view.max_low;ae=this.view.max_high;ad=(view.max_high-view.max_low)/ab;am=1/ad}this.before_draw();this.tiles_div.children().addClass("remove");var Z=Math.floor(ai/(ad*P)),ah=true,al=[],af=function(an){return(an&&"track" in an)};while((Z*P*ad)<ae){var aj=this.draw_helper(aa,ab,Z,ad,this.tiles_div,am);if(af(aj)){al.push(aj)}else{ah=false}Z+=1}if(!ak){this.tiles_div.children(".remove").removeClass("remove").remove()}var ac=this;if(ah){this.tiles_div.children(".remove").remove();ac.postdraw_actions(al,ab,am,ak)}},postdraw_actions:function(ab,ac,ae,Z){var ad=false;for(var aa=0;aa<ab.length;aa++){if(ab[aa].has_icons){ad=true;break}}if(ad){for(var aa=0;aa<ab.length;aa++){tile=ab[aa];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(Z,al,aq,ao,ae,af,am){var ak=this,au=this._gen_tile_cache_key(al,af,aq),ac=this._get_tile_bounds(aq,ao);if(!am){am={}}var at=(Z?undefined:ak.tile_cache.get_elt(au));if(at){ak.show_tile(at,ae,af);return at}var ai=true;var ap=ak.data_manager.get_data(ac,ak.mode,ao,ak.data_url_extra_params);if(is_deferred(ap)){ai=false}var ag;if(view.reference_track&&af>view.canvas_manager.char_width_px){ag=view.reference_track.data_manager.get_data(ac,ak.mode,ao,view.reference_track.data_url_extra_params);if(is_deferred(ag)){ai=false}}if(ai){o(ap,am.more_tile_data);var ah=ak.mode;if(ah==="Auto"){ah=ak.get_mode(ap);ak.update_auto_mode(ah)}var ab=ak.view.canvas_manager.new_canvas(),ar=ac.get("start"),aa=ac.get("end"),al=Math.ceil((aa-ar)*af)+ak.left_offset,aj=ak.get_canvas_height(ap,ah,af,al);ab.width=al;ab.height=aj;var an=ab.getContext("2d");an.translate(this.left_offset,0);var at=ak.draw_tile(ap,an,ah,ao,ac,af,ag);if(at!==undefined){ak.tile_cache.set_elt(au,at);ak.show_tile(at,ae,af)}return at}var ad=$.Deferred();$.when(ap,ag).then(function(){view.request_redraw(false,false,false,ak);ad.resolve()});return ad},get_canvas_height:function(Z,ab,ac,aa){return this.visible_height_px},draw_tile:function(Z,aa,ae,ac,ad,af,ab){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ab,ad,ae){var aa=this,Z=ab.html_elt;ab.predisplay_actions();var ac=(ab.low-(this.is_overview?this.view.max_low:this.view.low))*ae;if(this.left_offset){ac-=this.left_offset}Z.css({position:"absolute",top:0,left:ac});if(Z.hasClass("remove")){Z.removeClass("remove")}else{ad.append(Z)}aa.after_show_tile(ab)},after_show_tile:function(Z){this.max_height_px=Math.max(this.max_height_px,Z.html_elt.height());Z.html_elt.parent().children().css("height",this.max_height_px+"px");var aa=this.max_height_px;if(this.visible_height_px!==0){aa=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",aa+"px")},_get_tile_bounds:function(Z,aa){var ac=Math.floor(Z*P*aa),ad=Math.ceil(P*aa),ab=(ac+ad<=this.view.max_high?ac+ad:this.view.max_high);return new GenomeRegion({chrom:this.view.chrom,start:ac,end:ab})},tool_region_and_parameters_str:function(ab,Z,ac){var aa=this,ad=(ab!==undefined&&Z!==undefined&&ac!==undefined?ab+":"+Z+"-"+ac:"all");return" - region=["+ad+"], parameters=["+aa.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(Z,aa){return true},can_subset:function(Z){return false},init_for_tool_data:function(){this.data_manager.set("data_url",raw_data_url);this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ab,ac,ae,Z){var aa=this;aa.normal_postdraw_actions(ab,ac,ae,Z);aa.dataset_state_url=converted_datasets_state_url;aa.data_query_wait=H;var ad=new ServerStateDeferred({url:aa.dataset_state_url,url_params:{dataset_id:aa.dataset_id,hda_ldda:aa.hda_ldda},interval:aa.data_query_wait,success_fn:function(af){return af!=="pending"}});$.when(ad.go()).then(function(){aa.data_manager.set("data_url",default_data_url)});aa.postdraw_actions=aa.normal_postdraw_actions}}});var W=function(aa,Z){var ab={resize:false};h.call(this,aa,Z,ab);this.container_div.addClass("label-track")};o(W.prototype,h.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ab=this.view,ac=ab.high-ab.low,af=Math.floor(Math.pow(10,Math.floor(Math.log(ac)/Math.log(10)))),Z=Math.floor(ab.low/af)*af,ad=this.view.container.width(),aa=$("<div style='position: relative; height: 1.3em;'></div>");while(Z<ab.high){var ae=(Z-ab.low)/ac*ad;aa.append($("<div class='label'>"+commatize(Z)+"</div>").css({position:"absolute",left:ae-1}));Z+=af}this.content_div.children(":first").remove();this.content_div.append(aa)}});var g=function(aa,Z,ad){J.call(this,aa,Z,ad);this.drawables=[];this.left_offset=0;if("drawables" in ad){var ac;for(var ab=0;ab<ad.drawables.length;ab++){ac=ad.drawables[ab];this.drawables[ab]=object_from_template(ac,aa,null);if(ac.left_offset>this.left_offset){this.left_offset=ac.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};o(g.prototype,J.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_group()}}].concat(J.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(Z){J.prototype.change_mode.call(this,Z);for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].change_mode(Z)}},init:function(){var ab=[];for(var aa=0;aa<this.drawables.length;aa++){ab.push(this.drawables[aa].init())}var Z=this;$.when.apply($,ab).then(function(){Z.enabled=true;Z.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,draw_helper:function(aa,ap,aw,at,ah,aj,aq){var ao=this,aA=this._gen_tile_cache_key(ap,aj,aw),ae=this._get_tile_bounds(aw,at);if(!aq){aq={}}var az=(aa?undefined:ao.tile_cache.get_elt(aA));if(az){ao.show_tile(az,ah,aj);return az}var ai=[],ao,am=true,au,ak;for(var av=0;av<this.drawables.length;av++){ao=this.drawables[av];au=ao.data_manager.get_data(ae,ao.mode,at,ao.data_url_extra_params);if(is_deferred(au)){am=false}ai.push(au);ak=null;if(view.reference_track&&aj>view.canvas_manager.char_width_px){ak=view.reference_track.data_manager.get_data(ae,ao.mode,at,view.reference_track.data_url_extra_params);if(is_deferred(ak)){am=false}}ai.push(ak)}if(am){o(au,aq.more_tile_data);this.tile_predraw_init();var ad=ao.view.canvas_manager.new_canvas(),af=ao._get_tile_bounds(aw,at),ax=ae.get("start"),ab=ae.get("end"),ay=0,ap=Math.ceil((ab-ax)*aj)+this.left_offset,an=0,ac=[],av;var Z=0;for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];var al=ao.mode;if(al==="Auto"){al=ao.get_mode(au);ao.update_auto_mode(al)}ac.push(al);Z=ao.get_canvas_height(au,al,aj,ap);if(Z>an){an=Z}}ad.width=ap;ad.height=(aq.height?aq.height:an);ay=0;var ar=ad.getContext("2d");ar.translate(this.left_offset,0);ar.globalAlpha=0.5;ar.globalCompositeOperation="source-over";for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];ak=ai[ay+1];az=ao.draw_tile(au,ar,ac[av],at,ae,aj,ak)}this.tile_cache.set_elt(aA,az);this.show_tile(az,ah,aj);return az}var ag=$.Deferred(),ao=this;$.when.apply($,ai).then(function(){view.request_redraw(false,false,false,ao);ag.resolve()});return ag},show_group:function(){var ac=new M(this.view,this.container,{name:this.name}),Z;for(var ab=0;ab<this.drawables.length;ab++){Z=this.drawables[ab];Z.update_icons();ac.add_drawable(Z);Z.container=ac;ac.content_div.append(Z.container_div)}var aa=this.container.replace_drawable(this,ac,true);ac.request_draw()},tile_predraw_init:function(){var ac=Number.MAX_VALUE,Z=-ac,aa;for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];if(aa instanceof i){if(aa.prefs.min_value<ac){ac=aa.prefs.min_value}if(aa.prefs.max_value>Z){Z=aa.prefs.max_value}}}for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];aa.prefs.min_value=ac;aa.prefs.max_value=Z}},postdraw_actions:function(ab,ae,ag,aa){J.prototype.postdraw_actions.call(this,ab,ae,ag,aa);var ad=-1;for(var ac=0;ac<ab.length;ac++){var Z=ab[ac].html_elt.find("canvas").height();if(Z>ad){ad=Z}}for(var ac=0;ac<ab.length;ac++){var af=ab[ac];if(af.html_elt.find("canvas").height()!==ad){this.draw_helper(true,ae,af.index,af.resolution,af.html_elt.parent(),ag,{height:ad});af.html_elt.remove()}}}});var y=function(Z){J.call(this,Z,{content_div:Z.top_labeltrack},{resize:false});Z.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:Z.dbkey};this.data_manager=new ReferenceTrackDataManager({data_url:reference_url});this.hide_contents()};o(y.prototype,p.prototype,J.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:p.prototype.can_draw,draw_helper:function(ad,ab,Z,aa,ae,af,ac){if(af>this.view.canvas_manager.char_width_px){return J.prototype.draw_helper.call(this,ad,ab,Z,aa,ae,af,ac)}else{this.hide_contents();return null}},draw_tile:function(ah,ai,ad,ac,af,aj){var ab=this;if(aj>this.view.canvas_manager.char_width_px){if(ah.data===null){this.hide_contents();return}var aa=ai.canvas;ai.font=ai.canvas.manager.default_font;ai.textAlign="center";ah=ah.data;for(var ae=0,ag=ah.length;ae<ag;ae++){var Z=Math.floor(ae*aj);ai.fillText(ah[ae],Z,10)}this.show_contents();return new b(ab,af,ac,aa,ah)}this.hide_contents()}});var i=function(ab,aa,ac){var Z=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_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:32,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(i.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var Z=this;Z.vertical_range=undefined;return $.getJSON(Z.data_url,{stats:true,chrom:Z.view.chrom,low:0,high:Z.view.max_high,hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id},function(aa){Z.container_div.addClass("line-track");var ad=aa.data;if(isNaN(parseFloat(Z.prefs.min_value))||isNaN(parseFloat(Z.prefs.max_value))){var ab=ad.min,af=ad.max;ab=Math.floor(Math.min(0,Math.max(ab,ad.mean-2*ad.sd)));af=Math.ceil(Math.max(0,Math.min(af,ad.mean+2*ad.sd)));Z.prefs.min_value=ab;Z.prefs.max_value=af;$("#track_"+Z.dataset_id+"_minval").val(Z.prefs.min_value);$("#track_"+Z.dataset_id+"_maxval").val(Z.prefs.max_value)}Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.total_frequency=ad.total_frequency;Z.container_div.find(".yaxislabel").remove();var ae=$("<div/>").text(U(Z.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_min_value(ag)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+Z.dataset_id+"_minval").prependTo(Z.container_div),ac=$("<div/>").text(U(Z.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_max_value(ag)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+Z.dataset_id+"_maxval").prependTo(Z.container_div)})},draw_tile:function(ai,ag,ab,aa,ad,ah){var Z=ag.canvas,ac=ad.get("start"),af=ad.get("end"),ae=new I.LinePainter(ai.data,ac,af,this.prefs,ab);ae.draw(ag,Z.width,Z.height,ah);return new b(this,ad,aa,Z,ai.data)},can_subset:function(Z){return false}});var r=function(ab,aa,ac){var Z=this;this.display_modes=["Heatmap"];this.mode="Heatmap";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{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}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(r.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;this.tile_cache.clear();this.request_draw()},draw_tile:function(aj,ah,ae,ac,aa,ai){var ab=ah.canvas,Z=this._get_tile_bounds(aa,ac),ad=Z[0],ag=Z[1],af=new I.DiagonalHeatmapPainter(aj.data,ad,ag,this.prefs,ae);af.draw(ah,ab.width,ab.height,ai);return new b(this,aa,ac,ab,aj.data)}});var c=function(ac,ab,ae){var aa=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];J.call(this,ac,ab,ae);var ad=get_random_color(),Z=get_random_color([ad,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ad},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",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:this.visible_height_px,hidden:true}],saved_values:ae.prefs,onchange:function(){aa.set_name(aa.prefs.name);aa.tile_cache.clear();aa.set_painter_from_config();aa.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ae.hda_ldda;this.dataset_id=ae.dataset_id;this.original_dataset_id=ae.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,J.prototype,{set_dataset:function(Z){this.dataset_id=Z.get("id");this.hda_ldda=Z.get("hda_ldda");this.data_manager.set("dataset",Z)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=I.ArcLinkedFeaturePainter}else{this.painter=I.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ao,aj,ae,ad){J.prototype.postdraw_actions.call(this,ao,ad);var ai=this,al;if(ai.mode==="Coverage"){var aa=-1;for(al=0;al<ao.length;al++){var ak=ao[al].max_val;if(ak>aa){aa=ak}}for(al=0;al<ao.length;al++){var aq=ao[al];if(aq.max_val!==aa){aq.html_elt.remove();ai.draw_helper(true,aj,aq.index,aq.resolution,aq.html_elt.parent(),ae,{more_tile_data:{max:aa}})}}}if(ai.filters_manager){var af=ai.filters_manager.filters;for(var an=0;an<af.length;an++){af[an].update_ui_elt()}var ap=false,Z,ag;for(al=0;al<ao.length;al++){if(ao[al].data.length){Z=ao[al].data[0];for(var an=0;an<af.length;an++){ag=af[an];if(ag.applies_to(Z)&&ag.min!==ag.max){ap=true;break}}}}if(ai.filters_available!==ap){ai.filters_available=ap;if(!ai.filters_available){ai.filters_manager.hide()}ai.update_icons()}}this.container_div.find(".yaxislabel").remove();var ac=ao[0];if(ac instanceof j){var ah=(this.prefs.histogram_max?this.prefs.histogram_max:ac.max_val),ab=$("<div/>").text(ah).make_text_editable({num_cols:12,on_finish:function(ar){$(".bs-tooltip").remove();var ar=parseFloat(ar);ai.prefs.histogram_max=(!isNaN(ar)?ar:null);ai.tile_cache.clear();ai.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ab)}if(ac instanceof L){var am=true;for(al=0;al<ao.length;al++){if(!ao[al].all_slotted){am=false;break}}if(!am){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(Z){var Z;if(this.mode==="Auto"){if(Z==="no_detail"){Z="feature spans"}else{if(Z==="summary_tree"){Z="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+Z+")")}},incremental_slots:function(ad,Z,ac){var aa=this.view.canvas_manager.dummy_context,ab=this.slotters[ad];if(!ab||(ab.mode!==ac)){ab=new (s.FeatureSlotter)(ad,ac,x,function(ae){return aa.measureText(ae)});this.slotters[ad]=ab}return ab.slot_features(Z)},get_mode:function(Z){if(Z.dataset_type==="summary_tree"){mode="summary_tree"}else{if(Z.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>F){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(Z,ad,ae,aa){if(ad==="summary_tree"||ad==="Coverage"){return this.summary_draw_height}else{var ac=this.incremental_slots(ae,Z.data,ad);var ab=new (this.painter)(null,null,null,this.prefs,ad);return Math.max(Y,ab.get_required_height(ac,aa))}},draw_tile:function(aj,an,al,ao,ac,ag,ab){var am=this,aa=an.canvas,av=ac.get("start"),Z=ac.get("end"),ad=this.left_offset;if(al==="summary_tree"||al==="Coverage"){var ax=new I.SummaryTreePainter(aj,av,Z,this.prefs);ax.draw(an,aa.width,aa.height,ag);return new j(am,ac,ao,aa,aj.data,aj.max)}var af=[],ak=this.slotters[ag].slots;all_slotted=true;if(aj.data){var ah=this.filters_manager.filters;for(var ap=0,ar=aj.data.length;ap<ar;ap++){var ae=aj.data[ap];var aq=false;var ai;for(var au=0,az=ah.length;au<az;au++){ai=ah[au];ai.update_attrs(ae);if(!ai.keep(ae)){aq=true;break}}if(!aq){af.push(ae);if(!(ae[0] in ak)){all_slotted=false}}}}var ay=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aw=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var ax=new (this.painter)(af,av,Z,this.prefs,al,ay,aw,ab);var at=null;an.fillStyle=this.prefs.block_color;an.font=an.canvas.manager.default_font;an.textAlign="right";if(aj.data){at=ax.draw(an,aa.width,aa.height,ag,ak);at.translation=-ad}return new L(am,ac,ao,aa,aj.data,ag,al,aj.message,all_slotted,at)},data_and_mode_compatible:function(Z,aa){if(aa==="Auto"){return true}else{if(aa==="Coverage"){return Z.dataset_type==="summary_tree"}else{if(Z.extra_info==="no_detail"||Z.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(Z){if(Z.dataset_type==="summary_tree"||Z.message||Z.extra_info==="no_detail"){return false}return true}});var O=function(aa,Z,ab){c.call(this,aa,Z,ab);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_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_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ab.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter};o(O.prototype,p.prototype,J.prototype,c.prototype);var R=function(ab,aa,ad){c.call(this,ab,aa,ad);var ac=get_random_color(),Z=get_random_color([ac,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ac},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ad.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter;this.update_icons()};o(R.prototype,p.prototype,J.prototype,c.prototype);S.View=X;S.DrawableGroup=M;S.LineTrack=i;S.FeatureTrack=c;S.DiagonalHeatmapTrack=r;S.ReadTrack=R;S.VcfTrack=O;S.CompositeTrack=g};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(require,exports){var extend=require("class").extend;var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-1)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2]-1,feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,orig_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=0,char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var draw_last=[];if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){gap=Math.round(w_scale/2)}if(!cigar){cigar=[[0,orig_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=(feature_start-1)+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(gap>0){ctx.fillStyle=block_color;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=CONNECTOR_COLOR;for(var c=0,str_len=seq.length;c<str_len;c++){if(this.prefs.show_differences){if(this.ref_seq){var ref_char=this.ref_seq[seq_start-tile_low+c];if(!ref_char||ref_char.toLowerCase()===seq[c].toLowerCase()){continue}}else{continue}}if(seq_start+c>=tile_low&&seq_start+c<=tile_high){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start-gap,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color,gap=0;if((mode==="Pack"||this.mode==="Auto")&&w_scale>ctx.canvas.manager.char_width_px){var gap=Math.round(w_scale/2)}if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING-gap,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"4169E1",neg_color:"FF8C00"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};exports.Scaler=Scaler;exports.SummaryTreePainter=SummaryTreePainter;exports.LinePainter=LinePainter;exports.LinkedFeaturePainter=LinkedFeaturePainter;exports.ReadPainter=ReadPainter;exports.ArcLinkedFeaturePainter=ArcLinkedFeaturePainter;exports.DiagonalHeatmapPainter=DiagonalHeatmapPainter};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var g=arguments[0];for(var f=1;f<arguments.length;f++){var d=arguments[f];for(var e in d){g[e]=d[e]}}return g};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tooltip().click(a)};var trackster_module=function(d,S){var o=d("class").extend,s=d("slotting"),I=d("painters");var m={};var k=function(Z,aa){m[Z.attr("id")]=aa};var l=function(Z,ab,ad,ac){ad=".group";var aa={};m[Z.attr("id")]=ac;Z.bind("drag",{handle:"."+ab,relative:true},function(al,am){var ak=$(this),ap=$(this).parent(),ah=ap.children(),aj=m[$(this).attr("id")],ag,af,an,ae,ai;af=$(this).parents(ad);if(af.length!==0){an=af.position().top;ae=an+af.outerHeight();if(am.offsetY<an){$(this).insertBefore(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable_before(aj,ao);return}else{if(am.offsetY>ae){$(this).insertAfter(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable(aj);return}}}af=null;for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));an=ag.position().top;ae=an+ag.outerHeight();if(ag.is(ad)&&this!==ag.get(0)&&am.offsetY>=an&&am.offsetY<=ae){if(am.offsetY-an<ae-am.offsetY){ag.find(".content-div").prepend(this)}else{ag.find(".content-div").append(this)}if(aj.container){aj.container.remove_drawable(aj)}m[ag.attr("id")].add_drawable(aj);return}}for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));if(am.offsetY<ag.position().top&&!(ag.hasClass("reference-track")||ag.hasClass("intro"))){break}}if(ai===ah.length){if(this!==ah.get(ai-1)){ap.append(this);m[ap.attr("id")].move_drawable(aj,ai)}}else{if(this!==ah.get(ai)){$(this).insertBefore(ah.get(ai));m[ap.attr("id")].move_drawable(aj,(am.deltaY>0?ai-1:ai))}}}).bind("dragstart",function(){aa["border-top"]=Z.css("border-top");aa["border-bottom"]=Z.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(aa)})};S.moveable=l;var Y=16,D=9,A=20,x=100,F=12000,P=400,H=5000,u=100,n="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",N=10,E=20;function U(aa,Z){if(!Z){Z=0}var ab=Math.pow(10,Z);return Math.round(aa*ab)/ab}var p=function(aa,Z,ac){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ac.name;this.view=aa;this.container=Z;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ac.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ac.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;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=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ad){ad.stopPropagation()});var ab=this;this.container_div.hover(function(){ab.icons_div.show()},function(){ab.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(Z){if(Z.content_visible){Z.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");Z.hide_contents();Z.content_visible=false}else{Z.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");Z.content_visible=true;Z.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(aa){var ac=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},Z=function(){aa.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(ad){if((ad.keyCode||ad.which)===27){ac()}else{if((ad.keyCode||ad.which)===13){Z()}}};$(window).bind("keypress.check_enter_esc",ab);show_modal("Configure",aa.config.build_form(),{Cancel:ac,OK:Z})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(Z){this.old_name=this.name;this.name=Z;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var Z=this.view;this.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(aa,af,ae,ad,Z,ac){var ab=this;this.action_icons[aa]=$("<a/>").attr("href","javascript:void(0);").attr("title",af).addClass("icon-button").addClass(ae).tooltip().click(function(){ad(ab)}).appendTo(this.icons_div);if(ac){this.action_icons[aa].hide()}},build_action_icons:function(Z){var ab;for(var aa=0;aa<Z.length;aa++){ab=Z[aa];this.add_action_icon(ab.name,ab.title,ab.css_class,ab.on_click_fn,ab.prepend,ab.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var w=function(aa,Z,ab){p.call(this,aa,Z,ab);this.obj_type=ab.obj_type;this.drawables=[]};o(w.prototype,p.prototype,{unpack_drawables:function(ab){this.drawables=[];var aa;for(var Z=0;Z<ab.length;Z++){aa=object_from_template(ab[Z],this.view,this);this.add_drawable(aa)}},init:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].init()}},_draw:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z]._draw()}},to_dict:function(){var aa=[];for(var Z=0;Z<this.drawables.length;Z++){aa.push(this.drawables[Z].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:aa}},add_drawable:function(Z){this.drawables.push(Z);Z.container=this;this.changed()},add_drawable_before:function(ab,Z){this.changed();var aa=this.drawables.indexOf(Z);if(aa!==-1){this.drawables.splice(aa,0,ab);return true}return false},replace_drawable:function(ab,Z,aa){var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables[ac]=Z;if(aa){ab.container_div.replaceWith(Z.container_div)}this.changed()}return ac},remove_drawable:function(aa){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);aa.container=null;this.changed();return true}return false},move_drawable:function(aa,ab){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);this.drawables.splice(ab,0,aa);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var M=function(aa,Z,ac){o(ac,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,aa,Z,ac);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new V(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ac){this.unpack_drawables(ac.drawables)}if("filters" in ac){var ab=this.filters_manager;this.filters_manager=new V(this,ac.filters);ab.parent_div.replaceWith(this.filters_manager.parent_div);if(ac.filters.visible){this.setup_multitrack_filtering()}}};o(M.prototype,p.prototype,w.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters();Z._restore_filter_managers()}else{Z.setup_multitrack_filtering();Z.request_draw(true)}Z.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var Z=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(Z)}return Z},build_header_div:function(){var Z=$("<div/>").addClass("track-header");Z.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(Z);return Z},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ab=this.drawables.length;if(ab===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ab===1){if(this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ah,af,al=true,ad=this.drawables[0].get_type(),Z=0;for(ai=0;ai<ab;ai++){af=this.drawables[ai];if(af.get_type()!==ad){can_composite=false;break}if(af instanceof c){Z++}}if(al||Z===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(Z>1&&Z===this.drawables.length){var am={},aa;af=this.drawables[0];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];am[aa.name]=[aa]}for(ai=1;ai<this.drawables.length;ai++){af=this.drawables[ai];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];if(aa.name in am){am[aa.name].push(aa)}}}this.filters_manager.remove_all();var ac,ae,ag,aj;for(var ak in am){ac=am[ak];if(ac.length===Z){ae=new Q({name:ac[0].name,index:ac[0].index});this.filters_manager.add_filter(ae)}}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 Z=0;Z<this.drawables.length;Z++){this.drawables[Z].filters_manager=this.saved_filters_managers[Z]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var Z=0;Z<this.drawables.length;Z++){drawable=this.drawables[Z];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=[];for(var aa=0;aa<this.drawables.length;aa++){ad.push(this.drawables[aa].name)}var ab="Composite Track of "+this.drawables.length+" tracks ("+ad.join(", ")+")";var ac=new g(this.view,this.view,{name:ab,drawables:this.drawables});var Z=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);this.update_icons()},remove_drawable:function(Z){w.prototype.remove_drawable.call(this,Z);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var Z=o(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return Z},request_draw:function(Z,ab){for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].request_draw(Z,ab)}}});var X=function(Z){o(Z,{obj_type:"View"});w.call(this,"View",Z.container,Z);this.chrom=null;this.vis_id=Z.vis_id;this.dbkey=Z.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.init();this.canvas_manager=new CanvasManager(this.container.get(0).ownerDocument);this.reset()};_.extend(X.prototype,Backbone.Events);o(X.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ab=this.container,Z=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ab);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ab);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ab);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,Z);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ac=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_datasets(add_datasets_url,add_track_async_url,function(ad){_.each(ad,function(ae){Z.add_drawable(object_from_template(ae,Z,Z))})})});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("href","javascript:void(0);").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=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var aa=function(ad){if(ad.type==="focusout"||(ad.keyCode||ad.which)===13||(ad.keyCode||ad.which)===27){if((ad.keyCode||ad.which)!==27){Z.go_to($(this).val())}$(this).hide();$(this).val("");Z.location_span.show();Z.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",aa).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){Z.location_span.hide();Z.chrom_select.hide();Z.nav_input.val(Z.chrom+":"+Z.low+"-"+Z.high);Z.nav_input.css("display","inline-block");Z.nav_input.select();Z.nav_input.focus();Z.nav_input.autocomplete({source:function(af,ad){var ag=[],ae=$.map(Z.get_drawables(),function(ah){return ah.data_manager.search_features(af.term).success(function(ai){ag=ag.concat(ai)})});$.when.apply($,ae).done(function(){ad($.map(ag,function(ah){return{label:ah[0],value:ah[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(){Z.zoom_out();Z.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){Z.zoom_in();Z.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){Z.change_chrom(Z.chrom_select.val())});this.browser_content_div.click(function(ad){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ad){Z.zoom_in(ad.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ad,ae){this.current_x=ae.offsetX}).bind("drag",function(ad,af){var ag=af.offsetX-this.current_x;this.current_x=af.offsetX;var ae=Math.round(ag/Z.viewport_container.width()*(Z.max_high-Z.max_low));Z.move_delta(-ae)});this.overview_close.click(function(){Z.reset_overview()});this.viewport_container.bind("draginit",function(ad,ae){if(ad.clientX>Z.viewport_container.width()-16){return false}}).bind("dragstart",function(ad,ae){ae.original_low=Z.low;ae.current_height=ad.clientY;ae.current_x=ae.offsetX}).bind("drag",function(af,ah){var ad=$(this);var ai=ah.offsetX-ah.current_x;var ae=ad.scrollTop()-(af.clientY-ah.current_height);ad.scrollTop(ae);ah.current_height=af.clientY;ah.current_x=ah.offsetX;var ag=Math.round(ai/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}).bind("mousewheel",function(af,ah,ae,ad){if(ae){ae*=50;var ag=Math.round(-ae/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}});this.top_labeltrack.bind("dragstart",function(ad,ae){return $("<div />").css({height:Z.browser_content_div.height()+Z.top_labeltrack.height()+Z.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ah,ai){$(ai.proxy).css({left:Math.min(ah.pageX,ai.startX)-Z.container.offset().left,width:Math.abs(ah.pageX-ai.startX)});var ae=Math.min(ah.pageX,ai.startX)-Z.container.offset().left,ad=Math.max(ah.pageX,ai.startX)-Z.container.offset().left,ag=(Z.high-Z.low),af=Z.viewport_container.width();Z.update_location(Math.round(ae/af*ag)+Z.low,Math.round(ad/af*ag)+Z.low)}).bind("dragend",function(ai,aj){var ae=Math.min(ai.pageX,aj.startX),ad=Math.max(ai.pageX,aj.startX),ag=(Z.high-Z.low),af=Z.viewport_container.width(),ah=Z.low;Z.low=Math.round(ae/af*ag)+ah;Z.high=Math.round(ad/af*ag)+ah;$(aj.proxy).remove();Z.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}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){Z.resize_window()},500)});$(document).bind("redraw",function(){Z.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(aa,ac,Z,ad){if(this.timer){clearTimeout(this.timer)}if(ad){var ab=this;this.timer=setTimeout(function(){ab.trigger("navigate",aa+":"+ac+"-"+Z)},500)}else{view.trigger("navigate",aa+":"+ac+"-"+Z)}},update_location:function(Z,ab){this.location_span.text(commatize(Z)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(Z)+"-"+commatize(ab));var aa=view.chrom_select.val();if(aa!==""){this.trigger_navigate(aa,view.low,view.high,true)}},load_chroms:function(ab){ab.num=u;ab.dbkey=this.dbkey;var Z=this,aa=$.Deferred();$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ad){if(ad.chrom_info.length===0){return}if(ad.reference){Z.add_label_track(new y(Z))}Z.chrom_data=ad.chrom_info;var ag='<option value="">Select Chrom/Contig</option>';for(var af=0,ac=Z.chrom_data.length;af<ac;af++){var ae=Z.chrom_data[af].chrom;ag+='<option value="'+ae+'">'+ae+"</option>"}if(ad.prev_chroms){ag+='<option value="previous">Previous '+u+"</option>"}if(ad.next_chroms){ag+='<option value="next">Next '+u+"</option>"}Z.chrom_select.html(ag);Z.chrom_start_index=ad.start_index;aa.resolve(ad)},error:function(){alert("Could not load chroms for this dbkey:",Z.dbkey)}});return aa},change_chrom:function(ae,aa,ag){var ab=this;if(!ab.chrom_data){ab.load_chroms_deferred.then(function(){ab.change_chrom(ae,aa,ag)});return}if(!ae||ae==="None"){return}if(ae==="previous"){ab.load_chroms({low:this.chrom_start_index-u});return}if(ae==="next"){ab.load_chroms({low:this.chrom_start_index+u});return}var af=$.grep(ab.chrom_data,function(ah,ai){return ah.chrom===ae})[0];if(af===undefined){ab.load_chroms({chrom:ae},function(){ab.change_chrom(ae,aa,ag)});return}else{if(ae!==ab.chrom){ab.chrom=ae;ab.chrom_select.val(ab.chrom);ab.max_high=af.len-1;ab.reset();ab.request_redraw(true);for(var ad=0,Z=ab.drawables.length;ad<Z;ad++){var ac=ab.drawables[ad];if(ac.init){ac.init()}}if(ab.reference_track){ab.reference_track.init()}}if(aa!==undefined&&ag!==undefined){ab.low=Math.max(aa,0);ab.high=Math.min(ag,ab.max_high)}else{ab.low=0;ab.high=ab.max_high}ab.reset_overview();ab.request_redraw()}},go_to:function(ad){ad=ad.replace(/ |,/g,"");var ah=this,Z,ac,aa=ad.split(":"),af=aa[0],ag=aa[1];if(ag!==undefined){try{var ae=ag.split("-");Z=parseInt(ae[0],10);ac=parseInt(ae[1],10)}catch(ab){return false}}ah.change_chrom(af,Z,ac)},move_fraction:function(ab){var Z=this;var aa=Z.high-Z.low;this.move_delta(ab*aa)},move_delta:function(ac){var Z=this;var ab=Z.high-Z.low;if(Z.low-ac<Z.max_low){Z.low=Z.max_low;Z.high=Z.max_low+ab}else{if(Z.high-ac>Z.max_high){Z.high=Z.max_high;Z.low=Z.max_high-ab}else{Z.high-=ac;Z.low-=ac}}Z.request_redraw();var aa=Z.chrom_select.val();this.trigger_navigate(aa,Z.low,Z.high,true)},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);Z.init();this.changed();this.update_intro_div()},add_label_track:function(Z){Z.view=this;Z.init();this.label_tracks.push(Z)},remove_drawable:function(ab,aa){w.prototype.remove_drawable.call(this,ab);if(aa){var Z=this;ab.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ah,Z,ag,ai){var af=this,ae=(ai?[ai]:af.drawables),ab;var aa;for(var ad=0;ad<ae.length;ad++){aa=ae[ad];ab=-1;for(var ac=0;ac<af.tracks_to_be_redrawn.length;ac++){if(af.tracks_to_be_redrawn[ac][0]===aa){ab=ac;break}}if(ab<0){af.tracks_to_be_redrawn.push([aa,Z,ag])}else{af.tracks_to_be_redrawn[ad][1]=Z;af.tracks_to_be_redrawn[ad][2]=ag}}if(!this.requested_redraw){requestAnimationFrame(function(){af._redraw(ah)});this.requested_redraw=true}},_redraw:function(aj){this.requested_redraw=false;var ag=this.low,ac=this.high;if(ag<this.max_low){ag=this.max_low}if(ac>this.max_high){ac=this.max_high}var ai=this.high-this.low;if(this.high!==0&&ai<this.min_separation){ac=ag+this.min_separation}this.low=Math.floor(ag);this.high=Math.ceil(ac);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var Z=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=13;this.overview_box.css({left:Z,width:Math.max(ak,af)}).show();if(af<ak){this.overview_box.css("left",Z-(ak-af)/2)}if(this.overview_highlight){this.overview_highlight.css({left:Z,width:af})}if(!aj){var ab,aa,ah;for(var ad=0,ae=this.tracks_to_be_redrawn.length;ad<ae;ad++){ab=this.tracks_to_be_redrawn[ad][0];aa=this.tracks_to_be_redrawn[ad][1];ah=this.tracks_to_be_redrawn[ad][2];if(ab){ab._draw(aa,ah)}}this.tracks_to_be_redrawn=[];for(ad=0,ae=this.label_tracks.length;ad<ae;ad++){this.label_tracks[ad]._draw()}}},zoom_in:function(aa,ab){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ac=this.high-this.low,ad=ac/2+this.low,Z=(ac/this.zoom_factor)/2;if(aa){ad=aa/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ad-Z);this.high=Math.round(ad+Z);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var aa=this.high-this.low,ab=aa/2+this.low,Z=(aa*this.zoom_factor)/2;this.low=Math.round(ab-Z);this.high=Math.round(ab+Z);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(ab){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ab.dataset_id){return}this.overview_viewport.find(".track").remove()}var aa=ab.copy({content_div:this.overview_viewport}),Z=this;aa.header_div.hide();aa.is_overview=true;Z.overview_drawable=aa;this.overview_drawable.postdraw_actions=function(){Z.overview_highlight.show().height(Z.overview_drawable.content_div.height());Z.overview_viewport.height(Z.overview_drawable.content_div.height()+Z.overview_box.outerHeight());Z.overview_close.show();Z.resize_window()};Z.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-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 q=function(ab,ag,ac){this.track=ab;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],aa=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params.push(new e(aa,am,ae,(aa in ac?ac[aa]:ao),ai.min,ai.max))}else{if(ak==="select"){this.params.push(new K(aa,am,ae,(aa in ac?ac[aa]:ao)))}else{console.log("WARNING: unrecognized tool parameter type:",aa,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).click(function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("param-input").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: both;'/>").appendTo(au)});this.parent_div.find("input").click(function(){$(this).select()});var ap=$("<div>").addClass("param-row").appendTo(this.parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ap);var Z=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ap);Z.click(function(){ah.run_on_region()});af.click(function(){ah.run_on_dataset()});if("visible" in ac&&ac.visible){this.parent_div.show()}};o(q.prototype,{update_params:function(){for(var Z=0;Z<this.params.length;Z++){this.params[Z].update_value()}},state_dict:function(){var aa={};for(var Z=0;Z<this.params.length;Z++){aa[this.params[Z].name]=this.params[Z].value}aa.visible=this.parent_div.is(":visible");return aa},get_param_values_dict:function(){var Z={};this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();Z[aa]=ab});return Z},get_param_values:function(){var Z=[];this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();if(aa){Z[Z.length]=ab}});return Z},run_on_dataset:function(){var Z=this;Z.run({target_dataset_id:this.track.original_dataset_id,tool_id:Z.name},null,function(aa){show_modal(Z.name+" is Running",Z.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ae=this.track,ab=aa.tool_id+ae.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),Z;if(ae.container===view){var ad=new M(view,view,{name:this.name});var ac=ae.container.replace_drawable(ae,ad,false);ad.container_div.insertBefore(ae.view.content_div.children()[ac]);ad.add_drawable(ae);ae.container_div.appendTo(ad.content_div);Z=ad}else{Z=ae.container}var af=new ae.constructor(view,Z,{name:ab,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ae.mode);af.set_filters_manager(ae.filters_manager.copy(af));af.update_icons();Z.add_drawable(af);af.tiles_div.text("Starting job.");this.update_params();this.run(aa,af,function(ag){af.set_dataset(new Dataset(ag));af.tiles_div.text("Running job.");af.init()})},run:function(Z,ab,ac){Z.inputs=this.get_param_values_dict();var aa=new ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(Z),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ad){return ad!=="pending"}});$.when(aa.go()).then(function(ad){if(ad==="no converter"){ab.container_div.addClass("error");ab.content_div.text(G)}else{if(ad.error){ab.container_div.addClass("error");ab.content_div.text(v+ad.message)}else{ac(ad)}}})}});var K=function(aa,Z,ab,ac){this.name=aa;this.label=Z;this.html=$(ab);this.value=ac};o(K.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ab,aa,ad,ae,ac,Z){K.call(this,ab,aa,ad,ae);this.min=ac;this.max=Z};o(e.prototype,K.prototype,{update_value:function(){K.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var f=function(Z){this.manager=null;this.name=Z.name;this.index=Z.index;this.tool_id=Z.tool_id;this.tool_exp_name=Z.tool_exp_name};o(f.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var Q=function(ah){f.call(this,ah);this.low=("low" in ah?ah.low:-Number.MAX_VALUE);this.high=("high" in ah?ah.high:Number.MAX_VALUE);this.min=("min" in ah?ah.min:Number.MAX_VALUE);this.max=("max" in ah?ah.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ad=function(ai,aj,ak){ai.click(function(){var ap=aj.text(),an=parseFloat(ak.slider("option","max")),am=(an<=1?4:an<=1000000?an.toString().length:6),ao=false,al=$(this).parents(".slider-row");al.addClass("input");if(ak.slider("option","values")){am=2*am+1;ao=true}aj.text("");$("<input type='text'/>").attr("size",am).attr("maxlength",am).attr("value",ap).appendTo(aj).focus().select().click(function(aq){aq.stopPropagation()}).blur(function(){$(this).remove();aj.text(ap);al.removeClass("input")}).keyup(function(av){if(av.keyCode===27){$(this).trigger("blur")}else{if(av.keyCode===13){var at=ak.slider("option","min"),aq=ak.slider("option","max"),au=function(aw){return(isNaN(aw)||aw>aq||aw<at)},ar=$(this).val();if(!ao){ar=parseFloat(ar);if(au(ar)){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}else{ar=ar.split("-");ar=[parseFloat(ar[0]),parseFloat(ar[1])];if(au(ar[0])||au(ar[1])){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}ak.slider((ao?"values":"value"),ar);al.removeClass("input")}}})})};var aa=this;aa.parent_div=$("<div/>").addClass("filter-row slider-row");var Z=$("<div/>").addClass("elt-label").appendTo(aa.parent_div),af=$("<span/>").addClass("slider-name").text(aa.name+" ").appendTo(Z),ab=$("<span/>").text(this.low+"-"+this.high),ac=$("<span/>").addClass("slider-value").appendTo(Z).append("[").append(ab).append("]");aa.values_span=ab;var ae=$("<div/>").addClass("slider").appendTo(aa.parent_div);aa.control_element=$("<div/>").attr("id",aa.name+"-filter-control").appendTo(ae);aa.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(ai,aj){aa.slide(ai,aj)},change:function(ai,aj){aa.control_element.slider("option","slide").call(aa.control_element,ai,aj)}});aa.slider=aa.control_element;aa.slider_label=ab;ad(ac,ab,aa.control_element);var ag=$("<div/>").addClass("display-controls").appendTo(aa.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(aa.manager.alpha_filter!==aa){aa.manager.alpha_filter=aa;aa.manager.parent_div.find(".layer-transparent").removeClass("active").hide();aa.transparency_icon.addClass("active").show()}else{aa.manager.alpha_filter=null;aa.transparency_icon.removeClass("active")}aa.manager.track.request_draw(true,true)}).appendTo(ag).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(aa.manager.height_filter!==aa){aa.manager.height_filter=aa;aa.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();aa.height_icon.addClass("active").show()}else{aa.manager.height_filter=null;aa.height_icon.removeClass("active")}aa.manager.track.request_draw(true,true)}).appendTo(ag).hide();aa.parent_div.hover(function(){aa.transparency_icon.show();aa.height_icon.show()},function(){if(aa.manager.alpha_filter!==aa){aa.transparency_icon.hide()}if(aa.manager.height_filter!==aa){aa.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(aa.parent_div)};o(Q.prototype,{to_dict:function(){var Z=f.prototype.to_dict.call(this);return o(Z,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new Q({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ab,Z){var aa=Z-ab;return(aa<=2?0.01:1)},slide:function(ab,ac){var aa=ac.values;this.values_span.text(aa[0]+"-"+aa[1]);this.low=aa[0];this.high=aa[1];var Z=this;setTimeout(function(){if(aa[0]===Z.low&&aa[1]===Z.high){Z.manager.track.request_draw(true,true)}},25)},applies_to:function(Z){if(Z.length>this.index){return true}return false},_keep_val:function(Z){return(isNaN(Z)||(Z>=this.low&&Z<=this.high))},keep:function(aa){if(!this.applies_to(aa)){return true}var ac=this;var ad=aa[this.index];if(ad instanceof Array){var ab=true;for(var Z=0;Z<ad.length;Z++){if(!this._keep_val(ad[Z])){ab=false;break}}return ab}else{return this._keep_val(aa[this.index])}},update_attrs:function(ac){var Z=false;if(!this.applies_to(ac)){return Z}var aa=ac[this.index];if(!(aa instanceof Array)){aa=[aa]}for(var ab=0;ab<aa.length;ab++){var ad=aa[ab];if(ad<this.min){this.min=Math.floor(ad);Z=true}if(ad>this.max){this.max=Math.ceil(ad);Z=true}}return Z},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var aa=this.slider.slider("option","min"),Z=this.slider.slider("option","max");if(this.min<aa||this.max>Z){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var V=function(ab,ah){this.track=ab;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aj){aj.stopPropagation()}).click(function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()}).bind("keydown",function(aj){aj.stopPropagation()});if(ah&&"filters" in ah){var Z=("alpha_filter" in ah?ah.alpha_filter:null),ac=("height_filter" in ah?ah.height_filter:null),ae=ah.filters,aa;for(var af=0;af<ae.length;af++){if(ae[af].type==="number"){aa=new Q(ae[af]);this.add_filter(aa);if(aa.name===Z){this.alpha_filter=aa;aa.transparency_icon.addClass("active").show()}if(aa.name===ac){this.height_filter=aa;aa.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ah&&ah.visible){this.parent_div.show()}}if(this.filters.length!==0){var ai=$("<div/>").addClass("param-row").appendTo(this.parent_div);var ag=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ai);var ad=this;ag.click(function(){ad.run_on_dataset()})}};o(V.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var ac={},ab=[],aa;for(var Z=0;Z<this.filters.length;Z++){aa=this.filters[Z];ab.push(aa.to_dict())}ac.filters=ab;ac.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);ac.height_filter=(this.height_filter?this.height_filter.name:null);ac.visible=this.parent_div.is(":visible");return ac},copy:function(aa){var ab=new V(aa);for(var Z=0;Z<this.filters.length;Z++){ab.add_filter(this.filters[Z].copy())}return ab},add_filter:function(Z){Z.manager=this;this.parent_div.append(Z.parent_div);this.filters.push(Z)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.update_ui_elt()}},clear_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.slider.slider("option","values",[aa.min,aa.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var af=function(aj,ah,ai){if(!(ah in aj)){aj[ah]=ai}return aj[ah]};var ae={},ag,Z;for(var ad=0;ad<this.filters.length;ad++){ag=this.filters[ad];if(ag.tool_id){if(ag.min!==ag.low){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" >= "+ag.low}if(ag.max!==ag.high){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" <= "+ag.high}}}var aa=[];for(var ac in ae){aa[aa.length]=[ac,ae[ac]]}(function ab(an,ak){var ai=ak[0],aj=ai[0],am=ai[1],al="("+am.join(") and (")+")",ah={cond:al,input:an,target_dataset_id:an,tool_id:aj},ak=ak.slice(1);$.getJSON(run_tool_url,ah,function(ao){if(ao.error){show_modal("Filter Dataset","Error running tool "+aj,{Close:hide_modal})}else{if(ak.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ab(ao.dataset_id,ak)}}})})(this.track.dataset_id,aa)}});var z=function(Z,aa){I.Scaler.call(this,aa);this.filter=Z};z.prototype.gen_val=function(Z){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(Z[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(Z){this.track=Z.track;this.params=Z.params;this.values={};this.restore_values((Z.saved_values?Z.saved_values:{}));this.onchange=Z.onchange};o(C.prototype,{restore_values:function(Z){var aa=this;$.each(this.params,function(ab,ac){if(Z[ac.key]!==undefined){aa.values[ac.key]=Z[ac.key]}else{aa.values[ac.key]=ac.default_value}})},build_form:function(){var ac=this;var Z=$("<div />");var ab;function aa(ah,ad){for(var al=0;al<ah.length;al++){ab=ah[al];if(ab.hidden){continue}var af="param_"+al;var ap=ac.values[ab.key];var ar=$("<div class='form-row' />").appendTo(ad);ar.append($("<label />").attr("for",af).text(ab.label+":"));if(ab.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",af).attr("name",af).attr("checked",ap))}else{if(ab.type==="text"){ar.append($('<input type="text"/>').attr("id",af).val(ap).click(function(){$(this).select()}))}else{if(ab.type==="select"){var an=$("<select />").attr("id",af);for(var aj=0;aj<ab.options.length;aj++){$("<option/>").text(ab.options[aj].label).attr("value",ab.options[aj].value).appendTo(an)}an.val(ap);ar.append(an)}else{if(ab.type==="color"){var aq=$("<div/>").appendTo(ar),am=$("<input />").attr("id",af).attr("name",af).val(ap).css("float","left").appendTo(aq).click(function(au){$(".bs-tooltip").removeClass("in");var at=$(this).siblings(".bs-tooltip").addClass("in");at.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(at).height()/2)+($(this).height()/2)}).show();at.click(function(av){av.stopPropagation()});$(document).bind("click.color-picker",function(){at.hide();$(document).unbind("click.color-picker")});au.stopPropagation()}),ak=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aq).attr("title","Set new random color").tooltip(),ao=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aq).hide(),ag=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ao),ae=$("<div class='tooltip-arrow'></div>").appendTo(ao),ai=$.farbtastic(ag,{width:100,height:100,callback:am,color:ap});aq.append($("<div/>").css("clear","both"));(function(at){ak.click(function(){at.setColor(get_random_color())})})(ai)}else{ar.append($("<input />").attr("id",af).attr("name",af).val(ap))}}}}if(ab.help){ar.append($("<div class='help'/>").text(ab.help))}}}aa(this.params,Z);return Z},update_from_form:function(Z){var ab=this;var aa=false;$.each(this.params,function(ac,ae){if(!ae.hidden){var af="param_"+ac;var ad=Z.find("#"+af).val();if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad)}else{if(ae.type==="bool"){ad=Z.find("#"+af).is(":checked")}}}if(ad!==ab.values[ae.key]){ab.values[ae.key]=ad;aa=true}}});if(aa){this.onchange();this.track.changed()}}});var b=function(Z,ad,ab,aa,ac){this.track=Z;this.region=ad;this.low=ad.get("start");this.high=ad.get("end");this.resolution=ab;this.html_elt=$("<div class='track-tile'/>").append(aa).height($(aa).attr("height"));this.data=ac;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(Z,ae,ab,aa,ac,ad){b.call(this,Z,ae,ab,aa,ac);this.max_val=ad};o(j.prototype,b.prototype);var L=function(ac,ak,ad,ab,af,am,ag,an,aa,aj){b.call(this,ac,ak,ad,ab,af);this.mode=ag;this.all_slotted=aa;this.feature_mapper=aj;this.has_icons=false;if(an){this.has_icons=true;var ah=this;ab=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ab.width}).prependTo(this.html_elt);var ai=new GenomeRegion({chrom:ac.view.chrom,start:this.low,end:this.high}),al=af.length,ae=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),Z=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ae.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()});Z.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()})}};o(L.prototype,b.prototype);L.prototype.predisplay_actions=function(){var aa=this,Z={};if(aa.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(al){if(!this.hovered){return}var ag=$(this).offset(),ak=al.pageX-ag.left,aj=al.pageY-ag.top,ap=aa.feature_mapper.get_feature_data(ak,aj),ah=(ap?ap[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ah||$(this).attr("id")!==ah.toString()){$(this).remove()}});if(ap){var ac=Z[ah];if(!ac){var ah=ap[0],am={name:ap[3],start:ap[1],end:ap[2],strand:ap[4]},af=aa.track.filters_manager.filters,ae;for(var ai=0;ai<af.length;ai++){ae=af[ai];am[ae.name]=ap[ae.index]}var ac=$("<div/>").attr("id",ah).addClass("feature-popup"),aq=$("<table/>"),ao,an,ar;for(ao in am){an=am[ao];ar=$("<tr/>").appendTo(aq);$("<th/>").appendTo(ar).text(ao);$("<td/>").attr("align","left").appendTo(ar).text(typeof(an)==="number"?U(an,2):an)}ac.append($("<div class='feature-popup-inner'>").append(aq));Z[ah]=ac}ac.appendTo($(this).parents(".track-content").children(".overlay"));var ad=ak+parseInt(aa.html_elt.css("left"))-ac.width()/2,ab=aj+parseInt(aa.html_elt.css("top"))+7;ac.css("left",ad+"px").css("top",ab+"px")}else{if(!al.isPropagationStopped()){al.stopPropagation();$(this).siblings().each(function(){$(this).trigger(al)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var h=function(ab,aa,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ab,aa,ad);this.data_url=("data_url" in ad?ad.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:H);this.dataset_check_url=("converted_datasets_state_url" in ad?ad.converted_datasets_state_url:converted_datasets_state_url);this.feature_search_url=("feature_search_url" in ad?ad.feature_search_url:feature_search_url);var Z=this,ac=new Dataset({id:ad.dataset_id,hda_ldda:ad.hda_ldda});this.data_manager=("data_manager" in ad?ad.data_manager:new GenomeDataManager({dataset:ac,data_url:Z.data_url,dataset_state_url:Z.dataset_check_url,feature_search_url:Z.feature_search_url,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(h.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(Z){Z.view.set_overview(Z)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters()}else{Z.filters_manager.init_filters()}Z.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(Z){Z.dynamic_tool_div.toggle();if(Z.dynamic_tool_div.is(":visible")){Z.set_name(Z.name+Z.tool_region_and_parameters_str())}else{Z.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(Z){var ac='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ab=_.template(ac,{track:Z});var ae=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aa=function(){var ag=$('select[name="regions"] option:selected').val(),ai,af=new GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ah=_.map($(".bookmark"),function(aj){return new GenomeRegion({from_str:$(aj).children(".position").text()})});if(ag==="cur"){ai=[af]}else{if(ag==="bookmarks"){ai=ah}else{ai=[af].concat(ah)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:Z.dataset_id,hda_ldda:Z.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ai).toJSON())})},ad=function(af){if((af.keyCode||af.which)===27){ae()}else{if((af.keyCode||af.which)===13){aa()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ab,{No:ae,Yes:aa})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var Z=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(Z)}this.name_div=$("<div/>").addClass("track-name").appendTo(Z).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return Z},on_resize:function(){},add_resize_handle:function(){var Z=this;var ac=false;var ab=false;var aa=$("<div class='track-resize'>");$(Z.container_div).hover(function(){if(Z.content_visible){ac=true;aa.show()}},function(){ac=false;if(!ab){aa.hide()}});aa.hide().bind("dragstart",function(ad,ae){ab=true;ae.original_height=$(Z.content_div).height()}).bind("drag",function(ae,af){var ad=Math.min(Math.max(af.original_height+af.deltaY,Z.min_height_px),Z.max_height_px);$(Z.tiles_div).css("height",ad);Z.visible_height_px=(Z.max_height_px===ad?0:ad);Z.on_resize()}).bind("dragend",function(ad,ae){Z.tile_cache.clear();ab=false;if(!ac){aa.hide()}Z.config.values.height=Z.visible_height_px;Z.changed()}).appendTo(Z.container_div)},set_display_modes:function(ac,af){this.display_modes=ac;this.mode=(af?af:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var aa=this,ad={};for(var ab=0,Z=aa.display_modes.length;ab<Z;ab++){var ae=aa.display_modes[ab];ad[ae]=function(ag){return function(){aa.change_mode(ag);aa.icons_div.show();aa.container_div.mouseleave(function(){aa.icons_div.hide()})}}(ae)}make_popupmenu(this.action_icons.mode_icon,ad)},build_action_icons:function(){p.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 y){return"ReferenceTrack"}else{if(this instanceof i){return"LineTrack"}else{if(this instanceof R){return"ReadTrack"}else{if(this instanceof O){return"VcfTrack"}else{if(this instanceof g){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.content_div.css("height","auto");aa.tiles_div.children().remove();aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}var Z=$.Deferred();$.getJSON(this.dataset_check_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.tiles_div.text(n);if(ab.message){var ac=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.tiles_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.tiles_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.tiles_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.tiles_div.html(t);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab==="data"||ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.update_icons()}aa.tiles_div.text(T);if(aa.view.chrom){aa.tiles_div.text("");aa.tiles_div.css("height",aa.visible_height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){Z.resolve();aa.container_div.removeClass("nodata error pending");aa.request_draw()})}else{Z.resolve()}}}}}}});this.update_icons();return Z},predraw_init:function(){},get_drawables:function(){return this}});var J=function(ab,aa,ac){h.call(this,ab,aa,ac);var Z=this;l(Z.container_div,Z.drag_handle_class,".group",Z);this.filters_manager=new V(this,("filters" in ac?ac.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ac&&ac.tool?new q(this,ac.tool,ac.tool_state):null);this.tile_cache=new Cache(N);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ac.mode){this.change_mode(ac.mode)}};o(J.prototype,p.prototype,h.prototype,{action_icons_def:h.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(Z){$(".bs-tooltip").remove();Z.slotters[Z.view.resolution_px_b].max_rows*=2;Z.request_draw(true)},hide:true}]),copy:function(Z){var aa=this.to_dict();o(aa,{data_manager:this.data_manager});var ab=new this.constructor(this.view,Z,aa);ab.change_mode(this.mode);ab.enabled=this.enabled;return ab},set_filters_manager:function(Z){this.filters_manager=Z;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(aa){var Z=this;Z.mode=aa;Z.config.values.mode=aa;Z.tile_cache.clear();Z.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+Z.mode+")");return Z},update_icons:function(){var Z=this;if(Z.filters_available){Z.action_icons.filters_icon.show()}else{Z.action_icons.filters_icon.hide()}if(Z.tool){Z.action_icons.tools_icon.show();Z.action_icons.param_space_viz_icon.show()}else{Z.action_icons.tools_icon.hide();Z.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(aa,ab,Z){return aa+"_"+ab+"_"+Z},request_draw:function(aa,Z){this.view.request_redraw(false,aa,Z,this)},before_draw:function(){},_draw:function(aa,ak){if(!this.can_draw()){return}var ai=this.view.low,ae=this.view.high,ag=ae-ai,ab=this.view.container.width(),am=this.view.resolution_px_b,ad=this.view.resolution_b_px;if(this.is_overview){ai=this.view.max_low;ae=this.view.max_high;ad=(view.max_high-view.max_low)/ab;am=1/ad}this.before_draw();this.tiles_div.children().addClass("remove");var Z=Math.floor(ai/(ad*P)),ah=true,al=[],af=function(an){return(an&&"track" in an)};while((Z*P*ad)<ae){var aj=this.draw_helper(aa,ab,Z,ad,this.tiles_div,am);if(af(aj)){al.push(aj)}else{ah=false}Z+=1}if(!ak){this.tiles_div.children(".remove").removeClass("remove").remove()}var ac=this;if(ah){this.tiles_div.children(".remove").remove();ac.postdraw_actions(al,ab,am,ak)}},postdraw_actions:function(ab,ac,ae,Z){var ad=false;for(var aa=0;aa<ab.length;aa++){if(ab[aa].has_icons){ad=true;break}}if(ad){for(var aa=0;aa<ab.length;aa++){tile=ab[aa];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(Z,al,aq,ao,ae,af,am){var ak=this,au=this._gen_tile_cache_key(al,af,aq),ac=this._get_tile_bounds(aq,ao);if(!am){am={}}var at=(Z?undefined:ak.tile_cache.get_elt(au));if(at){ak.show_tile(at,ae,af);return at}var ai=true;var ap=ak.data_manager.get_data(ac,ak.mode,ao,ak.data_url_extra_params);if(is_deferred(ap)){ai=false}var ag;if(view.reference_track&&af>view.canvas_manager.char_width_px){ag=view.reference_track.data_manager.get_data(ac,ak.mode,ao,view.reference_track.data_url_extra_params);if(is_deferred(ag)){ai=false}}if(ai){o(ap,am.more_tile_data);var ah=ak.mode;if(ah==="Auto"){ah=ak.get_mode(ap);ak.update_auto_mode(ah)}var ab=ak.view.canvas_manager.new_canvas(),ar=ac.get("start"),aa=ac.get("end"),al=Math.ceil((aa-ar)*af)+ak.left_offset,aj=ak.get_canvas_height(ap,ah,af,al);ab.width=al;ab.height=aj;var an=ab.getContext("2d");an.translate(this.left_offset,0);var at=ak.draw_tile(ap,an,ah,ao,ac,af,ag);if(at!==undefined){ak.tile_cache.set_elt(au,at);ak.show_tile(at,ae,af)}return at}var ad=$.Deferred();$.when(ap,ag).then(function(){view.request_redraw(false,false,false,ak);ad.resolve()});return ad},get_canvas_height:function(Z,ab,ac,aa){return this.visible_height_px},draw_tile:function(Z,aa,ae,ac,ad,af,ab){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ab,ad,ae){var aa=this,Z=ab.html_elt;ab.predisplay_actions();var ac=(ab.low-(this.is_overview?this.view.max_low:this.view.low))*ae;if(this.left_offset){ac-=this.left_offset}Z.css({position:"absolute",top:0,left:ac});if(Z.hasClass("remove")){Z.removeClass("remove")}else{ad.append(Z)}aa.after_show_tile(ab)},after_show_tile:function(Z){this.max_height_px=Math.max(this.max_height_px,Z.html_elt.height());Z.html_elt.parent().children().css("height",this.max_height_px+"px");var aa=this.max_height_px;if(this.visible_height_px!==0){aa=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",aa+"px")},_get_tile_bounds:function(Z,aa){var ac=Math.floor(Z*P*aa),ad=Math.ceil(P*aa),ab=(ac+ad<=this.view.max_high?ac+ad:this.view.max_high);return new GenomeRegion({chrom:this.view.chrom,start:ac,end:ab})},tool_region_and_parameters_str:function(ab,Z,ac){var aa=this,ad=(ab!==undefined&&Z!==undefined&&ac!==undefined?ab+":"+Z+"-"+ac:"all");return" - region=["+ad+"], parameters=["+aa.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(Z,aa){return true},can_subset:function(Z){return false},init_for_tool_data:function(){this.data_manager.set("data_url",raw_data_url);this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ab,ac,ae,Z){var aa=this;aa.normal_postdraw_actions(ab,ac,ae,Z);aa.dataset_state_url=converted_datasets_state_url;aa.data_query_wait=H;var ad=new ServerStateDeferred({url:aa.dataset_state_url,url_params:{dataset_id:aa.dataset_id,hda_ldda:aa.hda_ldda},interval:aa.data_query_wait,success_fn:function(af){return af!=="pending"}});$.when(ad.go()).then(function(){aa.data_manager.set("data_url",default_data_url)});aa.postdraw_actions=aa.normal_postdraw_actions}}});var W=function(aa,Z){var ab={resize:false};h.call(this,aa,Z,ab);this.container_div.addClass("label-track")};o(W.prototype,h.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ab=this.view,ac=ab.high-ab.low,af=Math.floor(Math.pow(10,Math.floor(Math.log(ac)/Math.log(10)))),Z=Math.floor(ab.low/af)*af,ad=this.view.container.width(),aa=$("<div style='position: relative; height: 1.3em;'></div>");while(Z<ab.high){var ae=(Z-ab.low)/ac*ad;aa.append($("<div class='label'>"+commatize(Z)+"</div>").css({position:"absolute",left:ae-1}));Z+=af}this.content_div.children(":first").remove();this.content_div.append(aa)}});var g=function(aa,Z,ad){J.call(this,aa,Z,ad);this.drawables=[];this.left_offset=0;if("drawables" in ad){var ac;for(var ab=0;ab<ad.drawables.length;ab++){ac=ad.drawables[ab];this.drawables[ab]=object_from_template(ac,aa,null);if(ac.left_offset>this.left_offset){this.left_offset=ac.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};o(g.prototype,J.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_group()}}].concat(J.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(Z){J.prototype.change_mode.call(this,Z);for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].change_mode(Z)}},init:function(){var ab=[];for(var aa=0;aa<this.drawables.length;aa++){ab.push(this.drawables[aa].init())}var Z=this;$.when.apply($,ab).then(function(){Z.enabled=true;Z.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,draw_helper:function(aa,ap,aw,at,ah,aj,aq){var ao=this,aA=this._gen_tile_cache_key(ap,aj,aw),ae=this._get_tile_bounds(aw,at);if(!aq){aq={}}var az=(aa?undefined:ao.tile_cache.get_elt(aA));if(az){ao.show_tile(az,ah,aj);return az}var ai=[],ao,am=true,au,ak;for(var av=0;av<this.drawables.length;av++){ao=this.drawables[av];au=ao.data_manager.get_data(ae,ao.mode,at,ao.data_url_extra_params);if(is_deferred(au)){am=false}ai.push(au);ak=null;if(view.reference_track&&aj>view.canvas_manager.char_width_px){ak=view.reference_track.data_manager.get_data(ae,ao.mode,at,view.reference_track.data_url_extra_params);if(is_deferred(ak)){am=false}}ai.push(ak)}if(am){o(au,aq.more_tile_data);this.tile_predraw_init();var ad=ao.view.canvas_manager.new_canvas(),af=ao._get_tile_bounds(aw,at),ax=ae.get("start"),ab=ae.get("end"),ay=0,ap=Math.ceil((ab-ax)*aj)+this.left_offset,an=0,ac=[],av;var Z=0;for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];var al=ao.mode;if(al==="Auto"){al=ao.get_mode(au);ao.update_auto_mode(al)}ac.push(al);Z=ao.get_canvas_height(au,al,aj,ap);if(Z>an){an=Z}}ad.width=ap;ad.height=(aq.height?aq.height:an);ay=0;var ar=ad.getContext("2d");ar.translate(this.left_offset,0);ar.globalAlpha=0.5;ar.globalCompositeOperation="source-over";for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];ak=ai[ay+1];az=ao.draw_tile(au,ar,ac[av],at,ae,aj,ak)}this.tile_cache.set_elt(aA,az);this.show_tile(az,ah,aj);return az}var ag=$.Deferred(),ao=this;$.when.apply($,ai).then(function(){view.request_redraw(false,false,false,ao);ag.resolve()});return ag},show_group:function(){var ac=new M(this.view,this.container,{name:this.name}),Z;for(var ab=0;ab<this.drawables.length;ab++){Z=this.drawables[ab];Z.update_icons();ac.add_drawable(Z);Z.container=ac;ac.content_div.append(Z.container_div)}var aa=this.container.replace_drawable(this,ac,true);ac.request_draw()},tile_predraw_init:function(){var ac=Number.MAX_VALUE,Z=-ac,aa;for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];if(aa instanceof i){if(aa.prefs.min_value<ac){ac=aa.prefs.min_value}if(aa.prefs.max_value>Z){Z=aa.prefs.max_value}}}for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];aa.prefs.min_value=ac;aa.prefs.max_value=Z}},postdraw_actions:function(ab,ae,ag,aa){J.prototype.postdraw_actions.call(this,ab,ae,ag,aa);var ad=-1;for(var ac=0;ac<ab.length;ac++){var Z=ab[ac].html_elt.find("canvas").height();if(Z>ad){ad=Z}}for(var ac=0;ac<ab.length;ac++){var af=ab[ac];if(af.html_elt.find("canvas").height()!==ad){this.draw_helper(true,ae,af.index,af.resolution,af.html_elt.parent(),ag,{height:ad});af.html_elt.remove()}}}});var y=function(Z){J.call(this,Z,{content_div:Z.top_labeltrack},{resize:false});Z.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:Z.dbkey};this.data_manager=new ReferenceTrackDataManager({data_url:reference_url});this.hide_contents()};o(y.prototype,p.prototype,J.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:p.prototype.can_draw,draw_helper:function(ad,ab,Z,aa,ae,af,ac){if(af>this.view.canvas_manager.char_width_px){return J.prototype.draw_helper.call(this,ad,ab,Z,aa,ae,af,ac)}else{this.hide_contents();return null}},draw_tile:function(ah,ai,ad,ac,af,aj){var ab=this;if(aj>this.view.canvas_manager.char_width_px){if(ah.data===null){this.hide_contents();return}var aa=ai.canvas;ai.font=ai.canvas.manager.default_font;ai.textAlign="center";ah=ah.data;for(var ae=0,ag=ah.length;ae<ag;ae++){var Z=Math.floor(ae*aj);ai.fillText(ah[ae],Z,10)}this.show_contents();return new b(ab,af,ac,aa,ah)}this.hide_contents()}});var i=function(ab,aa,ac){var Z=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_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:32,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(i.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var Z=this;Z.vertical_range=undefined;return $.getJSON(Z.data_url,{stats:true,chrom:Z.view.chrom,low:0,high:Z.view.max_high,hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id},function(aa){Z.container_div.addClass("line-track");var ad=aa.data;if(isNaN(parseFloat(Z.prefs.min_value))||isNaN(parseFloat(Z.prefs.max_value))){var ab=ad.min,af=ad.max;ab=Math.floor(Math.min(0,Math.max(ab,ad.mean-2*ad.sd)));af=Math.ceil(Math.max(0,Math.min(af,ad.mean+2*ad.sd)));Z.prefs.min_value=ab;Z.prefs.max_value=af;$("#track_"+Z.dataset_id+"_minval").val(Z.prefs.min_value);$("#track_"+Z.dataset_id+"_maxval").val(Z.prefs.max_value)}Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.total_frequency=ad.total_frequency;Z.container_div.find(".yaxislabel").remove();var ae=$("<div/>").text(U(Z.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_min_value(ag)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+Z.dataset_id+"_minval").prependTo(Z.container_div),ac=$("<div/>").text(U(Z.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_max_value(ag)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+Z.dataset_id+"_maxval").prependTo(Z.container_div)})},draw_tile:function(ai,ag,ab,aa,ad,ah){var Z=ag.canvas,ac=ad.get("start"),af=ad.get("end"),ae=new I.LinePainter(ai.data,ac,af,this.prefs,ab);ae.draw(ag,Z.width,Z.height,ah);return new b(this,ad,aa,Z,ai.data)},can_subset:function(Z){return false}});var r=function(ab,aa,ac){var Z=this;this.display_modes=["Heatmap"];this.mode="Heatmap";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{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}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(r.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;this.tile_cache.clear();this.request_draw()},draw_tile:function(aj,ah,ae,ac,aa,ai){var ab=ah.canvas,Z=this._get_tile_bounds(aa,ac),ad=Z[0],ag=Z[1],af=new I.DiagonalHeatmapPainter(aj.data,ad,ag,this.prefs,ae);af.draw(ah,ab.width,ab.height,ai);return new b(this,aa,ac,ab,aj.data)}});var c=function(ac,ab,ae){var aa=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];J.call(this,ac,ab,ae);var ad=get_random_color(),Z=get_random_color([ad,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ad},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",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:this.visible_height_px,hidden:true}],saved_values:ae.prefs,onchange:function(){aa.set_name(aa.prefs.name);aa.tile_cache.clear();aa.set_painter_from_config();aa.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ae.hda_ldda;this.dataset_id=ae.dataset_id;this.original_dataset_id=ae.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,J.prototype,{set_dataset:function(Z){this.dataset_id=Z.get("id");this.hda_ldda=Z.get("hda_ldda");this.data_manager.set("dataset",Z)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=I.ArcLinkedFeaturePainter}else{this.painter=I.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ao,aj,ae,ad){J.prototype.postdraw_actions.call(this,ao,ad);var ai=this,al;if(ai.mode==="Coverage"){var aa=-1;for(al=0;al<ao.length;al++){var ak=ao[al].max_val;if(ak>aa){aa=ak}}for(al=0;al<ao.length;al++){var aq=ao[al];if(aq.max_val!==aa){aq.html_elt.remove();ai.draw_helper(true,aj,aq.index,aq.resolution,aq.html_elt.parent(),ae,{more_tile_data:{max:aa}})}}}if(ai.filters_manager){var af=ai.filters_manager.filters;for(var an=0;an<af.length;an++){af[an].update_ui_elt()}var ap=false,Z,ag;for(al=0;al<ao.length;al++){if(ao[al].data.length){Z=ao[al].data[0];for(var an=0;an<af.length;an++){ag=af[an];if(ag.applies_to(Z)&&ag.min!==ag.max){ap=true;break}}}}if(ai.filters_available!==ap){ai.filters_available=ap;if(!ai.filters_available){ai.filters_manager.hide()}ai.update_icons()}}this.container_div.find(".yaxislabel").remove();var ac=ao[0];if(ac instanceof j){var ah=(this.prefs.histogram_max?this.prefs.histogram_max:ac.max_val),ab=$("<div/>").text(ah).make_text_editable({num_cols:12,on_finish:function(ar){$(".bs-tooltip").remove();var ar=parseFloat(ar);ai.prefs.histogram_max=(!isNaN(ar)?ar:null);ai.tile_cache.clear();ai.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ab)}if(ac instanceof L){var am=true;for(al=0;al<ao.length;al++){if(!ao[al].all_slotted){am=false;break}}if(!am){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(Z){var Z;if(this.mode==="Auto"){if(Z==="no_detail"){Z="feature spans"}else{if(Z==="summary_tree"){Z="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+Z+")")}},incremental_slots:function(ad,Z,ac){var aa=this.view.canvas_manager.dummy_context,ab=this.slotters[ad];if(!ab||(ab.mode!==ac)){ab=new (s.FeatureSlotter)(ad,ac,x,function(ae){return aa.measureText(ae)});this.slotters[ad]=ab}return ab.slot_features(Z)},get_mode:function(Z){if(Z.dataset_type==="summary_tree"){mode="summary_tree"}else{if(Z.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>F){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(Z,ad,ae,aa){if(ad==="summary_tree"||ad==="Coverage"){return this.summary_draw_height}else{var ac=this.incremental_slots(ae,Z.data,ad);var ab=new (this.painter)(null,null,null,this.prefs,ad);return Math.max(Y,ab.get_required_height(ac,aa))}},draw_tile:function(aj,an,al,ao,ac,ag,ab){var am=this,aa=an.canvas,av=ac.get("start"),Z=ac.get("end"),ad=this.left_offset;if(al==="summary_tree"||al==="Coverage"){var ax=new I.SummaryTreePainter(aj,av,Z,this.prefs);ax.draw(an,aa.width,aa.height,ag);return new j(am,ac,ao,aa,aj.data,aj.max)}var af=[],ak=this.slotters[ag].slots;all_slotted=true;if(aj.data){var ah=this.filters_manager.filters;for(var ap=0,ar=aj.data.length;ap<ar;ap++){var ae=aj.data[ap];var aq=false;var ai;for(var au=0,az=ah.length;au<az;au++){ai=ah[au];ai.update_attrs(ae);if(!ai.keep(ae)){aq=true;break}}if(!aq){af.push(ae);if(!(ae[0] in ak)){all_slotted=false}}}}var ay=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aw=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var ax=new (this.painter)(af,av,Z,this.prefs,al,ay,aw,ab);var at=null;an.fillStyle=this.prefs.block_color;an.font=an.canvas.manager.default_font;an.textAlign="right";if(aj.data){at=ax.draw(an,aa.width,aa.height,ag,ak);at.translation=-ad}return new L(am,ac,ao,aa,aj.data,ag,al,aj.message,all_slotted,at)},data_and_mode_compatible:function(Z,aa){if(aa==="Auto"){return true}else{if(aa==="Coverage"){return Z.dataset_type==="summary_tree"}else{if(Z.extra_info==="no_detail"||Z.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(Z){if(Z.dataset_type==="summary_tree"||Z.message||Z.extra_info==="no_detail"){return false}return true}});var O=function(aa,Z,ab){c.call(this,aa,Z,ab);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_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_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ab.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter};o(O.prototype,p.prototype,J.prototype,c.prototype);var R=function(ab,aa,ad){c.call(this,ab,aa,ad);var ac=get_random_color(),Z=get_random_color([ac,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ac},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ad.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter;this.update_icons()};o(R.prototype,p.prototype,J.prototype,c.prototype);S.View=X;S.DrawableGroup=M;S.LineTrack=i;S.FeatureTrack=c;S.DiagonalHeatmapTrack=r;S.ReadTrack=R;S.VcfTrack=O;S.CompositeTrack=g};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(require,exports){var extend=require("class").extend;var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-1)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2]-1,feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,orig_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=0,char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var draw_last=[];if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){gap=Math.round(w_scale/2)}if(!cigar){cigar=[[0,orig_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=(feature_start-1)+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(gap>0){ctx.fillStyle=block_color;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=CONNECTOR_COLOR;for(var c=0,str_len=seq.length;c<str_len;c++){if(this.prefs.show_differences){if(this.ref_seq){var ref_char=this.ref_seq[seq_start-tile_low+c];if(!ref_char||ref_char.toLowerCase()===seq[c].toLowerCase()){continue}}else{continue}}if(seq_start+c>=tile_low&&seq_start+c<=tile_high){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start-gap,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color,gap=0;if((mode==="Pack"||this.mode==="Auto")&&w_scale>ctx.canvas.manager.char_width_px){var gap=Math.round(w_scale/2)}if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING-gap,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"4169E1",neg_color:"FF8C00"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};exports.Scaler=Scaler;exports.SummaryTreePainter=SummaryTreePainter;exports.LinePainter=LinePainter;exports.LinkedFeaturePainter=LinkedFeaturePainter;exports.ReadPainter=ReadPainter;exports.ArcLinkedFeaturePainter=ArcLinkedFeaturePainter;exports.DiagonalHeatmapPainter=DiagonalHeatmapPainter};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff -r d5626302446db334804820f0a29fc4d0c7d72a0e -r e6444e7a16851514d3efa3ef34acab8362356f8c static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -var ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.Deferred(),c=this,f=c.get("ajax_settings"),e=c.get("success_fn"),b=c.get("interval"),a=function(){$.ajax(f).success(function(g){if(e(g)){d.resolve(g)}else{setTimeout(a,b)}})};a();return d}});var CanvasManager=function(a){this.default_font=a!==undefined?a:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};_.extend(CanvasManager.prototype,{load_pattern:function(a,e){var b=this.patterns,c=this.dummy_context,d=new Image();d.src=galaxy_paths.attributes.image_path+e;d.onload=function(){b[a]=c.createPattern(d,"repeat")}},get_pattern:function(a){return this.patterns[a]},new_canvas:function(){var a=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(a)}a.manager=this;return a}});var Cache=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(a){this.clear()},get_elt:function(b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,a=d.indexOf(b);if(a!==-1){if(c[b].stale){d.splice(a,1);delete c[b]}else{this.move_key_to_end(b,a)}}return c[b]},set_elt:function(b,d){var e=this.attributes.obj_cache,f=this.attributes.key_ary,c=this.attributes.num_elements;if(!e[b]){if(f.length>=c){var a=f.shift();delete e[a]}f.push(b)}e[b]=d;return d},move_key_to_end:function(b,a){this.attributes.key_ary.splice(a,1);this.attributes.key_ary.push(b)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var GenomeDataManager=Cache.extend({defaults:_.extend({},Cache.prototype.defaults,{dataset:null,filters_manager:null,data_url:null,dataset_state_url:null,genome_wide_summary_data:null,data_mode_compatible:function(a,b){return true},can_subset:function(a){return false}}),data_is_ready:function(){var c=this.get("dataset"),b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.get("dataset_state_url"),data:{dataset_id:c.id,hda_ldda:c.get("hda_ldda")},dataType:"json"},interval:5000,success_fn:function(d){return d!=="pending"}});$.when(a.go()).then(function(d){b.resolve(d==="ok"||d==="data")});return b},load_data:function(h,g,b,f){var d={chrom:h.get("chrom"),low:h.get("start"),high:h.get("end"),mode:g,resolution:b};dataset=this.get("dataset");if(dataset){d.dataset_id=dataset.id;d.hda_ldda=dataset.get("hda_ldda")}$.extend(d,f);var j=this.get("filters_manager");if(j){var k=[];var a=j.filters;for(var e=0;e<a.length;e++){k.push(a[e].name)}d.filter_cols=JSON.stringify(k)}var c=this;return $.getJSON(this.get("data_url"),d,function(i){c.set_data(h,i)})},get_data:function(g,f,c,e){var h=this.get_elt(g);if(h&&(is_deferred(h)||this.get("data_mode_compatible")(h,f))){return h}var j=this.get("key_ary"),b=this.get("obj_cache"),k,a;for(var d=0;d<j.length;d++){k=j[d];a=new GenomeRegion({from_str:k});if(a.contains(g)){h=b[k];if(is_deferred(h)||(this.get("data_mode_compatible")(h,f)&&this.get("can_subset")(h))){this.move_key_to_end(k,d);return h}}}h=this.load_data(g,f,c,e);this.set_data(g,h);return h},set_data:function(b,a){this.set_elt(b,a)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(i,h,d,g,e){var k=this.get_elt(i);if(!(k&&this.get("data_mode_compatible")(k,h))){console.log("ERROR: no current data for: ",dataset,i.toString(),h,d,g);return}k.stale=true;var c=i.get("start");if(e===this.DEEP_DATA_REQ){$.extend(g,{start_val:k.data.length+1})}else{if(e===this.BROAD_DATA_REQ){c=(k.max_high?k.max_high:k.data[k.data.length-1][2])+1}}var j=i.copy().set("start",c);var b=this,f=this.load_data(j,h,d,g),a=$.Deferred();this.set_data(i,a);$.when(f).then(function(l){if(l.data){l.data=k.data.concat(l.data);if(l.max_low){l.max_low=k.max_low}if(l.message){l.message=l.message.replace(/[0-9]+/,l.data.length)}}b.set_data(i,l);a.resolve(l)});return a},get_elt:function(a){return Cache.prototype.get_elt.call(this,a.toString())},set_elt:function(b,a){return Cache.prototype.set_elt.call(this,b.toString(),a)}});var ReferenceTrackDataManager=GenomeDataManager.extend({load_data:function(a,d,e,b,c){if(b>1){return{data:null}}return GenomeDataManager.prototype.load_data.call(this,a,d,e,b,c)}});var Genome=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var GenomeRegion=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(b){if(b.from_str){var d=b.from_str.split(":"),c=d[0],a=d[1].split("-");this.set({chrom:c,start:parseInt(a[0],10),end:parseInt(a[1],10)})}},copy:function(){return new GenomeRegion({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(h){var b=this.get("chrom"),g=h.get("chrom"),f=this.get("start"),d=h.get("start"),e=this.get("end"),c=h.get("end"),a;if(b&&g&&b!==g){return this.get("DIF_CHROMS")}if(f<d){if(e<d){a=this.get("BEFORE")}else{if(e<=c){a=this.get("OVERLAP_START")}else{a=this.get("CONTAINS")}}}else{if(f>c){a=this.get("AFTER")}else{if(e<=c){a=this.get("CONTAINED_BY")}else{a=this.get("OVERLAP_END")}}}return a},contains:function(a){return this.compute_overlap(a)===this.get("CONTAINS")},overlaps:function(a){return _.intersection([this.compute_overlap(a)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var GenomeRegionCollection=Backbone.Collection.extend({model:GenomeRegion});var BrowserBookmark=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:"GenomeRegion"}]});var BrowserBookmarkCollection=Backbone.Collection.extend({model:BrowserBookmark});var GenomeWideBigWigData=Backbone.Model.extend({defaults:{data:null,min:0,max:0},initialize:function(b){var a=_.flatten(_.map(this.get("data"),function(c){if(c.data.length!==0){return _.map(c.data,function(d){return d[1]})}else{return 0}}));this.set("max",_.max(a));this.set("min",_.min(a))}});var GenomeWideSummaryTreeData=Backbone.RelationalModel.extend({defaults:{data:null,min:0,max:0},initialize:function(b){var a=_.max(this.get("data"),function(c){if(!c||typeof c==="string"){return 0}return c[1]});this.attributes.max=(a&&typeof a!=="string"?a[1]:0)}});var BackboneTrack=Dataset.extend({initialize:function(a){this.set("id",a.dataset_id);var c=this.get("genome_wide_data");if(c){var b=(this.get("track_type")==="LineTrack"?GenomeWideBigWigData:GenomeWideSummaryTreeData);this.set("genome_wide_data",new b(c))}}});var Visualization=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:"BackboneTrack"}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var GenomeVisualization=Visualization.extend({defaults:_.extend({},Visualization.prototype.defaults,{bookmarks:null,viewport:null})});var TrackConfig=Backbone.Model.extend({});var CircsterDataLayout=Backbone.Model.extend({defaults:{genome:null,dataset:null,total_gap:null},chroms_layout:function(){var b=this.attributes.genome.get_chroms_info(),d=d3.layout.pie().value(function(f){return f.len}).sort(null),e=d(b),a=this.attributes.total_gap/b.length,c=_.map(e,function(h,g){var f=h.endAngle-a;h.endAngle=(f>h.startAngle?f:h.startAngle);return h});return c},chrom_data_layout:function(d,c,b,e,a){},genome_data_layout:function(){var b=this,a=this.chroms_layout(),f=this.get("track").get("genome_wide_data"),e=this.get("radius_start"),c=this.get("radius_end"),d=_.zip(a,f.get("data")),g=_.map(d,function(i){var j=i[0],h=i[1];return b.chrom_data_layout(j,h,e,c,f.get("min"),f.get("max"))});return g}});var CircsterSummaryTreeLayout=CircsterDataLayout.extend({chrom_data_layout:function(k,b,h,g,d,i){if(!b||typeof b==="string"){return null}var e=b[0],j=b[3],c=d3.scale.linear().domain([d,i]).range([h,g]),f=d3.layout.pie().value(function(l){return j}).startAngle(k.startAngle).endAngle(k.endAngle),a=f(e);_.each(e,function(l,m){a[m].outerRadius=c(l[1])});return a}});var CircsterBigWigLayout=CircsterDataLayout.extend({chrom_data_layout:function(j,b,h,g,d,i){var e=b.data;if(e.length===0){return}var c=d3.scale.linear().domain([d,i]).range([h,g]),f=d3.layout.pie().value(function(l,k){if(k+1===e.length){return 0}return e[k+1][0]-e[k][0]}).startAngle(j.startAngle).endAngle(j.endAngle),a=f(e);_.each(e,function(k,l){a[l].outerRadius=c(k[1])});return a}});var CircsterView=Backbone.View.extend({className:"circster",initialize:function(a){this.width=a.width;this.height=a.height;this.total_gap=a.total_gap;this.genome=a.genome;this.radius_start=a.radius_start;this.dataset_arc_height=a.dataset_arc_height;this.track_gap=5},render:function(){var b=this,c=this.dataset_arc_height;var a=d3.select(b.$el[0]).append("svg").attr("width",b.width).attr("height",b.height).append("g").attr("transform","translate("+b.width/2+","+b.height/2+")");this.model.get("tracks").each(function(f,l){var g=f.get("genome_wide_data"),k=b.radius_start+l*(c+b.track_gap),h=(g instanceof GenomeWideBigWigData?CircsterBigWigLayout:CircsterSummaryTreeLayout),n=new h({track:f,radius_start:k,radius_end:k+c,genome:b.genome,total_gap:b.total_gap}),d=n.chroms_layout(),i=n.genome_data_layout();var o=a.append("g").attr("id","inner-arc"),m=d3.svg.arc().innerRadius(k).outerRadius(k+c),e=o.selectAll("#inner-arc>path").data(d).enter().append("path").attr("d",m).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(q){return q.data.chrom});var p=f.get("prefs"),j=p.block_color;_.each(i,function(q){if(!q){return}var t=a.append("g"),s=d3.svg.arc().innerRadius(k),r=t.selectAll("path").data(q).enter().append("path").attr("d",s).style("stroke",j).style("fill",j)})})}});var TrackBrowserRouter=Backbone.Router.extend({initialize:function(b){this.view=b.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var a=this;a.view.on("navigate",function(c){a.navigate(c)})},change_location:function(a){this.view.go_to(a)}});var add_datasets=function(a,c,b){$.ajax({url:a,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(d){show_modal("Select datasets for new tracks",d,{Cancel:function(){hide_modal()},Add:function(){var e=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var f,g=$(this).val();if($(this).attr("name")==="id"){f={hda_id:g}}else{f={ldda_id:g}}e[e.length]=$.ajax({url:c,data:f,dataType:"json"})});$.when.apply($,e).then(function(){var f=(arguments[0] instanceof Array?$.map(arguments,function(g){return g[0]}):[arguments[0]]);b(f)});hide_modal()}})}})}; \ No newline at end of file +var ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.Deferred(),c=this,f=c.get("ajax_settings"),e=c.get("success_fn"),b=c.get("interval"),a=function(){$.ajax(f).success(function(g){if(e(g)){d.resolve(g)}else{setTimeout(a,b)}})};a();return d}});var CanvasManager=function(a){this.default_font=a!==undefined?a:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};_.extend(CanvasManager.prototype,{load_pattern:function(a,e){var b=this.patterns,c=this.dummy_context,d=new Image();d.src=galaxy_paths.attributes.image_path+e;d.onload=function(){b[a]=c.createPattern(d,"repeat")}},get_pattern:function(a){return this.patterns[a]},new_canvas:function(){var a=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(a)}a.manager=this;return a}});var Cache=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(a){this.clear()},get_elt:function(b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,a=d.indexOf(b);if(a!==-1){if(c[b].stale){d.splice(a,1);delete c[b]}else{this.move_key_to_end(b,a)}}return c[b]},set_elt:function(b,d){var e=this.attributes.obj_cache,f=this.attributes.key_ary,c=this.attributes.num_elements;if(!e[b]){if(f.length>=c){var a=f.shift();delete e[a]}f.push(b)}e[b]=d;return d},move_key_to_end:function(b,a){this.attributes.key_ary.splice(a,1);this.attributes.key_ary.push(b)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var GenomeDataManager=Cache.extend({defaults:_.extend({},Cache.prototype.defaults,{dataset:null,filters_manager:null,data_url:null,dataset_state_url:null,feature_search_url:null,genome_wide_summary_data:null,data_mode_compatible:function(a,b){return true},can_subset:function(a){return false}}),data_is_ready:function(){var c=this.get("dataset"),b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.get("dataset_state_url"),data:{dataset_id:c.id,hda_ldda:c.get("hda_ldda")},dataType:"json"},interval:5000,success_fn:function(d){return d!=="pending"}});$.when(a.go()).then(function(d){b.resolve(d==="ok"||d==="data")});return b},search_features:function(a){var b=this.get("dataset"),c={query:a,dataset_id:b.id,hda_ldda:b.get("hda_ldda")};return $.getJSON(this.get("feature_search_url"),c)},load_data:function(j,h,b,g){var d={chrom:j.get("chrom"),low:j.get("start"),high:j.get("end"),mode:h,resolution:b},e=this.get("dataset");if(e){d.dataset_id=e.id;d.hda_ldda=e.get("hda_ldda")}$.extend(d,g);var k=this.get("filters_manager");if(k){var l=[];var a=k.filters;for(var f=0;f<a.length;f++){l.push(a[f].name)}d.filter_cols=JSON.stringify(l)}var c=this;return $.getJSON(this.get("data_url"),d,function(i){c.set_data(j,i)})},get_data:function(g,f,c,e){var h=this.get_elt(g);if(h&&(is_deferred(h)||this.get("data_mode_compatible")(h,f))){return h}var j=this.get("key_ary"),b=this.get("obj_cache"),k,a;for(var d=0;d<j.length;d++){k=j[d];a=new GenomeRegion({from_str:k});if(a.contains(g)){h=b[k];if(is_deferred(h)||(this.get("data_mode_compatible")(h,f)&&this.get("can_subset")(h))){this.move_key_to_end(k,d);return h}}}h=this.load_data(g,f,c,e);this.set_data(g,h);return h},set_data:function(b,a){this.set_elt(b,a)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(i,h,d,g,e){var k=this.get_elt(i);if(!(k&&this.get("data_mode_compatible")(k,h))){console.log("ERROR: no current data for: ",dataset,i.toString(),h,d,g);return}k.stale=true;var c=i.get("start");if(e===this.DEEP_DATA_REQ){$.extend(g,{start_val:k.data.length+1})}else{if(e===this.BROAD_DATA_REQ){c=(k.max_high?k.max_high:k.data[k.data.length-1][2])+1}}var j=i.copy().set("start",c);var b=this,f=this.load_data(j,h,d,g),a=$.Deferred();this.set_data(i,a);$.when(f).then(function(l){if(l.data){l.data=k.data.concat(l.data);if(l.max_low){l.max_low=k.max_low}if(l.message){l.message=l.message.replace(/[0-9]+/,l.data.length)}}b.set_data(i,l);a.resolve(l)});return a},get_elt:function(a){return Cache.prototype.get_elt.call(this,a.toString())},set_elt:function(b,a){return Cache.prototype.set_elt.call(this,b.toString(),a)}});var ReferenceTrackDataManager=GenomeDataManager.extend({load_data:function(a,d,e,b,c){if(b>1){return{data:null}}return GenomeDataManager.prototype.load_data.call(this,a,d,e,b,c)}});var Genome=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var GenomeRegion=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(b){if(b.from_str){var d=b.from_str.split(":"),c=d[0],a=d[1].split("-");this.set({chrom:c,start:parseInt(a[0],10),end:parseInt(a[1],10)})}},copy:function(){return new GenomeRegion({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(h){var b=this.get("chrom"),g=h.get("chrom"),f=this.get("start"),d=h.get("start"),e=this.get("end"),c=h.get("end"),a;if(b&&g&&b!==g){return this.get("DIF_CHROMS")}if(f<d){if(e<d){a=this.get("BEFORE")}else{if(e<=c){a=this.get("OVERLAP_START")}else{a=this.get("CONTAINS")}}}else{if(f>c){a=this.get("AFTER")}else{if(e<=c){a=this.get("CONTAINED_BY")}else{a=this.get("OVERLAP_END")}}}return a},contains:function(a){return this.compute_overlap(a)===this.get("CONTAINS")},overlaps:function(a){return _.intersection([this.compute_overlap(a)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var GenomeRegionCollection=Backbone.Collection.extend({model:GenomeRegion});var BrowserBookmark=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:"GenomeRegion"}]});var BrowserBookmarkCollection=Backbone.Collection.extend({model:BrowserBookmark});var GenomeWideBigWigData=Backbone.Model.extend({defaults:{data:null,min:0,max:0},initialize:function(b){var a=_.flatten(_.map(this.get("data"),function(c){if(c.data.length!==0){return _.map(c.data,function(d){return d[1]})}else{return 0}}));this.set("max",_.max(a));this.set("min",_.min(a))}});var GenomeWideSummaryTreeData=Backbone.RelationalModel.extend({defaults:{data:null,min:0,max:0},initialize:function(b){var a=_.max(this.get("data"),function(c){if(!c||typeof c==="string"){return 0}return c[1]});this.attributes.max=(a&&typeof a!=="string"?a[1]:0)}});var BackboneTrack=Dataset.extend({initialize:function(a){this.set("id",a.dataset_id);var c=this.get("genome_wide_data");if(c){var b=(this.get("track_type")==="LineTrack"?GenomeWideBigWigData:GenomeWideSummaryTreeData);this.set("genome_wide_data",new b(c))}}});var Visualization=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:"BackboneTrack"}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var GenomeVisualization=Visualization.extend({defaults:_.extend({},Visualization.prototype.defaults,{bookmarks:null,viewport:null})});var TrackConfig=Backbone.Model.extend({});var CircsterDataLayout=Backbone.Model.extend({defaults:{genome:null,dataset:null,total_gap:null},chroms_layout:function(){var b=this.attributes.genome.get_chroms_info(),d=d3.layout.pie().value(function(f){return f.len}).sort(null),e=d(b),a=this.attributes.total_gap/b.length,c=_.map(e,function(h,g){var f=h.endAngle-a;h.endAngle=(f>h.startAngle?f:h.startAngle);return h});return c},chrom_data_layout:function(d,c,b,e,a){},genome_data_layout:function(){var b=this,a=this.chroms_layout(),f=this.get("track").get("genome_wide_data"),e=this.get("radius_start"),c=this.get("radius_end"),d=_.zip(a,f.get("data")),g=_.map(d,function(i){var j=i[0],h=i[1];return b.chrom_data_layout(j,h,e,c,f.get("min"),f.get("max"))});return g}});var CircsterSummaryTreeLayout=CircsterDataLayout.extend({chrom_data_layout:function(k,b,h,g,d,i){if(!b||typeof b==="string"){return null}var e=b[0],j=b[3],c=d3.scale.linear().domain([d,i]).range([h,g]),f=d3.layout.pie().value(function(l){return j}).startAngle(k.startAngle).endAngle(k.endAngle),a=f(e);_.each(e,function(l,m){a[m].outerRadius=c(l[1])});return a}});var CircsterBigWigLayout=CircsterDataLayout.extend({chrom_data_layout:function(j,b,h,g,d,i){var e=b.data;if(e.length===0){return}var c=d3.scale.linear().domain([d,i]).range([h,g]),f=d3.layout.pie().value(function(l,k){if(k+1===e.length){return 0}return e[k+1][0]-e[k][0]}).startAngle(j.startAngle).endAngle(j.endAngle),a=f(e);_.each(e,function(k,l){a[l].outerRadius=c(k[1])});return a}});var CircsterView=Backbone.View.extend({className:"circster",initialize:function(a){this.width=a.width;this.height=a.height;this.total_gap=a.total_gap;this.genome=a.genome;this.radius_start=a.radius_start;this.dataset_arc_height=a.dataset_arc_height;this.track_gap=5},render:function(){var b=this,c=this.dataset_arc_height;var a=d3.select(b.$el[0]).append("svg").attr("width",b.width).attr("height",b.height).append("g").attr("transform","translate("+b.width/2+","+b.height/2+")");this.model.get("tracks").each(function(f,l){var g=f.get("genome_wide_data"),k=b.radius_start+l*(c+b.track_gap),h=(g instanceof GenomeWideBigWigData?CircsterBigWigLayout:CircsterSummaryTreeLayout),n=new h({track:f,radius_start:k,radius_end:k+c,genome:b.genome,total_gap:b.total_gap}),d=n.chroms_layout(),i=n.genome_data_layout();var o=a.append("g").attr("id","inner-arc"),m=d3.svg.arc().innerRadius(k).outerRadius(k+c),e=o.selectAll("#inner-arc>path").data(d).enter().append("path").attr("d",m).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(q){return q.data.chrom});var p=f.get("prefs"),j=p.block_color;_.each(i,function(q){if(!q){return}var t=a.append("g"),s=d3.svg.arc().innerRadius(k),r=t.selectAll("path").data(q).enter().append("path").attr("d",s).style("stroke",j).style("fill",j)})})}});var TrackBrowserRouter=Backbone.Router.extend({initialize:function(b){this.view=b.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var a=this;a.view.on("navigate",function(c){a.navigate(c)})},change_location:function(a){this.view.go_to(a)}});var add_datasets=function(a,c,b){$.ajax({url:a,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(d){show_modal("Select datasets for new tracks",d,{Cancel:function(){hide_modal()},Add:function(){var e=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var f,g=$(this).val();if($(this).attr("name")==="id"){f={hda_id:g}}else{f={ldda_id:g}}e[e.length]=$.ajax({url:c,data:f,dataType:"json"})});$.when.apply($,e).then(function(){var f=(arguments[0] instanceof Array?$.map(arguments,function(g){return g[0]}):[arguments[0]]);b(f)});hide_modal()}})}})}; \ 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: jgoecks: Add feature search to Trackster; typing in location box will search tracks in visualization for features that start with entered text. Works with both GFF/GTF and BED datasets. Fixes #611
by Bitbucket 05 Sep '12

05 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d5626302446d/ changeset: d5626302446d user: jgoecks date: 2012-09-05 23:26:43 summary: Add feature search to Trackster; typing in location box will search tracks in visualization for features that start with entered text. Works with both GFF/GTF and BED datasets. Fixes #611 affected #: 12 files diff -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e -r d5626302446db334804820f0a29fc4d0c7d72a0e datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -19,6 +19,7 @@ <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/><converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <converter file="bed_to_fli_converter.xml" target_datatype="fli"/><display file="genetrack.xml" /><display file="igb/bed.xml" /> diff -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e -r d5626302446db334804820f0a29fc4d0c7d72a0e lib/galaxy/datatypes/converters/bed_to_fli_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/bed_to_fli_converter.xml @@ -0,0 +1,13 @@ +<tool id="CONVERTER_bed_to_fli_0" name="Convert BED to Feature Location Index"> +  +  + <command interpreter="python">interval_to_fli.py -B $input1 $output1</command> + <inputs> + <param format="bed" name="input1" type="data" label="Choose BED file"/> + </inputs> + <outputs> + <data format="fli" name="output1"/> + </outputs> + <help> + </help> +</tool> diff -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e -r d5626302446db334804820f0a29fc4d0c7d72a0e lib/galaxy/datatypes/converters/gff_to_fli.py --- a/lib/galaxy/datatypes/converters/gff_to_fli.py +++ /dev/null @@ -1,57 +0,0 @@ -''' -Creates a feature location index for a given GFF file. -''' - -import sys -from galaxy import eggs -from galaxy.datatypes.util.gff_util import read_unordered_gtf, convert_gff_coords_to_bed - -def main(): - # Process arguments. - in_fname = sys.argv[1] - out_fname = sys.argv[2] - - # Create dict of name-location pairings. - name_loc_dict = {} - for feature in read_unordered_gtf( open( in_fname, 'r' ) ): - for name in feature.attributes: - val = feature.attributes[ name ] - try: - float( val ) - continue - except: - convert_gff_coords_to_bed( feature ) - # Value is not a number, so it can be indexed. - if val not in name_loc_dict: - # Value is not in dictionary. - name_loc_dict[ val ] = { - 'contig': feature.chrom, - 'start': feature.start, - 'end': feature.end - } - else: - # Value already in dictionary, so update dictionary. - loc = name_loc_dict[ val ] - if feature.start < loc[ 'start' ]: - loc[ 'start' ] = feature.start - if feature.end > loc[ 'end' ]: - loc[ 'end' ] = feature.end - - # Print name, loc in sorted order. - out = open( out_fname, 'w' ) - max_len = 0 - entries = [] - for name in sorted( name_loc_dict.iterkeys() ): - loc = name_loc_dict[ name ] - entry = '%s\t%s' % ( name, '%s:%i-%i' % ( loc[ 'contig' ], loc[ 'start' ], loc[ 'end' ] ) ) - if len( entry ) > max_len: - max_len = len( entry ) - entries.append( entry ) - - out.write( str( max_len + 1 ).ljust( max_len ) + '\n' ) - for entry in entries: - out.write( entry.ljust( max_len ) + '\n' ) - out.close() - -if __name__ == '__main__': - main() \ No newline at end of file diff -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e -r d5626302446db334804820f0a29fc4d0c7d72a0e lib/galaxy/datatypes/converters/gff_to_fli_converter.xml --- a/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml +++ b/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml @@ -1,7 +1,7 @@ <tool id="CONVERTER_gff_to_fli_0" name="Convert GFF to Feature Location Index"> - <command interpreter="python">gff_to_fli.py $input1 $output1</command> + <command interpreter="python">interval_to_fli.py -G $input1 $output1</command><inputs><param format="gff" name="input1" type="data" label="Choose GFF file"/></inputs> diff -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e -r d5626302446db334804820f0a29fc4d0c7d72a0e lib/galaxy/datatypes/converters/interval_to_fli.py --- /dev/null +++ b/lib/galaxy/datatypes/converters/interval_to_fli.py @@ -0,0 +1,81 @@ +''' +Creates a feature location index (FLI) for a given BED/GFF file. +FLI index has the form: + [line_length] + <symbol1_in_lowercase><tab><symbol1><tab><location> + <symbol2_in_lowercase><tab><symbol2><tab><location> + ... +where location is formatted as: + contig:start-end +and symbols are sorted in lexigraphical order. +''' + +import sys, optparse +from galaxy import eggs +from galaxy.datatypes.util.gff_util import read_unordered_gtf, convert_gff_coords_to_bed + +def main(): + # Process arguments. + parser = optparse.OptionParser() + parser.add_option( '-B', '--bed', action="store_true", dest="bed_input" ) + parser.add_option( '-G', '--gff', action="store_true", dest="gff_input" ) + (options, args) = parser.parse_args() + in_fname, out_fname = args + + + # Create dict of name-location pairings. + name_loc_dict = {} + if options.gff_input: + # GFF format + for feature in read_unordered_gtf( open( in_fname, 'r' ) ): + for name in feature.attributes: + val = feature.attributes[ name ] + try: + float( val ) + continue + except: + convert_gff_coords_to_bed( feature ) + # Value is not a number, so it can be indexed. + if val not in name_loc_dict: + # Value is not in dictionary. + name_loc_dict[ val ] = { + 'contig': feature.chrom, + 'start': feature.start, + 'end': feature.end + } + else: + # Value already in dictionary, so update dictionary. + loc = name_loc_dict[ val ] + if feature.start < loc[ 'start' ]: + loc[ 'start' ] = feature.start + if feature.end > loc[ 'end' ]: + loc[ 'end' ] = feature.end + else: + # BED format. + for line in open( in_fname, 'r' ): + fields = line.split() + name_loc_dict[ fields[3] ] = { + 'contig': fields[0], + 'start': int( fields[1] ), + 'end': int ( fields[2] ) + } + + # Create sorted list of entries. + out = open( out_fname, 'w' ) + max_len = 0 + entries = [] + for name in sorted( name_loc_dict.iterkeys() ): + loc = name_loc_dict[ name ] + entry = '%s\t%s\t%s' % ( name.lower(), name, '%s:%i-%i' % ( loc[ 'contig' ], loc[ 'start' ], loc[ 'end' ] ) ) + if len( entry ) > max_len: + max_len = len( entry ) + entries.append( entry ) + + # Write padded entries. + out.write( str( max_len + 1 ).ljust( max_len ) + '\n' ) + for entry in entries: + out.write( entry.ljust( max_len ) + '\n' ) + out.close() + +if __name__ == '__main__': + main() \ No newline at end of file diff -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e -r d5626302446db334804820f0a29fc4d0c7d72a0e lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -512,7 +512,7 @@ except: return False def get_track_type( self ): - return "FeatureTrack", {"data": "tabix", "index": "summary_tree"} + return "FeatureTrack", {"data": "tabix", "index": "summary_tree", "feature_search": "fli"} class BedStrict( Bed ): """Tab delimited data in strict BED format - no non-standard columns allowed""" @@ -785,7 +785,7 @@ return False def get_track_type( self ): - return "FeatureTrack", {"data": "interval_index", "index": "summary_tree"} + return "FeatureTrack", {"data": "interval_index", "index": "summary_tree", "feature_search": "fli"} class Gff3( Gff ): @@ -962,10 +962,6 @@ return True except: return False - - def get_track_type( self ): - return "FeatureTrack", {"data": "interval_index", "index": "summary_tree"} - class Wiggle( Tabular, _RemoteCallMixin ): """Tab delimited data in wiggle format""" diff -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e -r d5626302446db334804820f0a29fc4d0c7d72a0e lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1188,6 +1188,8 @@ return None def get_converter_types(self): return self.datatype.get_converter_types( self, datatypes_registry ) + def can_convert_to(self, format): + return format in self.get_converter_types() def find_conversion_destination( self, accepted_formats, **kwd ): """Returns ( target_ext, existing converted dataset )""" return self.datatype.find_conversion_destination( self, accepted_formats, datatypes_registry, **kwd ) diff -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e -r d5626302446db334804820f0a29fc4d0c7d72a0e lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -73,6 +73,7 @@ textloc_file = open( self.converted_dataset.file_name, 'r' ) line_len = int( textloc_file.readline() ) file_len = os.path.getsize( self.converted_dataset.file_name ) + query = query.lower() # Find query in file using binary search. low = 0 @@ -84,7 +85,6 @@ # Compare line with query and update low, high. line = textloc_file.readline() - print '--', mid, line if line < query: low = mid + 1 else: @@ -93,14 +93,14 @@ position = low * line_len # At right point in file, generate hits. - result = [ ] + result = [] while True: line = textloc_file.readline() if not line.startswith( query ): break if line[ -1: ] == '\n': line = line[ :-1 ] - result.append( line.split() ) + result.append( line.split()[1:] ) textloc_file.close() return result diff -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e -r d5626302446db334804820f0a29fc4d0c7d72a0e lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -347,18 +347,20 @@ return { "status": messages.DATA, "valid_chroms": valid_chroms } @web.json - def feature_loc( self, trans, hda_ldda, dataset_id, query ): + def search_features( self, trans, hda_ldda, dataset_id, query ): """ Returns features, locations in dataset that match query. Format is a list of features; each feature is a list itself: [name, location] """ dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - converted_dataset = dataset.get_converted_dataset( trans, "fli" ) - data_provider = FeatureLocationIndexDataProvider( converted_dataset=converted_dataset ) - if data_provider: - return data_provider.get_data( query ) - else: - return 'None' + if dataset.can_convert_to( "fli" ): + converted_dataset = dataset.get_converted_dataset( trans, "fli" ) + if converted_dataset: + data_provider = FeatureLocationIndexDataProvider( converted_dataset=converted_dataset ) + if data_provider: + return data_provider.get_data( query ) + + return [] @web.json def data( self, trans, hda_ldda, dataset_id, chrom, low, high, start_val=0, max_vals=None, **kwargs ): diff -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e -r d5626302446db334804820f0a29fc4d0c7d72a0e static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -574,18 +574,26 @@ icon_dict.on_click_fn, icon_dict.prepend, icon_dict.hide); } }, + /** * Update icons. */ update_icons: function() {}, + /** * Hide drawable's contents. */ hide_contents: function () {}, + /** * Show drawable's contents. */ - show_contents: function() {} + show_contents: function() {}, + + /** + * Returns a shallow copy of all drawables in this drawable. + */ + get_drawables: function() {} }); /** @@ -611,6 +619,7 @@ this.add_drawable(drawable); } }, + /** * Init each drawable in the collection. */ @@ -619,6 +628,7 @@ this.drawables[i].init(); } }, + /** * Draw each drawable in the collection. */ @@ -627,6 +637,7 @@ this.drawables[i]._draw(); } }, + /** * Returns representation of object in a dictionary for easy saving. * Use from_dict to recreate object. @@ -643,6 +654,7 @@ drawables: dictified_drawables }; }, + /** * Add a drawable to the end of the collection. */ @@ -651,6 +663,7 @@ drawable.container = this; this.changed(); }, + /** * Add a drawable before another drawable. */ @@ -663,6 +676,7 @@ } return false; }, + /** * Replace one drawable with another. */ @@ -677,6 +691,7 @@ } return index; }, + /** * Remove drawable from this collection. */ @@ -691,6 +706,7 @@ } return false; }, + /** * Move drawable to another location in collection. */ @@ -705,6 +721,13 @@ return true; } return false; + }, + + /** + * Returns all drawables in this drawable. + */ + get_drawables: function() { + return this.drawables; } }); @@ -1070,7 +1093,7 @@ 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"}).css("width", "15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls); + this.chrom_select = $("<select/>").attr({ "name": "chrom"}).css("width", "15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls); var submit_nav = function(e) { if (e.type === "focusout" || (e.keyCode || e.which) === 13 || (e.keyCode || e.which) === 27 ) { if ((e.keyCode || e.which) !== 27) { // Not escape key @@ -1091,6 +1114,28 @@ view.nav_input.css("display", "inline-block"); view.nav_input.select(); view.nav_input.focus(); + // Set up autocomplete for tracks' features. + view.nav_input.autocomplete({ + source: function(request, response) { + // Using current text, query each track and create list of all matching features. + var all_features = [], + feature_search_deferreds = $.map(view.get_drawables(), function(drawable) { + return drawable.data_manager.search_features(request.term).success(function(dataset_features) { + all_features = all_features.concat(dataset_features); + }); + }); + + // When all searching is done, fill autocomplete. + $.when.apply($, feature_search_deferreds).done(function() { + response($.map(all_features, function(feature) { + return { + label: feature[0], + value: feature[1] + }; + })); + }); + } + }); }); if (this.vis_id !== undefined) { this.hidden_input = $("<input/>").attr("type", "hidden").val(this.vis_id).appendTo(this.nav_controls); @@ -1285,9 +1330,8 @@ data: url_parms, dataType: "json", success: function (result) { - // Show error if could not load chroms. + // Do nothing if could not load chroms. if (result.chrom_info.length === 0) { - alert("Invalid chromosome: " + url_parms.chrom); return; } @@ -2935,6 +2979,7 @@ this.data_url_extra_params = {}; this.data_query_wait = ('data_query_wait' in obj_dict ? obj_dict.data_query_wait : DEFAULT_DATA_QUERY_WAIT); this.dataset_check_url = ('converted_datasets_state_url' in obj_dict ? obj_dict.converted_datasets_state_url : converted_datasets_state_url); + this.feature_search_url = ('feature_search_url' in obj_dict ? obj_dict.feature_search_url : feature_search_url); // A little ugly creating data manager right now due to transition to Backbone-based objects. var track = this, @@ -2948,6 +2993,7 @@ dataset: dataset, data_url: track.data_url, dataset_state_url: track.dataset_check_url, + feature_search_url: track.feature_search_url, data_mode_compatible: this.data_and_mode_compatible, can_subset: this.can_subset })); @@ -3319,7 +3365,14 @@ /** * Additional initialization required before drawing track for the first time. */ - predraw_init: function() {} + predraw_init: function() {}, + + /** + * Returns all drawables in this drawable. + */ + get_drawables: function() { + return this; + } }); var TiledTrack = function(view, container, obj_dict) { diff -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e -r d5626302446db334804820f0a29fc4d0c7d72a0e static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -169,6 +169,7 @@ filters_manager: null, data_url: null, dataset_state_url: null, + feature_search_url: null, genome_wide_summary_data: null, data_mode_compatible: function(entry, mode) { return true; }, can_subset: function(entry) { return false; } @@ -199,9 +200,22 @@ }); return ready_deferred; }, + + /** + * Perform a feature search from server; returns Deferred object that resolves when data is available. + */ + search_features: function(query) { + var dataset = this.get('dataset'), + params = { + query: query, + dataset_id: dataset.id, + hda_ldda: dataset.get('hda_ldda') + }; + return $.getJSON(this.get('feature_search_url'), params); + }, /** - * Load data from server; returns AJAX object so that use of Deferred is possible. + * Load data from server; returns Deferred object that resolves when data is available. */ load_data: function(region, mode, resolution, extra_params) { // Setup data request params. @@ -211,7 +225,7 @@ "high": region.get('end'), "mode": mode, "resolution": resolution - }; + }, dataset = this.get('dataset'); // ReferenceDataManager does not have dataset. diff -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e -r d5626302446db334804820f0a29fc4d0c7d72a0e templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -39,6 +39,7 @@ chrom_url = "${h.url_for( action='chroms' )}", dataset_state_url = "${h.url_for( action='dataset_state' )}", converted_datasets_state_url = "${h.url_for( action='converted_datasets_state' )}", + feature_search_url = "${h.url_for( action='search_features' )}", view, browser_router; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Remove jQuery UI slider code because it's now integrated into jquery-ui custom package.
by Bitbucket 05 Sep '12

05 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/382c9cb6d601/ changeset: 382c9cb6d601 user: jgoecks date: 2012-09-05 15:50:23 summary: Remove jQuery UI slider code because it's now integrated into jquery-ui custom package. affected #: 3 files diff -r 9287f22c692087319003516fe1a5da0eb07c63da -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e static/scripts/libs/jquery/jquery.ui.sortable.slider.js --- a/static/scripts/libs/jquery/jquery.ui.sortable.slider.js +++ /dev/null @@ -1,2458 +0,0 @@ -/*! - * jQuery UI 1.8.5 - * - * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI - */ -(function( $, undefined ) { - -// prevent duplicate loading -// this is only a problem because we proxy existing functions -// and we don't want to double proxy them -$.ui = $.ui || {}; -if ( $.ui.version ) { - return; -} - -$.extend( $.ui, { - version: "1.8.5", - - keyCode: { - ALT: 18, - BACKSPACE: 8, - CAPS_LOCK: 20, - COMMA: 188, - COMMAND: 91, - COMMAND_LEFT: 91, // COMMAND - COMMAND_RIGHT: 93, - CONTROL: 17, - DELETE: 46, - DOWN: 40, - END: 35, - ENTER: 13, - ESCAPE: 27, - HOME: 36, - INSERT: 45, - LEFT: 37, - MENU: 93, // COMMAND_RIGHT - NUMPAD_ADD: 107, - NUMPAD_DECIMAL: 110, - NUMPAD_DIVIDE: 111, - NUMPAD_ENTER: 108, - NUMPAD_MULTIPLY: 106, - NUMPAD_SUBTRACT: 109, - PAGE_DOWN: 34, - PAGE_UP: 33, - PERIOD: 190, - RIGHT: 39, - SHIFT: 16, - SPACE: 32, - TAB: 9, - UP: 38, - WINDOWS: 91 // COMMAND - } -}); - -// plugins -$.fn.extend({ - _focus: $.fn.focus, - focus: function( delay, fn ) { - return typeof delay === "number" ? - this.each(function() { - var elem = this; - setTimeout(function() { - $( elem ).focus(); - if ( fn ) { - fn.call( elem ); - } - }, delay ); - }) : - this._focus.apply( this, arguments ); - }, - - scrollParent: function() { - var scrollParent; - if (($.browser.msie && (/(static|relative)/).test(this.css('position'))) || (/absolute/).test(this.css('position'))) { - scrollParent = this.parents().filter(function() { - return (/(relative|absolute|fixed)/).test($.curCSS(this,'position',1)) && (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); - }).eq(0); - } else { - scrollParent = this.parents().filter(function() { - return (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); - }).eq(0); - } - - return (/fixed/).test(this.css('position')) || !scrollParent.length ? $(document) : scrollParent; - }, - - zIndex: function( zIndex ) { - if ( zIndex !== undefined ) { - return this.css( "zIndex", zIndex ); - } - - if ( this.length ) { - var elem = $( this[ 0 ] ), position, value; - while ( elem.length && elem[ 0 ] !== document ) { - // Ignore z-index if position is set to a value where z-index is ignored by the browser - // This makes behavior of this function consistent across browsers - // WebKit always returns auto if the element is positioned - position = elem.css( "position" ); - if ( position === "absolute" || position === "relative" || position === "fixed" ) { - // IE returns 0 when zIndex is not specified - // other browsers return a string - // we ignore the case of nested elements with an explicit value of 0 - // <div style="z-index: -10;"><div style="z-index: 0;"></div></div> - value = parseInt( elem.css( "zIndex" ) ); - if ( !isNaN( value ) && value != 0 ) { - return value; - } - } - elem = elem.parent(); - } - } - - return 0; - }, - - disableSelection: function() { - return this.bind( - "mousedown.ui-disableSelection selectstart.ui-disableSelection", - function( event ) { - event.preventDefault(); - }); - }, - - enableSelection: function() { - return this.unbind( ".ui-disableSelection" ); - } -}); - -$.each( [ "Width", "Height" ], function( i, name ) { - var side = name === "Width" ? [ "Left", "Right" ] : [ "Top", "Bottom" ], - type = name.toLowerCase(), - orig = { - innerWidth: $.fn.innerWidth, - innerHeight: $.fn.innerHeight, - outerWidth: $.fn.outerWidth, - outerHeight: $.fn.outerHeight - }; - - function reduce( elem, size, border, margin ) { - $.each( side, function() { - size -= parseFloat( $.curCSS( elem, "padding" + this, true) ) || 0; - if ( border ) { - size -= parseFloat( $.curCSS( elem, "border" + this + "Width", true) ) || 0; - } - if ( margin ) { - size -= parseFloat( $.curCSS( elem, "margin" + this, true) ) || 0; - } - }); - return size; - } - - $.fn[ "inner" + name ] = function( size ) { - if ( size === undefined ) { - return orig[ "inner" + name ].call( this ); - } - - return this.each(function() { - $.style( this, type, reduce( this, size ) + "px" ); - }); - }; - - $.fn[ "outer" + name] = function( size, margin ) { - if ( typeof size !== "number" ) { - return orig[ "outer" + name ].call( this, size ); - } - - return this.each(function() { - $.style( this, type, reduce( this, size, true, margin ) + "px" ); - }); - }; -}); - -// selectors -function visible( element ) { - return !$( element ).parents().andSelf().filter(function() { - return $.curCSS( this, "visibility" ) === "hidden" || - $.expr.filters.hidden( this ); - }).length; -} - -$.extend( $.expr[ ":" ], { - data: function( elem, i, match ) { - return !!$.data( elem, match[ 3 ] ); - }, - - focusable: function( element ) { - var nodeName = element.nodeName.toLowerCase(), - tabIndex = $.attr( element, "tabindex" ); - if ( "area" === nodeName ) { - var map = element.parentNode, - mapName = map.name, - img; - if ( !element.href || !mapName || map.nodeName.toLowerCase() !== "map" ) { - return false; - } - img = $( "img[usemap=#" + mapName + "]" )[0]; - return !!img && visible( img ); - } - return ( /input|select|textarea|button|object/.test( nodeName ) - ? !element.disabled - : "a" == nodeName - ? element.href || !isNaN( tabIndex ) - : !isNaN( tabIndex )) - // the element and all of its ancestors must be visible - && visible( element ); - }, - - tabbable: function( element ) { - var tabIndex = $.attr( element, "tabindex" ); - return ( isNaN( tabIndex ) || tabIndex >= 0 ) && $( element ).is( ":focusable" ); - } -}); - -// support -$(function() { - var div = document.createElement( "div" ), - body = document.body; - - $.extend( div.style, { - minHeight: "100px", - height: "auto", - padding: 0, - borderWidth: 0 - }); - - $.support.minHeight = body.appendChild( div ).offsetHeight === 100; - // set display to none to avoid a layout bug in IE - // http://dev.jquery.com/ticket/4014 - body.removeChild( div ).style.display = "none"; -}); - - - - - -// deprecated -$.extend( $.ui, { - // $.ui.plugin is deprecated. Use the proxy pattern instead. - plugin: { - add: function( module, option, set ) { - var proto = $.ui[ module ].prototype; - for ( var i in set ) { - proto.plugins[ i ] = proto.plugins[ i ] || []; - proto.plugins[ i ].push( [ option, set[ i ] ] ); - } - }, - call: function( instance, name, args ) { - var set = instance.plugins[ name ]; - if ( !set || !instance.element[ 0 ].parentNode ) { - return; - } - - for ( var i = 0; i < set.length; i++ ) { - if ( instance.options[ set[ i ][ 0 ] ] ) { - set[ i ][ 1 ].apply( instance.element, args ); - } - } - } - }, - - // will be deprecated when we switch to jQuery 1.4 - use jQuery.contains() - contains: function( a, b ) { - return document.compareDocumentPosition ? - a.compareDocumentPosition( b ) & 16 : - a !== b && a.contains( b ); - }, - - // only used by resizable - hasScroll: function( el, a ) { - - //If overflow is hidden, the element might have extra content, but the user wants to hide it - if ( $( el ).css( "overflow" ) === "hidden") { - return false; - } - - var scroll = ( a && a === "left" ) ? "scrollLeft" : "scrollTop", - has = false; - - if ( el[ scroll ] > 0 ) { - return true; - } - - // TODO: determine which cases actually cause this to happen - // if the element doesn't have the scroll set, see if it's possible to - // set the scroll - el[ scroll ] = 1; - has = ( el[ scroll ] > 0 ); - el[ scroll ] = 0; - return has; - }, - - // these are odd functions, fix the API or move into individual plugins - isOverAxis: function( x, reference, size ) { - //Determines when x coordinate is over "b" element axis - return ( x > reference ) && ( x < ( reference + size ) ); - }, - isOver: function( y, x, top, left, height, width ) { - //Determines when x, y coordinates is over "b" element - return $.ui.isOverAxis( y, top, height ) && $.ui.isOverAxis( x, left, width ); - } -}); - -})( jQuery ); -/*! - * jQuery UI Widget 1.8.5 - * - * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Widget - */ -(function( $, undefined ) { - -// jQuery 1.4+ -if ( $.cleanData ) { - var _cleanData = $.cleanData; - $.cleanData = function( elems ) { - for ( var i = 0, elem; (elem = elems[i]) != null; i++ ) { - $( elem ).triggerHandler( "remove" ); - } - _cleanData( elems ); - }; -} else { - var _remove = $.fn.remove; - $.fn.remove = function( selector, keepData ) { - return this.each(function() { - if ( !keepData ) { - if ( !selector || $.filter( selector, [ this ] ).length ) { - $( "*", this ).add( [ this ] ).each(function() { - $( this ).triggerHandler( "remove" ); - }); - } - } - return _remove.call( $(this), selector, keepData ); - }); - }; -} - -$.widget = function( name, base, prototype ) { - var namespace = name.split( "." )[ 0 ], - fullName; - name = name.split( "." )[ 1 ]; - fullName = namespace + "-" + name; - - if ( !prototype ) { - prototype = base; - base = $.Widget; - } - - // create selector for plugin - $.expr[ ":" ][ fullName ] = function( elem ) { - return !!$.data( elem, name ); - }; - - $[ namespace ] = $[ namespace ] || {}; - $[ namespace ][ name ] = function( options, element ) { - // allow instantiation without initializing for simple inheritance - if ( arguments.length ) { - this._createWidget( options, element ); - } - }; - - var basePrototype = new base(); - // we need to make the options hash a property directly on the new instance - // otherwise we'll modify the options hash on the prototype that we're - // inheriting from -// $.each( basePrototype, function( key, val ) { -// if ( $.isPlainObject(val) ) { -// basePrototype[ key ] = $.extend( {}, val ); -// } -// }); - basePrototype.options = $.extend( true, {}, basePrototype.options ); - $[ namespace ][ name ].prototype = $.extend( true, basePrototype, { - namespace: namespace, - widgetName: name, - widgetEventPrefix: $[ namespace ][ name ].prototype.widgetEventPrefix || name, - widgetBaseClass: fullName - }, prototype ); - - $.widget.bridge( name, $[ namespace ][ name ] ); -}; - -$.widget.bridge = function( name, object ) { - $.fn[ name ] = function( options ) { - var isMethodCall = typeof options === "string", - args = Array.prototype.slice.call( arguments, 1 ), - returnValue = this; - - // allow multiple hashes to be passed on init - options = !isMethodCall && args.length ? - $.extend.apply( null, [ true, options ].concat(args) ) : - options; - - // prevent calls to internal methods - if ( isMethodCall && options.substring( 0, 1 ) === "_" ) { - return returnValue; - } - - if ( isMethodCall ) { - this.each(function() { - var instance = $.data( this, name ); - if ( !instance ) { - throw "cannot call methods on " + name + " prior to initialization; " + - "attempted to call method '" + options + "'"; - } - if ( !$.isFunction( instance[options] ) ) { - throw "no such method '" + options + "' for " + name + " widget instance"; - } - var methodValue = instance[ options ].apply( instance, args ); - if ( methodValue !== instance && methodValue !== undefined ) { - returnValue = methodValue; - return false; - } - }); - } else { - this.each(function() { - var instance = $.data( this, name ); - if ( instance ) { - instance.option( options || {} )._init(); - } else { - $.data( this, name, new object( options, this ) ); - } - }); - } - - return returnValue; - }; -}; - -$.Widget = function( options, element ) { - // allow instantiation without initializing for simple inheritance - if ( arguments.length ) { - this._createWidget( options, element ); - } -}; - -$.Widget.prototype = { - widgetName: "widget", - widgetEventPrefix: "", - options: { - disabled: false - }, - _createWidget: function( options, element ) { - // $.widget.bridge stores the plugin instance, but we do it anyway - // so that it's stored even before the _create function runs - $.data( element, this.widgetName, this ); - this.element = $( element ); - this.options = $.extend( true, {}, - this.options, - $.metadata && $.metadata.get( element )[ this.widgetName ], - options ); - - var self = this; - this.element.bind( "remove." + this.widgetName, function() { - self.destroy(); - }); - - this._create(); - this._init(); - }, - _create: function() {}, - _init: function() {}, - - destroy: function() { - this.element - .unbind( "." + this.widgetName ) - .removeData( this.widgetName ); - this.widget() - .unbind( "." + this.widgetName ) - .removeAttr( "aria-disabled" ) - .removeClass( - this.widgetBaseClass + "-disabled " + - "ui-state-disabled" ); - }, - - widget: function() { - return this.element; - }, - - option: function( key, value ) { - var options = key, - self = this; - - if ( arguments.length === 0 ) { - // don't return a reference to the internal hash - return $.extend( {}, self.options ); - } - - if (typeof key === "string" ) { - if ( value === undefined ) { - return this.options[ key ]; - } - options = {}; - options[ key ] = value; - } - - $.each( options, function( key, value ) { - self._setOption( key, value ); - }); - - return self; - }, - _setOption: function( key, value ) { - this.options[ key ] = value; - - if ( key === "disabled" ) { - this.widget() - [ value ? "addClass" : "removeClass"]( - this.widgetBaseClass + "-disabled" + " " + - "ui-state-disabled" ) - .attr( "aria-disabled", value ); - } - - return this; - }, - - enable: function() { - return this._setOption( "disabled", false ); - }, - disable: function() { - return this._setOption( "disabled", true ); - }, - - _trigger: function( type, event, data ) { - var callback = this.options[ type ]; - - event = $.Event( event ); - event.type = ( type === this.widgetEventPrefix ? - type : - this.widgetEventPrefix + type ).toLowerCase(); - data = data || {}; - - // copy original event properties over to the new event - // this would happen if we could call $.event.fix instead of $.Event - // but we don't have a way to force an event to be fixed multiple times - if ( event.originalEvent ) { - for ( var i = $.event.props.length, prop; i; ) { - prop = $.event.props[ --i ]; - event[ prop ] = event.originalEvent[ prop ]; - } - } - - this.element.trigger( event, data ); - - return !( $.isFunction(callback) && - callback.call( this.element[0], event, data ) === false || - event.isDefaultPrevented() ); - } -}; - -})( jQuery ); -/*! - * jQuery UI Mouse 1.8.5 - * - * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Mouse - * - * Depends: - * jquery.ui.widget.js - */ -(function( $, undefined ) { - -$.widget("ui.mouse", { - options: { - cancel: ':input,option', - distance: 1, - delay: 0 - }, - _mouseInit: function() { - var self = this; - - this.element - .bind('mousedown.'+this.widgetName, function(event) { - return self._mouseDown(event); - }) - .bind('click.'+this.widgetName, function(event) { - if(self._preventClickEvent) { - self._preventClickEvent = false; - event.stopImmediatePropagation(); - return false; - } - }); - - this.started = false; - }, - - // TODO: make sure destroying one instance of mouse doesn't mess with - // other instances of mouse - _mouseDestroy: function() { - this.element.unbind('.'+this.widgetName); - }, - - _mouseDown: function(event) { - // don't let more than one widget handle mouseStart - // TODO: figure out why we have to use originalEvent - event.originalEvent = event.originalEvent || {}; - if (event.originalEvent.mouseHandled) { return; } - - // we may have missed mouseup (out of window) - (this._mouseStarted && this._mouseUp(event)); - - this._mouseDownEvent = event; - - var self = this, - btnIsLeft = (event.which == 1), - elIsCancel = (typeof this.options.cancel == "string" ? $(event.target).parents().add(event.target).filter(this.options.cancel).length : false); - if (!btnIsLeft || elIsCancel || !this._mouseCapture(event)) { - return true; - } - - this.mouseDelayMet = !this.options.delay; - if (!this.mouseDelayMet) { - this._mouseDelayTimer = setTimeout(function() { - self.mouseDelayMet = true; - }, this.options.delay); - } - - if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { - this._mouseStarted = (this._mouseStart(event) !== false); - if (!this._mouseStarted) { - event.preventDefault(); - return true; - } - } - - // these delegates are required to keep context - this._mouseMoveDelegate = function(event) { - return self._mouseMove(event); - }; - this._mouseUpDelegate = function(event) { - return self._mouseUp(event); - }; - $(document) - .bind('mousemove.'+this.widgetName, this._mouseMoveDelegate) - .bind('mouseup.'+this.widgetName, this._mouseUpDelegate); - - // preventDefault() is used to prevent the selection of text here - - // however, in Safari, this causes select boxes not to be selectable - // anymore, so this fix is needed - ($.browser.safari || event.preventDefault()); - - event.originalEvent.mouseHandled = true; - return true; - }, - - _mouseMove: function(event) { - // IE mouseup check - mouseup happened when mouse was out of window - if ($.browser.msie && !event.button) { - return this._mouseUp(event); - } - - if (this._mouseStarted) { - this._mouseDrag(event); - return event.preventDefault(); - } - - if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { - this._mouseStarted = - (this._mouseStart(this._mouseDownEvent, event) !== false); - (this._mouseStarted ? this._mouseDrag(event) : this._mouseUp(event)); - } - - return !this._mouseStarted; - }, - - _mouseUp: function(event) { - $(document) - .unbind('mousemove.'+this.widgetName, this._mouseMoveDelegate) - .unbind('mouseup.'+this.widgetName, this._mouseUpDelegate); - - if (this._mouseStarted) { - this._mouseStarted = false; - this._preventClickEvent = (event.target == this._mouseDownEvent.target); - this._mouseStop(event); - } - - return false; - }, - - _mouseDistanceMet: function(event) { - return (Math.max( - Math.abs(this._mouseDownEvent.pageX - event.pageX), - Math.abs(this._mouseDownEvent.pageY - event.pageY) - ) >= this.options.distance - ); - }, - - _mouseDelayMet: function(event) { - return this.mouseDelayMet; - }, - - // These are placeholder methods, to be overriden by extending plugin - _mouseStart: function(event) {}, - _mouseDrag: function(event) {}, - _mouseStop: function(event) {}, - _mouseCapture: function(event) { return true; } -}); - -})(jQuery); -/* - * jQuery UI Sortable 1.8.5 - * - * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Sortables - * - * Depends: - * jquery.ui.core.js - * jquery.ui.mouse.js - * jquery.ui.widget.js - */ -(function( $, undefined ) { - -$.widget("ui.sortable", $.ui.mouse, { - widgetEventPrefix: "sort", - options: { - appendTo: "parent", - axis: false, - connectWith: false, - containment: false, - cursor: 'auto', - cursorAt: false, - dropOnEmpty: true, - forcePlaceholderSize: false, - forceHelperSize: false, - grid: false, - handle: false, - helper: "original", - items: '> *', - opacity: false, - placeholder: false, - revert: false, - scroll: true, - scrollSensitivity: 20, - scrollSpeed: 20, - scope: "default", - tolerance: "intersect", - zIndex: 1000 - }, - _create: function() { - - var o = this.options; - this.containerCache = {}; - this.element.addClass("ui-sortable"); - - //Get the items - this.refresh(); - - //Let's determine if the items are floating - this.floating = this.items.length ? (/left|right/).test(this.items[0].item.css('float')) : false; - - //Let's determine the parent's offset - this.offset = this.element.offset(); - - //Initialize mouse events for interaction - this._mouseInit(); - - }, - - destroy: function() { - this.element - .removeClass("ui-sortable ui-sortable-disabled") - .removeData("sortable") - .unbind(".sortable"); - this._mouseDestroy(); - - for ( var i = this.items.length - 1; i >= 0; i-- ) - this.items[i].item.removeData("sortable-item"); - - return this; - }, - - _setOption: function(key, value){ - if ( key === "disabled" ) { - this.options[ key ] = value; - - this.widget() - [ value ? "addClass" : "removeClass"]( "ui-sortable-disabled" ); - } else { - // Don't call widget base _setOption for disable as it adds ui-state-disabled class - $.Widget.prototype._setOption.apply(this, arguments); - } - }, - - _mouseCapture: function(event, overrideHandle) { - - if (this.reverting) { - return false; - } - - if(this.options.disabled || this.options.type == 'static') return false; - - //We have to refresh the items data once first - this._refreshItems(event); - - //Find out if the clicked node (or one of its parents) is a actual item in this.items - var currentItem = null, self = this, nodes = $(event.target).parents().each(function() { - if($.data(this, 'sortable-item') == self) { - currentItem = $(this); - return false; - } - }); - if($.data(event.target, 'sortable-item') == self) currentItem = $(event.target); - - if(!currentItem) return false; - if(this.options.handle && !overrideHandle) { - var validHandle = false; - - $(this.options.handle, currentItem).find("*").andSelf().each(function() { if(this == event.target) validHandle = true; }); - if(!validHandle) return false; - } - - this.currentItem = currentItem; - this._removeCurrentsFromItems(); - return true; - - }, - - _mouseStart: function(event, overrideHandle, noActivation) { - - var o = this.options, self = this; - this.currentContainer = this; - - //We only need to call refreshPositions, because the refreshItems call has been moved to mouseCapture - this.refreshPositions(); - - //Create and append the visible helper - this.helper = this._createHelper(event); - - //Cache the helper size - this._cacheHelperProportions(); - - /* - * - Position generation - - * This block generates everything position related - it's the core of draggables. - */ - - //Cache the margins of the original element - this._cacheMargins(); - - //Get the next scrolling parent - this.scrollParent = this.helper.scrollParent(); - - //The element's absolute position on the page minus margins - this.offset = this.currentItem.offset(); - this.offset = { - top: this.offset.top - this.margins.top, - left: this.offset.left - this.margins.left - }; - - // Only after we got the offset, we can change the helper's position to absolute - // TODO: Still need to figure out a way to make relative sorting possible - this.helper.css("position", "absolute"); - this.cssPosition = this.helper.css("position"); - - $.extend(this.offset, { - click: { //Where the click happened, relative to the element - left: event.pageX - this.offset.left, - top: event.pageY - this.offset.top - }, - parent: this._getParentOffset(), - relative: this._getRelativeOffset() //This is a relative to absolute position minus the actual position calculation - only used for relative positioned helper - }); - - //Generate the original position - this.originalPosition = this._generatePosition(event); - this.originalPageX = event.pageX; - this.originalPageY = event.pageY; - - //Adjust the mouse offset relative to the helper if 'cursorAt' is supplied - (o.cursorAt && this._adjustOffsetFromHelper(o.cursorAt)); - - //Cache the former DOM position - this.domPosition = { prev: this.currentItem.prev()[0], parent: this.currentItem.parent()[0] }; - - //If the helper is not the original, hide the original so it's not playing any role during the drag, won't cause anything bad this way - if(this.helper[0] != this.currentItem[0]) { - this.currentItem.hide(); - } - - //Create the placeholder - this._createPlaceholder(); - - //Set a containment if given in the options - if(o.containment) - this._setContainment(); - - if(o.cursor) { // cursor option - if ($('body').css("cursor")) this._storedCursor = $('body').css("cursor"); - $('body').css("cursor", o.cursor); - } - - if(o.opacity) { // opacity option - if (this.helper.css("opacity")) this._storedOpacity = this.helper.css("opacity"); - this.helper.css("opacity", o.opacity); - } - - if(o.zIndex) { // zIndex option - if (this.helper.css("zIndex")) this._storedZIndex = this.helper.css("zIndex"); - this.helper.css("zIndex", o.zIndex); - } - - //Prepare scrolling - if(this.scrollParent[0] != document && this.scrollParent[0].tagName != 'HTML') - this.overflowOffset = this.scrollParent.offset(); - - //Call callbacks - this._trigger("start", event, this._uiHash()); - - //Recache the helper size - if(!this._preserveHelperProportions) - this._cacheHelperProportions(); - - - //Post 'activate' events to possible containers - if(!noActivation) { - for (var i = this.containers.length - 1; i >= 0; i--) { this.containers[i]._trigger("activate", event, self._uiHash(this)); } - } - - //Prepare possible droppables - if($.ui.ddmanager) - $.ui.ddmanager.current = this; - - if ($.ui.ddmanager && !o.dropBehaviour) - $.ui.ddmanager.prepareOffsets(this, event); - - this.dragging = true; - - this.helper.addClass("ui-sortable-helper"); - this._mouseDrag(event); //Execute the drag once - this causes the helper not to be visible before getting its correct position - return true; - - }, - - _mouseDrag: function(event) { - - //Compute the helpers position - this.position = this._generatePosition(event); - this.positionAbs = this._convertPositionTo("absolute"); - - if (!this.lastPositionAbs) { - this.lastPositionAbs = this.positionAbs; - } - - //Do scrolling - if(this.options.scroll) { - var o = this.options, scrolled = false; - if(this.scrollParent[0] != document && this.scrollParent[0].tagName != 'HTML') { - - if((this.overflowOffset.top + this.scrollParent[0].offsetHeight) - event.pageY < o.scrollSensitivity) - this.scrollParent[0].scrollTop = scrolled = this.scrollParent[0].scrollTop + o.scrollSpeed; - else if(event.pageY - this.overflowOffset.top < o.scrollSensitivity) - this.scrollParent[0].scrollTop = scrolled = this.scrollParent[0].scrollTop - o.scrollSpeed; - - if((this.overflowOffset.left + this.scrollParent[0].offsetWidth) - event.pageX < o.scrollSensitivity) - this.scrollParent[0].scrollLeft = scrolled = this.scrollParent[0].scrollLeft + o.scrollSpeed; - else if(event.pageX - this.overflowOffset.left < o.scrollSensitivity) - this.scrollParent[0].scrollLeft = scrolled = this.scrollParent[0].scrollLeft - o.scrollSpeed; - - } else { - - if(event.pageY - $(document).scrollTop() < o.scrollSensitivity) - scrolled = $(document).scrollTop($(document).scrollTop() - o.scrollSpeed); - else if($(window).height() - (event.pageY - $(document).scrollTop()) < o.scrollSensitivity) - scrolled = $(document).scrollTop($(document).scrollTop() + o.scrollSpeed); - - if(event.pageX - $(document).scrollLeft() < o.scrollSensitivity) - scrolled = $(document).scrollLeft($(document).scrollLeft() - o.scrollSpeed); - else if($(window).width() - (event.pageX - $(document).scrollLeft()) < o.scrollSensitivity) - scrolled = $(document).scrollLeft($(document).scrollLeft() + o.scrollSpeed); - - } - - if(scrolled !== false && $.ui.ddmanager && !o.dropBehaviour) - $.ui.ddmanager.prepareOffsets(this, event); - } - - //Regenerate the absolute position used for position checks - this.positionAbs = this._convertPositionTo("absolute"); - - //Set the helper position - if(!this.options.axis || this.options.axis != "y") this.helper[0].style.left = this.position.left+'px'; - if(!this.options.axis || this.options.axis != "x") this.helper[0].style.top = this.position.top+'px'; - - //Rearrange - for (var i = this.items.length - 1; i >= 0; i--) { - - //Cache variables and intersection, continue if no intersection - var item = this.items[i], itemElement = item.item[0], intersection = this._intersectsWithPointer(item); - if (!intersection) continue; - - if(itemElement != this.currentItem[0] //cannot intersect with itself - && this.placeholder[intersection == 1 ? "next" : "prev"]()[0] != itemElement //no useless actions that have been done before - && !$.ui.contains(this.placeholder[0], itemElement) //no action if the item moved is the parent of the item checked - && (this.options.type == 'semi-dynamic' ? !$.ui.contains(this.element[0], itemElement) : true) - //&& itemElement.parentNode == this.placeholder[0].parentNode // only rearrange items within the same container - ) { - - this.direction = intersection == 1 ? "down" : "up"; - - if (this.options.tolerance == "pointer" || this._intersectsWithSides(item)) { - this._rearrange(event, item); - } else { - break; - } - - this._trigger("change", event, this._uiHash()); - break; - } - } - - //Post events to containers - this._contactContainers(event); - - //Interconnect with droppables - if($.ui.ddmanager) $.ui.ddmanager.drag(this, event); - - //Call callbacks - this._trigger('sort', event, this._uiHash()); - - this.lastPositionAbs = this.positionAbs; - return false; - - }, - - _mouseStop: function(event, noPropagation) { - - if(!event) return; - - //If we are using droppables, inform the manager about the drop - if ($.ui.ddmanager && !this.options.dropBehaviour) - $.ui.ddmanager.drop(this, event); - - if(this.options.revert) { - var self = this; - var cur = self.placeholder.offset(); - - self.reverting = true; - - $(this.helper).animate({ - left: cur.left - this.offset.parent.left - self.margins.left + (this.offsetParent[0] == document.body ? 0 : this.offsetParent[0].scrollLeft), - top: cur.top - this.offset.parent.top - self.margins.top + (this.offsetParent[0] == document.body ? 0 : this.offsetParent[0].scrollTop) - }, parseInt(this.options.revert, 10) || 500, function() { - self._clear(event); - }); - } else { - this._clear(event, noPropagation); - } - - return false; - - }, - - cancel: function() { - - var self = this; - - if(this.dragging) { - - this._mouseUp(); - - if(this.options.helper == "original") - this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper"); - else - this.currentItem.show(); - - //Post deactivating events to containers - for (var i = this.containers.length - 1; i >= 0; i--){ - this.containers[i]._trigger("deactivate", null, self._uiHash(this)); - if(this.containers[i].containerCache.over) { - this.containers[i]._trigger("out", null, self._uiHash(this)); - this.containers[i].containerCache.over = 0; - } - } - - } - - //$(this.placeholder[0]).remove(); would have been the jQuery way - unfortunately, it unbinds ALL events from the original node! - if(this.placeholder[0].parentNode) this.placeholder[0].parentNode.removeChild(this.placeholder[0]); - if(this.options.helper != "original" && this.helper && this.helper[0].parentNode) this.helper.remove(); - - $.extend(this, { - helper: null, - dragging: false, - reverting: false, - _noFinalSort: null - }); - - if(this.domPosition.prev) { - $(this.domPosition.prev).after(this.currentItem); - } else { - $(this.domPosition.parent).prepend(this.currentItem); - } - - return this; - - }, - - serialize: function(o) { - - var items = this._getItemsAsjQuery(o && o.connected); - var str = []; o = o || {}; - - $(items).each(function() { - var res = ($(o.item || this).attr(o.attribute || 'id') || '').match(o.expression || (/(.+)[-=_](.+)/)); - if(res) str.push((o.key || res[1]+'[]')+'='+(o.key && o.expression ? res[1] : res[2])); - }); - - if(!str.length && o.key) { - str.push(o.key + '='); - } - - return str.join('&'); - - }, - - toArray: function(o) { - - var items = this._getItemsAsjQuery(o && o.connected); - var ret = []; o = o || {}; - - items.each(function() { ret.push($(o.item || this).attr(o.attribute || 'id') || ''); }); - return ret; - - }, - - /* Be careful with the following core functions */ - _intersectsWith: function(item) { - - var x1 = this.positionAbs.left, - x2 = x1 + this.helperProportions.width, - y1 = this.positionAbs.top, - y2 = y1 + this.helperProportions.height; - - var l = item.left, - r = l + item.width, - t = item.top, - b = t + item.height; - - var dyClick = this.offset.click.top, - dxClick = this.offset.click.left; - - var isOverElement = (y1 + dyClick) > t && (y1 + dyClick) < b && (x1 + dxClick) > l && (x1 + dxClick) < r; - - if( this.options.tolerance == "pointer" - || this.options.forcePointerForContainers - || (this.options.tolerance != "pointer" && this.helperProportions[this.floating ? 'width' : 'height'] > item[this.floating ? 'width' : 'height']) - ) { - return isOverElement; - } else { - - return (l < x1 + (this.helperProportions.width / 2) // Right Half - && x2 - (this.helperProportions.width / 2) < r // Left Half - && t < y1 + (this.helperProportions.height / 2) // Bottom Half - && y2 - (this.helperProportions.height / 2) < b ); // Top Half - - } - }, - - _intersectsWithPointer: function(item) { - - var isOverElementHeight = $.ui.isOverAxis(this.positionAbs.top + this.offset.click.top, item.top, item.height), - isOverElementWidth = $.ui.isOverAxis(this.positionAbs.left + this.offset.click.left, item.left, item.width), - isOverElement = isOverElementHeight && isOverElementWidth, - verticalDirection = this._getDragVerticalDirection(), - horizontalDirection = this._getDragHorizontalDirection(); - - if (!isOverElement) - return false; - - return this.floating ? - ( ((horizontalDirection && horizontalDirection == "right") || verticalDirection == "down") ? 2 : 1 ) - : ( verticalDirection && (verticalDirection == "down" ? 2 : 1) ); - - }, - - _intersectsWithSides: function(item) { - - var isOverBottomHalf = $.ui.isOverAxis(this.positionAbs.top + this.offset.click.top, item.top + (item.height/2), item.height), - isOverRightHalf = $.ui.isOverAxis(this.positionAbs.left + this.offset.click.left, item.left + (item.width/2), item.width), - verticalDirection = this._getDragVerticalDirection(), - horizontalDirection = this._getDragHorizontalDirection(); - - if (this.floating && horizontalDirection) { - return ((horizontalDirection == "right" && isOverRightHalf) || (horizontalDirection == "left" && !isOverRightHalf)); - } else { - return verticalDirection && ((verticalDirection == "down" && isOverBottomHalf) || (verticalDirection == "up" && !isOverBottomHalf)); - } - - }, - - _getDragVerticalDirection: function() { - var delta = this.positionAbs.top - this.lastPositionAbs.top; - return delta != 0 && (delta > 0 ? "down" : "up"); - }, - - _getDragHorizontalDirection: function() { - var delta = this.positionAbs.left - this.lastPositionAbs.left; - return delta != 0 && (delta > 0 ? "right" : "left"); - }, - - refresh: function(event) { - this._refreshItems(event); - this.refreshPositions(); - return this; - }, - - _connectWith: function() { - var options = this.options; - return options.connectWith.constructor == String - ? [options.connectWith] - : options.connectWith; - }, - - _getItemsAsjQuery: function(connected) { - - var self = this; - var items = []; - var queries = []; - var connectWith = this._connectWith(); - - if(connectWith && connected) { - for (var i = connectWith.length - 1; i >= 0; i--){ - var cur = $(connectWith[i]); - for (var j = cur.length - 1; j >= 0; j--){ - var inst = $.data(cur[j], 'sortable'); - if(inst && inst != this && !inst.options.disabled) { - queries.push([$.isFunction(inst.options.items) ? inst.options.items.call(inst.element) : $(inst.options.items, inst.element).not(".ui-sortable-helper").not('.ui-sortable-placeholder'), inst]); - } - }; - }; - } - - queries.push([$.isFunction(this.options.items) ? this.options.items.call(this.element, null, { options: this.options, item: this.currentItem }) : $(this.options.items, this.element).not(".ui-sortable-helper").not('.ui-sortable-placeholder'), this]); - - for (var i = queries.length - 1; i >= 0; i--){ - queries[i][0].each(function() { - items.push(this); - }); - }; - - return $(items); - - }, - - _removeCurrentsFromItems: function() { - - var list = this.currentItem.find(":data(sortable-item)"); - - for (var i=0; i < this.items.length; i++) { - - for (var j=0; j < list.length; j++) { - if(list[j] == this.items[i].item[0]) - this.items.splice(i,1); - }; - - }; - - }, - - _refreshItems: function(event) { - - this.items = []; - this.containers = [this]; - var items = this.items; - var self = this; - var queries = [[$.isFunction(this.options.items) ? this.options.items.call(this.element[0], event, { item: this.currentItem }) : $(this.options.items, this.element), this]]; - var connectWith = this._connectWith(); - - if(connectWith) { - for (var i = connectWith.length - 1; i >= 0; i--){ - var cur = $(connectWith[i]); - for (var j = cur.length - 1; j >= 0; j--){ - var inst = $.data(cur[j], 'sortable'); - if(inst && inst != this && !inst.options.disabled) { - queries.push([$.isFunction(inst.options.items) ? inst.options.items.call(inst.element[0], event, { item: this.currentItem }) : $(inst.options.items, inst.element), inst]); - this.containers.push(inst); - } - }; - }; - } - - for (var i = queries.length - 1; i >= 0; i--) { - var targetData = queries[i][1]; - var _queries = queries[i][0]; - - for (var j=0, queriesLength = _queries.length; j < queriesLength; j++) { - var item = $(_queries[j]); - - item.data('sortable-item', targetData); // Data for target checking (mouse manager) - - items.push({ - item: item, - instance: targetData, - width: 0, height: 0, - left: 0, top: 0 - }); - }; - }; - - }, - - refreshPositions: function(fast) { - - //This has to be redone because due to the item being moved out/into the offsetParent, the offsetParent's position will change - if(this.offsetParent && this.helper) { - this.offset.parent = this._getParentOffset(); - } - - for (var i = this.items.length - 1; i >= 0; i--){ - var item = this.items[i]; - - var t = this.options.toleranceElement ? $(this.options.toleranceElement, item.item) : item.item; - - if (!fast) { - item.width = t.outerWidth(); - item.height = t.outerHeight(); - } - - var p = t.offset(); - item.left = p.left; - item.top = p.top; - }; - - if(this.options.custom && this.options.custom.refreshContainers) { - this.options.custom.refreshContainers.call(this); - } else { - for (var i = this.containers.length - 1; i >= 0; i--){ - var p = this.containers[i].element.offset(); - this.containers[i].containerCache.left = p.left; - this.containers[i].containerCache.top = p.top; - this.containers[i].containerCache.width = this.containers[i].element.outerWidth(); - this.containers[i].containerCache.height = this.containers[i].element.outerHeight(); - }; - } - - return this; - }, - - _createPlaceholder: function(that) { - - var self = that || this, o = self.options; - - if(!o.placeholder || o.placeholder.constructor == String) { - var className = o.placeholder; - o.placeholder = { - element: function() { - - var el = $(document.createElement(self.currentItem[0].nodeName)) - .addClass(className || self.currentItem[0].className+" ui-sortable-placeholder") - .removeClass("ui-sortable-helper")[0]; - - if(!className) - el.style.visibility = "hidden"; - - return el; - }, - update: function(container, p) { - - // 1. If a className is set as 'placeholder option, we don't force sizes - the class is responsible for that - // 2. The option 'forcePlaceholderSize can be enabled to force it even if a class name is specified - if(className && !o.forcePlaceholderSize) return; - - //If the element doesn't have a actual height by itself (without styles coming from a stylesheet), it receives the inline height from the dragged item - if(!p.height()) { p.height(self.currentItem.innerHeight() - parseInt(self.currentItem.css('paddingTop')||0, 10) - parseInt(self.currentItem.css('paddingBottom')||0, 10)); }; - if(!p.width()) { p.width(self.currentItem.innerWidth() - parseInt(self.currentItem.css('paddingLeft')||0, 10) - parseInt(self.currentItem.css('paddingRight')||0, 10)); }; - } - }; - } - - //Create the placeholder - self.placeholder = $(o.placeholder.element.call(self.element, self.currentItem)); - - //Append it after the actual current item - self.currentItem.after(self.placeholder); - - //Update the size of the placeholder (TODO: Logic to fuzzy, see line 316/317) - o.placeholder.update(self, self.placeholder); - - }, - - _contactContainers: function(event) { - - // get innermost container that intersects with item - var innermostContainer = null, innermostIndex = null; - - - for (var i = this.containers.length - 1; i >= 0; i--){ - - // never consider a container that's located within the item itself - if($.ui.contains(this.currentItem[0], this.containers[i].element[0])) - continue; - - if(this._intersectsWith(this.containers[i].containerCache)) { - - // if we've already found a container and it's more "inner" than this, then continue - if(innermostContainer && $.ui.contains(this.containers[i].element[0], innermostContainer.element[0])) - continue; - - innermostContainer = this.containers[i]; - innermostIndex = i; - - } else { - // container doesn't intersect. trigger "out" event if necessary - if(this.containers[i].containerCache.over) { - this.containers[i]._trigger("out", event, this._uiHash(this)); - this.containers[i].containerCache.over = 0; - } - } - - } - - // if no intersecting containers found, return - if(!innermostContainer) return; - - // move the item into the container if it's not there already - if(this.containers.length === 1) { - this.containers[innermostIndex]._trigger("over", event, this._uiHash(this)); - this.containers[innermostIndex].containerCache.over = 1; - } else if(this.currentContainer != this.containers[innermostIndex]) { - - //When entering a new container, we will find the item with the least distance and append our item near it - var dist = 10000; var itemWithLeastDistance = null; var base = this.positionAbs[this.containers[innermostIndex].floating ? 'left' : 'top']; - for (var j = this.items.length - 1; j >= 0; j--) { - if(!$.ui.contains(this.containers[innermostIndex].element[0], this.items[j].item[0])) continue; - var cur = this.items[j][this.containers[innermostIndex].floating ? 'left' : 'top']; - if(Math.abs(cur - base) < dist) { - dist = Math.abs(cur - base); itemWithLeastDistance = this.items[j]; - } - } - - if(!itemWithLeastDistance && !this.options.dropOnEmpty) //Check if dropOnEmpty is enabled - return; - - this.currentContainer = this.containers[innermostIndex]; - itemWithLeastDistance ? this._rearrange(event, itemWithLeastDistance, null, true) : this._rearrange(event, null, this.containers[innermostIndex].element, true); - this._trigger("change", event, this._uiHash()); - this.containers[innermostIndex]._trigger("change", event, this._uiHash(this)); - - //Update the placeholder - this.options.placeholder.update(this.currentContainer, this.placeholder); - - this.containers[innermostIndex]._trigger("over", event, this._uiHash(this)); - this.containers[innermostIndex].containerCache.over = 1; - } - - - }, - - _createHelper: function(event) { - - var o = this.options; - var helper = $.isFunction(o.helper) ? $(o.helper.apply(this.element[0], [event, this.currentItem])) : (o.helper == 'clone' ? this.currentItem.clone() : this.currentItem); - - if(!helper.parents('body').length) //Add the helper to the DOM if that didn't happen already - $(o.appendTo != 'parent' ? o.appendTo : this.currentItem[0].parentNode)[0].appendChild(helper[0]); - - if(helper[0] == this.currentItem[0]) - this._storedCSS = { width: this.currentItem[0].style.width, height: this.currentItem[0].style.height, position: this.currentItem.css("position"), top: this.currentItem.css("top"), left: this.currentItem.css("left") }; - - if(helper[0].style.width == '' || o.forceHelperSize) helper.width(this.currentItem.width()); - if(helper[0].style.height == '' || o.forceHelperSize) helper.height(this.currentItem.height()); - - return helper; - - }, - - _adjustOffsetFromHelper: function(obj) { - if (typeof obj == 'string') { - obj = obj.split(' '); - } - if ($.isArray(obj)) { - obj = {left: +obj[0], top: +obj[1] || 0}; - } - if ('left' in obj) { - this.offset.click.left = obj.left + this.margins.left; - } - if ('right' in obj) { - this.offset.click.left = this.helperProportions.width - obj.right + this.margins.left; - } - if ('top' in obj) { - this.offset.click.top = obj.top + this.margins.top; - } - if ('bottom' in obj) { - this.offset.click.top = this.helperProportions.height - obj.bottom + this.margins.top; - } - }, - - _getParentOffset: function() { - - - //Get the offsetParent and cache its position - this.offsetParent = this.helper.offsetParent(); - var po = this.offsetParent.offset(); - - // This is a special case where we need to modify a offset calculated on start, since the following happened: - // 1. The position of the helper is absolute, so it's position is calculated based on the next positioned parent - // 2. The actual offset parent is a child of the scroll parent, and the scroll parent isn't the document, which means that - // the scroll is included in the initial calculation of the offset of the parent, and never recalculated upon drag - if(this.cssPosition == 'absolute' && this.scrollParent[0] != document && $.ui.contains(this.scrollParent[0], this.offsetParent[0])) { - po.left += this.scrollParent.scrollLeft(); - po.top += this.scrollParent.scrollTop(); - } - - if((this.offsetParent[0] == document.body) //This needs to be actually done for all browsers, since pageX/pageY includes this information - || (this.offsetParent[0].tagName && this.offsetParent[0].tagName.toLowerCase() == 'html' && $.browser.msie)) //Ugly IE fix - po = { top: 0, left: 0 }; - - return { - top: po.top + (parseInt(this.offsetParent.css("borderTopWidth"),10) || 0), - left: po.left + (parseInt(this.offsetParent.css("borderLeftWidth"),10) || 0) - }; - - }, - - _getRelativeOffset: function() { - - if(this.cssPosition == "relative") { - var p = this.currentItem.position(); - return { - top: p.top - (parseInt(this.helper.css("top"),10) || 0) + this.scrollParent.scrollTop(), - left: p.left - (parseInt(this.helper.css("left"),10) || 0) + this.scrollParent.scrollLeft() - }; - } else { - return { top: 0, left: 0 }; - } - - }, - - _cacheMargins: function() { - this.margins = { - left: (parseInt(this.currentItem.css("marginLeft"),10) || 0), - top: (parseInt(this.currentItem.css("marginTop"),10) || 0) - }; - }, - - _cacheHelperProportions: function() { - this.helperProportions = { - width: this.helper.outerWidth(), - height: this.helper.outerHeight() - }; - }, - - _setContainment: function() { - - var o = this.options; - if(o.containment == 'parent') o.containment = this.helper[0].parentNode; - if(o.containment == 'document' || o.containment == 'window') this.containment = [ - 0 - this.offset.relative.left - this.offset.parent.left, - 0 - this.offset.relative.top - this.offset.parent.top, - $(o.containment == 'document' ? document : window).width() - this.helperProportions.width - this.margins.left, - ($(o.containment == 'document' ? document : window).height() || document.body.parentNode.scrollHeight) - this.helperProportions.height - this.margins.top - ]; - - if(!(/^(document|window|parent)$/).test(o.containment)) { - var ce = $(o.containment)[0]; - var co = $(o.containment).offset(); - var over = ($(ce).css("overflow") != 'hidden'); - - this.containment = [ - co.left + (parseInt($(ce).css("borderLeftWidth"),10) || 0) + (parseInt($(ce).css("paddingLeft"),10) || 0) - this.margins.left, - co.top + (parseInt($(ce).css("borderTopWidth"),10) || 0) + (parseInt($(ce).css("paddingTop"),10) || 0) - this.margins.top, - co.left+(over ? Math.max(ce.scrollWidth,ce.offsetWidth) : ce.offsetWidth) - (parseInt($(ce).css("borderLeftWidth"),10) || 0) - (parseInt($(ce).css("paddingRight"),10) || 0) - this.helperProportions.width - this.margins.left, - co.top+(over ? Math.max(ce.scrollHeight,ce.offsetHeight) : ce.offsetHeight) - (parseInt($(ce).css("borderTopWidth"),10) || 0) - (parseInt($(ce).css("paddingBottom"),10) || 0) - this.helperProportions.height - this.margins.top - ]; - } - - }, - - _convertPositionTo: function(d, pos) { - - if(!pos) pos = this.position; - var mod = d == "absolute" ? 1 : -1; - var o = this.options, scroll = this.cssPosition == 'absolute' && !(this.scrollParent[0] != document && $.ui.contains(this.scrollParent[0], this.offsetParent[0])) ? this.offsetParent : this.scrollParent, scrollIsRootNode = (/(html|body)/i).test(scroll[0].tagName); - - return { - top: ( - pos.top // The absolute mouse position - + this.offset.relative.top * mod // Only for relative positioned nodes: Relative offset from element to offset parent - + this.offset.parent.top * mod // The offsetParent's offset without borders (offset + border) - - ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollTop() : ( scrollIsRootNode ? 0 : scroll.scrollTop() ) ) * mod) - ), - left: ( - pos.left // The absolute mouse position - + this.offset.relative.left * mod // Only for relative positioned nodes: Relative offset from element to offset parent - + this.offset.parent.left * mod // The offsetParent's offset without borders (offset + border) - - ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollLeft() : scrollIsRootNode ? 0 : scroll.scrollLeft() ) * mod) - ) - }; - - }, - - _generatePosition: function(event) { - - var o = this.options, scroll = this.cssPosition == 'absolute' && !(this.scrollParent[0] != document && $.ui.contains(this.scrollParent[0], this.offsetParent[0])) ? this.offsetParent : this.scrollParent, scrollIsRootNode = (/(html|body)/i).test(scroll[0].tagName); - - // This is another very weird special case that only happens for relative elements: - // 1. If the css position is relative - // 2. and the scroll parent is the document or similar to the offset parent - // we have to refresh the relative offset during the scroll so there are no jumps - if(this.cssPosition == 'relative' && !(this.scrollParent[0] != document && this.scrollParent[0] != this.offsetParent[0])) { - this.offset.relative = this._getRelativeOffset(); - } - - var pageX = event.pageX; - var pageY = event.pageY; - - /* - * - Position constraining - - * Constrain the position to a mix of grid, containment. - */ - - if(this.originalPosition) { //If we are not dragging yet, we won't check for options - - if(this.containment) { - if(event.pageX - this.offset.click.left < this.containment[0]) pageX = this.containment[0] + this.offset.click.left; - if(event.pageY - this.offset.click.top < this.containment[1]) pageY = this.containment[1] + this.offset.click.top; - if(event.pageX - this.offset.click.left > this.containment[2]) pageX = this.containment[2] + this.offset.click.left; - if(event.pageY - this.offset.click.top > this.containment[3]) pageY = this.containment[3] + this.offset.click.top; - } - - if(o.grid) { - var top = this.originalPageY + Math.round((pageY - this.originalPageY) / o.grid[1]) * o.grid[1]; - pageY = this.containment ? (!(top - this.offset.click.top < this.containment[1] || top - this.offset.click.top > this.containment[3]) ? top : (!(top - this.offset.click.top < this.containment[1]) ? top - o.grid[1] : top + o.grid[1])) : top; - - var left = this.originalPageX + Math.round((pageX - this.originalPageX) / o.grid[0]) * o.grid[0]; - pageX = this.containment ? (!(left - this.offset.click.left < this.containment[0] || left - this.offset.click.left > this.containment[2]) ? left : (!(left - this.offset.click.left < this.containment[0]) ? left - o.grid[0] : left + o.grid[0])) : left; - } - - } - - return { - top: ( - pageY // The absolute mouse position - - this.offset.click.top // Click offset (relative to the element) - - this.offset.relative.top // Only for relative positioned nodes: Relative offset from element to offset parent - - this.offset.parent.top // The offsetParent's offset without borders (offset + border) - + ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollTop() : ( scrollIsRootNode ? 0 : scroll.scrollTop() ) )) - ), - left: ( - pageX // The absolute mouse position - - this.offset.click.left // Click offset (relative to the element) - - this.offset.relative.left // Only for relative positioned nodes: Relative offset from element to offset parent - - this.offset.parent.left // The offsetParent's offset without borders (offset + border) - + ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollLeft() : scrollIsRootNode ? 0 : scroll.scrollLeft() )) - ) - }; - - }, - - _rearrange: function(event, i, a, hardRefresh) { - - a ? a[0].appendChild(this.placeholder[0]) : i.item[0].parentNode.insertBefore(this.placeholder[0], (this.direction == 'down' ? i.item[0] : i.item[0].nextSibling)); - - //Various things done here to improve the performance: - // 1. we create a setTimeout, that calls refreshPositions - // 2. on the instance, we have a counter variable, that get's higher after every append - // 3. on the local scope, we copy the counter variable, and check in the timeout, if it's still the same - // 4. this lets only the last addition to the timeout stack through - this.counter = this.counter ? ++this.counter : 1; - var self = this, counter = this.counter; - - window.setTimeout(function() { - if(counter == self.counter) self.refreshPositions(!hardRefresh); //Precompute after each DOM insertion, NOT on mousemove - },0); - - }, - - _clear: function(event, noPropagation) { - - this.reverting = false; - // We delay all events that have to be triggered to after the point where the placeholder has been removed and - // everything else normalized again - var delayedTriggers = [], self = this; - - // We first have to update the dom position of the actual currentItem - // Note: don't do it if the current item is already removed (by a user), or it gets reappended (see #4088) - if(!this._noFinalSort && this.currentItem[0].parentNode) this.placeholder.before(this.currentItem); - this._noFinalSort = null; - - if(this.helper[0] == this.currentItem[0]) { - for(var i in this._storedCSS) { - if(this._storedCSS[i] == 'auto' || this._storedCSS[i] == 'static') this._storedCSS[i] = ''; - } - this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper"); - } else { - this.currentItem.show(); - } - - if(this.fromOutside && !noPropagation) delayedTriggers.push(function(event) { this._trigger("receive", event, this._uiHash(this.fromOutside)); }); - if((this.fromOutside || this.domPosition.prev != this.currentItem.prev().not(".ui-sortable-helper")[0] || this.domPosition.parent != this.currentItem.parent()[0]) && !noPropagation) delayedTriggers.push(function(event) { this._trigger("update", event, this._uiHash()); }); //Trigger update callback if the DOM position has changed - if(!$.ui.contains(this.element[0], this.currentItem[0])) { //Node was moved out of the current element - if(!noPropagation) delayedTriggers.push(function(event) { this._trigger("remove", event, this._uiHash()); }); - for (var i = this.containers.length - 1; i >= 0; i--){ - if($.ui.contains(this.containers[i].element[0], this.currentItem[0]) && !noPropagation) { - delayedTriggers.push((function(c) { return function(event) { c._trigger("receive", event, this._uiHash(this)); }; }).call(this, this.containers[i])); - delayedTriggers.push((function(c) { return function(event) { c._trigger("update", event, this._uiHash(this)); }; }).call(this, this.containers[i])); - } - }; - }; - - //Post events to containers - for (var i = this.containers.length - 1; i >= 0; i--){ - if(!noPropagation) delayedTriggers.push((function(c) { return function(event) { c._trigger("deactivate", event, this._uiHash(this)); }; }).call(this, this.containers[i])); - if(this.containers[i].containerCache.over) { - delayedTriggers.push((function(c) { return function(event) { c._trigger("out", event, this._uiHash(this)); }; }).call(this, this.containers[i])); - this.containers[i].containerCache.over = 0; - } - } - - //Do what was originally in plugins - if(this._storedCursor) $('body').css("cursor", this._storedCursor); //Reset cursor - if(this._storedOpacity) this.helper.css("opacity", this._storedOpacity); //Reset opacity - if(this._storedZIndex) this.helper.css("zIndex", this._storedZIndex == 'auto' ? '' : this._storedZIndex); //Reset z-index - - this.dragging = false; - if(this.cancelHelperRemoval) { - if(!noPropagation) { - this._trigger("beforeStop", event, this._uiHash()); - for (var i=0; i < delayedTriggers.length; i++) { delayedTriggers[i].call(this, event); }; //Trigger all delayed events - this._trigger("stop", event, this._uiHash()); - } - return false; - } - - if(!noPropagation) this._trigger("beforeStop", event, this._uiHash()); - - //$(this.placeholder[0]).remove(); would have been the jQuery way - unfortunately, it unbinds ALL events from the original node! - this.placeholder[0].parentNode.removeChild(this.placeholder[0]); - - if(this.helper[0] != this.currentItem[0]) this.helper.remove(); this.helper = null; - - if(!noPropagation) { - for (var i=0; i < delayedTriggers.length; i++) { delayedTriggers[i].call(this, event); }; //Trigger all delayed events - this._trigger("stop", event, this._uiHash()); - } - - this.fromOutside = false; - return true; - - }, - - _trigger: function() { - if ($.Widget.prototype._trigger.apply(this, arguments) === false) { - this.cancel(); - } - }, - - _uiHash: function(inst) { - var self = inst || this; - return { - helper: self.helper, - placeholder: self.placeholder || $([]), - position: self.position, - originalPosition: self.originalPosition, - offset: self.positionAbs, - item: self.currentItem, - sender: inst ? inst.element : null - }; - } - -}); - -$.extend($.ui.sortable, { - version: "1.8.5" -}); - -})(jQuery); -/* - * jQuery UI Slider 1.8.5 - * - * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Slider - * - * Depends: - * jquery.ui.core.js - * jquery.ui.mouse.js - * jquery.ui.widget.js - */ -(function( $, undefined ) { - -// number of pages in a slider -// (how many times can you page up/down to go through the whole range) -var numPages = 5; - -$.widget( "ui.slider", $.ui.mouse, { - - widgetEventPrefix: "slide", - - options: { - animate: false, - distance: 0, - max: 100, - min: 0, - orientation: "horizontal", - range: false, - step: 1, - value: 0, - values: null - }, - - _create: function() { - var self = this, - o = this.options; - - this._keySliding = false; - this._mouseSliding = false; - this._animateOff = true; - this._handleIndex = null; - this._detectOrientation(); - this._mouseInit(); - - this.element - .addClass( "ui-slider" + - " ui-slider-" + this.orientation + - " ui-widget" + - " ui-widget-content" + - " ui-corner-all" ); - - if ( o.disabled ) { - this.element.addClass( "ui-slider-disabled ui-disabled" ); - } - - this.range = $([]); - - if ( o.range ) { - if ( o.range === true ) { - this.range = $( "<div></div>" ); - if ( !o.values ) { - o.values = [ this._valueMin(), this._valueMin() ]; - } - if ( o.values.length && o.values.length !== 2 ) { - o.values = [ o.values[0], o.values[0] ]; - } - } else { - this.range = $( "<div></div>" ); - } - - this.range - .appendTo( this.element ) - .addClass( "ui-slider-range" ); - - if ( o.range === "min" || o.range === "max" ) { - this.range.addClass( "ui-slider-range-" + o.range ); - } - - // note: this isn't the most fittingly semantic framework class for this element, - // but worked best visually with a variety of themes - this.range.addClass( "ui-widget-header" ); - } - - if ( $( ".ui-slider-handle", this.element ).length === 0 ) { - $( "<a href='#'></a>" ) - .appendTo( this.element ) - .addClass( "ui-slider-handle" ); - } - - if ( o.values && o.values.length ) { - while ( $(".ui-slider-handle", this.element).length < o.values.length ) { - $( "<a href='#'></a>" ) - .appendTo( this.element ) - .addClass( "ui-slider-handle" ); - } - } - - this.handles = $( ".ui-slider-handle", this.element ) - .addClass( "ui-state-default" + - " ui-corner-all" ); - - this.handle = this.handles.eq( 0 ); - - this.handles.add( this.range ).filter( "a" ) - .click(function( event ) { - event.preventDefault(); - }) - .hover(function() { - if ( !o.disabled ) { - $( this ).addClass( "ui-state-hover" ); - } - }, function() { - $( this ).removeClass( "ui-state-hover" ); - }) - .focus(function() { - if ( !o.disabled ) { - $( ".ui-slider .ui-state-focus" ).removeClass( "ui-state-focus" ); - $( this ).addClass( "ui-state-focus" ); - } else { - $( this ).blur(); - } - }) - .blur(function() { - $( this ).removeClass( "ui-state-focus" ); - }); - - this.handles.each(function( i ) { - $( this ).data( "index.ui-slider-handle", i ); - }); - - this.handles - .keydown(function( event ) { - var ret = true, - index = $( this ).data( "index.ui-slider-handle" ), - allowed, - curVal, - newVal, - step; - - if ( self.options.disabled ) { - return; - } - - switch ( event.keyCode ) { - case $.ui.keyCode.HOME: - case $.ui.keyCode.END: - case $.ui.keyCode.PAGE_UP: - case $.ui.keyCode.PAGE_DOWN: - case $.ui.keyCode.UP: - case $.ui.keyCode.RIGHT: - case $.ui.keyCode.DOWN: - case $.ui.keyCode.LEFT: - ret = false; - if ( !self._keySliding ) { - self._keySliding = true; - $( this ).addClass( "ui-state-active" ); - allowed = self._start( event, index ); - if ( allowed === false ) { - return; - } - } - break; - } - - step = self.options.step; - if ( self.options.values && self.options.values.length ) { - curVal = newVal = self.values( index ); - } else { - curVal = newVal = self.value(); - } - - switch ( event.keyCode ) { - case $.ui.keyCode.HOME: - newVal = self._valueMin(); - break; - case $.ui.keyCode.END: - newVal = self._valueMax(); - break; - case $.ui.keyCode.PAGE_UP: - newVal = self._trimAlignValue( curVal + ( (self._valueMax() - self._valueMin()) / numPages ) ); - break; - case $.ui.keyCode.PAGE_DOWN: - newVal = self._trimAlignValue( curVal - ( (self._valueMax() - self._valueMin()) / numPages ) ); - break; - case $.ui.keyCode.UP: - case $.ui.keyCode.RIGHT: - if ( curVal === self._valueMax() ) { - return; - } - newVal = self._trimAlignValue( curVal + step ); - break; - case $.ui.keyCode.DOWN: - case $.ui.keyCode.LEFT: - if ( curVal === self._valueMin() ) { - return; - } - newVal = self._trimAlignValue( curVal - step ); - break; - } - - self._slide( event, index, newVal ); - - return ret; - - }) - .keyup(function( event ) { - var index = $( this ).data( "index.ui-slider-handle" ); - - if ( self._keySliding ) { - self._keySliding = false; - self._stop( event, index ); - self._change( event, index ); - $( this ).removeClass( "ui-state-active" ); - } - - }); - - this._refreshValue(); - - this._animateOff = false; - }, - - destroy: function() { - this.handles.remove(); - this.range.remove(); - - this.element - .removeClass( "ui-slider" + - " ui-slider-horizontal" + - " ui-slider-vertical" + - " ui-slider-disabled" + - " ui-widget" + - " ui-widget-content" + - " ui-corner-all" ) - .removeData( "slider" ) - .unbind( ".slider" ); - - this._mouseDestroy(); - - return this; - }, - - _mouseCapture: function( event ) { - var o = this.options, - position, - normValue, - distance, - closestHandle, - self, - index, - allowed, - offset, - mouseOverHandle; - - if ( o.disabled ) { - return false; - } - - this.elementSize = { - width: this.element.outerWidth(), - height: this.element.outerHeight() - }; - this.elementOffset = this.element.offset(); - - position = { x: event.pageX, y: event.pageY }; - normValue = this._normValueFromMouse( position ); - distance = this._valueMax() - this._valueMin() + 1; - self = this; - this.handles.each(function( i ) { - var thisDistance = Math.abs( normValue - self.values(i) ); - if ( distance > thisDistance ) { - distance = thisDistance; - closestHandle = $( this ); - index = i; - } - }); - - // workaround for bug #3736 (if both handles of a range are at 0, - // the first is always used as the one with least distance, - // and moving it is obviously prevented by preventing negative ranges) - if( o.range === true && this.values(1) === o.min ) { - index += 1; - closestHandle = $( this.handles[index] ); - } - - allowed = this._start( event, index ); - if ( allowed === false ) { - return false; - } - this._mouseSliding = true; - - self._handleIndex = index; - - closestHandle - .addClass( "ui-state-active" ) - .focus(); - - offset = closestHandle.offset(); - mouseOverHandle = !$( event.target ).parents().andSelf().is( ".ui-slider-handle" ); - this._clickOffset = mouseOverHandle ? { left: 0, top: 0 } : { - left: event.pageX - offset.left - ( closestHandle.width() / 2 ), - top: event.pageY - offset.top - - ( closestHandle.height() / 2 ) - - ( parseInt( closestHandle.css("borderTopWidth"), 10 ) || 0 ) - - ( parseInt( closestHandle.css("borderBottomWidth"), 10 ) || 0) + - ( parseInt( closestHandle.css("marginTop"), 10 ) || 0) - }; - - this._slide( event, index, normValue ); - this._animateOff = true; - return true; - }, - - _mouseStart: function( event ) { - return true; - }, - - _mouseDrag: function( event ) { - var position = { x: event.pageX, y: event.pageY }, - normValue = this._normValueFromMouse( position ); - - this._slide( event, this._handleIndex, normValue ); - - return false; - }, - - _mouseStop: function( event ) { - this.handles.removeClass( "ui-state-active" ); - this._mouseSliding = false; - - this._stop( event, this._handleIndex ); - this._change( event, this._handleIndex ); - - this._handleIndex = null; - this._clickOffset = null; - this._animateOff = false; - - return false; - }, - - _detectOrientation: function() { - this.orientation = ( this.options.orientation === "vertical" ) ? "vertical" : "horizontal"; - }, - - _normValueFromMouse: function( position ) { - var pixelTotal, - pixelMouse, - percentMouse, - valueTotal, - valueMouse; - - if ( this.orientation === "horizontal" ) { - pixelTotal = this.elementSize.width; - pixelMouse = position.x - this.elementOffset.left - ( this._clickOffset ? this._clickOffset.left : 0 ); - } else { - pixelTotal = this.elementSize.height; - pixelMouse = position.y - this.elementOffset.top - ( this._clickOffset ? this._clickOffset.top : 0 ); - } - - percentMouse = ( pixelMouse / pixelTotal ); - if ( percentMouse > 1 ) { - percentMouse = 1; - } - if ( percentMouse < 0 ) { - percentMouse = 0; - } - if ( this.orientation === "vertical" ) { - percentMouse = 1 - percentMouse; - } - - valueTotal = this._valueMax() - this._valueMin(); - valueMouse = this._valueMin() + percentMouse * valueTotal; - - return this._trimAlignValue( valueMouse ); - }, - - _start: function( event, index ) { - var uiHash = { - handle: this.handles[ index ], - value: this.value() - }; - if ( this.options.values && this.options.values.length ) { - uiHash.value = this.values( index ); - uiHash.values = this.values(); - } - return this._trigger( "start", event, uiHash ); - }, - - _slide: function( event, index, newVal ) { - var otherVal, - newValues, - allowed; - - if ( this.options.values && this.options.values.length ) { - otherVal = this.values( index ? 0 : 1 ); - - if ( ( this.options.values.length === 2 && this.options.range === true ) && - ( ( index === 0 && newVal > otherVal) || ( index === 1 && newVal < otherVal ) ) - ) { - newVal = otherVal; - } - - if ( newVal !== this.values( index ) ) { - newValues = this.values(); - newValues[ index ] = newVal; - // A slide can be canceled by returning false from the slide callback - allowed = this._trigger( "slide", event, { - handle: this.handles[ index ], - value: newVal, - values: newValues - } ); - otherVal = this.values( index ? 0 : 1 ); - if ( allowed !== false ) { - this.values( index, newVal, true ); - } - } - } else { - if ( newVal !== this.value() ) { - // A slide can be canceled by returning false from the slide callback - allowed = this._trigger( "slide", event, { - handle: this.handles[ index ], - value: newVal - } ); - if ( allowed !== false ) { - this.value( newVal ); - } - } - } - }, - - _stop: function( event, index ) { - var uiHash = { - handle: this.handles[ index ], - value: this.value() - }; - if ( this.options.values && this.options.values.length ) { - uiHash.value = this.values( index ); - uiHash.values = this.values(); - } - - this._trigger( "stop", event, uiHash ); - }, - - _change: function( event, index ) { - if ( !this._keySliding && !this._mouseSliding ) { - var uiHash = { - handle: this.handles[ index ], - value: this.value() - }; - if ( this.options.values && this.options.values.length ) { - uiHash.value = this.values( index ); - uiHash.values = this.values(); - } - - this._trigger( "change", event, uiHash ); - } - }, - - value: function( newValue ) { - if ( arguments.length ) { - this.options.value = this._trimAlignValue( newValue ); - this._refreshValue(); - this._change( null, 0 ); - } - - return this._value(); - }, - - values: function( index, newValue ) { - var vals, - newValues, - i; - - if ( arguments.length > 1 ) { - this.options.values[ index ] = this._trimAlignValue( newValue ); - this._refreshValue(); - this._change( null, index ); - } - - if ( arguments.length ) { - if ( $.isArray( arguments[ 0 ] ) ) { - vals = this.options.values; - newValues = arguments[ 0 ]; - for ( i = 0; i < vals.length; i += 1 ) { - vals[ i ] = this._trimAlignValue( newValues[ i ] ); - this._change( null, i ); - } - this._refreshValue(); - } else { - if ( this.options.values && this.options.values.length ) { - return this._values( index ); - } else { - return this.value(); - } - } - } else { - return this._values(); - } - }, - - _setOption: function( key, value ) { - var i, - valsLength = 0; - - if ( $.isArray( this.options.values ) ) { - valsLength = this.options.values.length; - } - - $.Widget.prototype._setOption.apply( this, arguments ); - - switch ( key ) { - case "disabled": - if ( value ) { - this.handles.filter( ".ui-state-focus" ).blur(); - this.handles.removeClass( "ui-state-hover" ); - this.handles.attr( "disabled", "disabled" ); - this.element.addClass( "ui-disabled" ); - } else { - this.handles.removeAttr( "disabled" ); - this.element.removeClass( "ui-disabled" ); - } - break; - case "orientation": - this._detectOrientation(); - this.element - .removeClass( "ui-slider-horizontal ui-slider-vertical" ) - .addClass( "ui-slider-" + this.orientation ); - this._refreshValue(); - break; - case "value": - this._animateOff = true; - this._refreshValue(); - this._change( null, 0 ); - this._animateOff = false; - break; - case "values": - this._animateOff = true; - this._refreshValue(); - for ( i = 0; i < valsLength; i += 1 ) { - this._change( null, i ); - } - this._animateOff = false; - break; - } - }, - - //internal value getter - // _value() returns value trimmed by min and max, aligned by step - _value: function() { - var val = this.options.value; - val = this._trimAlignValue( val ); - - return val; - }, - - //internal values getter - // _values() returns array of values trimmed by min and max, aligned by step - // _values( index ) returns single value trimmed by min and max, aligned by step - _values: function( index ) { - var val, - vals, - i; - - if ( arguments.length ) { - val = this.options.values[ index ]; - val = this._trimAlignValue( val ); - - return val; - } else { - // .slice() creates a copy of the array - // this copy gets trimmed by min and max and then returned - vals = this.options.values.slice(); - for ( i = 0; i < vals.length; i+= 1) { - vals[ i ] = this._trimAlignValue( vals[ i ] ); - } - - return vals; - } - }, - - // returns the step-aligned value that val is closest to, between (inclusive) min and max - _trimAlignValue: function( val ) { - if ( val < this._valueMin() ) { - return this._valueMin(); - } - if ( val > this._valueMax() ) { - return this._valueMax(); - } - var step = ( this.options.step > 0 ) ? this.options.step : 1, - valModStep = val % step, - alignValue = val - valModStep; - - if ( Math.abs(valModStep) * 2 >= step ) { - alignValue += ( valModStep > 0 ) ? step : ( -step ); - } - - // Since JavaScript has problems with large floats, round - // the final value to 5 digits after the decimal point (see #4124) - return parseFloat( alignValue.toFixed(5) ); - }, - - _valueMin: function() { - return this.options.min; - }, - - _valueMax: function() { - return this.options.max; - }, - - _refreshValue: function() { - var oRange = this.options.range, - o = this.options, - self = this, - animate = ( !this._animateOff ) ? o.animate : false, - valPercent, - _set = {}, - lastValPercent, - value, - valueMin, - valueMax; - - if ( this.options.values && this.options.values.length ) { - this.handles.each(function( i, j ) { - valPercent = ( self.values(i) - self._valueMin() ) / ( self._valueMax() - self._valueMin() ) * 100; - _set[ self.orientation === "horizontal" ? "left" : "bottom" ] = valPercent + "%"; - $( this ).stop( 1, 1 )[ animate ? "animate" : "css" ]( _set, o.animate ); - if ( self.options.range === true ) { - if ( self.orientation === "horizontal" ) { - if ( i === 0 ) { - self.range.stop( 1, 1 )[ animate ? "animate" : "css" ]( { left: valPercent + "%" }, o.animate ); - } - if ( i === 1 ) { - self.range[ animate ? "animate" : "css" ]( { width: ( valPercent - lastValPercent ) + "%" }, { queue: false, duration: o.animate } ); - } - } else { - if ( i === 0 ) { - self.range.stop( 1, 1 )[ animate ? "animate" : "css" ]( { bottom: ( valPercent ) + "%" }, o.animate ); - } - if ( i === 1 ) { - self.range[ animate ? "animate" : "css" ]( { height: ( valPercent - lastValPercent ) + "%" }, { queue: false, duration: o.animate } ); - } - } - } - lastValPercent = valPercent; - }); - } else { - value = this.value(); - valueMin = this._valueMin(); - valueMax = this._valueMax(); - valPercent = ( valueMax !== valueMin ) ? - ( value - valueMin ) / ( valueMax - valueMin ) * 100 : - 0; - _set[ self.orientation === "horizontal" ? "left" : "bottom" ] = valPercent + "%"; - this.handle.stop( 1, 1 )[ animate ? "animate" : "css" ]( _set, o.animate ); - - if ( oRange === "min" && this.orientation === "horizontal" ) { - this.range.stop( 1, 1 )[ animate ? "animate" : "css" ]( { width: valPercent + "%" }, o.animate ); - } - if ( oRange === "max" && this.orientation === "horizontal" ) { - this.range[ animate ? "animate" : "css" ]( { width: ( 100 - valPercent ) + "%" }, { queue: false, duration: o.animate } ); - } - if ( oRange === "min" && this.orientation === "vertical" ) { - this.range.stop( 1, 1 )[ animate ? "animate" : "css" ]( { height: valPercent + "%" }, o.animate ); - } - if ( oRange === "max" && this.orientation === "vertical" ) { - this.range[ animate ? "animate" : "css" ]( { height: ( 100 - valPercent ) + "%" }, { queue: false, duration: o.animate } ); - } - } - } - -}); - -$.extend( $.ui.slider, { - version: "1.8.5" -}); - -}(jQuery)); diff -r 9287f22c692087319003516fe1a5da0eb07c63da -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e static/scripts/packed/libs/jquery/jquery.ui.sortable.slider.js --- a/static/scripts/packed/libs/jquery/jquery.ui.sortable.slider.js +++ /dev/null @@ -1,33 +0,0 @@ -/* - * jQuery UI 1.8.5 - * - * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI - */ -(function(a,c){a.ui=a.ui||{};if(a.ui.version){return}a.extend(a.ui,{version:"1.8.5",keyCode:{ALT:18,BACKSPACE:8,CAPS_LOCK:20,COMMA:188,COMMAND:91,COMMAND_LEFT:91,COMMAND_RIGHT:93,CONTROL:17,DELETE:46,DOWN:40,END:35,ENTER:13,ESCAPE:27,HOME:36,INSERT:45,LEFT:37,MENU:93,NUMPAD_ADD:107,NUMPAD_DECIMAL:110,NUMPAD_DIVIDE:111,NUMPAD_ENTER:108,NUMPAD_MULTIPLY:106,NUMPAD_SUBTRACT:109,PAGE_DOWN:34,PAGE_UP:33,PERIOD:190,RIGHT:39,SHIFT:16,SPACE:32,TAB:9,UP:38,WINDOWS:91}});a.fn.extend({_focus:a.fn.focus,focus:function(d,e){return typeof d==="number"?this.each(function(){var f=this;setTimeout(function(){a(f).focus();if(e){e.call(f)}},d)}):this._focus.apply(this,arguments)},scrollParent:function(){var d;if((a.browser.msie&&(/(static|relative)/).test(this.css("position")))||(/absolute/).test(this.css("position"))){d=this.parents().filter(function(){return(/(relative|absolute|fixed)/).test(a.curCSS(this,"position",1))&&(/(auto|scroll)/).test(a.curCSS(this,"overflow",1)+a.curCSS(this,"overflow-y",1)+a.curCSS(this,"overflow-x",1))}).eq(0)}else{d=this.parents().filter(function(){return(/(auto|scroll)/).test(a.curCSS(this,"overflow",1)+a.curCSS(this,"overflow-y",1)+a.curCSS(this,"overflow-x",1))}).eq(0)}return(/fixed/).test(this.css("position"))||!d.length?a(document):d},zIndex:function(g){if(g!==c){return this.css("zIndex",g)}if(this.length){var e=a(this[0]),d,f;while(e.length&&e[0]!==document){d=e.css("position");if(d==="absolute"||d==="relative"||d==="fixed"){f=parseInt(e.css("zIndex"));if(!isNaN(f)&&f!=0){return f}}e=e.parent()}}return 0},disableSelection:function(){return this.bind("mousedown.ui-disableSelection 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a.curCSS(this,"visibility")==="hidden"||a.expr.filters.hidden(this)}).length}a.extend(a.expr[":"],{data:function(f,e,d){return !!a.data(f,d[3])},focusable:function(f){var i=f.nodeName.toLowerCase(),d=a.attr(f,"tabindex");if("area"===i){var h=f.parentNode,g=h.name,e;if(!f.href||!g||h.nodeName.toLowerCase()!=="map"){return false}e=a("img[usemap=#"+g+"]")[0];return !!e&&b(e)}return(/input|select|textarea|button|object/.test(i)?!f.disabled:"a"==i?f.href||!isNaN(d):!isNaN(d))&&b(f)},tabbable:function(e){var d=a.attr(e,"tabindex");return(isNaN(d)||d>=0)&&a(e).is(":focusable")}});a(function(){var e=document.createElement("div"),d=document.body;a.extend(e.style,{minHeight:"100px",height:"auto",padding:0,borderWidth:0});a.support.minHeight=d.appendChild(e).offsetHeight===100;d.removeChild(e).style.display="none"});a.extend(a.ui,{plugin:{add:function(e,f,h){var g=a.ui[e].prototype;for(var d in h){g.plugins[d]=g.plugins[d]||[];g.plugins[d].push([f,h[d]])}},call:function(d,f,e){var h=d.plugins[f];if(!h||!d.element[0].parentNode){return}for(var g=0;g<h.length;g++){if(d.options[h[g][0]]){h[g][1].apply(d.element,e)}}}},contains:function(e,d){return document.compareDocumentPosition?e.compareDocumentPosition(d)&16:e!==d&&e.contains(d)},hasScroll:function(g,e){if(a(g).css("overflow")==="hidden"){return false}var d=(e&&e==="left")?"scrollLeft":"scrollTop",f=false;if(g[d]>0){return true}g[d]=1;f=(g[d]>0);g[d]=0;return f},isOverAxis:function(e,d,f){return(e>d)&&(e<(d+f))},isOver:function(i,e,h,g,d,f){return a.ui.isOverAxis(i,h,d)&&a.ui.isOverAxis(e,g,f)}})})(jQuery); -/* - * jQuery UI Widget 1.8.5 - * - * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Widget - */ -(function(b,d){if(b.cleanData){var c=b.cleanData;b.cleanData=function(e){for(var f=0,g;(g=e[f])!=null;f++){b(g).triggerHandler("remove")}c(e)}}else{var a=b.fn.remove;b.fn.remove=function(e,f){return this.each(function(){if(!f){if(!e||b.filter(e,[this]).length){b("*",this).add([this]).each(function(){b(this).triggerHandler("remove")})}}return a.call(b(this),e,f)})}}b.widget=function(f,h,e){var g=f.split(".")[0],j;f=f.split(".")[1];j=g+"-"+f;if(!e){e=h;h=b.Widget}b.expr[":"][j]=function(k){return !!b.data(k,f)};b[g]=b[g]||{};b[g][f]=function(k,l){if(arguments.length){this._createWidget(k,l)}};var i=new h();i.options=b.extend(true,{},i.options);b[g][f].prototype=b.extend(true,i,{namespace:g,widgetName:f,widgetEventPrefix:b[g][f].prototype.widgetEventPrefix||f,widgetBaseClass:j},e);b.widget.bridge(f,b[g][f])};b.widget.bridge=function(f,e){b.fn[f]=function(i){var g=typeof i==="string",h=Array.prototype.slice.call(arguments,1),j=this;i=!g&&h.length?b.extend.apply(null,[true,i].concat(h)):i;if(g&&i.substring(0,1)==="_"){return j}if(g){this.each(function(){var k=b.data(this,f);if(!k){throw"cannot call methods on "+f+" prior to initialization; attempted to call method '"+i+"'"}if(!b.isFunction(k[i])){throw"no such method '"+i+"' for "+f+" widget instance"}var l=k[i].apply(k,h);if(l!==k&&l!==d){j=l;return false}})}else{this.each(function(){var k=b.data(this,f);if(k){k.option(i||{})._init()}else{b.data(this,f,new e(i,this))}})}return j}};b.Widget=function(e,f){if(arguments.length){this._createWidget(e,f)}};b.Widget.prototype={widgetName:"widget",widgetEventPrefix:"",options:{disabled:false},_createWidget:function(f,g){b.data(g,this.widgetName,this);this.element=b(g);this.options=b.extend(true,{},this.options,b.metadata&&b.metadata.get(g)[this.widgetName],f);var e=this;this.element.bind("remove."+this.widgetName,function(){e.destroy()});this._create();this._init()},_create:function(){},_init:function(){},destroy:function(){this.element.unbind("."+this.widgetName).removeData(this.widgetName);this.widget().unbind("."+this.widgetName).removeAttr("aria-disabled").removeClass(this.widgetBaseClass+"-disabled 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Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Mouse - * - * Depends: - * jquery.ui.widget.js - */ -(function(a,b){a.widget("ui.mouse",{options:{cancel:":input,option",distance:1,delay:0},_mouseInit:function(){var c=this;this.element.bind("mousedown."+this.widgetName,function(d){return c._mouseDown(d)}).bind("click."+this.widgetName,function(d){if(c._preventClickEvent){c._preventClickEvent=false;d.stopImmediatePropagation();return false}});this.started=false},_mouseDestroy:function(){this.element.unbind("."+this.widgetName)},_mouseDown:function(e){e.originalEvent=e.originalEvent||{};if(e.originalEvent.mouseHandled){return}(this._mouseStarted&&this._mouseUp(e));this._mouseDownEvent=e;var d=this,f=(e.which==1),c=(typeof this.options.cancel=="string"?a(e.target).parents().add(e.target).filter(this.options.cancel).length:false);if(!f||c||!this._mouseCapture(e)){return true}this.mouseDelayMet=!this.options.delay;if(!this.mouseDelayMet){this._mouseDelayTimer=setTimeout(function(){d.mouseDelayMet=true},this.options.delay)}if(this._mouseDistanceMet(e)&&this._mouseDelayMet(e)){this._mouseStarted=(this._mouseStart(e)!==false);if(!this._mouseStarted){e.preventDefault();return true}}this._mouseMoveDelegate=function(g){return d._mouseMove(g)};this._mouseUpDelegate=function(g){return d._mouseUp(g)};a(document).bind("mousemove."+this.widgetName,this._mouseMoveDelegate).bind("mouseup."+this.widgetName,this._mouseUpDelegate);(a.browser.safari||e.preventDefault());e.originalEvent.mouseHandled=true;return true},_mouseMove:function(c){if(a.browser.msie&&!c.button){return this._mouseUp(c)}if(this._mouseStarted){this._mouseDrag(c);return c.preventDefault()}if(this._mouseDistanceMet(c)&&this._mouseDelayMet(c)){this._mouseStarted=(this._mouseStart(this._mouseDownEvent,c)!==false);(this._mouseStarted?this._mouseDrag(c):this._mouseUp(c))}return !this._mouseStarted},_mouseUp:function(c){a(document).unbind("mousemove."+this.widgetName,this._mouseMoveDelegate).unbind("mouseup."+this.widgetName,this._mouseUpDelegate);if(this._mouseStarted){this._mouseStarted=false;this._preventClickEvent=(c.target==this._mouseDownEvent.target);this._mouseStop(c)}return false},_mouseDistanceMet:function(c){return(Math.max(Math.abs(this._mouseDownEvent.pageX-c.pageX),Math.abs(this._mouseDownEvent.pageY-c.pageY))>=this.options.distance)},_mouseDelayMet:function(c){return this.mouseDelayMet},_mouseStart:function(c){},_mouseDrag:function(c){},_mouseStop:function(c){},_mouseCapture:function(c){return true}})})(jQuery);(function(a,b){a.widget("ui.sortable",a.ui.mouse,{widgetEventPrefix:"sort",options:{appendTo:"parent",axis:false,connectWith:false,containment:false,cursor:"auto",cursorAt:false,dropOnEmpty:true,forcePlaceholderSize:false,forceHelperSize:false,grid:false,handle:false,helper:"original",items:"> *",opacity:false,placeholder:false,revert:false,scroll:true,scrollSensitivity:20,scrollSpeed:20,scope:"default",tolerance:"intersect",zIndex:1000},_create:function(){var c=this.options;this.containerCache={};this.element.addClass("ui-sortable");this.refresh();this.floating=this.items.length?(/left|right/).test(this.items[0].item.css("float")):false;this.offset=this.element.offset();this._mouseInit()},destroy:function(){this.element.removeClass("ui-sortable ui-sortable-disabled").removeData("sortable").unbind(".sortable");this._mouseDestroy();for(var c=this.items.length-1;c>=0;c--){this.items[c].item.removeData("sortable-item")}return this},_setOption:function(c,d){if(c==="disabled"){this.options[c]=d;this.widget()[d?"addClass":"removeClass"]("ui-sortable-disabled")}else{a.Widget.prototype._setOption.apply(this,arguments)}},_mouseCapture:function(f,g){if(this.reverting){return false}if(this.options.disabled||this.options.type=="static"){return false}this._refreshItems(f);var e=null,d=this,c=a(f.target).parents().each(function(){if(a.data(this,"sortable-item")==d){e=a(this);return false}});if(a.data(f.target,"sortable-item")==d){e=a(f.target)}if(!e){return false}if(this.options.handle&&!g){var h=false;a(this.options.handle,e).find("*").andSelf().each(function(){if(this==f.target){h=true}});if(!h){return false}}this.currentItem=e;this._removeCurrentsFromItems();return true},_mouseStart:function(f,g,c){var h=this.options,d=this;this.currentContainer=this;this.refreshPositions();this.helper=this._createHelper(f);this._cacheHelperProportions();this._cacheMargins();this.scrollParent=this.helper.scrollParent();this.offset=this.currentItem.offset();this.offset={top:this.offset.top-this.margins.top,left:this.offset.left-this.margins.left};this.helper.css("position","absolute");this.cssPosition=this.helper.css("position");a.extend(this.offset,{click:{left:f.pageX-this.offset.left,top:f.pageY-this.offset.top},parent:this._getParentOffset(),relative:this._getRelativeOffset()});this.originalPosition=this._generatePosition(f);this.originalPageX=f.pageX;this.originalPageY=f.pageY;(h.cursorAt&&this._adjustOffsetFromHelper(h.cursorAt));this.domPosition={prev:this.currentItem.prev()[0],parent:this.currentItem.parent()[0]};if(this.helper[0]!=this.currentItem[0]){this.currentItem.hide()}this._createPlaceholder();if(h.containment){this._setContainment()}if(h.cursor){if(a("body").css("cursor")){this._storedCursor=a("body").css("cursor")}a("body").css("cursor",h.cursor)}if(h.opacity){if(this.helper.css("opacity")){this._storedOpacity=this.helper.css("opacity")}this.helper.css("opacity",h.opacity)}if(h.zIndex){if(this.helper.css("zIndex")){this._storedZIndex=this.helper.css("zIndex")}this.helper.css("zIndex",h.zIndex)}if(this.scrollParent[0]!=document&&this.scrollParent[0].tagName!="HTML"){this.overflowOffset=this.scrollParent.offset()}this._trigger("start",f,this._uiHash());if(!this._preserveHelperProportions){this._cacheHelperProportions()}if(!c){for(var e=this.containers.length-1;e>=0;e--){this.containers[e]._trigger("activate",f,d._uiHash(this))}}if(a.ui.ddmanager){a.ui.ddmanager.current=this}if(a.ui.ddmanager&&!h.dropBehaviour){a.ui.ddmanager.prepareOffsets(this,f)}this.dragging=true;this.helper.addClass("ui-sortable-helper");this._mouseDrag(f);return true},_mouseDrag:function(g){this.position=this._generatePosition(g);this.positionAbs=this._convertPositionTo("absolute");if(!this.lastPositionAbs){this.lastPositionAbs=this.positionAbs}if(this.options.scroll){var h=this.options,c=false;if(this.scrollParent[0]!=document&&this.scrollParent[0].tagName!="HTML"){if((this.overflowOffset.top+this.scrollParent[0].offsetHeight)-g.pageY<h.scrollSensitivity){this.scrollParent[0].scrollTop=c=this.scrollParent[0].scrollTop+h.scrollSpeed}else{if(g.pageY-this.overflowOffset.top<h.scrollSensitivity){this.scrollParent[0].scrollTop=c=this.scrollParent[0].scrollTop-h.scrollSpeed}}if((this.overflowOffset.left+this.scrollParent[0].offsetWidth)-g.pageX<h.scrollSensitivity){this.scrollParent[0].scrollLeft=c=this.scrollParent[0].scrollLeft+h.scrollSpeed}else{if(g.pageX-this.overflowOffset.left<h.scrollSensitivity){this.scrollParent[0].scrollLeft=c=this.scrollParent[0].scrollLeft-h.scrollSpeed}}}else{if(g.pageY-a(document).scrollTop()<h.scrollSensitivity){c=a(document).scrollTop(a(document).scrollTop()-h.scrollSpeed)}else{if(a(window).height()-(g.pageY-a(document).scrollTop())<h.scrollSensitivity){c=a(document).scrollTop(a(document).scrollTop()+h.scrollSpeed)}}if(g.pageX-a(document).scrollLeft()<h.scrollSensitivity){c=a(document).scrollLeft(a(document).scrollLeft()-h.scrollSpeed)}else{if(a(window).width()-(g.pageX-a(document).scrollLeft())<h.scrollSensitivity){c=a(document).scrollLeft(a(document).scrollLeft()+h.scrollSpeed)}}}if(c!==false&&a.ui.ddmanager&&!h.dropBehaviour){a.ui.ddmanager.prepareOffsets(this,g)}}this.positionAbs=this._convertPositionTo("absolute");if(!this.options.axis||this.options.axis!="y"){this.helper[0].style.left=this.position.left+"px"}if(!this.options.axis||this.options.axis!="x"){this.helper[0].style.top=this.position.top+"px"}for(var e=this.items.length-1;e>=0;e--){var f=this.items[e],d=f.item[0],j=this._intersectsWithPointer(f);if(!j){continue}if(d!=this.currentItem[0]&&this.placeholder[j==1?"next":"prev"]()[0]!=d&&!a.ui.contains(this.placeholder[0],d)&&(this.options.type=="semi-dynamic"?!a.ui.contains(this.element[0],d):true)){this.direction=j==1?"down":"up";if(this.options.tolerance=="pointer"||this._intersectsWithSides(f)){this._rearrange(g,f)}else{break}this._trigger("change",g,this._uiHash());break}}this._contactContainers(g);if(a.ui.ddmanager){a.ui.ddmanager.drag(this,g)}this._trigger("sort",g,this._uiHash());this.lastPositionAbs=this.positionAbs;return false},_mouseStop:function(d,e){if(!d){return}if(a.ui.ddmanager&&!this.options.dropBehaviour){a.ui.ddmanager.drop(this,d)}if(this.options.revert){var c=this;var f=c.placeholder.offset();c.reverting=true;a(this.helper).animate({left:f.left-this.offset.parent.left-c.margins.left+(this.offsetParent[0]==document.body?0:this.offsetParent[0].scrollLeft),top:f.top-this.offset.parent.top-c.margins.top+(this.offsetParent[0]==document.body?0:this.offsetParent[0].scrollTop)},parseInt(this.options.revert,10)||500,function(){c._clear(d)})}else{this._clear(d,e)}return false},cancel:function(){var c=this;if(this.dragging){this._mouseUp();if(this.options.helper=="original"){this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper")}else{this.currentItem.show()}for(var d=this.containers.length-1;d>=0;d--){this.containers[d]._trigger("deactivate",null,c._uiHash(this));if(this.containers[d].containerCache.over){this.containers[d]._trigger("out",null,c._uiHash(this));this.containers[d].containerCache.over=0}}}if(this.placeholder[0].parentNode){this.placeholder[0].parentNode.removeChild(this.placeholder[0])}if(this.options.helper!="original"&&this.helper&&this.helper[0].parentNode){this.helper.remove()}a.extend(this,{helper:null,dragging:false,reverting:false,_noFinalSort:null});if(this.domPosition.prev){a(this.domPosition.prev).after(this.currentItem)}else{a(this.domPosition.parent).prepend(this.currentItem)}return this},serialize:function(e){var c=this._getItemsAsjQuery(e&&e.connected);var d=[];e=e||{};a(c).each(function(){var f=(a(e.item||this).attr(e.attribute||"id")||"").match(e.expression||(/(.+)[-=_](.+)/));if(f){d.push((e.key||f[1]+"[]")+"="+(e.key&&e.expression?f[1]:f[2]))}});if(!d.length&&e.key){d.push(e.key+"=")}return d.join("&")},toArray:function(e){var c=this._getItemsAsjQuery(e&&e.connected);var d=[];e=e||{};c.each(function(){d.push(a(e.item||this).attr(e.attribute||"id")||"")});return d},_intersectsWith:function(m){var e=this.positionAbs.left,d=e+this.helperProportions.width,k=this.positionAbs.top,j=k+this.helperProportions.height;var f=m.left,c=f+m.width,n=m.top,i=n+m.height;var o=this.offset.click.top,h=this.offset.click.left;var g=(k+o)>n&&(k+o)<i&&(e+h)>f&&(e+h)<c;if(this.options.tolerance=="pointer"||this.options.forcePointerForContainers||(this.options.tolerance!="pointer"&&this.helperProportions[this.floating?"width":"height"]>m[this.floating?"width":"height"])){return g}else{return(f<e+(this.helperProportions.width/2)&&d-(this.helperProportions.width/2)<c&&n<k+(this.helperProportions.height/2)&&j-(this.helperProportions.height/2)<i)}},_intersectsWithPointer:function(e){var f=a.ui.isOverAxis(this.positionAbs.top+this.offset.click.top,e.top,e.height),d=a.ui.isOverAxis(this.positionAbs.left+this.offset.click.left,e.left,e.width),h=f&&d,c=this._getDragVerticalDirection(),g=this._getDragHorizontalDirection();if(!h){return false}return this.floating?(((g&&g=="right")||c=="down")?2:1):(c&&(c=="down"?2:1))},_intersectsWithSides:function(f){var d=a.ui.isOverAxis(this.positionAbs.top+this.offset.click.top,f.top+(f.height/2),f.height),e=a.ui.isOverAxis(this.positionAbs.left+this.offset.click.left,f.left+(f.width/2),f.width),c=this._getDragVerticalDirection(),g=this._getDragHorizontalDirection();if(this.floating&&g){return((g=="right"&&e)||(g=="left"&&!e))}else{return c&&((c=="down"&&d)||(c=="up"&&!d))}},_getDragVerticalDirection:function(){var c=this.positionAbs.top-this.lastPositionAbs.top;return c!=0&&(c>0?"down":"up")},_getDragHorizontalDirection:function(){var c=this.positionAbs.left-this.lastPositionAbs.left;return c!=0&&(c>0?"right":"left")},refresh:function(c){this._refreshItems(c);this.refreshPositions();return this},_connectWith:function(){var c=this.options;return c.connectWith.constructor==String?[c.connectWith]:c.connectWith},_getItemsAsjQuery:function(c){var m=this;var h=[];var f=[];var k=this._connectWith();if(k&&c){for(var e=k.length-1;e>=0;e--){var l=a(k[e]);for(var d=l.length-1;d>=0;d--){var g=a.data(l[d],"sortable");if(g&&g!=this&&!g.options.disabled){f.push([a.isFunction(g.options.items)?g.options.items.call(g.element):a(g.options.items,g.element).not(".ui-sortable-helper").not(".ui-sortable-placeholder"),g])}}}}f.push([a.isFunction(this.options.items)?this.options.items.call(this.element,null,{options:this.options,item:this.currentItem}):a(this.options.items,this.element).not(".ui-sortable-helper").not(".ui-sortable-placeholder"),this]);for(var e=f.length-1;e>=0;e--){f[e][0].each(function(){h.push(this)})}return a(h)},_removeCurrentsFromItems:function(){var e=this.currentItem.find(":data(sortable-item)");for(var d=0;d<this.items.length;d++){for(var c=0;c<e.length;c++){if(e[c]==this.items[d].item[0]){this.items.splice(d,1)}}}},_refreshItems:function(c){this.items=[];this.containers=[this];var k=this.items;var q=this;var g=[[a.isFunction(this.options.items)?this.options.items.call(this.element[0],c,{item:this.currentItem}):a(this.options.items,this.element),this]];var m=this._connectWith();if(m){for(var f=m.length-1;f>=0;f--){var n=a(m[f]);for(var e=n.length-1;e>=0;e--){var h=a.data(n[e],"sortable");if(h&&h!=this&&!h.options.disabled){g.push([a.isFunction(h.options.items)?h.options.items.call(h.element[0],c,{item:this.currentItem}):a(h.options.items,h.element),h]);this.containers.push(h)}}}}for(var f=g.length-1;f>=0;f--){var l=g[f][1];var d=g[f][0];for(var e=0,o=d.length;e<o;e++){var p=a(d[e]);p.data("sortable-item",l);k.push({item:p,instance:l,width:0,height:0,left:0,top:0})}}},refreshPositions:function(c){if(this.offsetParent&&this.helper){this.offset.parent=this._getParentOffset()}for(var e=this.items.length-1;e>=0;e--){var f=this.items[e];var d=this.options.toleranceElement?a(this.options.toleranceElement,f.item):f.item;if(!c){f.width=d.outerWidth();f.height=d.outerHeight()}var g=d.offset();f.left=g.left;f.top=g.top}if(this.options.custom&&this.options.custom.refreshContainers){this.options.custom.refreshContainers.call(this)}else{for(var e=this.containers.length-1;e>=0;e--){var g=this.containers[e].element.offset();this.containers[e].containerCache.left=g.left;this.containers[e].containerCache.top=g.top;this.containers[e].containerCache.width=this.containers[e].element.outerWidth();this.containers[e].containerCache.height=this.containers[e].element.outerHeight()}}return this},_createPlaceholder:function(e){var c=e||this,f=c.options;if(!f.placeholder||f.placeholder.constructor==String){var d=f.placeholder;f.placeholder={element:function(){var g=a(document.createElement(c.currentItem[0].nodeName)).addClass(d||c.currentItem[0].className+" ui-sortable-placeholder").removeClass("ui-sortable-helper")[0];if(!d){g.style.visibility="hidden"}return g},update:function(g,h){if(d&&!f.forcePlaceholderSize){return}if(!h.height()){h.height(c.currentItem.innerHeight()-parseInt(c.currentItem.css("paddingTop")||0,10)-parseInt(c.currentItem.css("paddingBottom")||0,10))}if(!h.width()){h.width(c.currentItem.innerWidth()-parseInt(c.currentItem.css("paddingLeft")||0,10)-parseInt(c.currentItem.css("paddingRight")||0,10))}}}}c.placeholder=a(f.placeholder.element.call(c.element,c.currentItem));c.currentItem.after(c.placeholder);f.placeholder.update(c,c.placeholder)},_contactContainers:function(c){var e=null,l=null;for(var g=this.containers.length-1;g>=0;g--){if(a.ui.contains(this.currentItem[0],this.containers[g].element[0])){continue}if(this._intersectsWith(this.containers[g].containerCache)){if(e&&a.ui.contains(this.containers[g].element[0],e.element[0])){continue}e=this.containers[g];l=g}else{if(this.containers[g].containerCache.over){this.containers[g]._trigger("out",c,this._uiHash(this));this.containers[g].containerCache.over=0}}}if(!e){return}if(this.containers.length===1){this.containers[l]._trigger("over",c,this._uiHash(this));this.containers[l].containerCache.over=1}else{if(this.currentContainer!=this.containers[l]){var k=10000;var h=null;var d=this.positionAbs[this.containers[l].floating?"left":"top"];for(var f=this.items.length-1;f>=0;f--){if(!a.ui.contains(this.containers[l].element[0],this.items[f].item[0])){continue}var m=this.items[f][this.containers[l].floating?"left":"top"];if(Math.abs(m-d)<k){k=Math.abs(m-d);h=this.items[f]}}if(!h&&!this.options.dropOnEmpty){return}this.currentContainer=this.containers[l];h?this._rearrange(c,h,null,true):this._rearrange(c,null,this.containers[l].element,true);this._trigger("change",c,this._uiHash());this.containers[l]._trigger("change",c,this._uiHash(this));this.options.placeholder.update(this.currentContainer,this.placeholder);this.containers[l]._trigger("over",c,this._uiHash(this));this.containers[l].containerCache.over=1}}},_createHelper:function(d){var e=this.options;var c=a.isFunction(e.helper)?a(e.helper.apply(this.element[0],[d,this.currentItem])):(e.helper=="clone"?this.currentItem.clone():this.currentItem);if(!c.parents("body").length){a(e.appendTo!="parent"?e.appendTo:this.currentItem[0].parentNode)[0].appendChild(c[0])}if(c[0]==this.currentItem[0]){this._storedCSS={width:this.currentItem[0].style.width,height:this.currentItem[0].style.height,position:this.currentItem.css("position"),top:this.currentItem.css("top"),left:this.currentItem.css("left")}}if(c[0].style.width==""||e.forceHelperSize){c.width(this.currentItem.width())}if(c[0].style.height==""||e.forceHelperSize){c.height(this.currentItem.height())}return c},_adjustOffsetFromHelper:function(c){if(typeof c=="string"){c=c.split(" ")}if(a.isArray(c)){c={left:+c[0],top:+c[1]||0}}if("left" in c){this.offset.click.left=c.left+this.margins.left}if("right" in c){this.offset.click.left=this.helperProportions.width-c.right+this.margins.left}if("top" in c){this.offset.click.top=c.top+this.margins.top}if("bottom" in c){this.offset.click.top=this.helperProportions.height-c.bottom+this.margins.top}},_getParentOffset:function(){this.offsetParent=this.helper.offsetParent();var c=this.offsetParent.offset();if(this.cssPosition=="absolute"&&this.scrollParent[0]!=document&&a.ui.contains(this.scrollParent[0],this.offsetParent[0])){c.left+=this.scrollParent.scrollLeft();c.top+=this.scrollParent.scrollTop()}if((this.offsetParent[0]==document.body)||(this.offsetParent[0].tagName&&this.offsetParent[0].tagName.toLowerCase()=="html"&&a.browser.msie)){c={top:0,left:0}}return{top:c.top+(parseInt(this.offsetParent.css("borderTopWidth"),10)||0),left:c.left+(parseInt(this.offsetParent.css("borderLeftWidth"),10)||0)}},_getRelativeOffset:function(){if(this.cssPosition=="relative"){var c=this.currentItem.position();return{top:c.top-(parseInt(this.helper.css("top"),10)||0)+this.scrollParent.scrollTop(),left:c.left-(parseInt(this.helper.css("left"),10)||0)+this.scrollParent.scrollLeft()}}else{return{top:0,left:0}}},_cacheMargins:function(){this.margins={left:(parseInt(this.currentItem.css("marginLeft"),10)||0),top:(parseInt(this.currentItem.css("marginTop"),10)||0)}},_cacheHelperProportions:function(){this.helperProportions={width:this.helper.outerWidth(),height:this.helper.outerHeight()}},_setContainment:function(){var f=this.options;if(f.containment=="parent"){f.containment=this.helper[0].parentNode}if(f.containment=="document"||f.containment=="window"){this.containment=[0-this.offset.relative.left-this.offset.parent.left,0-this.offset.relative.top-this.offset.parent.top,a(f.containment=="document"?document:window).width()-this.helperProportions.width-this.margins.left,(a(f.containment=="document"?document:window).height()||document.body.parentNode.scrollHeight)-this.helperProportions.height-this.margins.top]}if(!(/^(document|window|parent)$/).test(f.containment)){var d=a(f.containment)[0];var e=a(f.containment).offset();var c=(a(d).css("overflow")!="hidden");this.containment=[e.left+(parseInt(a(d).css("borderLeftWidth"),10)||0)+(parseInt(a(d).css("paddingLeft"),10)||0)-this.margins.left,e.top+(parseInt(a(d).css("borderTopWidth"),10)||0)+(parseInt(a(d).css("paddingTop"),10)||0)-this.margins.top,e.left+(c?Math.max(d.scrollWidth,d.offsetWidth):d.offsetWidth)-(parseInt(a(d).css("borderLeftWidth"),10)||0)-(parseInt(a(d).css("paddingRight"),10)||0)-this.helperProportions.width-this.margins.left,e.top+(c?Math.max(d.scrollHeight,d.offsetHeight):d.offsetHeight)-(parseInt(a(d).css("borderTopWidth"),10)||0)-(parseInt(a(d).css("paddingBottom"),10)||0)-this.helperProportions.height-this.margins.top]}},_convertPositionTo:function(g,i){if(!i){i=this.position}var e=g=="absolute"?1:-1;var f=this.options,c=this.cssPosition=="absolute"&&!(this.scrollParent[0]!=document&&a.ui.contains(this.scrollParent[0],this.offsetParent[0]))?this.offsetParent:this.scrollParent,h=(/(html|body)/i).test(c[0].tagName);return{top:(i.top+this.offset.relative.top*e+this.offset.parent.top*e-(a.browser.safari&&this.cssPosition=="fixed"?0:(this.cssPosition=="fixed"?-this.scrollParent.scrollTop():(h?0:c.scrollTop()))*e)),left:(i.left+this.offset.relative.left*e+this.offset.parent.left*e-(a.browser.safari&&this.cssPosition=="fixed"?0:(this.cssPosition=="fixed"?-this.scrollParent.scrollLeft():h?0:c.scrollLeft())*e))}},_generatePosition:function(f){var i=this.options,c=this.cssPosition=="absolute"&&!(this.scrollParent[0]!=document&&a.ui.contains(this.scrollParent[0],this.offsetParent[0]))?this.offsetParent:this.scrollParent,j=(/(html|body)/i).test(c[0].tagName);if(this.cssPosition=="relative"&&!(this.scrollParent[0]!=document&&this.scrollParent[0]!=this.offsetParent[0])){this.offset.relative=this._getRelativeOffset()}var e=f.pageX;var d=f.pageY;if(this.originalPosition){if(this.containment){if(f.pageX-this.offset.click.left<this.containment[0]){e=this.containment[0]+this.offset.click.left}if(f.pageY-this.offset.click.top<this.containment[1]){d=this.containment[1]+this.offset.click.top}if(f.pageX-this.offset.click.left>this.containment[2]){e=this.containment[2]+this.offset.click.left}if(f.pageY-this.offset.click.top>this.containment[3]){d=this.containment[3]+this.offset.click.top}}if(i.grid){var h=this.originalPageY+Math.round((d-this.originalPageY)/i.grid[1])*i.grid[1];d=this.containment?(!(h-this.offset.click.top<this.containment[1]||h-this.offset.click.top>this.containment[3])?h:(!(h-this.offset.click.top<this.containment[1])?h-i.grid[1]:h+i.grid[1])):h;var g=this.originalPageX+Math.round((e-this.originalPageX)/i.grid[0])*i.grid[0];e=this.containment?(!(g-this.offset.click.left<this.containment[0]||g-this.offset.click.left>this.containment[2])?g:(!(g-this.offset.click.left<this.containment[0])?g-i.grid[0]:g+i.grid[0])):g}}return{top:(d-this.offset.click.top-this.offset.relative.top-this.offset.parent.top+(a.browser.safari&&this.cssPosition=="fixed"?0:(this.cssPosition=="fixed"?-this.scrollParent.scrollTop():(j?0:c.scrollTop())))),left:(e-this.offset.click.left-this.offset.relative.left-this.offset.parent.left+(a.browser.safari&&this.cssPosition=="fixed"?0:(this.cssPosition=="fixed"?-this.scrollParent.scrollLeft():j?0:c.scrollLeft())))}},_rearrange:function(h,g,d,f){d?d[0].appendChild(this.placeholder[0]):g.item[0].parentNode.insertBefore(this.placeholder[0],(this.direction=="down"?g.item[0]:g.item[0].nextSibling));this.counter=this.counter?++this.counter:1;var e=this,c=this.counter;window.setTimeout(function(){if(c==e.counter){e.refreshPositions(!f)}},0)},_clear:function(e,f){this.reverting=false;var g=[],c=this;if(!this._noFinalSort&&this.currentItem[0].parentNode){this.placeholder.before(this.currentItem)}this._noFinalSort=null;if(this.helper[0]==this.currentItem[0]){for(var d in this._storedCSS){if(this._storedCSS[d]=="auto"||this._storedCSS[d]=="static"){this._storedCSS[d]=""}}this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper")}else{this.currentItem.show()}if(this.fromOutside&&!f){g.push(function(h){this._trigger("receive",h,this._uiHash(this.fromOutside))})}if((this.fromOutside||this.domPosition.prev!=this.currentItem.prev().not(".ui-sortable-helper")[0]||this.domPosition.parent!=this.currentItem.parent()[0])&&!f){g.push(function(h){this._trigger("update",h,this._uiHash())})}if(!a.ui.contains(this.element[0],this.currentItem[0])){if(!f){g.push(function(h){this._trigger("remove",h,this._uiHash())})}for(var d=this.containers.length-1;d>=0;d--){if(a.ui.contains(this.containers[d].element[0],this.currentItem[0])&&!f){g.push((function(h){return function(i){h._trigger("receive",i,this._uiHash(this))}}).call(this,this.containers[d]));g.push((function(h){return function(i){h._trigger("update",i,this._uiHash(this))}}).call(this,this.containers[d]))}}}for(var d=this.containers.length-1;d>=0;d--){if(!f){g.push((function(h){return function(i){h._trigger("deactivate",i,this._uiHash(this))}}).call(this,this.containers[d]))}if(this.containers[d].containerCache.over){g.push((function(h){return function(i){h._trigger("out",i,this._uiHash(this))}}).call(this,this.containers[d]));this.containers[d].containerCache.over=0}}if(this._storedCursor){a("body").css("cursor",this._storedCursor)}if(this._storedOpacity){this.helper.css("opacity",this._storedOpacity)}if(this._storedZIndex){this.helper.css("zIndex",this._storedZIndex=="auto"?"":this._storedZIndex)}this.dragging=false;if(this.cancelHelperRemoval){if(!f){this._trigger("beforeStop",e,this._uiHash());for(var d=0;d<g.length;d++){g[d].call(this,e)}this._trigger("stop",e,this._uiHash())}return false}if(!f){this._trigger("beforeStop",e,this._uiHash())}this.placeholder[0].parentNode.removeChild(this.placeholder[0]);if(this.helper[0]!=this.currentItem[0]){this.helper.remove()}this.helper=null;if(!f){for(var d=0;d<g.length;d++){g[d].call(this,e)}this._trigger("stop",e,this._uiHash())}this.fromOutside=false;return true},_trigger:function(){if(a.Widget.prototype._trigger.apply(this,arguments)===false){this.cancel()}},_uiHash:function(d){var c=d||this;return{helper:c.helper,placeholder:c.placeholder||a([]),position:c.position,originalPosition:c.originalPosition,offset:c.positionAbs,item:c.currentItem,sender:d?d.element:null}}});a.extend(a.ui.sortable,{version:"1.8.5"})})(jQuery);(function(b,c){var a=5;b.widget("ui.slider",b.ui.mouse,{widgetEventPrefix:"slide",options:{animate:false,distance:0,max:100,min:0,orientation:"horizontal",range:false,step:1,value:0,values:null},_create:function(){var d=this,e=this.options;this._keySliding=false;this._mouseSliding=false;this._animateOff=true;this._handleIndex=null;this._detectOrientation();this._mouseInit();this.element.addClass("ui-slider ui-slider-"+this.orientation+" ui-widget ui-widget-content ui-corner-all");if(e.disabled){this.element.addClass("ui-slider-disabled ui-disabled")}this.range=b([]);if(e.range){if(e.range===true){this.range=b("<div></div>");if(!e.values){e.values=[this._valueMin(),this._valueMin()]}if(e.values.length&&e.values.length!==2){e.values=[e.values[0],e.values[0]]}}else{this.range=b("<div></div>")}this.range.appendTo(this.element).addClass("ui-slider-range");if(e.range==="min"||e.range==="max"){this.range.addClass("ui-slider-range-"+e.range)}this.range.addClass("ui-widget-header")}if(b(".ui-slider-handle",this.element).length===0){b("<a href='#'></a>").appendTo(this.element).addClass("ui-slider-handle")}if(e.values&&e.values.length){while(b(".ui-slider-handle",this.element).length<e.values.length){b("<a href='#'></a>").appendTo(this.element).addClass("ui-slider-handle")}}this.handles=b(".ui-slider-handle",this.element).addClass("ui-state-default ui-corner-all");this.handle=this.handles.eq(0);this.handles.add(this.range).filter("a").click(function(f){f.preventDefault()}).hover(function(){if(!e.disabled){b(this).addClass("ui-state-hover")}},function(){b(this).removeClass("ui-state-hover")}).focus(function(){if(!e.disabled){b(".ui-slider .ui-state-focus").removeClass("ui-state-focus");b(this).addClass("ui-state-focus")}else{b(this).blur()}}).blur(function(){b(this).removeClass("ui-state-focus")});this.handles.each(function(f){b(this).data("index.ui-slider-handle",f)});this.handles.keydown(function(k){var h=true,g=b(this).data("index.ui-slider-handle"),l,i,f,j;if(d.options.disabled){return}switch(k.keyCode){case b.ui.keyCode.HOME:case b.ui.keyCode.END:case b.ui.keyCode.PAGE_UP:case b.ui.keyCode.PAGE_DOWN:case b.ui.keyCode.UP:case b.ui.keyCode.RIGHT:case b.ui.keyCode.DOWN:case b.ui.keyCode.LEFT:h=false;if(!d._keySliding){d._keySliding=true;b(this).addClass("ui-state-active");l=d._start(k,g);if(l===false){return}}break}j=d.options.step;if(d.options.values&&d.options.values.length){i=f=d.values(g)}else{i=f=d.value()}switch(k.keyCode){case b.ui.keyCode.HOME:f=d._valueMin();break;case b.ui.keyCode.END:f=d._valueMax();break;case b.ui.keyCode.PAGE_UP:f=d._trimAlignValue(i+((d._valueMax()-d._valueMin())/a));break;case b.ui.keyCode.PAGE_DOWN:f=d._trimAlignValue(i-((d._valueMax()-d._valueMin())/a));break;case b.ui.keyCode.UP:case b.ui.keyCode.RIGHT:if(i===d._valueMax()){return}f=d._trimAlignValue(i+j);break;case b.ui.keyCode.DOWN:case b.ui.keyCode.LEFT:if(i===d._valueMin()){return}f=d._trimAlignValue(i-j);break}d._slide(k,g,f);return h}).keyup(function(g){var f=b(this).data("index.ui-slider-handle");if(d._keySliding){d._keySliding=false;d._stop(g,f);d._change(g,f);b(this).removeClass("ui-state-active")}});this._refreshValue();this._animateOff=false},destroy:function(){this.handles.remove();this.range.remove();this.element.removeClass("ui-slider ui-slider-horizontal ui-slider-vertical ui-slider-disabled ui-widget ui-widget-content ui-corner-all").removeData("slider").unbind(".slider");this._mouseDestroy();return this},_mouseCapture:function(f){var g=this.options,j,l,e,h,n,k,m,i,d;if(g.disabled){return false}this.elementSize={width:this.element.outerWidth(),height:this.element.outerHeight()};this.elementOffset=this.element.offset();j={x:f.pageX,y:f.pageY};l=this._normValueFromMouse(j);e=this._valueMax()-this._valueMin()+1;n=this;this.handles.each(function(o){var p=Math.abs(l-n.values(o));if(e>p){e=p;h=b(this);k=o}});if(g.range===true&&this.values(1)===g.min){k+=1;h=b(this.handles[k])}m=this._start(f,k);if(m===false){return 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\ No newline at end of file diff -r 9287f22c692087319003516fe1a5da0eb07c63da -r 382c9cb6d6016ea58a50d5b2fd5a02ca484f4f6e templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -21,7 +21,7 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/libs/IE/excanvas.js')}"></script><![endif]--> -${h.js( "galaxy.base", "galaxy.panels", "libs/json2", "libs/jquery/jquery", "libs/bootstrap", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery-ui-1.8.23.custom.min", "mvc/data", "viz/visualization", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.ui.sortable.slider", "libs/farbtastic" )} +${h.js( "galaxy.base", "galaxy.panels", "libs/json2", "libs/jquery/jquery", "libs/bootstrap", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery-ui-1.8.23.custom.min", "mvc/data", "viz/visualization", "viz/trackster", "viz/trackster_ui", "libs/farbtastic" )} <script type="text/javascript"> // 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: jgoecks: jQuery UI enhancements: (a) update to v1.8.23; (b) remove core script and replace with script that includes core, autocomplete, sliders, and dependencies; (c) replace overcast theme with smoothness theme; and (d) add directory for jQuery UI styles.
by Bitbucket 05 Sep '12

05 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9287f22c6920/ changeset: 9287f22c6920 user: jgoecks date: 2012-09-05 15:35:21 summary: jQuery UI enhancements: (a) update to v1.8.23; (b) remove core script and replace with script that includes core, autocomplete, sliders, and dependencies; (c) replace overcast theme with smoothness theme; and (d) add directory for jQuery UI styles. affected #: 33 files diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da static/june_2007_style/blue/jquery-ui/smoothness/images/ui-bg_flat_0_aaaaaa_40x100.png Binary file static/june_2007_style/blue/jquery-ui/smoothness/images/ui-bg_flat_0_aaaaaa_40x100.png has changed diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da static/june_2007_style/blue/jquery-ui/smoothness/images/ui-bg_flat_75_ffffff_40x100.png Binary file 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static/june_2007_style/blue/jquery-ui/smoothness/images/ui-icons_222222_256x240.png Binary file static/june_2007_style/blue/jquery-ui/smoothness/images/ui-icons_222222_256x240.png has changed diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da static/june_2007_style/blue/jquery-ui/smoothness/images/ui-icons_2e83ff_256x240.png Binary file static/june_2007_style/blue/jquery-ui/smoothness/images/ui-icons_2e83ff_256x240.png has changed diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da static/june_2007_style/blue/jquery-ui/smoothness/images/ui-icons_454545_256x240.png Binary file static/june_2007_style/blue/jquery-ui/smoothness/images/ui-icons_454545_256x240.png has changed diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da static/june_2007_style/blue/jquery-ui/smoothness/images/ui-icons_888888_256x240.png Binary file static/june_2007_style/blue/jquery-ui/smoothness/images/ui-icons_888888_256x240.png has changed diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da static/june_2007_style/blue/jquery-ui/smoothness/images/ui-icons_cd0a0a_256x240.png Binary file static/june_2007_style/blue/jquery-ui/smoothness/images/ui-icons_cd0a0a_256x240.png has changed diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da static/june_2007_style/blue/jquery-ui/smoothness/jquery-ui-1.8.23.custom.css --- /dev/null +++ b/static/june_2007_style/blue/jquery-ui/smoothness/jquery-ui-1.8.23.custom.css @@ -0,0 +1,363 @@ +/*! + * jQuery UI CSS Framework 1.8.23 + * + * Copyright 2012, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Theming/API + */ + +/* Layout helpers +----------------------------------*/ +.ui-helper-hidden { display: none; } +.ui-helper-hidden-accessible { position: absolute !important; clip: rect(1px 1px 1px 1px); clip: rect(1px,1px,1px,1px); } +.ui-helper-reset { margin: 0; padding: 0; border: 0; outline: 0; line-height: 1.3; text-decoration: none; font-size: 100%; list-style: none; } +.ui-helper-clearfix:before, .ui-helper-clearfix:after { content: ""; display: table; } +.ui-helper-clearfix:after { clear: both; } +.ui-helper-clearfix { zoom: 1; } +.ui-helper-zfix { width: 100%; height: 100%; top: 0; left: 0; position: absolute; opacity: 0; filter:Alpha(Opacity=0); } + + +/* Interaction Cues +----------------------------------*/ +.ui-state-disabled { cursor: default !important; } + + +/* Icons +----------------------------------*/ + +/* states and images */ +.ui-icon { display: block; text-indent: -99999px; overflow: hidden; background-repeat: no-repeat; } + + +/* Misc visuals +----------------------------------*/ + +/* Overlays */ +.ui-widget-overlay { position: absolute; top: 0; left: 0; width: 100%; height: 100%; } + + +/*! + * jQuery UI CSS Framework 1.8.23 + * + * Copyright 2012, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Theming/API + * + * To view and modify this theme, visit http://jqueryui.com/themeroller/?ffDefault=Verdana,Arial,sans-serif&fwDefau… + */ + + +/* Component containers +----------------------------------*/ +.ui-widget { font-family: Verdana,Arial,sans-serif; font-size: 1.1em; } +.ui-widget .ui-widget { font-size: 1em; } +.ui-widget input, .ui-widget select, .ui-widget textarea, .ui-widget button { font-family: Verdana,Arial,sans-serif; font-size: 1em; } +.ui-widget-content { border: 1px solid #aaaaaa; background: #ffffff url(images/ui-bg_flat_75_ffffff_40x100.png) 50% 50% repeat-x; color: #222222; } +.ui-widget-content a { color: #222222; } +.ui-widget-header { border: 1px solid #aaaaaa; background: #cccccc url(images/ui-bg_highlight-soft_75_cccccc_1x100.png) 50% 50% repeat-x; color: #222222; font-weight: bold; } +.ui-widget-header a { color: #222222; } + +/* Interaction states +----------------------------------*/ +.ui-state-default, .ui-widget-content .ui-state-default, .ui-widget-header .ui-state-default { border: 1px solid #d3d3d3; background: #e6e6e6 url(images/ui-bg_glass_75_e6e6e6_1x400.png) 50% 50% repeat-x; font-weight: normal; color: #555555; } +.ui-state-default a, .ui-state-default a:link, .ui-state-default a:visited { color: #555555; text-decoration: none; } +.ui-state-hover, .ui-widget-content .ui-state-hover, .ui-widget-header .ui-state-hover, .ui-state-focus, .ui-widget-content .ui-state-focus, .ui-widget-header .ui-state-focus { border: 1px solid #999999; background: #dadada url(images/ui-bg_glass_75_dadada_1x400.png) 50% 50% repeat-x; font-weight: normal; color: #212121; } +.ui-state-hover a, .ui-state-hover a:hover { color: #212121; text-decoration: none; } +.ui-state-active, .ui-widget-content .ui-state-active, .ui-widget-header .ui-state-active { border: 1px solid #aaaaaa; background: #ffffff url(images/ui-bg_glass_65_ffffff_1x400.png) 50% 50% repeat-x; font-weight: normal; color: #212121; } +.ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited { color: #212121; text-decoration: none; } +.ui-widget :active { outline: none; } + +/* Interaction Cues +----------------------------------*/ +.ui-state-highlight, .ui-widget-content .ui-state-highlight, .ui-widget-header .ui-state-highlight {border: 1px solid #fcefa1; background: #fbf9ee url(images/ui-bg_glass_55_fbf9ee_1x400.png) 50% 50% repeat-x; color: #363636; } +.ui-state-highlight a, .ui-widget-content .ui-state-highlight a,.ui-widget-header .ui-state-highlight a { color: #363636; } +.ui-state-error, .ui-widget-content .ui-state-error, .ui-widget-header .ui-state-error {border: 1px solid #cd0a0a; background: #fef1ec url(images/ui-bg_glass_95_fef1ec_1x400.png) 50% 50% repeat-x; color: #cd0a0a; } +.ui-state-error a, .ui-widget-content .ui-state-error a, .ui-widget-header .ui-state-error a { color: #cd0a0a; } +.ui-state-error-text, .ui-widget-content .ui-state-error-text, .ui-widget-header .ui-state-error-text { color: #cd0a0a; } +.ui-priority-primary, .ui-widget-content .ui-priority-primary, .ui-widget-header .ui-priority-primary { font-weight: bold; } +.ui-priority-secondary, .ui-widget-content .ui-priority-secondary, .ui-widget-header .ui-priority-secondary { opacity: .7; filter:Alpha(Opacity=70); font-weight: normal; } +.ui-state-disabled, .ui-widget-content .ui-state-disabled, .ui-widget-header .ui-state-disabled { opacity: .35; filter:Alpha(Opacity=35); background-image: none; } + +/* Icons +----------------------------------*/ + +/* states and images */ +.ui-icon { width: 16px; height: 16px; background-image: url(images/ui-icons_222222_256x240.png); } +.ui-widget-content .ui-icon {background-image: url(images/ui-icons_222222_256x240.png); } +.ui-widget-header .ui-icon {background-image: url(images/ui-icons_222222_256x240.png); } +.ui-state-default .ui-icon { background-image: url(images/ui-icons_888888_256x240.png); } +.ui-state-hover .ui-icon, .ui-state-focus .ui-icon {background-image: url(images/ui-icons_454545_256x240.png); } +.ui-state-active .ui-icon {background-image: url(images/ui-icons_454545_256x240.png); } +.ui-state-highlight .ui-icon {background-image: url(images/ui-icons_2e83ff_256x240.png); } +.ui-state-error .ui-icon, .ui-state-error-text .ui-icon {background-image: url(images/ui-icons_cd0a0a_256x240.png); } + +/* positioning */ +.ui-icon-carat-1-n { background-position: 0 0; } +.ui-icon-carat-1-ne { background-position: -16px 0; } +.ui-icon-carat-1-e { background-position: -32px 0; } +.ui-icon-carat-1-se { background-position: -48px 0; } +.ui-icon-carat-1-s { background-position: -64px 0; } +.ui-icon-carat-1-sw { background-position: -80px 0; } +.ui-icon-carat-1-w { background-position: -96px 0; } +.ui-icon-carat-1-nw { background-position: -112px 0; } +.ui-icon-carat-2-n-s { background-position: -128px 0; } +.ui-icon-carat-2-e-w { background-position: -144px 0; } +.ui-icon-triangle-1-n { background-position: 0 -16px; } +.ui-icon-triangle-1-ne { background-position: -16px -16px; } +.ui-icon-triangle-1-e { background-position: -32px -16px; } +.ui-icon-triangle-1-se { background-position: -48px -16px; } +.ui-icon-triangle-1-s { background-position: -64px -16px; } +.ui-icon-triangle-1-sw { background-position: -80px -16px; } +.ui-icon-triangle-1-w { background-position: -96px -16px; } +.ui-icon-triangle-1-nw { background-position: -112px -16px; } +.ui-icon-triangle-2-n-s { background-position: -128px -16px; } +.ui-icon-triangle-2-e-w { background-position: -144px -16px; } +.ui-icon-arrow-1-n { background-position: 0 -32px; } +.ui-icon-arrow-1-ne { background-position: -16px -32px; } +.ui-icon-arrow-1-e { background-position: -32px -32px; } +.ui-icon-arrow-1-se { background-position: -48px -32px; } +.ui-icon-arrow-1-s { background-position: -64px -32px; } +.ui-icon-arrow-1-sw { background-position: -80px -32px; } +.ui-icon-arrow-1-w { background-position: -96px -32px; } +.ui-icon-arrow-1-nw { background-position: -112px -32px; } +.ui-icon-arrow-2-n-s { background-position: -128px -32px; } +.ui-icon-arrow-2-ne-sw { background-position: -144px -32px; } +.ui-icon-arrow-2-e-w { background-position: -160px -32px; } +.ui-icon-arrow-2-se-nw { background-position: -176px -32px; } +.ui-icon-arrowstop-1-n { background-position: -192px -32px; } +.ui-icon-arrowstop-1-e { background-position: -208px -32px; } +.ui-icon-arrowstop-1-s { background-position: -224px -32px; } +.ui-icon-arrowstop-1-w { background-position: -240px -32px; } +.ui-icon-arrowthick-1-n { background-position: 0 -48px; } +.ui-icon-arrowthick-1-ne { background-position: -16px -48px; } +.ui-icon-arrowthick-1-e { background-position: -32px -48px; } +.ui-icon-arrowthick-1-se { background-position: -48px -48px; } +.ui-icon-arrowthick-1-s { background-position: -64px -48px; } +.ui-icon-arrowthick-1-sw { background-position: -80px -48px; } +.ui-icon-arrowthick-1-w { background-position: -96px -48px; } +.ui-icon-arrowthick-1-nw { background-position: -112px -48px; } +.ui-icon-arrowthick-2-n-s { background-position: -128px -48px; } +.ui-icon-arrowthick-2-ne-sw { background-position: -144px -48px; } +.ui-icon-arrowthick-2-e-w { background-position: -160px -48px; } +.ui-icon-arrowthick-2-se-nw { background-position: -176px -48px; } +.ui-icon-arrowthickstop-1-n { background-position: -192px -48px; } +.ui-icon-arrowthickstop-1-e { background-position: -208px -48px; } +.ui-icon-arrowthickstop-1-s { background-position: -224px -48px; } +.ui-icon-arrowthickstop-1-w { background-position: -240px -48px; } +.ui-icon-arrowreturnthick-1-w { background-position: 0 -64px; } +.ui-icon-arrowreturnthick-1-n { background-position: -16px -64px; } +.ui-icon-arrowreturnthick-1-e { background-position: -32px -64px; } +.ui-icon-arrowreturnthick-1-s { background-position: -48px -64px; } +.ui-icon-arrowreturn-1-w { background-position: -64px -64px; } +.ui-icon-arrowreturn-1-n { background-position: -80px -64px; } +.ui-icon-arrowreturn-1-e { background-position: -96px -64px; } +.ui-icon-arrowreturn-1-s { background-position: -112px -64px; } +.ui-icon-arrowrefresh-1-w { background-position: -128px -64px; } +.ui-icon-arrowrefresh-1-n { background-position: -144px -64px; } +.ui-icon-arrowrefresh-1-e { background-position: -160px -64px; } +.ui-icon-arrowrefresh-1-s { background-position: -176px -64px; } +.ui-icon-arrow-4 { background-position: 0 -80px; } +.ui-icon-arrow-4-diag { background-position: -16px -80px; } +.ui-icon-extlink { background-position: -32px -80px; } +.ui-icon-newwin { background-position: -48px -80px; } +.ui-icon-refresh { background-position: -64px -80px; } +.ui-icon-shuffle { background-position: -80px -80px; } +.ui-icon-transfer-e-w { background-position: -96px -80px; } +.ui-icon-transferthick-e-w { background-position: -112px -80px; } +.ui-icon-folder-collapsed { background-position: 0 -96px; } +.ui-icon-folder-open { background-position: -16px -96px; } +.ui-icon-document { background-position: -32px -96px; } +.ui-icon-document-b { background-position: -48px -96px; } +.ui-icon-note { background-position: -64px -96px; } +.ui-icon-mail-closed { background-position: -80px -96px; } +.ui-icon-mail-open { background-position: -96px -96px; } +.ui-icon-suitcase { background-position: -112px -96px; } +.ui-icon-comment { background-position: -128px -96px; } +.ui-icon-person { background-position: -144px -96px; } +.ui-icon-print { background-position: -160px -96px; } +.ui-icon-trash { background-position: -176px -96px; } +.ui-icon-locked { background-position: -192px -96px; } +.ui-icon-unlocked { background-position: -208px -96px; } +.ui-icon-bookmark { background-position: -224px -96px; } +.ui-icon-tag { background-position: -240px -96px; } +.ui-icon-home { background-position: 0 -112px; } +.ui-icon-flag { background-position: -16px -112px; } +.ui-icon-calendar { background-position: -32px -112px; } +.ui-icon-cart { background-position: -48px -112px; } +.ui-icon-pencil { background-position: -64px -112px; } +.ui-icon-clock { background-position: -80px -112px; } +.ui-icon-disk { background-position: -96px -112px; } +.ui-icon-calculator { background-position: -112px -112px; } +.ui-icon-zoomin { background-position: -128px -112px; } +.ui-icon-zoomout { background-position: -144px -112px; } +.ui-icon-search { background-position: -160px -112px; } +.ui-icon-wrench { background-position: -176px -112px; } +.ui-icon-gear { background-position: -192px -112px; } +.ui-icon-heart { background-position: -208px -112px; } +.ui-icon-star { background-position: -224px -112px; } +.ui-icon-link { background-position: -240px -112px; } +.ui-icon-cancel { background-position: 0 -128px; } +.ui-icon-plus { background-position: -16px -128px; } +.ui-icon-plusthick { background-position: -32px -128px; } +.ui-icon-minus { background-position: -48px -128px; } +.ui-icon-minusthick { background-position: -64px -128px; } +.ui-icon-close { background-position: -80px -128px; } +.ui-icon-closethick { background-position: -96px -128px; } +.ui-icon-key { background-position: -112px -128px; } +.ui-icon-lightbulb { background-position: -128px -128px; } +.ui-icon-scissors { background-position: -144px -128px; } +.ui-icon-clipboard { background-position: -160px -128px; } +.ui-icon-copy { background-position: -176px -128px; } +.ui-icon-contact { background-position: -192px -128px; } +.ui-icon-image { background-position: -208px -128px; } +.ui-icon-video { background-position: -224px -128px; } +.ui-icon-script { background-position: -240px -128px; } +.ui-icon-alert { background-position: 0 -144px; } +.ui-icon-info { background-position: -16px -144px; } +.ui-icon-notice { background-position: -32px -144px; } +.ui-icon-help { background-position: -48px -144px; } +.ui-icon-check { background-position: -64px -144px; } +.ui-icon-bullet { background-position: -80px -144px; } +.ui-icon-radio-off { background-position: -96px -144px; } +.ui-icon-radio-on { background-position: -112px -144px; } +.ui-icon-pin-w { background-position: -128px -144px; } +.ui-icon-pin-s { background-position: -144px -144px; } +.ui-icon-play { background-position: 0 -160px; } +.ui-icon-pause { background-position: -16px -160px; } +.ui-icon-seek-next { background-position: -32px -160px; } +.ui-icon-seek-prev { background-position: -48px -160px; } +.ui-icon-seek-end { background-position: -64px -160px; } +.ui-icon-seek-start { background-position: -80px -160px; } +/* ui-icon-seek-first is deprecated, use ui-icon-seek-start instead */ +.ui-icon-seek-first { background-position: -80px -160px; } +.ui-icon-stop { background-position: -96px -160px; } +.ui-icon-eject { background-position: -112px -160px; } +.ui-icon-volume-off { background-position: -128px -160px; } +.ui-icon-volume-on { background-position: -144px -160px; } +.ui-icon-power { background-position: 0 -176px; } +.ui-icon-signal-diag { background-position: -16px -176px; } +.ui-icon-signal { background-position: -32px -176px; } +.ui-icon-battery-0 { background-position: -48px -176px; } +.ui-icon-battery-1 { background-position: -64px -176px; } +.ui-icon-battery-2 { background-position: -80px -176px; } +.ui-icon-battery-3 { background-position: -96px -176px; } +.ui-icon-circle-plus { background-position: 0 -192px; } +.ui-icon-circle-minus { background-position: -16px -192px; } +.ui-icon-circle-close { background-position: -32px -192px; } +.ui-icon-circle-triangle-e { background-position: -48px -192px; } +.ui-icon-circle-triangle-s { background-position: -64px -192px; } +.ui-icon-circle-triangle-w { background-position: -80px -192px; } +.ui-icon-circle-triangle-n { background-position: -96px -192px; } +.ui-icon-circle-arrow-e { background-position: -112px -192px; } +.ui-icon-circle-arrow-s { background-position: -128px -192px; } +.ui-icon-circle-arrow-w { background-position: -144px -192px; } +.ui-icon-circle-arrow-n { background-position: -160px -192px; } +.ui-icon-circle-zoomin { background-position: -176px -192px; } +.ui-icon-circle-zoomout { background-position: -192px -192px; } +.ui-icon-circle-check { background-position: -208px -192px; } +.ui-icon-circlesmall-plus { background-position: 0 -208px; } +.ui-icon-circlesmall-minus { background-position: -16px -208px; } +.ui-icon-circlesmall-close { background-position: -32px -208px; } +.ui-icon-squaresmall-plus { background-position: -48px -208px; } +.ui-icon-squaresmall-minus { background-position: -64px -208px; } +.ui-icon-squaresmall-close { background-position: -80px -208px; } +.ui-icon-grip-dotted-vertical { background-position: 0 -224px; } +.ui-icon-grip-dotted-horizontal { background-position: -16px -224px; } +.ui-icon-grip-solid-vertical { background-position: -32px -224px; } +.ui-icon-grip-solid-horizontal { background-position: -48px -224px; } +.ui-icon-gripsmall-diagonal-se { background-position: -64px -224px; } +.ui-icon-grip-diagonal-se { background-position: -80px -224px; } + + +/* Misc visuals +----------------------------------*/ + +/* Corner radius */ +.ui-corner-all, .ui-corner-top, .ui-corner-left, .ui-corner-tl { -moz-border-radius-topleft: 4px; -webkit-border-top-left-radius: 4px; -khtml-border-top-left-radius: 4px; border-top-left-radius: 4px; } +.ui-corner-all, .ui-corner-top, .ui-corner-right, .ui-corner-tr { -moz-border-radius-topright: 4px; -webkit-border-top-right-radius: 4px; -khtml-border-top-right-radius: 4px; border-top-right-radius: 4px; } +.ui-corner-all, .ui-corner-bottom, .ui-corner-left, .ui-corner-bl { -moz-border-radius-bottomleft: 4px; -webkit-border-bottom-left-radius: 4px; -khtml-border-bottom-left-radius: 4px; border-bottom-left-radius: 4px; } +.ui-corner-all, .ui-corner-bottom, .ui-corner-right, .ui-corner-br { -moz-border-radius-bottomright: 4px; -webkit-border-bottom-right-radius: 4px; -khtml-border-bottom-right-radius: 4px; border-bottom-right-radius: 4px; } + +/* Overlays */ +.ui-widget-overlay { background: #aaaaaa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x; opacity: .30;filter:Alpha(Opacity=30); } +.ui-widget-shadow { margin: -8px 0 0 -8px; padding: 8px; background: #aaaaaa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x; opacity: .30;filter:Alpha(Opacity=30); -moz-border-radius: 8px; -khtml-border-radius: 8px; -webkit-border-radius: 8px; border-radius: 8px; }/*! + * jQuery UI Autocomplete 1.8.23 + * + * Copyright 2012, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Autocomplete#theming + */ +.ui-autocomplete { position: absolute; cursor: default; } + +/* workarounds */ +* html .ui-autocomplete { width:1px; } /* without this, the menu expands to 100% in IE6 */ + +/* + * jQuery UI Menu 1.8.23 + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Menu#theming + */ +.ui-menu { + list-style:none; + padding: 2px; + margin: 0; + display:block; + float: left; +} +.ui-menu .ui-menu { + margin-top: -3px; +} +.ui-menu .ui-menu-item { + margin:0; + padding: 0; + zoom: 1; + float: left; + clear: left; + width: 100%; +} +.ui-menu .ui-menu-item a { + text-decoration:none; + display:block; + padding:.2em .4em; + line-height:1.5; + zoom:1; +} +.ui-menu .ui-menu-item a.ui-state-hover, +.ui-menu .ui-menu-item a.ui-state-active { + font-weight: normal; + margin: -1px; +} +/*! + * jQuery UI Slider 1.8.23 + * + * Copyright 2012, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Slider#theming + */ +.ui-slider { position: relative; text-align: left; } +.ui-slider .ui-slider-handle { position: absolute; z-index: 2; width: 1.2em; height: 1.2em; cursor: default; } +.ui-slider .ui-slider-range { position: absolute; z-index: 1; font-size: .7em; display: block; border: 0; background-position: 0 0; } + +.ui-slider-horizontal { height: .8em; } +.ui-slider-horizontal .ui-slider-handle { top: -.3em; margin-left: -.6em; } +.ui-slider-horizontal .ui-slider-range { top: 0; height: 100%; } +.ui-slider-horizontal .ui-slider-range-min { left: 0; } +.ui-slider-horizontal .ui-slider-range-max { right: 0; } + +.ui-slider-vertical { width: .8em; height: 100px; } +.ui-slider-vertical .ui-slider-handle { left: -.3em; margin-left: 0; margin-bottom: -.6em; } +.ui-slider-vertical .ui-slider-range { left: 0; width: 100%; } +.ui-slider-vertical .ui-slider-range-min { bottom: 0; } +.ui-slider-vertical .ui-slider-range-max { top: 0; } \ No newline at end of file diff -r 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static/june_2007_style/blue/overcast/images/ui-bg_inset-hard_75_999999_1x100.png has changed diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da static/june_2007_style/blue/overcast/images/ui-bg_inset-soft_50_c9c9c9_1x100.png Binary file static/june_2007_style/blue/overcast/images/ui-bg_inset-soft_50_c9c9c9_1x100.png has changed diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da static/june_2007_style/blue/overcast/jquery-ui-1.8.5.custom.css --- a/static/june_2007_style/blue/overcast/jquery-ui-1.8.5.custom.css +++ /dev/null @@ -1,318 +0,0 @@ -/* - * jQuery UI CSS Framework @VERSION - * - * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Theming/API - */ - -/* Layout helpers -----------------------------------*/ -.ui-helper-hidden { display: none; } -.ui-helper-hidden-accessible { position: absolute; left: -99999999px; } -.ui-helper-reset { margin: 0; padding: 0; border: 0; outline: 0; line-height: 1.3; text-decoration: none; font-size: 100%; list-style: none; } -.ui-helper-clearfix:after { content: "."; display: block; height: 0; clear: both; visibility: hidden; } -.ui-helper-clearfix { display: inline-block; } -/* required comment for clearfix to work in Opera \*/ -* html .ui-helper-clearfix { height:1%; } -.ui-helper-clearfix { display:block; } -/* end clearfix */ -.ui-helper-zfix { width: 100%; height: 100%; top: 0; left: 0; position: absolute; opacity: 0; filter:Alpha(Opacity=0); } - - -/* Interaction Cues -----------------------------------*/ -.ui-state-disabled { cursor: default !important; } - - -/* Icons -----------------------------------*/ - -/* states and images */ -.ui-icon { display: block; text-indent: -99999px; overflow: hidden; background-repeat: no-repeat; } - - -/* Misc visuals -----------------------------------*/ - -/* Overlays */ -.ui-widget-overlay { position: absolute; top: 0; left: 0; width: 100%; height: 100%; } - - -/* - * jQuery UI CSS Framework @VERSION - * - * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Theming/API - * - * To view and modify this theme, visit http://jqueryui.com/themeroller/?ffDefault=Trebuchet%20MS,%20Helvetica,%20A… - */ - - -/* Component containers -----------------------------------*/ -.ui-widget { font-family: Trebuchet MS, Helvetica, Arial, sans-serif; font-size: 1.1em; } -.ui-widget .ui-widget { font-size: 1em; } -.ui-widget input, .ui-widget select, .ui-widget textarea, .ui-widget button { font-family: Trebuchet MS, Helvetica, Arial, sans-serif; font-size: 1em; } -.ui-widget-content { border: 1px solid #aaaaaa; background: #c9c9c9 url(images/ui-bg_inset-soft_50_c9c9c9_1x100.png) 50% bottom repeat-x; color: #333333; } -.ui-widget-content a { color: #333333; } -.ui-widget-header { border: 1px solid #bbbbbb; background: #dddddd url(images/ui-bg_glass_35_dddddd_1x400.png) 50% 50% repeat-x; color: #444444; font-weight: bold; } -.ui-widget-header a { color: #444444; } - -/* Interaction states -----------------------------------*/ -.ui-state-default, .ui-widget-content .ui-state-default, .ui-widget-header .ui-state-default { border: 1px solid #cccccc; background: #eeeeee url(images/ui-bg_glass_60_eeeeee_1x400.png) 50% 50% repeat-x; font-weight: bold; color: #3383bb; } -.ui-state-default a, .ui-state-default a:link, .ui-state-default a:visited { color: #3383bb; text-decoration: none; } -.ui-state-hover, .ui-widget-content .ui-state-hover, .ui-widget-header .ui-state-hover, .ui-state-focus, .ui-widget-content .ui-state-focus, .ui-widget-header .ui-state-focus { border: 1px solid #bbbbbb; background: #f8f8f8 url(images/ui-bg_glass_100_f8f8f8_1x400.png) 50% 50% repeat-x; font-weight: bold; color: #599fcf; } -.ui-state-hover a, .ui-state-hover a:hover { color: #599fcf; text-decoration: none; } -.ui-state-active, .ui-widget-content .ui-state-active, .ui-widget-header .ui-state-active { border: 1px solid #999999; background: #999999 url(images/ui-bg_inset-hard_75_999999_1x100.png) 50% 50% repeat-x; font-weight: bold; color: #ffffff; } -.ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited { color: #ffffff; text-decoration: none; } -.ui-widget :active { outline: none; } - -/* Interaction Cues -----------------------------------*/ -.ui-state-highlight, .ui-widget-content .ui-state-highlight, .ui-widget-header .ui-state-highlight {border: 1px solid #ffffff; background: #eeeeee url(images/ui-bg_flat_55_eeeeee_40x100.png) 50% 50% repeat-x; color: #444444; } -.ui-state-highlight a, .ui-widget-content .ui-state-highlight a,.ui-widget-header .ui-state-highlight a { color: #444444; } -.ui-state-error, .ui-widget-content .ui-state-error, .ui-widget-header .ui-state-error {border: 1px solid #c0402a; background: #c0402a url(images/ui-bg_flat_55_c0402a_40x100.png) 50% 50% repeat-x; color: #ffffff; } -.ui-state-error a, .ui-widget-content .ui-state-error a, .ui-widget-header .ui-state-error a { color: #ffffff; } -.ui-state-error-text, .ui-widget-content .ui-state-error-text, .ui-widget-header .ui-state-error-text { color: #ffffff; } -.ui-priority-primary, .ui-widget-content .ui-priority-primary, .ui-widget-header .ui-priority-primary { font-weight: bold; } -.ui-priority-secondary, .ui-widget-content .ui-priority-secondary, .ui-widget-header .ui-priority-secondary { opacity: .7; filter:Alpha(Opacity=70); font-weight: normal; } -.ui-state-disabled, .ui-widget-content .ui-state-disabled, .ui-widget-header .ui-state-disabled { opacity: .35; filter:Alpha(Opacity=35); background-image: none; } - -/* Icons -----------------------------------*/ - -/* states and images */ -.ui-icon { width: 16px; height: 16px; background-image: 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\ No newline at end of file diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da static/scripts/libs/jquery/jquery.ui.core.js --- a/static/scripts/libs/jquery/jquery.ui.core.js +++ /dev/null @@ -1,519 +0,0 @@ -/* - * jQuery UI 1.7.1 - * - * Copyright (c) 2009 AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT (MIT-LICENSE.txt) - * and GPL (GPL-LICENSE.txt) licenses. - * - * http://docs.jquery.com/UI - */ -;jQuery.ui || (function($) { - -var _remove = $.fn.remove, - isFF2 = $.browser.mozilla && (parseFloat($.browser.version) < 1.9); - -//Helper functions and ui object -$.ui = { - version: "1.7.1", - - // $.ui.plugin is deprecated. Use the proxy pattern instead. - plugin: { - add: function(module, option, set) { - var proto = $.ui[module].prototype; - for(var i in set) { - proto.plugins[i] = proto.plugins[i] || []; - proto.plugins[i].push([option, set[i]]); - } - }, - call: function(instance, name, args) { - var set = instance.plugins[name]; - if(!set || !instance.element[0].parentNode) { return; } - - for (var i = 0; i < set.length; i++) { - if (instance.options[set[i][0]]) { - set[i][1].apply(instance.element, args); - } - } - } - }, - - contains: function(a, b) { - return document.compareDocumentPosition - ? a.compareDocumentPosition(b) & 16 - : a !== b && a.contains(b); - }, - - hasScroll: function(el, a) { - - //If overflow is hidden, the element might have extra content, but the user wants to hide it - if ($(el).css('overflow') == 'hidden') { return false; } - - var scroll = (a && a == 'left') ? 'scrollLeft' : 'scrollTop', - has = false; - - if (el[scroll] > 0) { return true; } - - // TODO: determine which cases actually cause this to happen - // if the element doesn't have the scroll set, see if it's possible to - // set the scroll - el[scroll] = 1; - has = (el[scroll] > 0); - el[scroll] = 0; - return has; - }, - - isOverAxis: function(x, reference, size) { - //Determines when x coordinate is over "b" element axis - return (x > reference) && (x < (reference + size)); - }, - - isOver: function(y, x, top, left, height, width) { - //Determines when x, y coordinates is over "b" element - return $.ui.isOverAxis(y, top, height) && $.ui.isOverAxis(x, left, width); - }, - - keyCode: { - BACKSPACE: 8, - CAPS_LOCK: 20, - COMMA: 188, - CONTROL: 17, - DELETE: 46, - DOWN: 40, - END: 35, - ENTER: 13, - ESCAPE: 27, - HOME: 36, - INSERT: 45, - LEFT: 37, - NUMPAD_ADD: 107, - NUMPAD_DECIMAL: 110, - NUMPAD_DIVIDE: 111, - NUMPAD_ENTER: 108, - NUMPAD_MULTIPLY: 106, - NUMPAD_SUBTRACT: 109, - PAGE_DOWN: 34, - PAGE_UP: 33, - PERIOD: 190, - RIGHT: 39, - SHIFT: 16, - SPACE: 32, - TAB: 9, - UP: 38 - } -}; - -// WAI-ARIA normalization -if (isFF2) { - var attr = $.attr, - removeAttr = $.fn.removeAttr, - ariaNS = "http://www.w3.org/2005/07/aaa", - ariaState = /^aria-/, - ariaRole = /^wairole:/; - - $.attr = function(elem, name, value) { - var set = value !== undefined; - - return (name == 'role' - ? (set - ? attr.call(this, elem, name, "wairole:" + value) - : (attr.apply(this, arguments) || "").replace(ariaRole, "")) - : (ariaState.test(name) - ? (set - ? elem.setAttributeNS(ariaNS, - name.replace(ariaState, "aaa:"), value) - : attr.call(this, elem, name.replace(ariaState, "aaa:"))) - : attr.apply(this, arguments))); - }; - - $.fn.removeAttr = function(name) { - return (ariaState.test(name) - ? this.each(function() { - this.removeAttributeNS(ariaNS, name.replace(ariaState, "")); - }) : removeAttr.call(this, name)); - }; -} - -//jQuery plugins -$.fn.extend({ - remove: function() { - // Safari has a native remove event which actually removes DOM elements, - // so we have to use triggerHandler instead of trigger (#3037). - $("*", this).add(this).each(function() { - $(this).triggerHandler("remove"); - }); - return _remove.apply(this, arguments ); - }, - - enableSelection: function() { - return this - .attr('unselectable', 'off') - .css('MozUserSelect', '') - .unbind('selectstart.ui'); - }, - - disableSelection: function() { - return this - .attr('unselectable', 'on') - .css('MozUserSelect', 'none') - .bind('selectstart.ui', function() { return false; }); - }, - - scrollParent: function() { - var scrollParent; - if(($.browser.msie && (/(static|relative)/).test(this.css('position'))) || (/absolute/).test(this.css('position'))) { - scrollParent = this.parents().filter(function() { - return (/(relative|absolute|fixed)/).test($.curCSS(this,'position',1)) && (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); - }).eq(0); - } else { - scrollParent = this.parents().filter(function() { - return (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); - }).eq(0); - } - - return (/fixed/).test(this.css('position')) || !scrollParent.length ? $(document) : scrollParent; - } -}); - - -//Additional selectors -$.extend($.expr[':'], { - data: function(elem, i, match) { - return !!$.data(elem, match[3]); - }, - - focusable: function(element) { - var nodeName = element.nodeName.toLowerCase(), - tabIndex = $.attr(element, 'tabindex'); - return (/input|select|textarea|button|object/.test(nodeName) - ? !element.disabled - : 'a' == nodeName || 'area' == nodeName - ? element.href || !isNaN(tabIndex) - : !isNaN(tabIndex)) - // the element and all of its ancestors must be visible - // the browser may report that the area is hidden - && !$(element)['area' == nodeName ? 'parents' : 'closest'](':hidden').length; - }, - - tabbable: function(element) { - var tabIndex = $.attr(element, 'tabindex'); - return (isNaN(tabIndex) || tabIndex >= 0) && $(element).is(':focusable'); - } -}); - - -// $.widget is a factory to create jQuery plugins -// taking some boilerplate code out of the plugin code -function getter(namespace, plugin, method, args) { - function getMethods(type) { - var methods = $[namespace][plugin][type] || []; - return (typeof methods == 'string' ? methods.split(/,?\s+/) : methods); - } - - var methods = getMethods('getter'); - if (args.length == 1 && typeof args[0] == 'string') { - methods = methods.concat(getMethods('getterSetter')); - } - return ($.inArray(method, methods) != -1); -} - -$.widget = function(name, prototype) { - var namespace = name.split(".")[0]; - name = name.split(".")[1]; - - // create plugin method - $.fn[name] = function(options) { - var isMethodCall = (typeof options == 'string'), - args = Array.prototype.slice.call(arguments, 1); - - // prevent calls to internal methods - if (isMethodCall && options.substring(0, 1) == '_') { - return this; - } - - // handle getter methods - if (isMethodCall && getter(namespace, name, options, args)) { - var instance = $.data(this[0], name); - return (instance ? instance[options].apply(instance, args) - : undefined); - } - - // handle initialization and non-getter methods - return this.each(function() { - var instance = $.data(this, name); - - // constructor - (!instance && !isMethodCall && - $.data(this, name, new $[namespace][name](this, options))._init()); - - // method call - (instance && isMethodCall && $.isFunction(instance[options]) && - instance[options].apply(instance, args)); - }); - }; - - // create widget constructor - $[namespace] = $[namespace] || {}; - $[namespace][name] = function(element, options) { - var self = this; - - this.namespace = namespace; - this.widgetName = name; - this.widgetEventPrefix = $[namespace][name].eventPrefix || name; - this.widgetBaseClass = namespace + '-' + name; - - this.options = $.extend({}, - $.widget.defaults, - $[namespace][name].defaults, - $.metadata && $.metadata.get(element)[name], - options); - - this.element = $(element) - .bind('setData.' + name, function(event, key, value) { - if (event.target == element) { - return self._setData(key, value); - } - }) - .bind('getData.' + name, function(event, key) { - if (event.target == element) { - return self._getData(key); - } - }) - .bind('remove', function() { - return self.destroy(); - }); - }; - - // add widget prototype - $[namespace][name].prototype = $.extend({}, $.widget.prototype, prototype); - - // TODO: merge getter and getterSetter properties from widget prototype - // and plugin prototype - $[namespace][name].getterSetter = 'option'; -}; - -$.widget.prototype = { - _init: function() {}, - destroy: function() { - this.element.removeData(this.widgetName) - .removeClass(this.widgetBaseClass + '-disabled' + ' ' + this.namespace + '-state-disabled') - .removeAttr('aria-disabled'); - }, - - option: function(key, value) { - var options = key, - self = this; - - if (typeof key == "string") { - if (value === undefined) { - return this._getData(key); - } - options = {}; - options[key] = value; - } - - $.each(options, function(key, value) { - self._setData(key, value); - }); - }, - _getData: function(key) { - return this.options[key]; - }, - _setData: function(key, value) { - this.options[key] = value; - - if (key == 'disabled') { - this.element - [value ? 'addClass' : 'removeClass']( - this.widgetBaseClass + '-disabled' + ' ' + - this.namespace + '-state-disabled') - .attr("aria-disabled", value); - } - }, - - enable: function() { - this._setData('disabled', false); - }, - disable: function() { - this._setData('disabled', true); - }, - - _trigger: function(type, event, data) { - var callback = this.options[type], - eventName = (type == this.widgetEventPrefix - ? type : this.widgetEventPrefix + type); - - event = $.Event(event); - event.type = eventName; - - // copy original event properties over to the new event - // this would happen if we could call $.event.fix instead of $.Event - // but we don't have a way to force an event to be fixed multiple times - if (event.originalEvent) { - for (var i = $.event.props.length, prop; i;) { - prop = $.event.props[--i]; - event[prop] = event.originalEvent[prop]; - } - } - - this.element.trigger(event, data); - - return !($.isFunction(callback) && callback.call(this.element[0], event, data) === false - || event.isDefaultPrevented()); - } -}; - -$.widget.defaults = { - disabled: false -}; - - -/** Mouse Interaction Plugin **/ - -$.ui.mouse = { - _mouseInit: function() { - var self = this; - - this.element - .bind('mousedown.'+this.widgetName, function(event) { - return self._mouseDown(event); - }) - .bind('click.'+this.widgetName, function(event) { - if(self._preventClickEvent) { - self._preventClickEvent = false; - event.stopImmediatePropagation(); - return false; - } - }); - - // Prevent text selection in IE - if ($.browser.msie) { - this._mouseUnselectable = this.element.attr('unselectable'); - this.element.attr('unselectable', 'on'); - } - - this.started = false; - }, - - // TODO: make sure destroying one instance of mouse doesn't mess with - // other instances of mouse - _mouseDestroy: function() { - this.element.unbind('.'+this.widgetName); - - // Restore text selection in IE - ($.browser.msie - && this.element.attr('unselectable', this._mouseUnselectable)); - }, - - _mouseDown: function(event) { - // don't let more than one widget handle mouseStart - // TODO: figure out why we have to use originalEvent - event.originalEvent = event.originalEvent || {}; - if (event.originalEvent.mouseHandled) { return; } - - // we may have missed mouseup (out of window) - (this._mouseStarted && this._mouseUp(event)); - - this._mouseDownEvent = event; - - var self = this, - btnIsLeft = (event.which == 1), - elIsCancel = (typeof this.options.cancel == "string" ? $(event.target).parents().add(event.target).filter(this.options.cancel).length : false); - if (!btnIsLeft || elIsCancel || !this._mouseCapture(event)) { - return true; - } - - this.mouseDelayMet = !this.options.delay; - if (!this.mouseDelayMet) { - this._mouseDelayTimer = setTimeout(function() { - self.mouseDelayMet = true; - }, this.options.delay); - } - - if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { - this._mouseStarted = (this._mouseStart(event) !== false); - if (!this._mouseStarted) { - event.preventDefault(); - return true; - } - } - - // these delegates are required to keep context - this._mouseMoveDelegate = function(event) { - return self._mouseMove(event); - }; - this._mouseUpDelegate = function(event) { - return self._mouseUp(event); - }; - $(document) - .bind('mousemove.'+this.widgetName, this._mouseMoveDelegate) - .bind('mouseup.'+this.widgetName, this._mouseUpDelegate); - - // preventDefault() is used to prevent the selection of text here - - // however, in Safari, this causes select boxes not to be selectable - // anymore, so this fix is needed - ($.browser.safari || event.preventDefault()); - - event.originalEvent.mouseHandled = true; - return true; - }, - - _mouseMove: function(event) { - // IE mouseup check - mouseup happened when mouse was out of window - if ($.browser.msie && !event.button) { - return this._mouseUp(event); - } - - if (this._mouseStarted) { - this._mouseDrag(event); - return event.preventDefault(); - } - - if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { - this._mouseStarted = - (this._mouseStart(this._mouseDownEvent, event) !== false); - (this._mouseStarted ? this._mouseDrag(event) : this._mouseUp(event)); - } - - return !this._mouseStarted; - }, - - _mouseUp: function(event) { - $(document) - .unbind('mousemove.'+this.widgetName, this._mouseMoveDelegate) - .unbind('mouseup.'+this.widgetName, this._mouseUpDelegate); - - if (this._mouseStarted) { - this._mouseStarted = false; - this._preventClickEvent = (event.target == this._mouseDownEvent.target); - this._mouseStop(event); - } - - return false; - }, - - _mouseDistanceMet: function(event) { - return (Math.max( - Math.abs(this._mouseDownEvent.pageX - event.pageX), - Math.abs(this._mouseDownEvent.pageY - event.pageY) - ) >= this.options.distance - ); - }, - - _mouseDelayMet: function(event) { - return this.mouseDelayMet; - }, - - // These are placeholder methods, to be overriden by extending plugin - _mouseStart: function(event) {}, - _mouseDrag: function(event) {}, - _mouseStop: function(event) {}, - _mouseCapture: function(event) { return true; } -}; - -$.ui.mouse.defaults = { - cancel: null, - distance: 1, - delay: 0 -}; - -})(jQuery); diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da static/scripts/packed/libs/jquery/jquery-ui-1.8.23.custom.min.js --- /dev/null +++ b/static/scripts/packed/libs/jquery/jquery-ui-1.8.23.custom.min.js @@ -0,0 +1,30 @@ +/* jQuery UI - v1.8.23 - 2012-08-15 +* https://github.com/jquery/jquery-ui +* Includes: jquery.ui.core.js +* Copyright (c) 2012 AUTHORS.txt; Licensed MIT, GPL */ +(function(f,e){function h(a,l){var k=a.nodeName.toLowerCase();if("area"===k){var j=a.parentNode,i=j.name,d;return !a.href||!i||j.nodeName.toLowerCase()!=="map"?!1:(d=f("img[usemap=#"+i+"]")[0],!!d&&g(d))}return(/input|select|textarea|button|object/.test(k)?!a.disabled:"a"==k?a.href||l:l)&&g(a)}function g(a){return 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(c) 2012 AUTHORS.txt; Licensed MIT, GPL */ +(function(e,d){var f=!1;e(document).mouseup(function(b){f=!1}),e.widget("ui.mouse",{options:{cancel:":input,option",distance:1,delay:0},_mouseInit:function(){var a=this;this.element.bind("mousedown."+this.widgetName,function(b){return a._mouseDown(b)}).bind("click."+this.widgetName,function(b){if(!0===e.data(b.target,a.widgetName+".preventClickEvent")){return e.removeData(b.target,a.widgetName+".preventClickEvent"),b.stopImmediatePropagation(),!1}}),this.started=!1},_mouseDestroy:function(){this.element.unbind("."+this.widgetName),this._mouseMoveDelegate&&e(document).unbind("mousemove."+this.widgetName,this._mouseMoveDelegate).unbind("mouseup."+this.widgetName,this._mouseUpDelegate)},_mouseDown:function(a){if(f){return}this._mouseStarted&&this._mouseUp(a),this._mouseDownEvent=a;var h=this,g=a.which==1,c=typeof 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UI - v1.8.23 - 2012-08-15 +* https://github.com/jquery/jquery-ui +* Includes: jquery.ui.position.js +* Copyright (c) 2012 AUTHORS.txt; Licensed MIT, GPL */ +(function(j,i){j.ui=j.ui||{};var p=/left|center|right/,o=/top|center|bottom/,n="center",m={},l=j.fn.position,k=j.fn.offset;j.fn.position=function(c){if(!c||!c.of){return l.apply(this,arguments)}c=j.extend({},c);var q=j(c.of),g=q[0],f=(c.collision||"flip").split(" "),e=c.offset?c.offset.split(" "):[0,0],d,a,r;return g.nodeType===9?(d=q.width(),a=q.height(),r={top:0,left:0}):g.setTimeout?(d=q.width(),a=q.height(),r={top:q.scrollTop(),left:q.scrollLeft()}):g.preventDefault?(c.at="left top",d=a=0,r={top:c.of.pageY,left:c.of.pageX}):(d=q.outerWidth(),a=q.outerHeight(),r=q.offset()),j.each(["my","at"],function(){var b=(c[this]||"").split(" 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g=j(window),f=h.collisionPosition.top+h.collisionHeight-g.height()-g.scrollTop();a.top=f>0?a.top-f:Math.max(a.top-h.collisionPosition.top,a.top)}},flip:{left:function(a,u){if(u.at[0]===n){return}var t=j(window),s=u.collisionPosition.left+u.collisionWidth-t.width()-t.scrollLeft(),r=u.my[0]==="left"?-u.elemWidth:u.my[0]==="right"?u.elemWidth:0,q=u.at[0]==="left"?u.targetWidth:-u.targetWidth,e=-2*u.offset[0];a.left+=u.collisionPosition.left<0?r+q+e:s>0?r+q+e:0},top:function(a,u){if(u.at[1]===n){return}var t=j(window),s=u.collisionPosition.top+u.collisionHeight-t.height()-t.scrollTop(),r=u.my[1]==="top"?-u.elemHeight:u.my[1]==="bottom"?u.elemHeight:0,q=u.at[1]==="top"?u.targetHeight:-u.targetHeight,e=-2*u.offset[1];a.top+=u.collisionPosition.top<0?r+q+e:s>0?r+q+e:0}}},j.offset.setOffset||(j.offset.setOffset=function(a,v){/static/.test(j.curCSS(a,"position"))&&(a.style.position="relative");var 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c}).offset(),u.innerHTML="",t.removeChild(u),q=r.top+r.left+(a?2000:0),m.fractions=q>21&&q<22}()})(jQuery); +/* jQuery UI - v1.8.23 - 2012-08-15 +* https://github.com/jquery/jquery-ui +* Includes: jquery.ui.autocomplete.js +* Copyright (c) 2012 AUTHORS.txt; Licensed MIT, GPL */ +(function(e,d){var f=0;e.widget("ui.autocomplete",{options:{appendTo:"body",autoFocus:!1,delay:300,minLength:1,position:{my:"left top",at:"left bottom",collision:"none"},source:null},pending:0,_create:function(){var a=this,h=this.element[0].ownerDocument,g;this.isMultiLine=this.element.is("textarea"),this.element.addClass("ui-autocomplete-input").attr("autocomplete","off").attr({role:"textbox","aria-autocomplete":"list","aria-haspopup":"true"}).bind("keydown.autocomplete",function(i){if(a.options.disabled||a.element.propAttr("readOnly")){return}g=!1;var b=e.ui.keyCode;switch(i.keyCode){case b.PAGE_UP:a._move("previousPage",i);break;case b.PAGE_DOWN:a._move("nextPage",i);break;case 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b},_render_visibleWarning:function(){var b=null;if(!this.model.get("visible")&&this.model.get("unhide_url")){var a=HistoryItemView.TEMPLATES.hiddenMsg(this.model.attributes);b=$(HistoryItemView.TEMPLATES.warningMsg({warning:a}))}return b},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>'),b=this.model.get("for_editing");if(this.model.get("state")!==HistoryItem.STATES.UPLOAD){a.append(this._render_displayButton());if(b){a.append(this._render_editButton())}}if(b){a.append(this._render_deleteButton())}return a},_render_displayButton:function(){if(this.model.get("purged")){return $('<span class="icon-button display_disabled tooltip" title="Cannot display datasets removed from disk"></span>')}var b=this.model.get("id"),a={title:"Display data in browser",href:"/datasets/"+b+"/display/?preview=True",target:(this.model.get("for_editing"))?("galaxy_main"):(""),classes:["icon-button","tooltip","display"],dataset_id:b};return $(linkHTMLTemplate(a))},_render_editButton:function(){var c=this.model.get("id"),b=this.model.get("purged"),a=this.model.get("deleted");if(a||b){if(!b){return $('<span class="icon-button edit_disabled tooltip" title="Undelete dataset to edit attributes"></span>')}else{return $('<span class="icon-button edit_disabled tooltip" title="Cannot edit attributes of datasets removed from disk"></span>')}}return $(linkHTMLTemplate({title:"Edit attributes",href:"/datasets/"+c+"/edit",target:"galaxy_main",classes:["icon-button","tooltip","edit"]}))},_render_deleteButton:function(){var c=this.model.get("id"),b=this.model.get("purged"),a=this.model.get("deleted");if(b||a){return $('<span title="Dataset is already deleted" class="icon-button delete_disabled tooltip"></span>')}return $(linkHTMLTemplate({title:"Delete",href:"/datasets/"+c+"/delete?show_deleted_on_refresh=False",target:"galaxy_main",id:"historyItemDeleter-"+c,classes:["icon-button","tooltip","delete"]}))},_render_titleLink:function(){var b=this.model.get("name"),a=this.model.get("hid");title=(a+": "+b);return $(linkHTMLTemplate({href:"javascript:void(0);",text:'<span class="historyItemTitle">'+title+"</span>"}))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_showParamsAndRerun())},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_showParamsAndRerun())},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));var b=$(this._render_showParamsAndRerun());if(this.model.get("for_editing")){b.prepend($(linkHTMLTemplate({title:"View or report this error",href:this.model.get("report_errors_url"),target:"galaxy_main",classes:["icon-button","tooltip","bug"]})))}if(this.model.hasData()){b.prepend(this._render_downloadLinks())}a.append(b)},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_showParamsAndRerun())},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_showParamsAndRerun())},_render_body_failed_metadata:function(b){var c="An error occurred setting the metadata for this dataset.";if(this.model.isEditable()){var a=linkHTMLTemplate({text:"set it manually or retry auto-detection",href:this.model.get("edit_url"),target:"galaxy_main"});c+="You may be able to "+a+"."}b.append($(HistoryItemView.TEMPLATES.warningMsg({warning:c})));this._render_body_ok(b)},_render_body_ok:function(i){i.append(this._render_hdaSummary());if(this.model.get("misc_info")){i.append($('<div class="info">Info: '+this.model.get("misc_info")+"</div>"))}if(this.model.hasData()){var d=$("<div/>");d.append(this._render_downloadLinks());d.append($(linkHTMLTemplate({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",classes:["icon-button","tooltip","information"]})));if(this.model.get("for_editing")){d.append($(linkHTMLTemplate({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",classes:["icon-button","tooltip","arrow-circle"]})));if(this.model.get("trackster_urls")){var a=this.model.get("trackster_urls");d.append($(linkHTMLTemplate({title:"View in Trackster",href:"javascript:void(0)",classes:["icon-button","tooltip","chart_curve","trackster-add"],"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]})))}if(this.model.get("retag_url")&&this.model.get("annotate_url")){var e=$('<div style="float: right;"></div>');e.append($(linkHTMLTemplate({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),classes:["icon-button","tooltip","tags"]})));e.append($(linkHTMLTemplate({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotation_url"),classes:["icon-button","tooltip","annotate"]})));d.append(e);d.append('<div style="clear: both"></div>');var c=$('<div class="tag-area" style="display: none">');c.append("<strong>Tags:</strong>");c.append('<div class="tag-elt"></div>');d.append(c);var f=$(('<div id="${dataset_id}-annotation-area" class="annotation-area" style="display: none">'));f.append("<strong>Annotation:</strong>");f.append(('<div id="${dataset_id}-annotation-elt" style="margin: 1px 0px 1px 0px" class="annotation-elt tooltip editable-text" title="Edit dataset annotation"></div>'));d.append(f)}}d.append('<div style="clear: both;"></div>');i.append(d);var j=$("<div/>");if(this.model.get("display_apps")){var k=this.model.get("display_apps"),b=$("<span/>");for(app_name in k){var h=k[app_name],g=app_name+" ";for(location_name in h){g+=linkHTMLTemplate({text:location_name,href:h[location_name].url,target:h[location_name].target})+" "}b.append(g)}j.append(b)}i.append(j)}else{if(this.model.get("for_editing")){i.append(this._render_showParamsAndRerun())}}i.append(this._render_peek())},_render_body:function(){this.log(this+"_render_body");var b=this.model.get("state"),c=this.model.get("for_editing");this.log("state:",b,"for_editing",c);var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}return a},_render_hdaSummary:function(){var a=_.template('<span class="<%= dbkey %>"><%= dbkey %></span>',{dbkey:this.model.get("metadata_dbkey")});if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){a=linkHTMLTemplate({text:this.model.get("metadata_dbkey"),href:this.model.get("edit_url"),target:"galaxy_main"})}return(HistoryItemView.TEMPLATES.hdaSummary(_.extend({dbkeyHTML:a},this.model.attributes)))},_render_showParamsAndRerun:function(){var a=$("<div/>");a.append($(linkHTMLTemplate({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",classes:["icon-button","tooltip","information"]})));if(this.model.get("for_editing")){a.append($(linkHTMLTemplate({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",classes:["icon-button","tooltip","arrow-circle"]})))}return a},_render_downloadLinks:function(){if(this.model.get("purged")){return null}var a=linkHTMLTemplate({title:"Download",href:this.model.get("download_url"),classes:["icon-button","tooltip","disk"]});var d=this.model.get("download_meta_urls");if(!d){return a}var c=$('<div popupmenu="dataset-'+this.model.get("id")+'-popup"></div>');c.append(linkHTMLTemplate({text:"Download Dataset",title:"Download",href:this.model.get("download_url"),classes:["icon-button","tooltip","disk"]}));c.append("<a>Additional Files</a>");for(file_type in d){c.append(linkHTMLTemplate({text:"Download "+file_type,href:d[file_type],classes:["action-button"]}))}var b=$(('<div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"></div>'));b.append(a);c.append(b);return c},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(){this.log(this+".toggleBodyVisibility");this.$el.find(".historyItemBody").toggle()},toString:function(){var a=(this.model)?(this.model+""):("");return"HistoryItemView("+a+")"}});HistoryItemView.TEMPLATES={};HistoryItemView.TEMPLATES.warningMsg=_.template("<div class=warningmessagesmall><strong><%= warning %></strong></div>");HistoryItemView.TEMPLATES.undeleteLink=_.template('This dataset has been deleted. Click <a href="<%= undelete_url %>" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" target="galaxy_history">here</a> to undelete it.');HistoryItemView.TEMPLATES.purgeLink=_.template(' or <a href="<%= purge_url %>" class="historyItemPurge" id="historyItemPurger-{{ id }}" target="galaxy_history">here</a> to immediately remove it from disk.');HistoryItemView.TEMPLATES.hiddenMsg=_.template('This dataset has been hidden. Click <a href="<%= unhide_url %>" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" target="galaxy_history">here</a> to unhide it.');HistoryItemView.TEMPLATES.hdaSummary=_.template(["<%= misc_blurb %><br />",'format: <span class="<%= data_type %>"><%= data_type %></span>, ',"database: <%= dbkeyHTML %>"].join(""));HistoryItemView.STRINGS={};HistoryItemView.STRINGS.purgedMsg=HistoryItemView.TEMPLATES.warningMsg({warning:"This dataset has been deleted and removed from disk."});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=LoggingModel.extend({logger:console,defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0}},initialize:function(b,a){this.log(this+".initialize",b,a);this.items=new HistoryCollection()},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){a.log("loading dataset: ",f,e);var h=new HistoryItem(_.extend(f,{history_id:b}));a.log("as History:",h);a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=LoggingView.extend({logger:console,el:"body.historyPage",initialize:function(){this.log(this+".initialize");this.itemViews=[];var a=this;this.model.items.each(function(c){var b=new HistoryItemView({model:c});a.itemViews.push(b)})},render:function(){this.log(this+".render");var a=$("<div/>");_.each(this.itemViews,function(b){a.prepend(b.render())});this.$el.append(a.children());a.remove()},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});if(window.USE_MOCK_DATA){mockHistory={};mockHistory.data={template:{id:"a799d38679e985db",name:"template",data_type:"fastq",file_size:226297533,genome_build:"?",metadata_data_lines:0,metadata_dbkey:"?",metadata_sequences:0,misc_blurb:"215.8 MB",misc_info:"uploaded fastq file",model_class:"HistoryDatasetAssociation",download_url:"",state:"ok",visible:true,deleted:false,purged:false,hid:0,for_editing:true,undelete_url:"example.com/undelete",purge_url:"example.com/purge",unhide_url:"example.com/unhide",display_url:"example.com/display",edit_url:"example.com/edit",delete_url:"example.com/delete",show_params_url:"example.com/show_params",rerun_url:"example.com/rerun",retag_url:"example.com/retag",annotate_url:"example.com/annotate",peek:['<table cellspacing="0" cellpadding="3"><tr><th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th><th>5.MAPQ</th><th>6.CIGAR</th><th>7.MRNM</th><th>8.MPOS</th><th>9.ISIZE</th><th>10.SEQ</th><th>11.QUAL</th><th>12.OPT</th></tr>','<tr><td colspan="100%">@SQ SN:gi|87159884|ref|NC_007793.1| LN:2872769</td></tr>','<tr><td colspan="100%">@PG ID:bwa PN:bwa VN:0.5.9-r16</td></tr>','<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 73 gi|87159884|ref|NC_007793.1| 2720169 37 101M = 2720169 0 NAATATGACATTATTTTCAAAACAGCTGAAAATTTAGACGTACCGATTTATCTACATCCCGCGCCAGTTAACAGTGACATTTATCAATCATACTATAAAGG !!!!!!!!!!$!!!$!!!!!$!!!!!!$!$!$$$!!$!!$!!!!!!!!!!!$!</td></tr>','<tr><td colspan="100%">!!!$!$!$$!!$$!!$!!!!!!!!!!!!!!!!!!!!!!!!!!$!!$!! XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0A100</td></tr>','<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 133 gi|87159884|ref|NC_007793.1| 2720169 0 * = 2720169 0 NAAACTGTGGCTTCGTTNNNNNNNNNNNNNNNGTGANNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNCNAANNNNNNNNNNNNNNNNNNNNN !!!!!!!!!!!!$!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>','<tr><td colspan="100%">!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>',"</table>"].join("")}};_.extend(mockHistory.data,{deleted:_.extend(_.clone(mockHistory.data.template),{deleted:true}),purgedNotDeleted:_.extend(_.clone(mockHistory.data.template),{purged:true}),notvisible:_.extend(_.clone(mockHistory.data.template),{visible:false}),hasDisplayApps:_.extend(_.clone(mockHistory.data.template),{display_apps:{"display in IGB":{Web:"/display_application/63cd3858d057a6d1/igb_bam/Web",Local:"/display_application/63cd3858d057a6d1/igb_bam/Local"}}}),canTrackster:_.extend(_.clone(mockHistory.data.template),{trackster_urls:{"data-url":"example.com/trackster-data","action-url":"example.com/trackster-action","new-url":"example.com/trackster-new"}}),zeroSize:_.extend(_.clone(mockHistory.data.template),{file_size:0}),hasMetafiles:_.extend(_.clone(mockHistory.data.template),{download_meta_urls:{bam_index:"example.com/bam-index"}}),upload:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.UPLOAD}),queued:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.QUEUED}),running:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.RUNNING}),empty:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.EMPTY}),error:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.ERROR}),discarded:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.DISCARDED}),setting_metadata:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.SETTING_METADATA}),failed_metadata:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.FAILED_METADATA})});$(document).ready(function(){mockHistory.items={};mockHistory.views={};for(key in mockHistory.data){mockHistory.items[key]=new HistoryItem(mockHistory.data[key]);mockHistory.items[key].set("name",key);mockHistory.views[key]=new HistoryItemView({model:mockHistory.items[key]});$("body").append(mockHistory.views[key].render())}})}; \ No newline at end of file diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da static/scripts/packed/viz/phyloviz.js --- /dev/null +++ b/static/scripts/packed/viz/phyloviz.js @@ -0,0 +1,1 @@ +var UserMenuBase=Backbone.View.extend({className:"UserMenuBase",isAcceptableValue:function(e,c,a){var b=this,f=e.val(),g=e.attr("displayLabel")||e.attr("id").replace("phyloViz","");function d(h){return !isNaN(parseFloat(h))&&isFinite(h)}if(!d(f)){alert(g+" is not a number!");return false}if(f>a){alert(g+" is too large.");return false}else{if(f<c){alert(g+" is too small.");return false}}return true},hasIllegalJsonCharacters:function(a){if(a.val().search(/"|'|\\/)!==-1){alert("Named fields cannot contain these illegal characters: double quote(\"), single guote('), or back slash(\\). ");return true}return false}});function PhyloTreeLayout(){var j=this,e=d3.layout.hierarchy().sort(null).value(null),i=360,d="Linear",h=18,f=200,g=0,c=0.5,a=50;j.leafHeight=function(k){if(typeof k==="undefined"){return h}else{h=k;return j}};j.layoutMode=function(k){if(typeof k==="undefined"){return d}else{d=k;return j}};j.layoutAngle=function(k){if(typeof k==="undefined"){return i}if(isNaN(k)||k<0||k>360){return j}else{i=k;return j}};j.separation=function(k){if(typeof k==="undefined"){return f}else{f=k;return j}};j.links=function(k){return d3.layout.tree().links(k)};j.nodes=function(n,l){var m=e.call(j,n,l),k=[],p=0,o=0;m.forEach(function(q){var r=q.data;r.depth=q.depth;p=r.depth>p?r.depth:p;k.push(r)});k.forEach(function(q){if(!q.children){o+=1;q.depth=p}});h=d==="Circular"?i/o:h;g=0;b(k[0],p,h,null);return k};function b(o,q,n,m){var l=o.children,k=0;var p=o.dist||c;p=p>1?1:p;o.dist=p;if(m!==null){o.y0=m.y0+p*f}else{o.y0=a}if(!l){o.x0=g++*n}else{l.forEach(function(r){r.parent=o;k+=b(r,q,n,o)});o.x0=k/l.length}o.x=o.x0;o.y=o.y0;return o.x0}return j}var PhyloTree=Visualization.extend({defaults:{layout:"Linear",separation:250,leafHeight:18,type:"phyloviz",title:"Title",scaleFactor:1,translate:[0,0],fontSize:12,selectedNode:null,nodeAttrChangedTime:0},root:{},toggle:function(a){if(typeof a==="undefined"){return}if(a.children){a._children=a.children;a.children=null}else{a.children=a._children;a._children=null}},toggleAll:function(a){if(a.children&&a.children.length!==0){a.children.forEach(this.toggleAll);toggle(a)}},getData:function(){return this.root},save:function(){var a=this.root;b(a);this.set("root",a);function b(d){delete d.parent;if(d._selected){delete d._selected}d.children?d.children.forEach(b):0;d._children?d._children.forEach(b):0}var c=jQuery.extend(true,{},this.attributes);c.selectedNode=null;show_message("Saving to Galaxy","progress");return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(c)},success:function(d){var e=d.url.split("id=")[1].split("&")[0],f="/phyloviz/visualization?id="+e;window.history.pushState({},"",f+window.location.hash);hide_modal()}})}});var PhylovizLayoutBase=Backbone.View.extend({defaults:{nodeRadius:4.5},stdInit:function(b){var a=this;a.model.on("change:separation change:leafHeight change:fontSize change:nodeAttrChangedTime",a.updateAndRender,a);a.vis=b.vis;a.i=0;a.maxDepth=-1;a.width=b.width;a.height=b.height},updateAndRender:function(c){var b=d3.select(".vis"),a=this;c=c||a.model.root;a.renderNodes(c);a.renderLinks(c);a.addTooltips()},renderLinks:function(a){var j=this;var b=j.diagonal;var c=j.duration;var e=j.layoutMode;var g=j.vis.selectAll("g.completeLink").data(j.tree.links(j.nodes),function(k){return k.target.id});var i=function(k){k.pos0=k.source.y0+" "+k.source.x0;k.pos1=k.source.y0+" "+k.target.x0;k.pos2=k.target.y0+" "+k.target.x0};var h=g.enter().insert("svg:g","g.node").attr("class","completeLink");h.append("svg:path").attr("class","link").attr("d",function(k){i(k);return"M "+k.pos0+" L "+k.pos1});var f=g.transition().duration(500);f.select("path.link").attr("d",function(k){i(k);return"M "+k.pos0+" L "+k.pos1+" L "+k.pos2});var d=g.exit().remove()},selectNode:function(b){var a=this;d3.selectAll("g.node").classed("selectedHighlight",function(c){if(b.id===c.id){if(b._selected){delete b._selected;return false}else{b._selected=true;return true}}return false});a.model.set("selectedNode",b);$("#phyloVizSelectedNodeName").val(b.name);$("#phyloVizSelectedNodeDist").val(b.dist);$("#phyloVizSelectedNodeAnnotation").val(b.annotation||"")},addTooltips:function(){$(".bs-tooltip").remove();$(".node").attr("data-original-title",function(){var b=this.__data__,a=b.annotation||"None";return b?(b.name?b.name+"<br/>":"")+"Dist: "+b.dist+" <br/>Annotation: "+a:""}).tooltip({placement:"top",trigger:"hover"})}});var PhylovizLinearView=PhylovizLayoutBase.extend({initialize:function(b){var a=this;a.margins=b.margins;a.layoutMode="Linear";a.stdInit(b);a.layout();a.updateAndRender(a.model.root)},layout:function(){var a=this;a.tree=new PhyloTreeLayout().layoutMode("Linear");a.diagonal=d3.svg.diagonal().projection(function(b){return[b.y,b.x]})},renderNodes:function(a){var h=this,i=h.model.get("fontSize")+"px";h.tree.separation(h.model.get("separation")).leafHeight(h.model.get("leafHeight"));var d=500,b=h.tree.separation(h.model.get("separation")).nodes(h.model.root);var c=h.vis.selectAll("g.node").data(b,function(j){return j.name+j.id||(j.id=++h.i)});h.nodes=b;h.duration=d;var e=c.enter().append("svg:g").attr("class","node").on("dblclick",function(){d3.event.stopPropagation()}).on("click",function(j){if(d3.event.altKey){h.selectNode(j)}else{if(j.children&&j.children.length===0){return}h.model.toggle(j);h.updateAndRender(j)}});e.attr("transform",function(j){return"translate("+a.y0+","+a.x0+")"});e.append("svg:circle").attr("r",0.000001).style("fill",function(j){return j._children?"lightsteelblue":"#fff"});e.append("svg:text").attr("class","nodeLabel").attr("x",function(j){return j.children||j._children?-10:10}).attr("dy",".35em").attr("text-anchor",function(j){return j.children||j._children?"end":"start"}).style("fill-opacity",0.000001);var f=c.transition().duration(d);f.attr("transform",function(j){return"translate("+j.y+","+j.x+")"});f.select("circle").attr("r",h.defaults.nodeRadius).style("fill",function(j){return j._children?"lightsteelblue":"#fff"});f.select("text").style("fill-opacity",1).style("font-size",i).text(function(j){return j.name});var g=c.exit().transition().duration(d).remove();g.select("circle").attr("r",0.000001);g.select("text").style("fill-opacity",0.000001);b.forEach(function(j){j.x0=j.x;j.y0=j.y})}});var PhylovizView=Backbone.View.extend({className:"phyloviz",initialize:function(b){var a=this;a.MIN_SCALE=0.05;a.MAX_SCALE=5;a.MAX_DISPLACEMENT=500;a.margins=[10,60,10,80];a.width=$("#PhyloViz").width();a.height=$("#PhyloViz").height();a.radius=a.width;a.data=b.data;$(window).resize(function(){a.width=$("#PhyloViz").width();a.height=$("#PhyloViz").height();a.render()});a.phyloTree=new PhyloTree(b.config);a.phyloTree.root=a.data;a.zoomFunc=d3.behavior.zoom().scaleExtent([a.MIN_SCALE,a.MAX_SCALE]);a.zoomFunc.translate(a.phyloTree.get("translate"));a.zoomFunc.scale(a.phyloTree.get("scaleFactor"));a.navMenu=new HeaderButtons(a);a.settingsMenu=new SettingsMenu({phyloTree:a.phyloTree});a.nodeSelectionView=new NodeSelectionView({phyloTree:a.phyloTree});a.search=new PhyloVizSearch();setTimeout(function(){a.zoomAndPan()},1000)},render:function(){var b=this;$("#PhyloViz").empty();b.mainSVG=d3.select("#PhyloViz").append("svg:svg").attr("width",b.width).attr("height",b.height).attr("pointer-events","all").call(b.zoomFunc.on("zoom",function(){b.zoomAndPan()}));b.boundingRect=b.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",b.width).attr("height",b.height).attr("stroke","black").attr("fill","white");b.vis=b.mainSVG.append("svg:g").attr("class","vis");b.layoutOptions={model:b.phyloTree,width:b.width,height:b.height,vis:b.vis,margins:b.margins};$("#title").text("Phylogenetic Tree from "+b.phyloTree.get("title")+":");var a=new PhylovizLinearView(b.layoutOptions)},zoomAndPan:function(a){if(typeof a!=="undefined"){var g=a.zoom,c=a.translate}var j=this,e=j.zoomFunc.scale(),i=j.zoomFunc.translate(),f="",h="";switch(g){case"reset":e=1;i=[0,0];break;case"+":e*=1.1;break;case"-":e*=0.9;break;default:if(typeof g==="number"){e=g}else{if(d3.event!==null){e=d3.event.scale}}}if(e<j.MIN_SCALE||e>j.MAX_SCALE){return}j.zoomFunc.scale(e);f="translate("+j.margins[3]+","+j.margins[0]+") scale("+e+")";if(d3.event!==null){h="translate("+d3.event.translate+")"}else{if(typeof c!=="undefined"){var d=c.split(",")[0];var b=c.split(",")[1];if(!isNaN(d)&&!isNaN(b)){i=[i[0]+parseFloat(d),i[1]+parseFloat(b)]}}j.zoomFunc.translate(i);h="translate("+i+")"}j.phyloTree.set("scaleFactor",e);j.phyloTree.set("translate",i);j.vis.attr("transform",h+f)},reloadViz:function(){var b=this,d=$("#phylovizNexSelector :selected").val(),a=b.phyloTree.get("dataset_id"),c="phyloviz/getJsonData?dataset_id="+a+"&treeIndex="+String(d);$.getJSON(c,function(e){window.initPhyloViz(e.data,e.config)})}});var HeaderButtons=Backbone.View.extend({initialize:function(b){var a=this;a.phylovizView=b;$("#panelHeaderRightBtns").empty();$("#phyloVizNavBtns").empty();$("#phylovizNexSelector").off();a.initNavBtns();a.initRightHeaderBtns();$("#phylovizNexSelector").off().on("change",function(){a.phylovizView.reloadViz()})},initRightHeaderBtns:function(){var a=this;rightMenu=create_icon_buttons_menu([{icon_class:"gear",title:"PhyloViz Settings",on_click:function(){$("#SettingsMenu").show();a.settingsMenu.updateUI()}},{icon_class:"disk",title:"Save visualization",on_click:function(){var b=$("#phylovizNexSelector option:selected").text();if(b){a.phylovizView.phyloTree.set("title",b)}a.phylovizView.phyloTree.save()}},{icon_class:"chevron-expand",title:"Search / Edit Nodes",on_click:function(){$("#nodeSelectionView").show()}},{icon_class:"information",title:"Phyloviz Help",on_click:function(){window.open("http://wiki.g2.bx.psu.edu/Learn/Visualization/PhylogeneticTree")}}],{tooltip_config:{placement:"bottom"}});$("#panelHeaderRightBtns").append(rightMenu.$el)},initNavBtns:function(){var a=this,b=create_icon_buttons_menu([{icon_class:"zoom-in",title:"Zoom in",on_click:function(){a.phylovizView.zoomAndPan({zoom:"+"})}},{icon_class:"zoom-out",title:"Zoom out",on_click:function(){a.phylovizView.zoomAndPan({zoom:"-"})}},{icon_class:"arrow-circle",title:"Reset Zoom/Pan",on_click:function(){a.phylovizView.zoomAndPan({zoom:"reset"})}}],{tooltip_config:{placement:"bottom"}});$("#phyloVizNavBtns").append(b.$el)}});var SettingsMenu=UserMenuBase.extend({className:"Settings",initialize:function(b){var a=this;a.phyloTree=b.phyloTree;a.el=$("#SettingsMenu");a.inputs={separation:$("#phyloVizTreeSeparation"),leafHeight:$("#phyloVizTreeLeafHeight"),fontSize:$("#phyloVizTreeFontSize")};$("#settingsCloseBtn").off().on("click",function(){a.el.hide()});$("#phylovizResetSettingsBtn").off().on("click",function(){a.resetToDefaults()});$("#phylovizApplySettingsBtn").off().on("click",function(){a.apply()})},apply:function(){var a=this;if(!a.isAcceptableValue(a.inputs.separation,50,2500)||!a.isAcceptableValue(a.inputs.leafHeight,5,30)||!a.isAcceptableValue(a.inputs.fontSize,5,20)){return}$.each(a.inputs,function(b,c){a.phyloTree.set(b,c.val())})},updateUI:function(){var a=this;$.each(a.inputs,function(b,c){c.val(a.phyloTree.get(b))})},resetToDefaults:function(){$(".bs-tooltip").remove();var a=this;$.each(a.phyloTree.defaults,function(b,c){a.phyloTree.set(b,c)});a.updateUI()},render:function(){}});var NodeSelectionView=UserMenuBase.extend({className:"Settings",initialize:function(b){var a=this;a.el=$("#nodeSelectionView");a.phyloTree=b.phyloTree;a.UI={enableEdit:$("#phylovizEditNodesCheck"),saveChanges:$("#phylovizNodeSaveChanges"),cancelChanges:$("#phylovizNodeCancelChanges"),name:$("#phyloVizSelectedNodeName"),dist:$("#phyloVizSelectedNodeDist"),annotation:$("#phyloVizSelectedNodeAnnotation")};a.valuesOfConcern={name:null,dist:null,annotation:null};$("#nodeSelCloseBtn").off().on("click",function(){a.el.hide()});a.UI.saveChanges.off().on("click",function(){a.updateNodes()});a.UI.cancelChanges.off().on("click",function(){a.cancelChanges()});(function(c){c.fn.enable=function(d){return c(this).each(function(){if(d){c(this).removeAttr("disabled")}else{c(this).attr("disabled","disabled")}})}})(jQuery);a.UI.enableEdit.off().on("click",function(){a.toggleUI()})},toggleUI:function(){var a=this,b=a.UI.enableEdit.is(":checked");!b?a.cancelChanges():"";$.each(a.valuesOfConcern,function(c,d){a.UI[c].enable(b)});if(b){a.UI.saveChanges.show();a.UI.cancelChanges.show()}else{a.UI.saveChanges.hide();a.UI.cancelChanges.hide()}},cancelChanges:function(){var a=this,b=a.phyloTree.get("selectedNode");if(b){$.each(a.valuesOfConcern,function(c,d){a.UI[c].val(b[c])})}},updateNodes:function(){var a=this,b=a.phyloTree.get("selectedNode");if(b){if(!a.isAcceptableValue(a.UI.dist,0,1)||a.hasIllegalJsonCharacters(a.UI.name)||a.hasIllegalJsonCharacters(a.UI.annotation)){return}$.each(a.valuesOfConcern,function(c,d){(b[c])=a.UI[c].val()});a.phyloTree.set("nodeAttrChangedTime",new Date())}else{alert("No node selected")}}});var PhyloVizSearch=UserMenuBase.extend({initialize:function(){var a=this;$("#phyloVizSearchBtn").on("click",function(){var c=$("#phyloVizSearchTerm"),d=$("#phyloVizSearchCondition").val().split("-"),b=d[0],e=d[1];a.hasIllegalJsonCharacters(c);if(b==="dist"){a.isAcceptableValue(c,0,1)}a.searchTree(b,e,c.val())})},searchTree:function(a,c,b){d3.selectAll("g.node").classed("searchHighlight",function(f){var e=f[a];if(typeof e!=="undefined"&&e!==null){if(a==="dist"){switch(c){case"greaterEqual":return e>=+b;case"lesserEqual":return e<=+b;default:return}}else{if(a==="name"||a==="annotation"){return e.toLowerCase().indexOf(b.toLowerCase())!==-1}}}})}}); \ No newline at end of file diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da static/scripts/packed/viz/trackster.js --- a/static/scripts/packed/viz/trackster.js +++ b/static/scripts/packed/viz/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var g=arguments[0];for(var f=1;f<arguments.length;f++){var d=arguments[f];for(var e in d){g[e]=d[e]}}return g};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tooltip().click(a)};var trackster_module=function(d,S){var o=d("class").extend,s=d("slotting"),I=d("painters");var m={};var k=function(Z,aa){m[Z.attr("id")]=aa};var l=function(Z,ab,ad,ac){ad=".group";var aa={};m[Z.attr("id")]=ac;Z.bind("drag",{handle:"."+ab,relative:true},function(al,am){var ak=$(this),ap=$(this).parent(),ah=ap.children(),aj=m[$(this).attr("id")],ag,af,an,ae,ai;af=$(this).parents(ad);if(af.length!==0){an=af.position().top;ae=an+af.outerHeight();if(am.offsetY<an){$(this).insertBefore(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable_before(aj,ao);return}else{if(am.offsetY>ae){$(this).insertAfter(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable(aj);return}}}af=null;for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));an=ag.position().top;ae=an+ag.outerHeight();if(ag.is(ad)&&this!==ag.get(0)&&am.offsetY>=an&&am.offsetY<=ae){if(am.offsetY-an<ae-am.offsetY){ag.find(".content-div").prepend(this)}else{ag.find(".content-div").append(this)}if(aj.container){aj.container.remove_drawable(aj)}m[ag.attr("id")].add_drawable(aj);return}}for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));if(am.offsetY<ag.position().top&&!(ag.hasClass("reference-track")||ag.hasClass("intro"))){break}}if(ai===ah.length){if(this!==ah.get(ai-1)){ap.append(this);m[ap.attr("id")].move_drawable(aj,ai)}}else{if(this!==ah.get(ai)){$(this).insertBefore(ah.get(ai));m[ap.attr("id")].move_drawable(aj,(am.deltaY>0?ai-1:ai))}}}).bind("dragstart",function(){aa["border-top"]=Z.css("border-top");aa["border-bottom"]=Z.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(aa)})};S.moveable=l;var Y=16,D=9,A=20,x=100,F=12000,P=400,H=5000,u=100,n="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",N=10,E=20;function U(aa,Z){if(!Z){Z=0}var ab=Math.pow(10,Z);return Math.round(aa*ab)/ab}var p=function(aa,Z,ac){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ac.name;this.view=aa;this.container=Z;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ac.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ac.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;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=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ad){ad.stopPropagation()});var ab=this;this.container_div.hover(function(){ab.icons_div.show()},function(){ab.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(Z){if(Z.content_visible){Z.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");Z.hide_contents();Z.content_visible=false}else{Z.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");Z.content_visible=true;Z.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(aa){var ac=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},Z=function(){aa.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(ad){if((ad.keyCode||ad.which)===27){ac()}else{if((ad.keyCode||ad.which)===13){Z()}}};$(window).bind("keypress.check_enter_esc",ab);show_modal("Configure",aa.config.build_form(),{Cancel:ac,OK:Z})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(Z){this.old_name=this.name;this.name=Z;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var Z=this.view;this.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(aa,af,ae,ad,Z,ac){var ab=this;this.action_icons[aa]=$("<a/>").attr("href","javascript:void(0);").attr("title",af).addClass("icon-button").addClass(ae).tooltip().click(function(){ad(ab)}).appendTo(this.icons_div);if(ac){this.action_icons[aa].hide()}},build_action_icons:function(Z){var ab;for(var aa=0;aa<Z.length;aa++){ab=Z[aa];this.add_action_icon(ab.name,ab.title,ab.css_class,ab.on_click_fn,ab.prepend,ab.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(aa,Z,ab){p.call(this,aa,Z,ab);this.obj_type=ab.obj_type;this.drawables=[]};o(w.prototype,p.prototype,{unpack_drawables:function(ab){this.drawables=[];var aa;for(var Z=0;Z<ab.length;Z++){aa=object_from_template(ab[Z],this.view,this);this.add_drawable(aa)}},init:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].init()}},_draw:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z]._draw()}},to_dict:function(){var aa=[];for(var Z=0;Z<this.drawables.length;Z++){aa.push(this.drawables[Z].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:aa}},add_drawable:function(Z){this.drawables.push(Z);Z.container=this;this.changed()},add_drawable_before:function(ab,Z){this.changed();var aa=this.drawables.indexOf(Z);if(aa!==-1){this.drawables.splice(aa,0,ab);return true}return false},replace_drawable:function(ab,Z,aa){var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables[ac]=Z;if(aa){ab.container_div.replaceWith(Z.container_div)}this.changed()}return ac},remove_drawable:function(aa){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);aa.container=null;this.changed();return true}return false},move_drawable:function(aa,ab){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);this.drawables.splice(ab,0,aa);this.changed();return true}return false}});var M=function(aa,Z,ac){o(ac,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,aa,Z,ac);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new V(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ac){this.unpack_drawables(ac.drawables)}if("filters" in ac){var ab=this.filters_manager;this.filters_manager=new V(this,ac.filters);ab.parent_div.replaceWith(this.filters_manager.parent_div);if(ac.filters.visible){this.setup_multitrack_filtering()}}};o(M.prototype,p.prototype,w.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters();Z._restore_filter_managers()}else{Z.setup_multitrack_filtering();Z.request_draw(true)}Z.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var Z=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(Z)}return Z},build_header_div:function(){var Z=$("<div/>").addClass("track-header");Z.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(Z);return Z},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ab=this.drawables.length;if(ab===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ab===1){if(this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ah,af,al=true,ad=this.drawables[0].get_type(),Z=0;for(ai=0;ai<ab;ai++){af=this.drawables[ai];if(af.get_type()!==ad){can_composite=false;break}if(af instanceof c){Z++}}if(al||Z===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(Z>1&&Z===this.drawables.length){var am={},aa;af=this.drawables[0];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];am[aa.name]=[aa]}for(ai=1;ai<this.drawables.length;ai++){af=this.drawables[ai];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];if(aa.name in am){am[aa.name].push(aa)}}}this.filters_manager.remove_all();var ac,ae,ag,aj;for(var ak in am){ac=am[ak];if(ac.length===Z){ae=new Q({name:ac[0].name,index:ac[0].index});this.filters_manager.add_filter(ae)}}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 Z=0;Z<this.drawables.length;Z++){this.drawables[Z].filters_manager=this.saved_filters_managers[Z]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var Z=0;Z<this.drawables.length;Z++){drawable=this.drawables[Z];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=[];for(var aa=0;aa<this.drawables.length;aa++){ad.push(this.drawables[aa].name)}var ab="Composite Track of "+this.drawables.length+" tracks ("+ad.join(", ")+")";var ac=new g(this.view,this.view,{name:ab,drawables:this.drawables});var Z=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);this.update_icons()},remove_drawable:function(Z){w.prototype.remove_drawable.call(this,Z);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var Z=o(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return Z},request_draw:function(Z,ab){for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].request_draw(Z,ab)}}});var X=function(Z){o(Z,{obj_type:"View"});w.call(this,"View",Z.container,Z);this.chrom=null;this.vis_id=Z.vis_id;this.dbkey=Z.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.init();this.canvas_manager=new CanvasManager(this.container.get(0).ownerDocument);this.reset()};_.extend(X.prototype,Backbone.Events);o(X.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ab=this.container,Z=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ab);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ab);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ab);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,Z);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ac=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_datasets(add_datasets_url,add_track_async_url,function(ad){_.each(ad,function(ae){Z.add_drawable(object_from_template(ae,Z,Z))})})});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("href","javascript:void(0);").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=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var aa=function(ad){if(ad.type==="focusout"||(ad.keyCode||ad.which)===13||(ad.keyCode||ad.which)===27){if((ad.keyCode||ad.which)!==27){Z.go_to($(this).val())}$(this).hide();$(this).val("");Z.location_span.show();Z.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",aa).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){Z.location_span.hide();Z.chrom_select.hide();Z.nav_input.val(Z.chrom+":"+Z.low+"-"+Z.high);Z.nav_input.css("display","inline-block");Z.nav_input.select();Z.nav_input.focus()});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(){Z.zoom_out();Z.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){Z.zoom_in();Z.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){Z.change_chrom(Z.chrom_select.val())});this.browser_content_div.click(function(ad){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ad){Z.zoom_in(ad.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ad,ae){this.current_x=ae.offsetX}).bind("drag",function(ad,af){var ag=af.offsetX-this.current_x;this.current_x=af.offsetX;var ae=Math.round(ag/Z.viewport_container.width()*(Z.max_high-Z.max_low));Z.move_delta(-ae)});this.overview_close.click(function(){Z.reset_overview()});this.viewport_container.bind("draginit",function(ad,ae){if(ad.clientX>Z.viewport_container.width()-16){return false}}).bind("dragstart",function(ad,ae){ae.original_low=Z.low;ae.current_height=ad.clientY;ae.current_x=ae.offsetX}).bind("drag",function(af,ah){var ad=$(this);var ai=ah.offsetX-ah.current_x;var ae=ad.scrollTop()-(af.clientY-ah.current_height);ad.scrollTop(ae);ah.current_height=af.clientY;ah.current_x=ah.offsetX;var ag=Math.round(ai/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}).bind("mousewheel",function(af,ah,ae,ad){if(ae){ae*=50;var ag=Math.round(-ae/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}});this.top_labeltrack.bind("dragstart",function(ad,ae){return $("<div />").css({height:Z.browser_content_div.height()+Z.top_labeltrack.height()+Z.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ah,ai){$(ai.proxy).css({left:Math.min(ah.pageX,ai.startX)-Z.container.offset().left,width:Math.abs(ah.pageX-ai.startX)});var ae=Math.min(ah.pageX,ai.startX)-Z.container.offset().left,ad=Math.max(ah.pageX,ai.startX)-Z.container.offset().left,ag=(Z.high-Z.low),af=Z.viewport_container.width();Z.update_location(Math.round(ae/af*ag)+Z.low,Math.round(ad/af*ag)+Z.low)}).bind("dragend",function(ai,aj){var ae=Math.min(ai.pageX,aj.startX),ad=Math.max(ai.pageX,aj.startX),ag=(Z.high-Z.low),af=Z.viewport_container.width(),ah=Z.low;Z.low=Math.round(ae/af*ag)+ah;Z.high=Math.round(ad/af*ag)+ah;$(aj.proxy).remove();Z.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}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){Z.resize_window()},500)});$(document).bind("redraw",function(){Z.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(aa,ac,Z,ad){if(this.timer){clearTimeout(this.timer)}if(ad){var ab=this;this.timer=setTimeout(function(){ab.trigger("navigate",aa+":"+ac+"-"+Z)},500)}else{view.trigger("navigate",aa+":"+ac+"-"+Z)}},update_location:function(Z,ab){this.location_span.text(commatize(Z)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(Z)+"-"+commatize(ab));var aa=view.chrom_select.val();if(aa!==""){this.trigger_navigate(aa,view.low,view.high,true)}},load_chroms:function(ab){ab.num=u;ab.dbkey=this.dbkey;var Z=this,aa=$.Deferred();$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ad){if(ad.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ad.reference){Z.add_label_track(new y(Z))}Z.chrom_data=ad.chrom_info;var ag='<option value="">Select Chrom/Contig</option>';for(var af=0,ac=Z.chrom_data.length;af<ac;af++){var ae=Z.chrom_data[af].chrom;ag+='<option value="'+ae+'">'+ae+"</option>"}if(ad.prev_chroms){ag+='<option value="previous">Previous '+u+"</option>"}if(ad.next_chroms){ag+='<option value="next">Next '+u+"</option>"}Z.chrom_select.html(ag);Z.chrom_start_index=ad.start_index;aa.resolve(ad)},error:function(){alert("Could not load chroms for this dbkey:",Z.dbkey)}});return aa},change_chrom:function(ae,aa,ag){var ab=this;if(!ab.chrom_data){ab.load_chroms_deferred.then(function(){ab.change_chrom(ae,aa,ag)});return}if(!ae||ae==="None"){return}if(ae==="previous"){ab.load_chroms({low:this.chrom_start_index-u});return}if(ae==="next"){ab.load_chroms({low:this.chrom_start_index+u});return}var af=$.grep(ab.chrom_data,function(ah,ai){return ah.chrom===ae})[0];if(af===undefined){ab.load_chroms({chrom:ae},function(){ab.change_chrom(ae,aa,ag)});return}else{if(ae!==ab.chrom){ab.chrom=ae;ab.chrom_select.val(ab.chrom);ab.max_high=af.len-1;ab.reset();ab.request_redraw(true);for(var ad=0,Z=ab.drawables.length;ad<Z;ad++){var ac=ab.drawables[ad];if(ac.init){ac.init()}}if(ab.reference_track){ab.reference_track.init()}}if(aa!==undefined&&ag!==undefined){ab.low=Math.max(aa,0);ab.high=Math.min(ag,ab.max_high)}else{ab.low=0;ab.high=ab.max_high}ab.reset_overview();ab.request_redraw()}},go_to:function(ad){ad=ad.replace(/ |,/g,"");var ah=this,Z,ac,aa=ad.split(":"),af=aa[0],ag=aa[1];if(ag!==undefined){try{var 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Z=this;ab.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ah,Z,ag,ai){var af=this,ae=(ai?[ai]:af.drawables),ab;var aa;for(var ad=0;ad<ae.length;ad++){aa=ae[ad];ab=-1;for(var ac=0;ac<af.tracks_to_be_redrawn.length;ac++){if(af.tracks_to_be_redrawn[ac][0]===aa){ab=ac;break}}if(ab<0){af.tracks_to_be_redrawn.push([aa,Z,ag])}else{af.tracks_to_be_redrawn[ad][1]=Z;af.tracks_to_be_redrawn[ad][2]=ag}}if(!this.requested_redraw){requestAnimationFrame(function(){af._redraw(ah)});this.requested_redraw=true}},_redraw:function(aj){this.requested_redraw=false;var ag=this.low,ac=this.high;if(ag<this.max_low){ag=this.max_low}if(ac>this.max_high){ac=this.max_high}var ai=this.high-this.low;if(this.high!==0&&ai<this.min_separation){ac=ag+this.min_separation}this.low=Math.floor(ag);this.high=Math.ceil(ac);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var Z=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=13;this.overview_box.css({left:Z,width:Math.max(ak,af)}).show();if(af<ak){this.overview_box.css("left",Z-(ak-af)/2)}if(this.overview_highlight){this.overview_highlight.css({left:Z,width:af})}if(!aj){var ab,aa,ah;for(var ad=0,ae=this.tracks_to_be_redrawn.length;ad<ae;ad++){ab=this.tracks_to_be_redrawn[ad][0];aa=this.tracks_to_be_redrawn[ad][1];ah=this.tracks_to_be_redrawn[ad][2];if(ab){ab._draw(aa,ah)}}this.tracks_to_be_redrawn=[];for(ad=0,ae=this.label_tracks.length;ad<ae;ad++){this.label_tracks[ad]._draw()}}},zoom_in:function(aa,ab){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ac=this.high-this.low,ad=ac/2+this.low,Z=(ac/this.zoom_factor)/2;if(aa){ad=aa/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ad-Z);this.high=Math.round(ad+Z);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var aa=this.high-this.low,ab=aa/2+this.low,Z=(aa*this.zoom_factor)/2;this.low=Math.round(ab-Z);this.high=Math.round(ab+Z);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(ab){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ab.dataset_id){return}this.overview_viewport.find(".track").remove()}var aa=ab.copy({content_div:this.overview_viewport}),Z=this;aa.header_div.hide();aa.is_overview=true;Z.overview_drawable=aa;this.overview_drawable.postdraw_actions=function(){Z.overview_highlight.show().height(Z.overview_drawable.content_div.height());Z.overview_viewport.height(Z.overview_drawable.content_div.height()+Z.overview_box.outerHeight());Z.overview_close.show();Z.resize_window()};Z.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-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 q=function(ab,ag,ac){this.track=ab;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],aa=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params.push(new e(aa,am,ae,(aa in ac?ac[aa]:ao),ai.min,ai.max))}else{if(ak==="select"){this.params.push(new K(aa,am,ae,(aa in ac?ac[aa]:ao)))}else{console.log("WARNING: unrecognized tool parameter type:",aa,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).click(function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("param-input").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: 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Z=[];this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();if(aa){Z[Z.length]=ab}});return Z},run_on_dataset:function(){var Z=this;Z.run({target_dataset_id:this.track.original_dataset_id,tool_id:Z.name},null,function(aa){show_modal(Z.name+" is Running",Z.name+" is running on the complete dataset. 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f=function(Z){this.manager=null;this.name=Z.name;this.index=Z.index;this.tool_id=Z.tool_id;this.tool_exp_name=Z.tool_exp_name};o(f.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var Q=function(ah){f.call(this,ah);this.low=("low" in ah?ah.low:-Number.MAX_VALUE);this.high=("high" in ah?ah.high:Number.MAX_VALUE);this.min=("min" in ah?ah.min:Number.MAX_VALUE);this.max=("max" in ah?ah.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ad=function(ai,aj,ak){ai.click(function(){var ap=aj.text(),an=parseFloat(ak.slider("option","max")),am=(an<=1?4:an<=1000000?an.toString().length:6),ao=false,al=$(this).parents(".slider-row");al.addClass("input");if(ak.slider("option","values")){am=2*am+1;ao=true}aj.text("");$("<input type='text'/>").attr("size",am).attr("maxlength",am).attr("value",ap).appendTo(aj).focus().select().click(function(aq){aq.stopPropagation()}).blur(function(){$(this).remove();aj.text(ap);al.removeClass("input")}).keyup(function(av){if(av.keyCode===27){$(this).trigger("blur")}else{if(av.keyCode===13){var at=ak.slider("option","min"),aq=ak.slider("option","max"),au=function(aw){return(isNaN(aw)||aw>aq||aw<at)},ar=$(this).val();if(!ao){ar=parseFloat(ar);if(au(ar)){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}else{ar=ar.split("-");ar=[parseFloat(ar[0]),parseFloat(ar[1])];if(au(ar[0])||au(ar[1])){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}ak.slider((ao?"values":"value"),ar);al.removeClass("input")}}})})};var aa=this;aa.parent_div=$("<div/>").addClass("filter-row slider-row");var Z=$("<div/>").addClass("elt-label").appendTo(aa.parent_div),af=$("<span/>").addClass("slider-name").text(aa.name+" ").appendTo(Z),ab=$("<span/>").text(this.low+"-"+this.high),ac=$("<span/>").addClass("slider-value").appendTo(Z).append("[").append(ab).append("]");aa.values_span=ab;var ae=$("<div/>").addClass("slider").appendTo(aa.parent_div);aa.control_element=$("<div/>").attr("id",aa.name+"-filter-control").appendTo(ae);aa.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(ai,aj){aa.slide(ai,aj)},change:function(ai,aj){aa.control_element.slider("option","slide").call(aa.control_element,ai,aj)}});aa.slider=aa.control_element;aa.slider_label=ab;ad(ac,ab,aa.control_element);var ag=$("<div/>").addClass("display-controls").appendTo(aa.parent_div);this.transparency_icon=create_action_icon("Use filter for data 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style='clear: both;'/>").appendTo(aa.parent_div)};o(Q.prototype,{to_dict:function(){var Z=f.prototype.to_dict.call(this);return o(Z,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new Q({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ab,Z){var aa=Z-ab;return(aa<=2?0.01:1)},slide:function(ab,ac){var aa=ac.values;this.values_span.text(aa[0]+"-"+aa[1]);this.low=aa[0];this.high=aa[1];var Z=this;setTimeout(function(){if(aa[0]===Z.low&&aa[1]===Z.high){Z.manager.track.request_draw(true,true)}},25)},applies_to:function(Z){if(Z.length>this.index){return true}return false},_keep_val:function(Z){return(isNaN(Z)||(Z>=this.low&&Z<=this.high))},keep:function(aa){if(!this.applies_to(aa)){return true}var ac=this;var ad=aa[this.index];if(ad instanceof Array){var ab=true;for(var Z=0;Z<ad.length;Z++){if(!this._keep_val(ad[Z])){ab=false;break}}return ab}else{return this._keep_val(aa[this.index])}},update_attrs:function(ac){var Z=false;if(!this.applies_to(ac)){return Z}var aa=ac[this.index];if(!(aa instanceof Array)){aa=[aa]}for(var ab=0;ab<aa.length;ab++){var ad=aa[ab];if(ad<this.min){this.min=Math.floor(ad);Z=true}if(ad>this.max){this.max=Math.ceil(ad);Z=true}}return Z},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var aa=this.slider.slider("option","min"),Z=this.slider.slider("option","max");if(this.min<aa||this.max>Z){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var V=function(ab,ah){this.track=ab;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aj){aj.stopPropagation()}).click(function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()}).bind("keydown",function(aj){aj.stopPropagation()});if(ah&&"filters" in ah){var Z=("alpha_filter" in ah?ah.alpha_filter:null),ac=("height_filter" in ah?ah.height_filter:null),ae=ah.filters,aa;for(var af=0;af<ae.length;af++){if(ae[af].type==="number"){aa=new Q(ae[af]);this.add_filter(aa);if(aa.name===Z){this.alpha_filter=aa;aa.transparency_icon.addClass("active").show()}if(aa.name===ac){this.height_filter=aa;aa.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ah&&ah.visible){this.parent_div.show()}}if(this.filters.length!==0){var ai=$("<div/>").addClass("param-row").appendTo(this.parent_div);var ag=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ai);var ad=this;ag.click(function(){ad.run_on_dataset()})}};o(V.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var ac={},ab=[],aa;for(var Z=0;Z<this.filters.length;Z++){aa=this.filters[Z];ab.push(aa.to_dict())}ac.filters=ab;ac.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);ac.height_filter=(this.height_filter?this.height_filter.name:null);ac.visible=this.parent_div.is(":visible");return ac},copy:function(aa){var ab=new V(aa);for(var Z=0;Z<this.filters.length;Z++){ab.add_filter(this.filters[Z].copy())}return ab},add_filter:function(Z){Z.manager=this;this.parent_div.append(Z.parent_div);this.filters.push(Z)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.update_ui_elt()}},clear_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.slider.slider("option","values",[aa.min,aa.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var af=function(aj,ah,ai){if(!(ah in aj)){aj[ah]=ai}return aj[ah]};var ae={},ag,Z;for(var ad=0;ad<this.filters.length;ad++){ag=this.filters[ad];if(ag.tool_id){if(ag.min!==ag.low){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" >= "+ag.low}if(ag.max!==ag.high){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" <= "+ag.high}}}var aa=[];for(var ac in ae){aa[aa.length]=[ac,ae[ac]]}(function ab(an,ak){var ai=ak[0],aj=ai[0],am=ai[1],al="("+am.join(") and (")+")",ah={cond:al,input:an,target_dataset_id:an,tool_id:aj},ak=ak.slice(1);$.getJSON(run_tool_url,ah,function(ao){if(ao.error){show_modal("Filter Dataset","Error running tool "+aj,{Close:hide_modal})}else{if(ak.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ab(ao.dataset_id,ak)}}})})(this.track.dataset_id,aa)}});var z=function(Z,aa){I.Scaler.call(this,aa);this.filter=Z};z.prototype.gen_val=function(Z){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(Z[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(Z){this.track=Z.track;this.params=Z.params;this.values={};this.restore_values((Z.saved_values?Z.saved_values:{}));this.onchange=Z.onchange};o(C.prototype,{restore_values:function(Z){var aa=this;$.each(this.params,function(ab,ac){if(Z[ac.key]!==undefined){aa.values[ac.key]=Z[ac.key]}else{aa.values[ac.key]=ac.default_value}})},build_form:function(){var ac=this;var Z=$("<div />");var ab;function aa(ah,ad){for(var al=0;al<ah.length;al++){ab=ah[al];if(ab.hidden){continue}var af="param_"+al;var ap=ac.values[ab.key];var ar=$("<div class='form-row' />").appendTo(ad);ar.append($("<label />").attr("for",af).text(ab.label+":"));if(ab.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",af).attr("name",af).attr("checked",ap))}else{if(ab.type==="text"){ar.append($('<input type="text"/>').attr("id",af).val(ap).click(function(){$(this).select()}))}else{if(ab.type==="select"){var an=$("<select />").attr("id",af);for(var aj=0;aj<ab.options.length;aj++){$("<option/>").text(ab.options[aj].label).attr("value",ab.options[aj].value).appendTo(an)}an.val(ap);ar.append(an)}else{if(ab.type==="color"){var aq=$("<div/>").appendTo(ar),am=$("<input />").attr("id",af).attr("name",af).val(ap).css("float","left").appendTo(aq).click(function(au){$(".bs-tooltip").removeClass("in");var at=$(this).siblings(".bs-tooltip").addClass("in");at.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(at).height()/2)+($(this).height()/2)}).show();at.click(function(av){av.stopPropagation()});$(document).bind("click.color-picker",function(){at.hide();$(document).unbind("click.color-picker")});au.stopPropagation()}),ak=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aq).attr("title","Set new random color").tooltip(),ao=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aq).hide(),ag=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ao),ae=$("<div class='tooltip-arrow'></div>").appendTo(ao),ai=$.farbtastic(ag,{width:100,height:100,callback:am,color:ap});aq.append($("<div/>").css("clear","both"));(function(at){ak.click(function(){at.setColor(get_random_color())})})(ai)}else{ar.append($("<input />").attr("id",af).attr("name",af).val(ap))}}}}if(ab.help){ar.append($("<div class='help'/>").text(ab.help))}}}aa(this.params,Z);return Z},update_from_form:function(Z){var ab=this;var aa=false;$.each(this.params,function(ac,ae){if(!ae.hidden){var af="param_"+ac;var ad=Z.find("#"+af).val();if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad)}else{if(ae.type==="bool"){ad=Z.find("#"+af).is(":checked")}}}if(ad!==ab.values[ae.key]){ab.values[ae.key]=ad;aa=true}}});if(aa){this.onchange();this.track.changed()}}});var b=function(Z,ad,ab,aa,ac){this.track=Z;this.region=ad;this.low=ad.get("start");this.high=ad.get("end");this.resolution=ab;this.html_elt=$("<div class='track-tile'/>").append(aa).height($(aa).attr("height"));this.data=ac;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(Z,ae,ab,aa,ac,ad){b.call(this,Z,ae,ab,aa,ac);this.max_val=ad};o(j.prototype,b.prototype);var L=function(ac,ak,ad,ab,af,am,ag,an,aa,aj){b.call(this,ac,ak,ad,ab,af);this.mode=ag;this.all_slotted=aa;this.feature_mapper=aj;this.has_icons=false;if(an){this.has_icons=true;var ah=this;ab=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ab.width}).prependTo(this.html_elt);var ai=new GenomeRegion({chrom:ac.view.chrom,start:this.low,end:this.high}),al=af.length,ae=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),Z=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ae.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()});Z.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()})}};o(L.prototype,b.prototype);L.prototype.predisplay_actions=function(){var aa=this,Z={};if(aa.mode!=="Pack"){return}$(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(al){if(!this.hovered){return}var ag=$(this).offset(),ak=al.pageX-ag.left,aj=al.pageY-ag.top,ap=aa.feature_mapper.get_feature_data(ak,aj),ah=(ap?ap[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ah||$(this).attr("id")!==ah.toString()){$(this).remove()}});if(ap){var ac=Z[ah];if(!ac){var ah=ap[0],am={name:ap[3],start:ap[1],end:ap[2],strand:ap[4]},af=aa.track.filters_manager.filters,ae;for(var ai=0;ai<af.length;ai++){ae=af[ai];am[ae.name]=ap[ae.index]}var ac=$("<div/>").attr("id",ah).addClass("feature-popup"),aq=$("<table/>"),ao,an,ar;for(ao in am){an=am[ao];ar=$("<tr/>").appendTo(aq);$("<th/>").appendTo(ar).text(ao);$("<td/>").attr("align","left").appendTo(ar).text(typeof(an)==="number"?U(an,2):an)}ac.append($("<div class='feature-popup-inner'>").append(aq));Z[ah]=ac}ac.appendTo($(this).parents(".track-content").children(".overlay"));var ad=ak+parseInt(aa.html_elt.css("left"))-ac.width()/2,ab=aj+parseInt(aa.html_elt.css("top"))+7;ac.css("left",ad+"px").css("top",ab+"px")}else{if(!al.isPropagationStopped()){al.stopPropagation();$(this).siblings().each(function(){$(this).trigger(al)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var h=function(ab,aa,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ab,aa,ad);this.data_url=("data_url" in ad?ad.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:H);this.dataset_check_url=("converted_datasets_state_url" in ad?ad.converted_datasets_state_url:converted_datasets_state_url);var Z=this,ac=new Dataset({id:ad.dataset_id,hda_ldda:ad.hda_ldda});this.data_manager=("data_manager" in ad?ad.data_manager:new GenomeDataManager({dataset:ac,data_url:Z.data_url,dataset_state_url:Z.dataset_check_url,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=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(h.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(Z){Z.view.set_overview(Z)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters()}else{Z.filters_manager.init_filters()}Z.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(Z){Z.dynamic_tool_div.toggle();if(Z.dynamic_tool_div.is(":visible")){Z.set_name(Z.name+Z.tool_region_and_parameters_str())}else{Z.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(Z){var ac='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.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>',ab=_.template(ac,{track:Z});var ae=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aa=function(){var ag=$('select[name="regions"] option:selected').val(),ai,af=new GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ah=_.map($(".bookmark"),function(aj){return new GenomeRegion({from_str:$(aj).children(".position").text()})});if(ag==="cur"){ai=[af]}else{if(ag==="bookmarks"){ai=ah}else{ai=[af].concat(ah)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:Z.dataset_id,hda_ldda:Z.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ai).toJSON())})},ad=function(af){if((af.keyCode||af.which)===27){ae()}else{if((af.keyCode||af.which)===13){aa()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ab,{No:ae,Yes:aa})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var Z=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(Z)}this.name_div=$("<div/>").addClass("track-name").appendTo(Z).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return Z},on_resize:function(){},add_resize_handle:function(){var Z=this;var ac=false;var ab=false;var aa=$("<div class='track-resize'>");$(Z.container_div).hover(function(){if(Z.content_visible){ac=true;aa.show()}},function(){ac=false;if(!ab){aa.hide()}});aa.hide().bind("dragstart",function(ad,ae){ab=true;ae.original_height=$(Z.content_div).height()}).bind("drag",function(ae,af){var ad=Math.min(Math.max(af.original_height+af.deltaY,Z.min_height_px),Z.max_height_px);$(Z.tiles_div).css("height",ad);Z.visible_height_px=(Z.max_height_px===ad?0:ad);Z.on_resize()}).bind("dragend",function(ad,ae){Z.tile_cache.clear();ab=false;if(!ac){aa.hide()}Z.config.values.height=Z.visible_height_px;Z.changed()}).appendTo(Z.container_div)},set_display_modes:function(ac,af){this.display_modes=ac;this.mode=(af?af:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var aa=this,ad={};for(var ab=0,Z=aa.display_modes.length;ab<Z;ab++){var ae=aa.display_modes[ab];ad[ae]=function(ag){return function(){aa.change_mode(ag);aa.icons_div.show();aa.container_div.mouseleave(function(){aa.icons_div.hide()})}}(ae)}make_popupmenu(this.action_icons.mode_icon,ad)},build_action_icons:function(){p.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 y){return"ReferenceTrack"}else{if(this instanceof i){return"LineTrack"}else{if(this instanceof R){return"ReadTrack"}else{if(this instanceof O){return"VcfTrack"}else{if(this instanceof g){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.content_div.css("height","auto");aa.tiles_div.children().remove();aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}var Z=$.Deferred();$.getJSON(this.dataset_check_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.tiles_div.text(n);if(ab.message){var ac=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.tiles_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.tiles_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.tiles_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.tiles_div.html(t);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab==="data"||ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.update_icons()}aa.tiles_div.text(T);if(aa.view.chrom){aa.tiles_div.text("");aa.tiles_div.css("height",aa.visible_height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){Z.resolve();aa.container_div.removeClass("nodata error pending");aa.request_draw()})}else{Z.resolve()}}}}}}});this.update_icons();return Z},predraw_init:function(){}});var J=function(ab,aa,ac){h.call(this,ab,aa,ac);var Z=this;l(Z.container_div,Z.drag_handle_class,".group",Z);this.filters_manager=new V(this,("filters" in ac?ac.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ac&&ac.tool?new q(this,ac.tool,ac.tool_state):null);this.tile_cache=new Cache(N);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ac.mode){this.change_mode(ac.mode)}};o(J.prototype,p.prototype,h.prototype,{action_icons_def:h.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(Z){$(".bs-tooltip").remove();Z.slotters[Z.view.resolution_px_b].max_rows*=2;Z.request_draw(true)},hide:true}]),copy:function(Z){var aa=this.to_dict();o(aa,{data_manager:this.data_manager});var ab=new this.constructor(this.view,Z,aa);ab.change_mode(this.mode);ab.enabled=this.enabled;return ab},set_filters_manager:function(Z){this.filters_manager=Z;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(aa){var Z=this;Z.mode=aa;Z.config.values.mode=aa;Z.tile_cache.clear();Z.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+Z.mode+")");return Z},update_icons:function(){var Z=this;if(Z.filters_available){Z.action_icons.filters_icon.show()}else{Z.action_icons.filters_icon.hide()}if(Z.tool){Z.action_icons.tools_icon.show();Z.action_icons.param_space_viz_icon.show()}else{Z.action_icons.tools_icon.hide();Z.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(aa,ab,Z){return aa+"_"+ab+"_"+Z},request_draw:function(aa,Z){this.view.request_redraw(false,aa,Z,this)},before_draw:function(){},_draw:function(aa,ak){if(!this.can_draw()){return}var ai=this.view.low,ae=this.view.high,ag=ae-ai,ab=this.view.container.width(),am=this.view.resolution_px_b,ad=this.view.resolution_b_px;if(this.is_overview){ai=this.view.max_low;ae=this.view.max_high;ad=(view.max_high-view.max_low)/ab;am=1/ad}this.before_draw();this.tiles_div.children().addClass("remove");var Z=Math.floor(ai/(ad*P)),ah=true,al=[],af=function(an){return(an&&"track" in an)};while((Z*P*ad)<ae){var aj=this.draw_helper(aa,ab,Z,ad,this.tiles_div,am);if(af(aj)){al.push(aj)}else{ah=false}Z+=1}if(!ak){this.tiles_div.children(".remove").removeClass("remove").remove()}var ac=this;if(ah){this.tiles_div.children(".remove").remove();ac.postdraw_actions(al,ab,am,ak)}},postdraw_actions:function(ab,ac,ae,Z){var ad=false;for(var aa=0;aa<ab.length;aa++){if(ab[aa].has_icons){ad=true;break}}if(ad){for(var aa=0;aa<ab.length;aa++){tile=ab[aa];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(Z,al,aq,ao,ae,af,am){var ak=this,au=this._gen_tile_cache_key(al,af,aq),ac=this._get_tile_bounds(aq,ao);if(!am){am={}}var at=(Z?undefined:ak.tile_cache.get_elt(au));if(at){ak.show_tile(at,ae,af);return at}var ai=true;var ap=ak.data_manager.get_data(ac,ak.mode,ao,ak.data_url_extra_params);if(is_deferred(ap)){ai=false}var ag;if(view.reference_track&&af>view.canvas_manager.char_width_px){ag=view.reference_track.data_manager.get_data(ac,ak.mode,ao,view.reference_track.data_url_extra_params);if(is_deferred(ag)){ai=false}}if(ai){o(ap,am.more_tile_data);var ah=ak.mode;if(ah==="Auto"){ah=ak.get_mode(ap);ak.update_auto_mode(ah)}var ab=ak.view.canvas_manager.new_canvas(),ar=ac.get("start"),aa=ac.get("end"),al=Math.ceil((aa-ar)*af)+ak.left_offset,aj=ak.get_canvas_height(ap,ah,af,al);ab.width=al;ab.height=aj;var an=ab.getContext("2d");an.translate(this.left_offset,0);var at=ak.draw_tile(ap,an,ah,ao,ac,af,ag);if(at!==undefined){ak.tile_cache.set_elt(au,at);ak.show_tile(at,ae,af)}return at}var ad=$.Deferred();$.when(ap,ag).then(function(){view.request_redraw(false,false,false,ak);ad.resolve()});return ad},get_canvas_height:function(Z,ab,ac,aa){return this.visible_height_px},draw_tile:function(Z,aa,ae,ac,ad,af,ab){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ab,ad,ae){var aa=this,Z=ab.html_elt;ab.predisplay_actions();var ac=(ab.low-(this.is_overview?this.view.max_low:this.view.low))*ae;if(this.left_offset){ac-=this.left_offset}Z.css({position:"absolute",top:0,left:ac});if(Z.hasClass("remove")){Z.removeClass("remove")}else{ad.append(Z)}aa.after_show_tile(ab)},after_show_tile:function(Z){this.max_height_px=Math.max(this.max_height_px,Z.html_elt.height());Z.html_elt.parent().children().css("height",this.max_height_px+"px");var aa=this.max_height_px;if(this.visible_height_px!==0){aa=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",aa+"px")},_get_tile_bounds:function(Z,aa){var ac=Math.floor(Z*P*aa),ad=Math.ceil(P*aa),ab=(ac+ad<=this.view.max_high?ac+ad:this.view.max_high);return new GenomeRegion({chrom:this.view.chrom,start:ac,end:ab})},tool_region_and_parameters_str:function(ab,Z,ac){var aa=this,ad=(ab!==undefined&&Z!==undefined&&ac!==undefined?ab+":"+Z+"-"+ac:"all");return" - region=["+ad+"], parameters=["+aa.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(Z,aa){return true},can_subset:function(Z){return false},init_for_tool_data:function(){this.data_manager.set("data_url",raw_data_url);this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ab,ac,ae,Z){var aa=this;aa.normal_postdraw_actions(ab,ac,ae,Z);aa.dataset_state_url=converted_datasets_state_url;aa.data_query_wait=H;var ad=new ServerStateDeferred({url:aa.dataset_state_url,url_params:{dataset_id:aa.dataset_id,hda_ldda:aa.hda_ldda},interval:aa.data_query_wait,success_fn:function(af){return af!=="pending"}});$.when(ad.go()).then(function(){aa.data_manager.set("data_url",default_data_url)});aa.postdraw_actions=aa.normal_postdraw_actions}}});var W=function(aa,Z){var ab={resize:false};h.call(this,aa,Z,ab);this.container_div.addClass("label-track")};o(W.prototype,h.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ab=this.view,ac=ab.high-ab.low,af=Math.floor(Math.pow(10,Math.floor(Math.log(ac)/Math.log(10)))),Z=Math.floor(ab.low/af)*af,ad=this.view.container.width(),aa=$("<div style='position: relative; height: 1.3em;'></div>");while(Z<ab.high){var ae=(Z-ab.low)/ac*ad;aa.append($("<div class='label'>"+commatize(Z)+"</div>").css({position:"absolute",left:ae-1}));Z+=af}this.content_div.children(":first").remove();this.content_div.append(aa)}});var g=function(aa,Z,ad){J.call(this,aa,Z,ad);this.drawables=[];this.left_offset=0;if("drawables" in ad){var ac;for(var ab=0;ab<ad.drawables.length;ab++){ac=ad.drawables[ab];this.drawables[ab]=object_from_template(ac,aa,null);if(ac.left_offset>this.left_offset){this.left_offset=ac.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};o(g.prototype,J.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_group()}}].concat(J.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(Z){J.prototype.change_mode.call(this,Z);for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].change_mode(Z)}},init:function(){var ab=[];for(var aa=0;aa<this.drawables.length;aa++){ab.push(this.drawables[aa].init())}var Z=this;$.when.apply($,ab).then(function(){Z.enabled=true;Z.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,draw_helper:function(aa,ap,aw,at,ah,aj,aq){var ao=this,aA=this._gen_tile_cache_key(ap,aj,aw),ae=this._get_tile_bounds(aw,at);if(!aq){aq={}}var az=(aa?undefined:ao.tile_cache.get_elt(aA));if(az){ao.show_tile(az,ah,aj);return az}var ai=[],ao,am=true,au,ak;for(var av=0;av<this.drawables.length;av++){ao=this.drawables[av];au=ao.data_manager.get_data(ae,ao.mode,at,ao.data_url_extra_params);if(is_deferred(au)){am=false}ai.push(au);ak=null;if(view.reference_track&&aj>view.canvas_manager.char_width_px){ak=view.reference_track.data_manager.get_data(ae,ao.mode,at,view.reference_track.data_url_extra_params);if(is_deferred(ak)){am=false}}ai.push(ak)}if(am){o(au,aq.more_tile_data);this.tile_predraw_init();var ad=ao.view.canvas_manager.new_canvas(),af=ao._get_tile_bounds(aw,at),ax=ae.get("start"),ab=ae.get("end"),ay=0,ap=Math.ceil((ab-ax)*aj)+this.left_offset,an=0,ac=[],av;var Z=0;for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];var al=ao.mode;if(al==="Auto"){al=ao.get_mode(au);ao.update_auto_mode(al)}ac.push(al);Z=ao.get_canvas_height(au,al,aj,ap);if(Z>an){an=Z}}ad.width=ap;ad.height=(aq.height?aq.height:an);ay=0;var ar=ad.getContext("2d");ar.translate(this.left_offset,0);ar.globalAlpha=0.5;ar.globalCompositeOperation="source-over";for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];ak=ai[ay+1];az=ao.draw_tile(au,ar,ac[av],at,ae,aj,ak)}this.tile_cache.set_elt(aA,az);this.show_tile(az,ah,aj);return az}var ag=$.Deferred(),ao=this;$.when.apply($,ai).then(function(){view.request_redraw(false,false,false,ao);ag.resolve()});return ag},show_group:function(){var ac=new M(this.view,this.container,{name:this.name}),Z;for(var ab=0;ab<this.drawables.length;ab++){Z=this.drawables[ab];Z.update_icons();ac.add_drawable(Z);Z.container=ac;ac.content_div.append(Z.container_div)}var aa=this.container.replace_drawable(this,ac,true);ac.request_draw()},tile_predraw_init:function(){var ac=Number.MAX_VALUE,Z=-ac,aa;for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];if(aa instanceof i){if(aa.prefs.min_value<ac){ac=aa.prefs.min_value}if(aa.prefs.max_value>Z){Z=aa.prefs.max_value}}}for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];aa.prefs.min_value=ac;aa.prefs.max_value=Z}},postdraw_actions:function(ab,ae,ag,aa){J.prototype.postdraw_actions.call(this,ab,ae,ag,aa);var ad=-1;for(var ac=0;ac<ab.length;ac++){var Z=ab[ac].html_elt.find("canvas").height();if(Z>ad){ad=Z}}for(var ac=0;ac<ab.length;ac++){var af=ab[ac];if(af.html_elt.find("canvas").height()!==ad){this.draw_helper(true,ae,af.index,af.resolution,af.html_elt.parent(),ag,{height:ad});af.html_elt.remove()}}}});var y=function(Z){J.call(this,Z,{content_div:Z.top_labeltrack},{resize:false});Z.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:Z.dbkey};this.data_manager=new ReferenceTrackDataManager({data_url:reference_url});this.hide_contents()};o(y.prototype,p.prototype,J.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:p.prototype.can_draw,draw_helper:function(ad,ab,Z,aa,ae,af,ac){if(af>this.view.canvas_manager.char_width_px){return J.prototype.draw_helper.call(this,ad,ab,Z,aa,ae,af,ac)}else{this.hide_contents();return null}},draw_tile:function(ah,ai,ad,ac,af,aj){var ab=this;if(aj>this.view.canvas_manager.char_width_px){if(ah.data===null){this.hide_contents();return}var aa=ai.canvas;ai.font=ai.canvas.manager.default_font;ai.textAlign="center";ah=ah.data;for(var ae=0,ag=ah.length;ae<ag;ae++){var Z=Math.floor(ae*aj);ai.fillText(ah[ae],Z,10)}this.show_contents();return new b(ab,af,ac,aa,ah)}this.hide_contents()}});var i=function(ab,aa,ac){var Z=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_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:32,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(i.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var Z=this;Z.vertical_range=undefined;return $.getJSON(Z.data_url,{stats:true,chrom:Z.view.chrom,low:0,high:Z.view.max_high,hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id},function(aa){Z.container_div.addClass("line-track");var ad=aa.data;if(isNaN(parseFloat(Z.prefs.min_value))||isNaN(parseFloat(Z.prefs.max_value))){var ab=ad.min,af=ad.max;ab=Math.floor(Math.min(0,Math.max(ab,ad.mean-2*ad.sd)));af=Math.ceil(Math.max(0,Math.min(af,ad.mean+2*ad.sd)));Z.prefs.min_value=ab;Z.prefs.max_value=af;$("#track_"+Z.dataset_id+"_minval").val(Z.prefs.min_value);$("#track_"+Z.dataset_id+"_maxval").val(Z.prefs.max_value)}Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.total_frequency=ad.total_frequency;Z.container_div.find(".yaxislabel").remove();var ae=$("<div/>").text(U(Z.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_min_value(ag)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+Z.dataset_id+"_minval").prependTo(Z.container_div),ac=$("<div/>").text(U(Z.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_max_value(ag)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+Z.dataset_id+"_maxval").prependTo(Z.container_div)})},draw_tile:function(ai,ag,ab,aa,ad,ah){var Z=ag.canvas,ac=ad.get("start"),af=ad.get("end"),ae=new I.LinePainter(ai.data,ac,af,this.prefs,ab);ae.draw(ag,Z.width,Z.height,ah);return new b(this,ad,aa,Z,ai.data)},can_subset:function(Z){return false}});var r=function(ab,aa,ac){var Z=this;this.display_modes=["Heatmap"];this.mode="Heatmap";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{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}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(r.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;this.tile_cache.clear();this.request_draw()},draw_tile:function(aj,ah,ae,ac,aa,ai){var ab=ah.canvas,Z=this._get_tile_bounds(aa,ac),ad=Z[0],ag=Z[1],af=new I.DiagonalHeatmapPainter(aj.data,ad,ag,this.prefs,ae);af.draw(ah,ab.width,ab.height,ai);return new b(this,aa,ac,ab,aj.data)}});var c=function(ac,ab,ae){var aa=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];J.call(this,ac,ab,ae);var ad=get_random_color(),Z=get_random_color([ad,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ad},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",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:this.visible_height_px,hidden:true}],saved_values:ae.prefs,onchange:function(){aa.set_name(aa.prefs.name);aa.tile_cache.clear();aa.set_painter_from_config();aa.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ae.hda_ldda;this.dataset_id=ae.dataset_id;this.original_dataset_id=ae.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,J.prototype,{set_dataset:function(Z){this.dataset_id=Z.get("id");this.hda_ldda=Z.get("hda_ldda");this.data_manager.set("dataset",Z)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=I.ArcLinkedFeaturePainter}else{this.painter=I.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ao,aj,ae,ad){J.prototype.postdraw_actions.call(this,ao,ad);var ai=this,al;if(ai.mode==="Coverage"){var aa=-1;for(al=0;al<ao.length;al++){var ak=ao[al].max_val;if(ak>aa){aa=ak}}for(al=0;al<ao.length;al++){var aq=ao[al];if(aq.max_val!==aa){aq.html_elt.remove();ai.draw_helper(true,aj,aq.index,aq.resolution,aq.html_elt.parent(),ae,{more_tile_data:{max:aa}})}}}if(ai.filters_manager){var af=ai.filters_manager.filters;for(var an=0;an<af.length;an++){af[an].update_ui_elt()}var ap=false,Z,ag;for(al=0;al<ao.length;al++){if(ao[al].data.length){Z=ao[al].data[0];for(var an=0;an<af.length;an++){ag=af[an];if(ag.applies_to(Z)&&ag.min!==ag.max){ap=true;break}}}}if(ai.filters_available!==ap){ai.filters_available=ap;if(!ai.filters_available){ai.filters_manager.hide()}ai.update_icons()}}this.container_div.find(".yaxislabel").remove();var ac=ao[0];if(ac instanceof j){var ah=(this.prefs.histogram_max?this.prefs.histogram_max:ac.max_val),ab=$("<div/>").text(ah).make_text_editable({num_cols:12,on_finish:function(ar){$(".bs-tooltip").remove();var ar=parseFloat(ar);ai.prefs.histogram_max=(!isNaN(ar)?ar:null);ai.tile_cache.clear();ai.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ab)}if(ac instanceof L){var am=true;for(al=0;al<ao.length;al++){if(!ao[al].all_slotted){am=false;break}}if(!am){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(Z){var Z;if(this.mode==="Auto"){if(Z==="no_detail"){Z="feature spans"}else{if(Z==="summary_tree"){Z="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+Z+")")}},incremental_slots:function(ad,Z,ac){var aa=this.view.canvas_manager.dummy_context,ab=this.slotters[ad];if(!ab||(ab.mode!==ac)){ab=new (s.FeatureSlotter)(ad,ac,x,function(ae){return aa.measureText(ae)});this.slotters[ad]=ab}return ab.slot_features(Z)},get_mode:function(Z){if(Z.dataset_type==="summary_tree"){mode="summary_tree"}else{if(Z.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>F){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(Z,ad,ae,aa){if(ad==="summary_tree"||ad==="Coverage"){return this.summary_draw_height}else{var ac=this.incremental_slots(ae,Z.data,ad);var ab=new (this.painter)(null,null,null,this.prefs,ad);return Math.max(Y,ab.get_required_height(ac,aa))}},draw_tile:function(aj,an,al,ao,ac,ag,ab){var am=this,aa=an.canvas,av=ac.get("start"),Z=ac.get("end"),ad=this.left_offset;if(al==="summary_tree"||al==="Coverage"){var ax=new I.SummaryTreePainter(aj,av,Z,this.prefs);ax.draw(an,aa.width,aa.height,ag);return new j(am,ac,ao,aa,aj.data,aj.max)}var af=[],ak=this.slotters[ag].slots;all_slotted=true;if(aj.data){var ah=this.filters_manager.filters;for(var ap=0,ar=aj.data.length;ap<ar;ap++){var ae=aj.data[ap];var aq=false;var ai;for(var au=0,az=ah.length;au<az;au++){ai=ah[au];ai.update_attrs(ae);if(!ai.keep(ae)){aq=true;break}}if(!aq){af.push(ae);if(!(ae[0] in ak)){all_slotted=false}}}}var ay=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aw=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var ax=new (this.painter)(af,av,Z,this.prefs,al,ay,aw,ab);var at=null;an.fillStyle=this.prefs.block_color;an.font=an.canvas.manager.default_font;an.textAlign="right";if(aj.data){at=ax.draw(an,aa.width,aa.height,ag,ak);at.translation=-ad}return new L(am,ac,ao,aa,aj.data,ag,al,aj.message,all_slotted,at)},data_and_mode_compatible:function(Z,aa){if(aa==="Auto"){return true}else{if(aa==="Coverage"){return Z.dataset_type==="summary_tree"}else{if(Z.extra_info==="no_detail"||Z.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(Z){if(Z.dataset_type==="summary_tree"||Z.message||Z.extra_info==="no_detail"){return false}return true}});var O=function(aa,Z,ab){c.call(this,aa,Z,ab);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_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_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ab.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter};o(O.prototype,p.prototype,J.prototype,c.prototype);var R=function(ab,aa,ad){c.call(this,ab,aa,ad);var ac=get_random_color(),Z=get_random_color([ac,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ac},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ad.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter;this.update_icons()};o(R.prototype,p.prototype,J.prototype,c.prototype);S.View=X;S.DrawableGroup=M;S.LineTrack=i;S.FeatureTrack=c;S.DiagonalHeatmapTrack=r;S.ReadTrack=R;S.VcfTrack=O;S.CompositeTrack=g};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(require,exports){var extend=require("class").extend;var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-1)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2]-1,feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,orig_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=0,char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var draw_last=[];if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){gap=Math.round(w_scale/2)}if(!cigar){cigar=[[0,orig_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=(feature_start-1)+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(gap>0){ctx.fillStyle=block_color;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=CONNECTOR_COLOR;for(var c=0,str_len=seq.length;c<str_len;c++){if(this.prefs.show_differences){if(this.ref_seq){var ref_char=this.ref_seq[seq_start-tile_low+c];if(!ref_char||ref_char.toLowerCase()===seq[c].toLowerCase()){continue}}else{continue}}if(seq_start+c>=tile_low&&seq_start+c<=tile_high){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start-gap,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color,gap=0;if((mode==="Pack"||this.mode==="Auto")&&w_scale>ctx.canvas.manager.char_width_px){var gap=Math.round(w_scale/2)}if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING-gap,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"4169E1",neg_color:"FF8C00"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};exports.Scaler=Scaler;exports.SummaryTreePainter=SummaryTreePainter;exports.LinePainter=LinePainter;exports.LinkedFeaturePainter=LinkedFeaturePainter;exports.ReadPainter=ReadPainter;exports.ArcLinkedFeaturePainter=ArcLinkedFeaturePainter;exports.DiagonalHeatmapPainter=DiagonalHeatmapPainter};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var g=arguments[0];for(var f=1;f<arguments.length;f++){var d=arguments[f];for(var e in d){g[e]=d[e]}}return g};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tooltip().click(a)};var trackster_module=function(d,S){var o=d("class").extend,s=d("slotting"),I=d("painters");var m={};var k=function(Z,aa){m[Z.attr("id")]=aa};var l=function(Z,ab,ad,ac){ad=".group";var aa={};m[Z.attr("id")]=ac;Z.bind("drag",{handle:"."+ab,relative:true},function(al,am){var ak=$(this),ap=$(this).parent(),ah=ap.children(),aj=m[$(this).attr("id")],ag,af,an,ae,ai;af=$(this).parents(ad);if(af.length!==0){an=af.position().top;ae=an+af.outerHeight();if(am.offsetY<an){$(this).insertBefore(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable_before(aj,ao);return}else{if(am.offsetY>ae){$(this).insertAfter(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable(aj);return}}}af=null;for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));an=ag.position().top;ae=an+ag.outerHeight();if(ag.is(ad)&&this!==ag.get(0)&&am.offsetY>=an&&am.offsetY<=ae){if(am.offsetY-an<ae-am.offsetY){ag.find(".content-div").prepend(this)}else{ag.find(".content-div").append(this)}if(aj.container){aj.container.remove_drawable(aj)}m[ag.attr("id")].add_drawable(aj);return}}for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));if(am.offsetY<ag.position().top&&!(ag.hasClass("reference-track")||ag.hasClass("intro"))){break}}if(ai===ah.length){if(this!==ah.get(ai-1)){ap.append(this);m[ap.attr("id")].move_drawable(aj,ai)}}else{if(this!==ah.get(ai)){$(this).insertBefore(ah.get(ai));m[ap.attr("id")].move_drawable(aj,(am.deltaY>0?ai-1:ai))}}}).bind("dragstart",function(){aa["border-top"]=Z.css("border-top");aa["border-bottom"]=Z.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(aa)})};S.moveable=l;var Y=16,D=9,A=20,x=100,F=12000,P=400,H=5000,u=100,n="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",N=10,E=20;function U(aa,Z){if(!Z){Z=0}var ab=Math.pow(10,Z);return Math.round(aa*ab)/ab}var p=function(aa,Z,ac){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ac.name;this.view=aa;this.container=Z;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ac.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ac.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;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=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ad){ad.stopPropagation()});var ab=this;this.container_div.hover(function(){ab.icons_div.show()},function(){ab.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(Z){if(Z.content_visible){Z.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");Z.hide_contents();Z.content_visible=false}else{Z.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");Z.content_visible=true;Z.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(aa){var ac=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},Z=function(){aa.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(ad){if((ad.keyCode||ad.which)===27){ac()}else{if((ad.keyCode||ad.which)===13){Z()}}};$(window).bind("keypress.check_enter_esc",ab);show_modal("Configure",aa.config.build_form(),{Cancel:ac,OK:Z})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(Z){this.old_name=this.name;this.name=Z;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var Z=this.view;this.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(aa,af,ae,ad,Z,ac){var ab=this;this.action_icons[aa]=$("<a/>").attr("href","javascript:void(0);").attr("title",af).addClass("icon-button").addClass(ae).tooltip().click(function(){ad(ab)}).appendTo(this.icons_div);if(ac){this.action_icons[aa].hide()}},build_action_icons:function(Z){var ab;for(var aa=0;aa<Z.length;aa++){ab=Z[aa];this.add_action_icon(ab.name,ab.title,ab.css_class,ab.on_click_fn,ab.prepend,ab.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(aa,Z,ab){p.call(this,aa,Z,ab);this.obj_type=ab.obj_type;this.drawables=[]};o(w.prototype,p.prototype,{unpack_drawables:function(ab){this.drawables=[];var aa;for(var Z=0;Z<ab.length;Z++){aa=object_from_template(ab[Z],this.view,this);this.add_drawable(aa)}},init:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].init()}},_draw:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z]._draw()}},to_dict:function(){var aa=[];for(var Z=0;Z<this.drawables.length;Z++){aa.push(this.drawables[Z].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:aa}},add_drawable:function(Z){this.drawables.push(Z);Z.container=this;this.changed()},add_drawable_before:function(ab,Z){this.changed();var aa=this.drawables.indexOf(Z);if(aa!==-1){this.drawables.splice(aa,0,ab);return true}return false},replace_drawable:function(ab,Z,aa){var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables[ac]=Z;if(aa){ab.container_div.replaceWith(Z.container_div)}this.changed()}return ac},remove_drawable:function(aa){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);aa.container=null;this.changed();return true}return false},move_drawable:function(aa,ab){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);this.drawables.splice(ab,0,aa);this.changed();return true}return false}});var M=function(aa,Z,ac){o(ac,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,aa,Z,ac);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new V(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ac){this.unpack_drawables(ac.drawables)}if("filters" in ac){var ab=this.filters_manager;this.filters_manager=new V(this,ac.filters);ab.parent_div.replaceWith(this.filters_manager.parent_div);if(ac.filters.visible){this.setup_multitrack_filtering()}}};o(M.prototype,p.prototype,w.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters();Z._restore_filter_managers()}else{Z.setup_multitrack_filtering();Z.request_draw(true)}Z.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var Z=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(Z)}return Z},build_header_div:function(){var Z=$("<div/>").addClass("track-header");Z.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(Z);return Z},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ab=this.drawables.length;if(ab===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ab===1){if(this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ah,af,al=true,ad=this.drawables[0].get_type(),Z=0;for(ai=0;ai<ab;ai++){af=this.drawables[ai];if(af.get_type()!==ad){can_composite=false;break}if(af instanceof c){Z++}}if(al||Z===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(Z>1&&Z===this.drawables.length){var am={},aa;af=this.drawables[0];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];am[aa.name]=[aa]}for(ai=1;ai<this.drawables.length;ai++){af=this.drawables[ai];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];if(aa.name in am){am[aa.name].push(aa)}}}this.filters_manager.remove_all();var ac,ae,ag,aj;for(var ak in am){ac=am[ak];if(ac.length===Z){ae=new Q({name:ac[0].name,index:ac[0].index});this.filters_manager.add_filter(ae)}}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 Z=0;Z<this.drawables.length;Z++){this.drawables[Z].filters_manager=this.saved_filters_managers[Z]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var Z=0;Z<this.drawables.length;Z++){drawable=this.drawables[Z];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=[];for(var aa=0;aa<this.drawables.length;aa++){ad.push(this.drawables[aa].name)}var ab="Composite Track of "+this.drawables.length+" tracks ("+ad.join(", ")+")";var ac=new g(this.view,this.view,{name:ab,drawables:this.drawables});var Z=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);this.update_icons()},remove_drawable:function(Z){w.prototype.remove_drawable.call(this,Z);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var Z=o(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return Z},request_draw:function(Z,ab){for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].request_draw(Z,ab)}}});var X=function(Z){o(Z,{obj_type:"View"});w.call(this,"View",Z.container,Z);this.chrom=null;this.vis_id=Z.vis_id;this.dbkey=Z.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.init();this.canvas_manager=new CanvasManager(this.container.get(0).ownerDocument);this.reset()};_.extend(X.prototype,Backbone.Events);o(X.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ab=this.container,Z=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ab);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ab);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ab);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,Z);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ac=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_datasets(add_datasets_url,add_track_async_url,function(ad){_.each(ad,function(ae){Z.add_drawable(object_from_template(ae,Z,Z))})})});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("href","javascript:void(0);").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=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var aa=function(ad){if(ad.type==="focusout"||(ad.keyCode||ad.which)===13||(ad.keyCode||ad.which)===27){if((ad.keyCode||ad.which)!==27){Z.go_to($(this).val())}$(this).hide();$(this).val("");Z.location_span.show();Z.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",aa).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){Z.location_span.hide();Z.chrom_select.hide();Z.nav_input.val(Z.chrom+":"+Z.low+"-"+Z.high);Z.nav_input.css("display","inline-block");Z.nav_input.select();Z.nav_input.focus()});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(){Z.zoom_out();Z.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){Z.zoom_in();Z.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){Z.change_chrom(Z.chrom_select.val())});this.browser_content_div.click(function(ad){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ad){Z.zoom_in(ad.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ad,ae){this.current_x=ae.offsetX}).bind("drag",function(ad,af){var ag=af.offsetX-this.current_x;this.current_x=af.offsetX;var ae=Math.round(ag/Z.viewport_container.width()*(Z.max_high-Z.max_low));Z.move_delta(-ae)});this.overview_close.click(function(){Z.reset_overview()});this.viewport_container.bind("draginit",function(ad,ae){if(ad.clientX>Z.viewport_container.width()-16){return false}}).bind("dragstart",function(ad,ae){ae.original_low=Z.low;ae.current_height=ad.clientY;ae.current_x=ae.offsetX}).bind("drag",function(af,ah){var ad=$(this);var ai=ah.offsetX-ah.current_x;var ae=ad.scrollTop()-(af.clientY-ah.current_height);ad.scrollTop(ae);ah.current_height=af.clientY;ah.current_x=ah.offsetX;var ag=Math.round(ai/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}).bind("mousewheel",function(af,ah,ae,ad){if(ae){ae*=50;var ag=Math.round(-ae/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}});this.top_labeltrack.bind("dragstart",function(ad,ae){return $("<div />").css({height:Z.browser_content_div.height()+Z.top_labeltrack.height()+Z.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ah,ai){$(ai.proxy).css({left:Math.min(ah.pageX,ai.startX)-Z.container.offset().left,width:Math.abs(ah.pageX-ai.startX)});var ae=Math.min(ah.pageX,ai.startX)-Z.container.offset().left,ad=Math.max(ah.pageX,ai.startX)-Z.container.offset().left,ag=(Z.high-Z.low),af=Z.viewport_container.width();Z.update_location(Math.round(ae/af*ag)+Z.low,Math.round(ad/af*ag)+Z.low)}).bind("dragend",function(ai,aj){var ae=Math.min(ai.pageX,aj.startX),ad=Math.max(ai.pageX,aj.startX),ag=(Z.high-Z.low),af=Z.viewport_container.width(),ah=Z.low;Z.low=Math.round(ae/af*ag)+ah;Z.high=Math.round(ad/af*ag)+ah;$(aj.proxy).remove();Z.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}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){Z.resize_window()},500)});$(document).bind("redraw",function(){Z.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(aa,ac,Z,ad){if(this.timer){clearTimeout(this.timer)}if(ad){var ab=this;this.timer=setTimeout(function(){ab.trigger("navigate",aa+":"+ac+"-"+Z)},500)}else{view.trigger("navigate",aa+":"+ac+"-"+Z)}},update_location:function(Z,ab){this.location_span.text(commatize(Z)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(Z)+"-"+commatize(ab));var aa=view.chrom_select.val();if(aa!==""){this.trigger_navigate(aa,view.low,view.high,true)}},load_chroms:function(ab){ab.num=u;ab.dbkey=this.dbkey;var Z=this,aa=$.Deferred();$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ad){if(ad.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ad.reference){Z.add_label_track(new y(Z))}Z.chrom_data=ad.chrom_info;var ag='<option value="">Select Chrom/Contig</option>';for(var af=0,ac=Z.chrom_data.length;af<ac;af++){var ae=Z.chrom_data[af].chrom;ag+='<option value="'+ae+'">'+ae+"</option>"}if(ad.prev_chroms){ag+='<option value="previous">Previous '+u+"</option>"}if(ad.next_chroms){ag+='<option value="next">Next '+u+"</option>"}Z.chrom_select.html(ag);Z.chrom_start_index=ad.start_index;aa.resolve(ad)},error:function(){alert("Could not load chroms for this dbkey:",Z.dbkey)}});return aa},change_chrom:function(ae,aa,ag){var ab=this;if(!ab.chrom_data){ab.load_chroms_deferred.then(function(){ab.change_chrom(ae,aa,ag)});return}if(!ae||ae==="None"){return}if(ae==="previous"){ab.load_chroms({low:this.chrom_start_index-u});return}if(ae==="next"){ab.load_chroms({low:this.chrom_start_index+u});return}var af=$.grep(ab.chrom_data,function(ah,ai){return ah.chrom===ae})[0];if(af===undefined){ab.load_chroms({chrom:ae},function(){ab.change_chrom(ae,aa,ag)});return}else{if(ae!==ab.chrom){ab.chrom=ae;ab.chrom_select.val(ab.chrom);ab.max_high=af.len-1;ab.reset();ab.request_redraw(true);for(var ad=0,Z=ab.drawables.length;ad<Z;ad++){var ac=ab.drawables[ad];if(ac.init){ac.init()}}if(ab.reference_track){ab.reference_track.init()}}if(aa!==undefined&&ag!==undefined){ab.low=Math.max(aa,0);ab.high=Math.min(ag,ab.max_high)}else{ab.low=0;ab.high=ab.max_high}ab.reset_overview();ab.request_redraw()}},go_to:function(ad){ad=ad.replace(/ |,/g,"");var ah=this,Z,ac,aa=ad.split(":"),af=aa[0],ag=aa[1];if(ag!==undefined){try{var ae=ag.split("-");Z=parseInt(ae[0],10);ac=parseInt(ae[1],10)}catch(ab){return false}}ah.change_chrom(af,Z,ac)},move_fraction:function(ab){var Z=this;var aa=Z.high-Z.low;this.move_delta(ab*aa)},move_delta:function(ac){var Z=this;var ab=Z.high-Z.low;if(Z.low-ac<Z.max_low){Z.low=Z.max_low;Z.high=Z.max_low+ab}else{if(Z.high-ac>Z.max_high){Z.high=Z.max_high;Z.low=Z.max_high-ab}else{Z.high-=ac;Z.low-=ac}}Z.request_redraw();var aa=Z.chrom_select.val();this.trigger_navigate(aa,Z.low,Z.high,true)},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);Z.init();this.changed();this.update_intro_div()},add_label_track:function(Z){Z.view=this;Z.init();this.label_tracks.push(Z)},remove_drawable:function(ab,aa){w.prototype.remove_drawable.call(this,ab);if(aa){var Z=this;ab.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ah,Z,ag,ai){var af=this,ae=(ai?[ai]:af.drawables),ab;var aa;for(var ad=0;ad<ae.length;ad++){aa=ae[ad];ab=-1;for(var ac=0;ac<af.tracks_to_be_redrawn.length;ac++){if(af.tracks_to_be_redrawn[ac][0]===aa){ab=ac;break}}if(ab<0){af.tracks_to_be_redrawn.push([aa,Z,ag])}else{af.tracks_to_be_redrawn[ad][1]=Z;af.tracks_to_be_redrawn[ad][2]=ag}}if(!this.requested_redraw){requestAnimationFrame(function(){af._redraw(ah)});this.requested_redraw=true}},_redraw:function(aj){this.requested_redraw=false;var ag=this.low,ac=this.high;if(ag<this.max_low){ag=this.max_low}if(ac>this.max_high){ac=this.max_high}var ai=this.high-this.low;if(this.high!==0&&ai<this.min_separation){ac=ag+this.min_separation}this.low=Math.floor(ag);this.high=Math.ceil(ac);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var Z=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=13;this.overview_box.css({left:Z,width:Math.max(ak,af)}).show();if(af<ak){this.overview_box.css("left",Z-(ak-af)/2)}if(this.overview_highlight){this.overview_highlight.css({left:Z,width:af})}if(!aj){var ab,aa,ah;for(var ad=0,ae=this.tracks_to_be_redrawn.length;ad<ae;ad++){ab=this.tracks_to_be_redrawn[ad][0];aa=this.tracks_to_be_redrawn[ad][1];ah=this.tracks_to_be_redrawn[ad][2];if(ab){ab._draw(aa,ah)}}this.tracks_to_be_redrawn=[];for(ad=0,ae=this.label_tracks.length;ad<ae;ad++){this.label_tracks[ad]._draw()}}},zoom_in:function(aa,ab){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ac=this.high-this.low,ad=ac/2+this.low,Z=(ac/this.zoom_factor)/2;if(aa){ad=aa/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ad-Z);this.high=Math.round(ad+Z);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var aa=this.high-this.low,ab=aa/2+this.low,Z=(aa*this.zoom_factor)/2;this.low=Math.round(ab-Z);this.high=Math.round(ab+Z);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(ab){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ab.dataset_id){return}this.overview_viewport.find(".track").remove()}var aa=ab.copy({content_div:this.overview_viewport}),Z=this;aa.header_div.hide();aa.is_overview=true;Z.overview_drawable=aa;this.overview_drawable.postdraw_actions=function(){Z.overview_highlight.show().height(Z.overview_drawable.content_div.height());Z.overview_viewport.height(Z.overview_drawable.content_div.height()+Z.overview_box.outerHeight());Z.overview_close.show();Z.resize_window()};Z.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-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 q=function(ab,ag,ac){this.track=ab;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],aa=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params.push(new e(aa,am,ae,(aa in ac?ac[aa]:ao),ai.min,ai.max))}else{if(ak==="select"){this.params.push(new K(aa,am,ae,(aa in ac?ac[aa]:ao)))}else{console.log("WARNING: unrecognized tool parameter type:",aa,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).click(function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("param-input").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: both;'/>").appendTo(au)});this.parent_div.find("input").click(function(){$(this).select()});var ap=$("<div>").addClass("param-row").appendTo(this.parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ap);var Z=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ap);Z.click(function(){ah.run_on_region()});af.click(function(){ah.run_on_dataset()});if("visible" in ac&&ac.visible){this.parent_div.show()}};o(q.prototype,{update_params:function(){for(var Z=0;Z<this.params.length;Z++){this.params[Z].update_value()}},state_dict:function(){var aa={};for(var Z=0;Z<this.params.length;Z++){aa[this.params[Z].name]=this.params[Z].value}aa.visible=this.parent_div.is(":visible");return aa},get_param_values_dict:function(){var Z={};this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();Z[aa]=ab});return Z},get_param_values:function(){var Z=[];this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();if(aa){Z[Z.length]=ab}});return Z},run_on_dataset:function(){var Z=this;Z.run({target_dataset_id:this.track.original_dataset_id,tool_id:Z.name},null,function(aa){show_modal(Z.name+" is Running",Z.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ae=this.track,ab=aa.tool_id+ae.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),Z;if(ae.container===view){var ad=new M(view,view,{name:this.name});var ac=ae.container.replace_drawable(ae,ad,false);ad.container_div.insertBefore(ae.view.content_div.children()[ac]);ad.add_drawable(ae);ae.container_div.appendTo(ad.content_div);Z=ad}else{Z=ae.container}var af=new ae.constructor(view,Z,{name:ab,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ae.mode);af.set_filters_manager(ae.filters_manager.copy(af));af.update_icons();Z.add_drawable(af);af.tiles_div.text("Starting job.");this.update_params();this.run(aa,af,function(ag){af.set_dataset(new Dataset(ag));af.tiles_div.text("Running 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f=function(Z){this.manager=null;this.name=Z.name;this.index=Z.index;this.tool_id=Z.tool_id;this.tool_exp_name=Z.tool_exp_name};o(f.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var Q=function(ah){f.call(this,ah);this.low=("low" in ah?ah.low:-Number.MAX_VALUE);this.high=("high" in ah?ah.high:Number.MAX_VALUE);this.min=("min" in ah?ah.min:Number.MAX_VALUE);this.max=("max" in ah?ah.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ad=function(ai,aj,ak){ai.click(function(){var ap=aj.text(),an=parseFloat(ak.slider("option","max")),am=(an<=1?4:an<=1000000?an.toString().length:6),ao=false,al=$(this).parents(".slider-row");al.addClass("input");if(ak.slider("option","values")){am=2*am+1;ao=true}aj.text("");$("<input type='text'/>").attr("size",am).attr("maxlength",am).attr("value",ap).appendTo(aj).focus().select().click(function(aq){aq.stopPropagation()}).blur(function(){$(this).remove();aj.text(ap);al.removeClass("input")}).keyup(function(av){if(av.keyCode===27){$(this).trigger("blur")}else{if(av.keyCode===13){var at=ak.slider("option","min"),aq=ak.slider("option","max"),au=function(aw){return(isNaN(aw)||aw>aq||aw<at)},ar=$(this).val();if(!ao){ar=parseFloat(ar);if(au(ar)){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}else{ar=ar.split("-");ar=[parseFloat(ar[0]),parseFloat(ar[1])];if(au(ar[0])||au(ar[1])){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}ak.slider((ao?"values":"value"),ar);al.removeClass("input")}}})})};var aa=this;aa.parent_div=$("<div/>").addClass("filter-row slider-row");var Z=$("<div/>").addClass("elt-label").appendTo(aa.parent_div),af=$("<span/>").addClass("slider-name").text(aa.name+" ").appendTo(Z),ab=$("<span/>").text(this.low+"-"+this.high),ac=$("<span/>").addClass("slider-value").appendTo(Z).append("[").append(ab).append("]");aa.values_span=ab;var ae=$("<div/>").addClass("slider").appendTo(aa.parent_div);aa.control_element=$("<div/>").attr("id",aa.name+"-filter-control").appendTo(ae);aa.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(ai,aj){aa.slide(ai,aj)},change:function(ai,aj){aa.control_element.slider("option","slide").call(aa.control_element,ai,aj)}});aa.slider=aa.control_element;aa.slider_label=ab;ad(ac,ab,aa.control_element);var ag=$("<div/>").addClass("display-controls").appendTo(aa.parent_div);this.transparency_icon=create_action_icon("Use filter for data 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this._keep_val(aa[this.index])}},update_attrs:function(ac){var Z=false;if(!this.applies_to(ac)){return Z}var aa=ac[this.index];if(!(aa instanceof Array)){aa=[aa]}for(var ab=0;ab<aa.length;ab++){var ad=aa[ab];if(ad<this.min){this.min=Math.floor(ad);Z=true}if(ad>this.max){this.max=Math.ceil(ad);Z=true}}return Z},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var aa=this.slider.slider("option","min"),Z=this.slider.slider("option","max");if(this.min<aa||this.max>Z){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var V=function(ab,ah){this.track=ab;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aj){aj.stopPropagation()}).click(function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()}).bind("keydown",function(aj){aj.stopPropagation()});if(ah&&"filters" in ah){var Z=("alpha_filter" in ah?ah.alpha_filter:null),ac=("height_filter" in ah?ah.height_filter:null),ae=ah.filters,aa;for(var af=0;af<ae.length;af++){if(ae[af].type==="number"){aa=new Q(ae[af]);this.add_filter(aa);if(aa.name===Z){this.alpha_filter=aa;aa.transparency_icon.addClass("active").show()}if(aa.name===ac){this.height_filter=aa;aa.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ah&&ah.visible){this.parent_div.show()}}if(this.filters.length!==0){var ai=$("<div/>").addClass("param-row").appendTo(this.parent_div);var ag=$("<input 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Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.update_ui_elt()}},clear_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.slider.slider("option","values",[aa.min,aa.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var af=function(aj,ah,ai){if(!(ah in aj)){aj[ah]=ai}return aj[ah]};var ae={},ag,Z;for(var ad=0;ad<this.filters.length;ad++){ag=this.filters[ad];if(ag.tool_id){if(ag.min!==ag.low){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" >= "+ag.low}if(ag.max!==ag.high){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" <= "+ag.high}}}var aa=[];for(var ac in ae){aa[aa.length]=[ac,ae[ac]]}(function ab(an,ak){var ai=ak[0],aj=ai[0],am=ai[1],al="("+am.join(") and (")+")",ah={cond:al,input:an,target_dataset_id:an,tool_id:aj},ak=ak.slice(1);$.getJSON(run_tool_url,ah,function(ao){if(ao.error){show_modal("Filter Dataset","Error running tool 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Click to get more data including depth").tooltip().appendTo(message_div),Z=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+al+" features in this region were obtained from server. 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ag=$(this).offset(),ak=al.pageX-ag.left,aj=al.pageY-ag.top,ap=aa.feature_mapper.get_feature_data(ak,aj),ah=(ap?ap[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ah||$(this).attr("id")!==ah.toString()){$(this).remove()}});if(ap){var ac=Z[ah];if(!ac){var ah=ap[0],am={name:ap[3],start:ap[1],end:ap[2],strand:ap[4]},af=aa.track.filters_manager.filters,ae;for(var ai=0;ai<af.length;ai++){ae=af[ai];am[ae.name]=ap[ae.index]}var ac=$("<div/>").attr("id",ah).addClass("feature-popup"),aq=$("<table/>"),ao,an,ar;for(ao in am){an=am[ao];ar=$("<tr/>").appendTo(aq);$("<th/>").appendTo(ar).text(ao);$("<td/>").attr("align","left").appendTo(ar).text(typeof(an)==="number"?U(an,2):an)}ac.append($("<div class='feature-popup-inner'>").append(aq));Z[ah]=ac}ac.appendTo($(this).parents(".track-content").children(".overlay"));var 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bookmarks</option></select>',ab=_.template(ac,{track:Z});var ae=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aa=function(){var ag=$('select[name="regions"] option:selected').val(),ai,af=new GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ah=_.map($(".bookmark"),function(aj){return new GenomeRegion({from_str:$(aj).children(".position").text()})});if(ag==="cur"){ai=[af]}else{if(ag==="bookmarks"){ai=ah}else{ai=[af].concat(ah)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:Z.dataset_id,hda_ldda:Z.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ai).toJSON())})},ad=function(af){if((af.keyCode||af.which)===27){ae()}else{if((af.keyCode||af.which)===13){aa()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ab,{No:ae,Yes:aa})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var Z=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(Z)}this.name_div=$("<div/>").addClass("track-name").appendTo(Z).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return Z},on_resize:function(){},add_resize_handle:function(){var Z=this;var ac=false;var ab=false;var aa=$("<div class='track-resize'>");$(Z.container_div).hover(function(){if(Z.content_visible){ac=true;aa.show()}},function(){ac=false;if(!ab){aa.hide()}});aa.hide().bind("dragstart",function(ad,ae){ab=true;ae.original_height=$(Z.content_div).height()}).bind("drag",function(ae,af){var ad=Math.min(Math.max(af.original_height+af.deltaY,Z.min_height_px),Z.max_height_px);$(Z.tiles_div).css("height",ad);Z.visible_height_px=(Z.max_height_px===ad?0:ad);Z.on_resize()}).bind("dragend",function(ad,ae){Z.tile_cache.clear();ab=false;if(!ac){aa.hide()}Z.config.values.height=Z.visible_height_px;Z.changed()}).appendTo(Z.container_div)},set_display_modes:function(ac,af){this.display_modes=ac;this.mode=(af?af:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var aa=this,ad={};for(var ab=0,Z=aa.display_modes.length;ab<Z;ab++){var ae=aa.display_modes[ab];ad[ae]=function(ag){return function(){aa.change_mode(ag);aa.icons_div.show();aa.container_div.mouseleave(function(){aa.icons_div.hide()})}}(ae)}make_popupmenu(this.action_icons.mode_icon,ad)},build_action_icons:function(){p.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 y){return"ReferenceTrack"}else{if(this instanceof i){return"LineTrack"}else{if(this instanceof R){return"ReadTrack"}else{if(this instanceof O){return"VcfTrack"}else{if(this instanceof g){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.content_div.css("height","auto");aa.tiles_div.children().remove();aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}var Z=$.Deferred();$.getJSON(this.dataset_check_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.tiles_div.text(n);if(ab.message){var ac=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.tiles_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.tiles_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.tiles_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.tiles_div.html(t);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab==="data"||ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.update_icons()}aa.tiles_div.text(T);if(aa.view.chrom){aa.tiles_div.text("");aa.tiles_div.css("height",aa.visible_height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){Z.resolve();aa.container_div.removeClass("nodata error pending");aa.request_draw()})}else{Z.resolve()}}}}}}});this.update_icons();return Z},predraw_init:function(){}});var J=function(ab,aa,ac){h.call(this,ab,aa,ac);var Z=this;l(Z.container_div,Z.drag_handle_class,".group",Z);this.filters_manager=new V(this,("filters" in ac?ac.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ac&&ac.tool?new q(this,ac.tool,ac.tool_state):null);this.tile_cache=new Cache(N);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ac.mode){this.change_mode(ac.mode)}};o(J.prototype,p.prototype,h.prototype,{action_icons_def:h.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(Z){$(".bs-tooltip").remove();Z.slotters[Z.view.resolution_px_b].max_rows*=2;Z.request_draw(true)},hide:true}]),copy:function(Z){var aa=this.to_dict();o(aa,{data_manager:this.data_manager});var ab=new this.constructor(this.view,Z,aa);ab.change_mode(this.mode);ab.enabled=this.enabled;return ab},set_filters_manager:function(Z){this.filters_manager=Z;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(aa){var Z=this;Z.mode=aa;Z.config.values.mode=aa;Z.tile_cache.clear();Z.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+Z.mode+")");return Z},update_icons:function(){var Z=this;if(Z.filters_available){Z.action_icons.filters_icon.show()}else{Z.action_icons.filters_icon.hide()}if(Z.tool){Z.action_icons.tools_icon.show();Z.action_icons.param_space_viz_icon.show()}else{Z.action_icons.tools_icon.hide();Z.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(aa,ab,Z){return aa+"_"+ab+"_"+Z},request_draw:function(aa,Z){this.view.request_redraw(false,aa,Z,this)},before_draw:function(){},_draw:function(aa,ak){if(!this.can_draw()){return}var ai=this.view.low,ae=this.view.high,ag=ae-ai,ab=this.view.container.width(),am=this.view.resolution_px_b,ad=this.view.resolution_b_px;if(this.is_overview){ai=this.view.max_low;ae=this.view.max_high;ad=(view.max_high-view.max_low)/ab;am=1/ad}this.before_draw();this.tiles_div.children().addClass("remove");var Z=Math.floor(ai/(ad*P)),ah=true,al=[],af=function(an){return(an&&"track" in an)};while((Z*P*ad)<ae){var aj=this.draw_helper(aa,ab,Z,ad,this.tiles_div,am);if(af(aj)){al.push(aj)}else{ah=false}Z+=1}if(!ak){this.tiles_div.children(".remove").removeClass("remove").remove()}var ac=this;if(ah){this.tiles_div.children(".remove").remove();ac.postdraw_actions(al,ab,am,ak)}},postdraw_actions:function(ab,ac,ae,Z){var ad=false;for(var aa=0;aa<ab.length;aa++){if(ab[aa].has_icons){ad=true;break}}if(ad){for(var aa=0;aa<ab.length;aa++){tile=ab[aa];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(Z,al,aq,ao,ae,af,am){var ak=this,au=this._gen_tile_cache_key(al,af,aq),ac=this._get_tile_bounds(aq,ao);if(!am){am={}}var at=(Z?undefined:ak.tile_cache.get_elt(au));if(at){ak.show_tile(at,ae,af);return at}var ai=true;var ap=ak.data_manager.get_data(ac,ak.mode,ao,ak.data_url_extra_params);if(is_deferred(ap)){ai=false}var ag;if(view.reference_track&&af>view.canvas_manager.char_width_px){ag=view.reference_track.data_manager.get_data(ac,ak.mode,ao,view.reference_track.data_url_extra_params);if(is_deferred(ag)){ai=false}}if(ai){o(ap,am.more_tile_data);var ah=ak.mode;if(ah==="Auto"){ah=ak.get_mode(ap);ak.update_auto_mode(ah)}var ab=ak.view.canvas_manager.new_canvas(),ar=ac.get("start"),aa=ac.get("end"),al=Math.ceil((aa-ar)*af)+ak.left_offset,aj=ak.get_canvas_height(ap,ah,af,al);ab.width=al;ab.height=aj;var an=ab.getContext("2d");an.translate(this.left_offset,0);var at=ak.draw_tile(ap,an,ah,ao,ac,af,ag);if(at!==undefined){ak.tile_cache.set_elt(au,at);ak.show_tile(at,ae,af)}return at}var ad=$.Deferred();$.when(ap,ag).then(function(){view.request_redraw(false,false,false,ak);ad.resolve()});return ad},get_canvas_height:function(Z,ab,ac,aa){return this.visible_height_px},draw_tile:function(Z,aa,ae,ac,ad,af,ab){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ab,ad,ae){var aa=this,Z=ab.html_elt;ab.predisplay_actions();var ac=(ab.low-(this.is_overview?this.view.max_low:this.view.low))*ae;if(this.left_offset){ac-=this.left_offset}Z.css({position:"absolute",top:0,left:ac});if(Z.hasClass("remove")){Z.removeClass("remove")}else{ad.append(Z)}aa.after_show_tile(ab)},after_show_tile:function(Z){this.max_height_px=Math.max(this.max_height_px,Z.html_elt.height());Z.html_elt.parent().children().css("height",this.max_height_px+"px");var aa=this.max_height_px;if(this.visible_height_px!==0){aa=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",aa+"px")},_get_tile_bounds:function(Z,aa){var ac=Math.floor(Z*P*aa),ad=Math.ceil(P*aa),ab=(ac+ad<=this.view.max_high?ac+ad:this.view.max_high);return new GenomeRegion({chrom:this.view.chrom,start:ac,end:ab})},tool_region_and_parameters_str:function(ab,Z,ac){var aa=this,ad=(ab!==undefined&&Z!==undefined&&ac!==undefined?ab+":"+Z+"-"+ac:"all");return" - region=["+ad+"], parameters=["+aa.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(Z,aa){return true},can_subset:function(Z){return false},init_for_tool_data:function(){this.data_manager.set("data_url",raw_data_url);this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ab,ac,ae,Z){var aa=this;aa.normal_postdraw_actions(ab,ac,ae,Z);aa.dataset_state_url=converted_datasets_state_url;aa.data_query_wait=H;var ad=new ServerStateDeferred({url:aa.dataset_state_url,url_params:{dataset_id:aa.dataset_id,hda_ldda:aa.hda_ldda},interval:aa.data_query_wait,success_fn:function(af){return af!=="pending"}});$.when(ad.go()).then(function(){aa.data_manager.set("data_url",default_data_url)});aa.postdraw_actions=aa.normal_postdraw_actions}}});var W=function(aa,Z){var ab={resize:false};h.call(this,aa,Z,ab);this.container_div.addClass("label-track")};o(W.prototype,h.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ab=this.view,ac=ab.high-ab.low,af=Math.floor(Math.pow(10,Math.floor(Math.log(ac)/Math.log(10)))),Z=Math.floor(ab.low/af)*af,ad=this.view.container.width(),aa=$("<div style='position: relative; height: 1.3em;'></div>");while(Z<ab.high){var ae=(Z-ab.low)/ac*ad;aa.append($("<div class='label'>"+commatize(Z)+"</div>").css({position:"absolute",left:ae-1}));Z+=af}this.content_div.children(":first").remove();this.content_div.append(aa)}});var g=function(aa,Z,ad){J.call(this,aa,Z,ad);this.drawables=[];this.left_offset=0;if("drawables" in ad){var ac;for(var ab=0;ab<ad.drawables.length;ab++){ac=ad.drawables[ab];this.drawables[ab]=object_from_template(ac,aa,null);if(ac.left_offset>this.left_offset){this.left_offset=ac.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};o(g.prototype,J.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_group()}}].concat(J.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(Z){J.prototype.change_mode.call(this,Z);for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].change_mode(Z)}},init:function(){var ab=[];for(var aa=0;aa<this.drawables.length;aa++){ab.push(this.drawables[aa].init())}var Z=this;$.when.apply($,ab).then(function(){Z.enabled=true;Z.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,draw_helper:function(aa,ap,aw,at,ah,aj,aq){var ao=this,aA=this._gen_tile_cache_key(ap,aj,aw),ae=this._get_tile_bounds(aw,at);if(!aq){aq={}}var az=(aa?undefined:ao.tile_cache.get_elt(aA));if(az){ao.show_tile(az,ah,aj);return az}var ai=[],ao,am=true,au,ak;for(var av=0;av<this.drawables.length;av++){ao=this.drawables[av];au=ao.data_manager.get_data(ae,ao.mode,at,ao.data_url_extra_params);if(is_deferred(au)){am=false}ai.push(au);ak=null;if(view.reference_track&&aj>view.canvas_manager.char_width_px){ak=view.reference_track.data_manager.get_data(ae,ao.mode,at,view.reference_track.data_url_extra_params);if(is_deferred(ak)){am=false}}ai.push(ak)}if(am){o(au,aq.more_tile_data);this.tile_predraw_init();var ad=ao.view.canvas_manager.new_canvas(),af=ao._get_tile_bounds(aw,at),ax=ae.get("start"),ab=ae.get("end"),ay=0,ap=Math.ceil((ab-ax)*aj)+this.left_offset,an=0,ac=[],av;var Z=0;for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];var al=ao.mode;if(al==="Auto"){al=ao.get_mode(au);ao.update_auto_mode(al)}ac.push(al);Z=ao.get_canvas_height(au,al,aj,ap);if(Z>an){an=Z}}ad.width=ap;ad.height=(aq.height?aq.height:an);ay=0;var ar=ad.getContext("2d");ar.translate(this.left_offset,0);ar.globalAlpha=0.5;ar.globalCompositeOperation="source-over";for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];ak=ai[ay+1];az=ao.draw_tile(au,ar,ac[av],at,ae,aj,ak)}this.tile_cache.set_elt(aA,az);this.show_tile(az,ah,aj);return az}var ag=$.Deferred(),ao=this;$.when.apply($,ai).then(function(){view.request_redraw(false,false,false,ao);ag.resolve()});return ag},show_group:function(){var ac=new M(this.view,this.container,{name:this.name}),Z;for(var ab=0;ab<this.drawables.length;ab++){Z=this.drawables[ab];Z.update_icons();ac.add_drawable(Z);Z.container=ac;ac.content_div.append(Z.container_div)}var aa=this.container.replace_drawable(this,ac,true);ac.request_draw()},tile_predraw_init:function(){var ac=Number.MAX_VALUE,Z=-ac,aa;for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];if(aa instanceof i){if(aa.prefs.min_value<ac){ac=aa.prefs.min_value}if(aa.prefs.max_value>Z){Z=aa.prefs.max_value}}}for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];aa.prefs.min_value=ac;aa.prefs.max_value=Z}},postdraw_actions:function(ab,ae,ag,aa){J.prototype.postdraw_actions.call(this,ab,ae,ag,aa);var ad=-1;for(var ac=0;ac<ab.length;ac++){var Z=ab[ac].html_elt.find("canvas").height();if(Z>ad){ad=Z}}for(var ac=0;ac<ab.length;ac++){var af=ab[ac];if(af.html_elt.find("canvas").height()!==ad){this.draw_helper(true,ae,af.index,af.resolution,af.html_elt.parent(),ag,{height:ad});af.html_elt.remove()}}}});var y=function(Z){J.call(this,Z,{content_div:Z.top_labeltrack},{resize:false});Z.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:Z.dbkey};this.data_manager=new ReferenceTrackDataManager({data_url:reference_url});this.hide_contents()};o(y.prototype,p.prototype,J.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:p.prototype.can_draw,draw_helper:function(ad,ab,Z,aa,ae,af,ac){if(af>this.view.canvas_manager.char_width_px){return J.prototype.draw_helper.call(this,ad,ab,Z,aa,ae,af,ac)}else{this.hide_contents();return null}},draw_tile:function(ah,ai,ad,ac,af,aj){var ab=this;if(aj>this.view.canvas_manager.char_width_px){if(ah.data===null){this.hide_contents();return}var aa=ai.canvas;ai.font=ai.canvas.manager.default_font;ai.textAlign="center";ah=ah.data;for(var ae=0,ag=ah.length;ae<ag;ae++){var Z=Math.floor(ae*aj);ai.fillText(ah[ae],Z,10)}this.show_contents();return new b(ab,af,ac,aa,ah)}this.hide_contents()}});var i=function(ab,aa,ac){var Z=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_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:32,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(i.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var Z=this;Z.vertical_range=undefined;return $.getJSON(Z.data_url,{stats:true,chrom:Z.view.chrom,low:0,high:Z.view.max_high,hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id},function(aa){Z.container_div.addClass("line-track");var ad=aa.data;if(isNaN(parseFloat(Z.prefs.min_value))||isNaN(parseFloat(Z.prefs.max_value))){var ab=ad.min,af=ad.max;ab=Math.floor(Math.min(0,Math.max(ab,ad.mean-2*ad.sd)));af=Math.ceil(Math.max(0,Math.min(af,ad.mean+2*ad.sd)));Z.prefs.min_value=ab;Z.prefs.max_value=af;$("#track_"+Z.dataset_id+"_minval").val(Z.prefs.min_value);$("#track_"+Z.dataset_id+"_maxval").val(Z.prefs.max_value)}Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.total_frequency=ad.total_frequency;Z.container_div.find(".yaxislabel").remove();var ae=$("<div/>").text(U(Z.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_min_value(ag)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+Z.dataset_id+"_minval").prependTo(Z.container_div),ac=$("<div/>").text(U(Z.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_max_value(ag)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+Z.dataset_id+"_maxval").prependTo(Z.container_div)})},draw_tile:function(ai,ag,ab,aa,ad,ah){var Z=ag.canvas,ac=ad.get("start"),af=ad.get("end"),ae=new I.LinePainter(ai.data,ac,af,this.prefs,ab);ae.draw(ag,Z.width,Z.height,ah);return new b(this,ad,aa,Z,ai.data)},can_subset:function(Z){return false}});var r=function(ab,aa,ac){var Z=this;this.display_modes=["Heatmap"];this.mode="Heatmap";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{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}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(r.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;this.tile_cache.clear();this.request_draw()},draw_tile:function(aj,ah,ae,ac,aa,ai){var ab=ah.canvas,Z=this._get_tile_bounds(aa,ac),ad=Z[0],ag=Z[1],af=new I.DiagonalHeatmapPainter(aj.data,ad,ag,this.prefs,ae);af.draw(ah,ab.width,ab.height,ai);return new b(this,aa,ac,ab,aj.data)}});var c=function(ac,ab,ae){var aa=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];J.call(this,ac,ab,ae);var ad=get_random_color(),Z=get_random_color([ad,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ad},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",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:this.visible_height_px,hidden:true}],saved_values:ae.prefs,onchange:function(){aa.set_name(aa.prefs.name);aa.tile_cache.clear();aa.set_painter_from_config();aa.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ae.hda_ldda;this.dataset_id=ae.dataset_id;this.original_dataset_id=ae.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,J.prototype,{set_dataset:function(Z){this.dataset_id=Z.get("id");this.hda_ldda=Z.get("hda_ldda");this.data_manager.set("dataset",Z)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=I.ArcLinkedFeaturePainter}else{this.painter=I.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ao,aj,ae,ad){J.prototype.postdraw_actions.call(this,ao,ad);var ai=this,al;if(ai.mode==="Coverage"){var aa=-1;for(al=0;al<ao.length;al++){var ak=ao[al].max_val;if(ak>aa){aa=ak}}for(al=0;al<ao.length;al++){var aq=ao[al];if(aq.max_val!==aa){aq.html_elt.remove();ai.draw_helper(true,aj,aq.index,aq.resolution,aq.html_elt.parent(),ae,{more_tile_data:{max:aa}})}}}if(ai.filters_manager){var af=ai.filters_manager.filters;for(var an=0;an<af.length;an++){af[an].update_ui_elt()}var ap=false,Z,ag;for(al=0;al<ao.length;al++){if(ao[al].data.length){Z=ao[al].data[0];for(var an=0;an<af.length;an++){ag=af[an];if(ag.applies_to(Z)&&ag.min!==ag.max){ap=true;break}}}}if(ai.filters_available!==ap){ai.filters_available=ap;if(!ai.filters_available){ai.filters_manager.hide()}ai.update_icons()}}this.container_div.find(".yaxislabel").remove();var ac=ao[0];if(ac instanceof j){var ah=(this.prefs.histogram_max?this.prefs.histogram_max:ac.max_val),ab=$("<div/>").text(ah).make_text_editable({num_cols:12,on_finish:function(ar){$(".bs-tooltip").remove();var ar=parseFloat(ar);ai.prefs.histogram_max=(!isNaN(ar)?ar:null);ai.tile_cache.clear();ai.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ab)}if(ac instanceof L){var am=true;for(al=0;al<ao.length;al++){if(!ao[al].all_slotted){am=false;break}}if(!am){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(Z){var Z;if(this.mode==="Auto"){if(Z==="no_detail"){Z="feature spans"}else{if(Z==="summary_tree"){Z="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+Z+")")}},incremental_slots:function(ad,Z,ac){var aa=this.view.canvas_manager.dummy_context,ab=this.slotters[ad];if(!ab||(ab.mode!==ac)){ab=new (s.FeatureSlotter)(ad,ac,x,function(ae){return aa.measureText(ae)});this.slotters[ad]=ab}return ab.slot_features(Z)},get_mode:function(Z){if(Z.dataset_type==="summary_tree"){mode="summary_tree"}else{if(Z.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>F){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(Z,ad,ae,aa){if(ad==="summary_tree"||ad==="Coverage"){return this.summary_draw_height}else{var ac=this.incremental_slots(ae,Z.data,ad);var ab=new (this.painter)(null,null,null,this.prefs,ad);return Math.max(Y,ab.get_required_height(ac,aa))}},draw_tile:function(aj,an,al,ao,ac,ag,ab){var am=this,aa=an.canvas,av=ac.get("start"),Z=ac.get("end"),ad=this.left_offset;if(al==="summary_tree"||al==="Coverage"){var ax=new I.SummaryTreePainter(aj,av,Z,this.prefs);ax.draw(an,aa.width,aa.height,ag);return new j(am,ac,ao,aa,aj.data,aj.max)}var af=[],ak=this.slotters[ag].slots;all_slotted=true;if(aj.data){var ah=this.filters_manager.filters;for(var ap=0,ar=aj.data.length;ap<ar;ap++){var ae=aj.data[ap];var aq=false;var ai;for(var au=0,az=ah.length;au<az;au++){ai=ah[au];ai.update_attrs(ae);if(!ai.keep(ae)){aq=true;break}}if(!aq){af.push(ae);if(!(ae[0] in ak)){all_slotted=false}}}}var ay=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aw=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var ax=new (this.painter)(af,av,Z,this.prefs,al,ay,aw,ab);var at=null;an.fillStyle=this.prefs.block_color;an.font=an.canvas.manager.default_font;an.textAlign="right";if(aj.data){at=ax.draw(an,aa.width,aa.height,ag,ak);at.translation=-ad}return new L(am,ac,ao,aa,aj.data,ag,al,aj.message,all_slotted,at)},data_and_mode_compatible:function(Z,aa){if(aa==="Auto"){return true}else{if(aa==="Coverage"){return Z.dataset_type==="summary_tree"}else{if(Z.extra_info==="no_detail"||Z.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(Z){if(Z.dataset_type==="summary_tree"||Z.message||Z.extra_info==="no_detail"){return false}return true}});var O=function(aa,Z,ab){c.call(this,aa,Z,ab);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_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_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ab.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter};o(O.prototype,p.prototype,J.prototype,c.prototype);var R=function(ab,aa,ad){c.call(this,ab,aa,ad);var ac=get_random_color(),Z=get_random_color([ac,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ac},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ad.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter;this.update_icons()};o(R.prototype,p.prototype,J.prototype,c.prototype);S.View=X;S.DrawableGroup=M;S.LineTrack=i;S.FeatureTrack=c;S.DiagonalHeatmapTrack=r;S.ReadTrack=R;S.VcfTrack=O;S.CompositeTrack=g};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(require,exports){var extend=require("class").extend;var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-1)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2]-1,feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,orig_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=0,char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var draw_last=[];if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){gap=Math.round(w_scale/2)}if(!cigar){cigar=[[0,orig_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=(feature_start-1)+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(gap>0){ctx.fillStyle=block_color;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=CONNECTOR_COLOR;for(var c=0,str_len=seq.length;c<str_len;c++){if(this.prefs.show_differences){if(this.ref_seq){var ref_char=this.ref_seq[seq_start-tile_low+c];if(!ref_char||ref_char.toLowerCase()===seq[c].toLowerCase()){continue}}else{continue}}if(seq_start+c>=tile_low&&seq_start+c<=tile_high){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start-gap,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color,gap=0;if((mode==="Pack"||this.mode==="Auto")&&w_scale>ctx.canvas.manager.char_width_px){var gap=Math.round(w_scale/2)}if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING-gap,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"4169E1",neg_color:"FF8C00"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};exports.Scaler=Scaler;exports.SummaryTreePainter=SummaryTreePainter;exports.LinePainter=LinePainter;exports.LinkedFeaturePainter=LinkedFeaturePainter;exports.ReadPainter=ReadPainter;exports.ArcLinkedFeaturePainter=ArcLinkedFeaturePainter;exports.DiagonalHeatmapPainter=DiagonalHeatmapPainter};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da templates/admin/requests/select_datasets_to_transfer.mako --- a/templates/admin/requests/select_datasets_to_transfer.mako +++ b/templates/admin/requests/select_datasets_to_transfer.mako @@ -8,7 +8,7 @@ ${common_javascripts()} </%def> -${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} +${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} ${h.css( "dynatree_skin/ui.dynatree" )} <script type="text/javascript"> diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da templates/admin/tool_shed_repository/browse_repository.mako --- a/templates/admin/tool_shed_repository/browse_repository.mako +++ b/templates/admin/tool_shed_repository/browse_repository.mako @@ -9,7 +9,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery.dynatree" )} ${browse_files(repository.name, repository.repo_files_directory(trans.app))} </%def> diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da templates/admin/tool_shed_repository/browse_tool_dependency.mako --- a/templates/admin/tool_shed_repository/browse_tool_dependency.mako +++ b/templates/admin/tool_shed_repository/browse_tool_dependency.mako @@ -9,7 +9,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery.dynatree" )} ${browse_files(tool_dependency.name, tool_dependency.installation_directory( trans.app ))} </%def> diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -11,7 +11,7 @@ <%def name="stylesheets()"> ${parent.stylesheets()} - ${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom", "library" )} + ${h.css( "history", "autocomplete_tagging", "trackster", "library", "jquery-ui/smoothness/jquery-ui-1.8.23.custom" )} </%def><%def name="javascripts()"> @@ -21,7 +21,7 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/libs/IE/excanvas.js')}"></script><![endif]--> -${h.js( "galaxy.base", "galaxy.panels", "libs/json2", "libs/jquery/jquery", "libs/bootstrap", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery.autocomplete", "mvc/data", "viz/visualization", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.ui.sortable.slider", "libs/farbtastic" )} +${h.js( "galaxy.base", "galaxy.panels", "libs/json2", "libs/jquery/jquery", "libs/bootstrap", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery-ui-1.8.23.custom.min", "mvc/data", "viz/visualization", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.ui.sortable.slider", "libs/farbtastic" )} <script type="text/javascript"> // diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da templates/webapps/community/repository/browse_repository.mako --- a/templates/webapps/community/repository/browse_repository.mako +++ b/templates/webapps/community/repository/browse_repository.mako @@ -57,7 +57,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery.ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} ${common_javascripts(repository)} </%def> diff -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 -r 9287f22c692087319003516fe1a5da0eb07c63da templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -28,7 +28,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} ${common_javascripts(repository)} <script type="text/javascript"> $( function() { 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: inithello: Added API integration for genome downloader. Improved detection of existing liftover files.
by Bitbucket 05 Sep '12

05 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/631c9dbca9bc/ changeset: 631c9dbca9bc user: inithello date: 2012-09-05 14:24:29 summary: Added API integration for genome downloader. Improved detection of existing liftover files. affected #: 4 files diff -r e4672c5b57b2234edc9f5e2c9d5abd6b7148fdca -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 lib/galaxy/jobs/deferred/liftover_transfer.py --- a/lib/galaxy/jobs/deferred/liftover_transfer.py +++ b/lib/galaxy/jobs/deferred/liftover_transfer.py @@ -77,7 +77,7 @@ self.sa_session.flush() return self.job_states.WAIT else: - log.error( "An error occurred while downloading from %s" % job.params[ 'url' ] ) + log.error( "An error occurred while downloading from %s" % job.transfer_job.params[ 'url' ] ) return self.job_states.INVALID elif job.params[ 'type' ] == 'extract_transfer': return self.job_states.READY diff -r e4672c5b57b2234edc9f5e2c9d5abd6b7148fdca -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 lib/galaxy/web/api/genomes.py --- a/lib/galaxy/web/api/genomes.py +++ b/lib/galaxy/web/api/genomes.py @@ -22,4 +22,73 @@ Returns information about build <id> """ - return self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low ) \ No newline at end of file + return self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low ) + + @web.expose_api + def create( self, trans, payload, **kwd ): + """ + POST /api/genomes + Download and/or index a genome. + + Parameters: + + dbkey DB key of the build to download, ignored unless 'UCSC' is specified as the source + ncbi_name NCBI's genome identifier, ignored unless NCBI is specified as the source + ensembl_dbkey Ensembl's genome identifier, ignored unless Ensembl is specified as the source + url_dbkey DB key to use for this build, ignored unless URL is specified as the source + source Data source for this build. Can be: UCSC, Ensembl, NCBI, URL + indexers POST array of indexers to run after downloading (indexers[] = first, indexers[] = second, ...) + func Allowed values: + 'download' Download and index + 'index' Index only + + Returns: + + If no error: + dict( status: 'ok', job: <job ID> ) + + If error: + dict( status: 'error', error: <error message> ) + + """ + params = util.Params( payload ) + from galaxy.web.controllers.data_admin import build_param_dict as massage + paramdict = massage( params, trans ) + func = params.get( 'func', 'download' ) + if func == 'download': + url = paramdict[ 'url' ] + liftover = paramdict[ 'liftover' ] + dbkey = paramdict[ 'dbkey' ] + indexers = paramdict[ 'indexers' ] + longname = paramdict[ 'longname' ] + jobid = trans.app.job_manager.deferred_job_queue.plugins['GenomeTransferPlugin'].create_job( trans, url, dbkey, longname, indexers ) + chainjob = [] + if liftover is not None: + for chain in liftover: + liftover_url = u'ftp://hgdownload.cse.ucsc.edu%s' % chain[0] + from_genome = chain[1] + to_genome = chain[2] + destfile = liftover_url.split('/')[-1].replace('.gz', '') + lochain = trans.app.job_manager.deferred_job_queue.plugins['LiftOverTransferPlugin'].create_job( trans, liftover_url, dbkey, from_genome, to_genome, destfile, jobid ) + chainjob.append( lochain ) + job = trans.app.job_manager.deferred_job_queue.plugins['GenomeTransferPlugin'].get_job_status( jobid ) + job.params['liftover'] = chainjob + trans.app.model.context.current.flush() + return dict( status='ok', job=jobid ) + elif func == 'index': + dbkey = paramdict[ 'dbkey' ] + indexer = [ params.get( 'indexer', None ) ] + longname = None + path = None + for build in trans.app.tool_data_tables.data_tables[ 'all_fasta' ].data: + if build[0] == dbkey: + longname = build[2] + path = build[3] + break + if longname is not None and indexer is not None and path is not None: + jobid = trans.app.job_manager.deferred_job_queue.plugins['GenomeIndexPlugin'].create_job( trans, path, indexer, dbkey, longname ) + return dict( status='ok', job=jobid ) + else: + return dict( status='error', error='Build not %s found in tool data table.' % dbkey ) + else: + return dict( status='error', error='Unkown function selected.' ) diff -r e4672c5b57b2234edc9f5e2c9d5abd6b7148fdca -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 lib/galaxy/web/controllers/data_admin.py --- a/lib/galaxy/web/controllers/data_admin.py +++ b/lib/galaxy/web/controllers/data_admin.py @@ -152,6 +152,8 @@ params = util.Params( kwd ) jobid = params.get( 'job', '' ) deferred = trans.app.model.context.current.query( model.DeferredJob ).filter_by( id=jobid ).first() + if deferred is None: + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='Invalid genome downloader job specified.' ) gname = deferred.params[ 'intname' ] indexers = ', '.join( deferred.params[ 'indexes' ] ) jobs = self._get_jobs( deferred, trans ) @@ -244,18 +246,20 @@ checker = [] liftover = [] newlift = [] + ftp.retrlines('NLST /goldenPath/%s/liftOver/*.chain.gz' % dbkey, liftover.append) try: - ftp.retrlines('NLST /goldenPath/%s/liftOver/*.chain.gz' % dbkey, liftover.append) for chain in liftover: + lifts = [] fname = chain.split( '/' )[-1] - target = fname.replace( '.over.chain.gz', '' ).split( 'To' )[1] - target = target[0].lower() + target[1:] - if not os.path.exists( os.path.join( trans.app.config.get( 'genome_data_path', 'tool-data/genome' ), dbkey, 'liftOver', fname ) ): - newlift.append( [ chain, dbkey, target ] ) - current = dbkey[0].upper() + dbkey[1:] - targetfile = '%sTo%s.over.chain.gz' % ( target, current ) - if not os.path.exists( os.path.join( trans.app.config.get( 'genome_data_path', 'tool-data/genome' ), target, 'liftOver', targetfile ) ): - newlift.append( [ '/goldenPath/%s/liftOver/%s' % ( target, targetfile ), target, dbkey ] ) + organisms = fname.replace( '.over.chain.gz', '' ).split( 'To' ) + lifts.append( [ organisms[0], organisms[1][0].lower() + organisms[1][1:] ] ) + lifts.append( [ organisms[1][0].lower() + organisms[1][1:], organisms[0] ] ) + for organism in lifts: + remotepath = '/goldenPath/%s/liftOver/%sTo%s.over.chain.gz' % ( organism[0], organism[0], organism[1][0].upper() + organism[1][1:] ) + localfile = '%sTo%s.over.chain' % ( organism[0], organism[1][0].upper() + organism[1][1:] ) + localpath = os.path.join( trans.app.config.get( 'genome_data_path', 'tool-data/genome' ), organism[0], 'liftOver', localfile ) + if not os.path.exists( localpath ) or os.path.getsize( localpath ) == 0: + newlift.append( [ remotepath, organism[0], organism[1] ] ) except: newlift = None pass diff -r e4672c5b57b2234edc9f5e2c9d5abd6b7148fdca -r 631c9dbca9bc83223b886e01c8ae7f676ae8c599 templates/admin/data_admin/local_data.mako --- a/templates/admin/data_admin/local_data.mako +++ b/templates/admin/data_admin/local_data.mako @@ -74,7 +74,7 @@ %endfor </table><h2>Recent jobs:</h2> - <p>Click the job ID to see job details. Note that this list only shows jobs initiated by your account.</p> + <p>Click the job ID to see job details and the status of any individual sub-jobs. Note that this list only shows jobs initiated by your account.</p><div id="recentJobs"> %for job in jobgrid: <div id="job-${job['deferred']}" data-dbkey="${job['dbkey']}" data-name="${job['intname']}" data-indexes="${job['indexers']}" data-jobid="${job['deferred']}" data-state="${job['state']}" class="historyItem-${job['state']} historyItemWrapper historyItem"> 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: carlfeberhard: Fix sniff.py blastxml doc/unittest, removal of func.test_get_data.py 0140 (megablast xml upload), increased lines_diff in cuffmerge_wrapper.xml to handle inconsistent oId assignment (cuffmerge.test_tool_000000)
by Bitbucket 04 Sep '12

04 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e4672c5b57b2/ changeset: e4672c5b57b2 user: carlfeberhard date: 2012-09-04 19:28:25 summary: Fix sniff.py blastxml doc/unittest, removal of func.test_get_data.py 0140 (megablast xml upload), increased lines_diff in cuffmerge_wrapper.xml to handle inconsistent oId assignment (cuffmerge.test_tool_000000) affected #: 3 files diff -r 7182b04a32a7cb70411cbf07a5b10bf6bd59206e -r e4672c5b57b2234edc9f5e2c9d5abd6b7148fdca lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -231,7 +231,7 @@ >>> fname = get_test_fname('megablast_xml_parser_test1.blastxml') >>> guess_ext(fname) - 'blastxml' + 'xml' >>> fname = get_test_fname('interval.interval') >>> guess_ext(fname) 'interval' diff -r 7182b04a32a7cb70411cbf07a5b10bf6bd59206e -r e4672c5b57b2234edc9f5e2c9d5abd6b7148fdca test/functional/test_get_data.py --- a/test/functional/test_get_data.py +++ b/test/functional/test_get_data.py @@ -360,16 +360,6 @@ self.check_history_for_string( '2,500 sequences format: <span class="csfasta">csfasta</span>, <td>>2_14_26_F3,-1282216.0</td>' ) self.check_metadata_for_string( 'value="shrimp_cs_test1.csfasta" value="\?" Change data type value="csfasta" selected="yes"' ) self.delete_history( id=self.security.encode_id( history.id ) ) - def test_0140_upload_file( self ): - """Test uploading megablast_xml_parser_test1.gz, NOT setting the file format""" - # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) - self.upload_file( 'megablast_xml_parser_test1.gz' ) - hda = get_latest_hda() - assert hda is not None, "Problem retrieving hda from database" - self.check_history_for_string( 'NCBI Blast XML data format: <span class="blastxml">blastxml</span>' ) - self.delete_history( id=self.security.encode_id( history.id ) ) def test_0145_upload_file( self ): """Test uploading 1.axt, NOT setting the file format""" # Logged in as admin_user diff -r 7182b04a32a7cb70411cbf07a5b10bf6bd59206e -r e4672c5b57b2234edc9f5e2c9d5abd6b7148fdca tools/ngs_rna/cuffmerge_wrapper.xml --- a/tools/ngs_rna/cuffmerge_wrapper.xml +++ b/tools/ngs_rna/cuffmerge_wrapper.xml @@ -87,7 +87,8 @@ <param name="use_ref_annotation" value="Yes"/><param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/><param name="use_seq_data" value="No"/> - <output name="merged_transcripts" file="cuffmerge_out1.gtf"/> +  + <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="8"/></test></tests> 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: 4 new changesets
by Bitbucket 04 Sep '12

04 Sep '12

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8bccff9db869/ changeset: 8bccff9db869 user: jmchilton date: 2012-08-16 06:35:28 summary: Remove hard-coding of unsniffable binary types array and manually checking each sniffable type with a seperate function in upload.py. Information on both types is now stored dynamically as static variables in the Binary class. affected #: 4 files diff -r a42eae47ae877073a077527463beb32e251d7035 -r 8bccff9db86973c924b17a4251573e25af7618a4 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -18,10 +18,31 @@ log = logging.getLogger(__name__) # Currently these supported binary data types must be manually set on upload -unsniffable_binary_formats = [ 'ab1', 'scf', 'h5' ] class Binary( data.Data ): """Binary data""" + sniffable_binary_formats = [] + unsniffable_binary_formats = [] + + @staticmethod + def register_sniffable_binary_format(data_type, ext, type_class): + Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext, "class": type_class}) + + @staticmethod + def register_unsniffable_binary_ext(ext): + Binary.unsniffable_binary_formats.append(ext) + + @staticmethod + def is_sniffable_binary(filename): + for format in Binary.sniffable_binary_formats: + if format["class"]().sniff(filename): + return (format["type"], format["ext"]) + return None + + @staticmethod + def is_ext_unsniffable(ext): + return ext in Binary.unsniffable_binary_formats + def set_peek( self, dataset, is_multi_byte=False ): """Set the peek and blurb text""" if not dataset.dataset.purged: @@ -62,6 +83,8 @@ except: return "Binary ab1 sequence file (%s)" % ( data.nice_size( dataset.get_size() ) ) +Binary.register_unsniffable_binary_ext("ab1") + class Bam( Binary ): """Class describing a BAM binary file""" file_ext = "bam" @@ -218,6 +241,8 @@ def get_track_type( self ): return "ReadTrack", {"data": "bai", "index": "summary_tree"} +Binary.register_sniffable_binary_format("bam", "bam", Bam) + class H5( Binary ): """Class describing an HDF5 file""" file_ext = "h5" @@ -235,6 +260,8 @@ except: return "Binary h5 sequence file (%s)" % ( data.nice_size( dataset.get_size() ) ) +Binary.register_unsniffable_binary_ext("h5") + class Scf( Binary ): """Class describing an scf binary sequence file""" file_ext = "scf" @@ -252,6 +279,8 @@ except: return "Binary scf sequence file (%s)" % ( data.nice_size( dataset.get_size() ) ) +Binary.register_unsniffable_binary_ext("scf") + class Sff( Binary ): """ Standard Flowgram Format (SFF) """ file_ext = "sff" @@ -281,6 +310,8 @@ except: return "Binary sff file (%s)" % ( data.nice_size( dataset.get_size() ) ) +Binary.register_sniffable_binary_format("sff", "sff", Sff) + class BigWig(Binary): """ Accessing binary BigWig files from UCSC. @@ -314,6 +345,8 @@ def get_track_type( self ): return "LineTrack", {"data_standalone": "bigwig"} +Binary.register_sniffable_binary_format("bigwig", "bigwig", BigWig) + class BigBed(BigWig): """BigBed support from UCSC.""" def __init__( self, **kwd ): @@ -323,6 +356,8 @@ def get_track_type( self ): return "LineTrack", {"data_standalone": "bigbed"} +Binary.register_sniffable_binary_format("bigbed", "bigbed", BigBed) + class TwoBit (Binary): """Class describing a TwoBit format nucleotide file""" diff -r a42eae47ae877073a077527463beb32e251d7035 -r 8bccff9db86973c924b17a4251573e25af7618a4 lib/galaxy/datatypes/images.py --- a/lib/galaxy/datatypes/images.py +++ b/lib/galaxy/datatypes/images.py @@ -4,6 +4,7 @@ import data import logging +from galaxy.datatypes.binary import Binary from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes import metadata from galaxy.datatypes.sniff import * @@ -154,6 +155,8 @@ except IndexError: return False +Binary.register_sniffable_binary_format("pdf", "pdf", Pdf) + def create_applet_tag_peek( class_name, archive, params ): text = """  diff -r a42eae47ae877073a077527463beb32e251d7035 -r 8bccff9db86973c924b17a4251573e25af7618a4 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -5,7 +5,6 @@ import registry from galaxy import util from galaxy.datatypes.checkers import * -from galaxy.datatypes.binary import unsniffable_binary_formats log = logging.getLogger(__name__) @@ -381,7 +380,7 @@ ext = guess_ext( filename, sniff_order = datatypes_registry.sniff_order, is_multi_byte=is_multi_byte ) if check_binary( filename ): - if ext not in unsniffable_binary_formats and not datatypes_registry.get_datatype_by_extension( ext ).sniff( filename ): + if not Binary.is_ext_unsniffable(ext) and not datatypes_registry.get_datatype_by_extension( ext ).sniff( filename ): raise InappropriateDatasetContentError, 'The binary uploaded file contains inappropriate content.' elif check_html( filename ): raise InappropriateDatasetContentError, 'The uploaded file contains inappropriate HTML content.' diff -r a42eae47ae877073a077527463beb32e251d7035 -r 8bccff9db86973c924b17a4251573e25af7618a4 tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -58,16 +58,6 @@ return [safe_dict(x) for x in d] else: return d -def check_bam( file_path ): - return Bam().sniff( file_path ) -def check_sff( file_path ): - return Sff().sniff( file_path ) -def check_pdf( file_path ): - return Pdf().sniff( file_path ) -def check_bigwig( file_path ): - return BigWig().sniff( file_path ) -def check_bigbed( file_path ): - return BigBed().sniff( file_path ) def parse_outputs( args ): rval = {} for arg in args: @@ -121,21 +111,11 @@ data_type = 'multi-byte char' ext = sniff.guess_ext( dataset.path, is_multi_byte=True ) # Is dataset content supported sniffable binary? - elif check_bam( dataset.path ): - ext = 'bam' - data_type = 'bam' - elif check_sff( dataset.path ): - ext = 'sff' - data_type = 'sff' - elif check_pdf( dataset.path ): - ext = 'pdf' - data_type = 'pdf' - elif check_bigwig( dataset.path ): - ext = 'bigwig' - data_type = 'bigwig' - elif check_bigbed( dataset.path ): - ext = 'bigbed' - data_type = 'bigbed' + else: + type_info = Binary.is_sniffable_binary( dataset.path ) + if type_info: + data_type = type_info[0] + ext = type_info[1] if not data_type: # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress is_gzipped, is_valid = check_gzip( dataset.path ) @@ -267,10 +247,10 @@ parts = dataset.name.split( "." ) if len( parts ) > 1: ext = parts[1].strip().lower() - if ext not in unsniffable_binary_formats: + if not Binary.is_ext_unsniffable(ext): file_err( 'The uploaded binary file contains inappropriate content', dataset, json_file ) return - elif ext in unsniffable_binary_formats and dataset.file_type != ext: + elif Binary.is_ext_unsniffable(ext) and dataset.file_type != ext: err_msg = "You must manually set the 'File Format' to '%s' when uploading %s files." % ( ext.capitalize(), ext ) file_err( err_msg, dataset, json_file ) return https://bitbucket.org/galaxy/galaxy-central/changeset/3338d7629e33/ changeset: 3338d7629e33 user: jmchilton date: 2012-09-04 05:14:36 summary: Merge. affected #: 308 files Diff too large to display. https://bitbucket.org/galaxy/galaxy-central/changeset/ee84b9493b94/ changeset: ee84b9493b94 user: jmchilton date: 2012-09-04 05:25:42 summary: I messed up the previous merge, this fixes that commit. affected #: 1 file diff -r 3338d7629e33fab90b6af8f84aa4a09a9798aafc -r ee84b9493b948a2d0b56ecab1f45e75a952ef631 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -5,7 +5,6 @@ import registry from galaxy import util from galaxy.datatypes.checkers import * -from galaxy.datatypes.binary import unsniffable_binary_formats from encodings import search_function as encodings_search_function log = logging.getLogger(__name__) https://bitbucket.org/galaxy/galaxy-central/changeset/7182b04a32a7/ changeset: 7182b04a32a7 user: natefoo date: 2012-09-04 17:07:45 summary: Merged in jmchilton/galaxy-central-binary-type-enhancements (pull request #59) affected #: 4 files diff -r 83434eb47d587fe729252fe9d7ef6e34e499afb8 -r 7182b04a32a7cb70411cbf07a5b10bf6bd59206e lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -18,10 +18,31 @@ log = logging.getLogger(__name__) # Currently these supported binary data types must be manually set on upload -unsniffable_binary_formats = [ 'ab1', 'scf', 'h5' ] class Binary( data.Data ): """Binary data""" + sniffable_binary_formats = [] + unsniffable_binary_formats = [] + + @staticmethod + def register_sniffable_binary_format(data_type, ext, type_class): + Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext, "class": type_class}) + + @staticmethod + def register_unsniffable_binary_ext(ext): + Binary.unsniffable_binary_formats.append(ext) + + @staticmethod + def is_sniffable_binary(filename): + for format in Binary.sniffable_binary_formats: + if format["class"]().sniff(filename): + return (format["type"], format["ext"]) + return None + + @staticmethod + def is_ext_unsniffable(ext): + return ext in Binary.unsniffable_binary_formats + def set_peek( self, dataset, is_multi_byte=False ): """Set the peek and blurb text""" if not dataset.dataset.purged: @@ -62,6 +83,8 @@ except: return "Binary ab1 sequence file (%s)" % ( data.nice_size( dataset.get_size() ) ) +Binary.register_unsniffable_binary_ext("ab1") + class Bam( Binary ): """Class describing a BAM binary file""" file_ext = "bam" @@ -218,6 +241,8 @@ def get_track_type( self ): return "ReadTrack", {"data": "bai", "index": "summary_tree"} +Binary.register_sniffable_binary_format("bam", "bam", Bam) + class H5( Binary ): """Class describing an HDF5 file""" file_ext = "h5" @@ -235,6 +260,8 @@ except: return "Binary h5 sequence file (%s)" % ( data.nice_size( dataset.get_size() ) ) +Binary.register_unsniffable_binary_ext("h5") + class Scf( Binary ): """Class describing an scf binary sequence file""" file_ext = "scf" @@ -252,6 +279,8 @@ except: return "Binary scf sequence file (%s)" % ( data.nice_size( dataset.get_size() ) ) +Binary.register_unsniffable_binary_ext("scf") + class Sff( Binary ): """ Standard Flowgram Format (SFF) """ file_ext = "sff" @@ -281,6 +310,8 @@ except: return "Binary sff file (%s)" % ( data.nice_size( dataset.get_size() ) ) +Binary.register_sniffable_binary_format("sff", "sff", Sff) + class BigWig(Binary): """ Accessing binary BigWig files from UCSC. @@ -314,6 +345,8 @@ def get_track_type( self ): return "LineTrack", {"data_standalone": "bigwig"} +Binary.register_sniffable_binary_format("bigwig", "bigwig", BigWig) + class BigBed(BigWig): """BigBed support from UCSC.""" def __init__( self, **kwd ): @@ -323,6 +356,8 @@ def get_track_type( self ): return "LineTrack", {"data_standalone": "bigbed"} +Binary.register_sniffable_binary_format("bigbed", "bigbed", BigBed) + class TwoBit (Binary): """Class describing a TwoBit format nucleotide file""" diff -r 83434eb47d587fe729252fe9d7ef6e34e499afb8 -r 7182b04a32a7cb70411cbf07a5b10bf6bd59206e lib/galaxy/datatypes/images.py --- a/lib/galaxy/datatypes/images.py +++ b/lib/galaxy/datatypes/images.py @@ -4,6 +4,7 @@ import data import logging +from galaxy.datatypes.binary import Binary from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes import metadata from galaxy.datatypes.sniff import * @@ -154,6 +155,8 @@ except IndexError: return False +Binary.register_sniffable_binary_format("pdf", "pdf", Pdf) + def create_applet_tag_peek( class_name, archive, params ): text = """  diff -r 83434eb47d587fe729252fe9d7ef6e34e499afb8 -r 7182b04a32a7cb70411cbf07a5b10bf6bd59206e lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -5,7 +5,6 @@ import registry from galaxy import util from galaxy.datatypes.checkers import * -from galaxy.datatypes.binary import unsniffable_binary_formats from encodings import search_function as encodings_search_function log = logging.getLogger(__name__) @@ -380,7 +379,7 @@ ext = guess_ext( filename, sniff_order = datatypes_registry.sniff_order, is_multi_byte=is_multi_byte ) if check_binary( filename ): - if ext not in unsniffable_binary_formats and not datatypes_registry.get_datatype_by_extension( ext ).sniff( filename ): + if not Binary.is_ext_unsniffable(ext) and not datatypes_registry.get_datatype_by_extension( ext ).sniff( filename ): raise InappropriateDatasetContentError, 'The binary uploaded file contains inappropriate content.' elif check_html( filename ): raise InappropriateDatasetContentError, 'The uploaded file contains inappropriate HTML content.' diff -r 83434eb47d587fe729252fe9d7ef6e34e499afb8 -r 7182b04a32a7cb70411cbf07a5b10bf6bd59206e tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -58,16 +58,6 @@ return [safe_dict(x) for x in d] else: return d -def check_bam( file_path ): - return Bam().sniff( file_path ) -def check_sff( file_path ): - return Sff().sniff( file_path ) -def check_pdf( file_path ): - return Pdf().sniff( file_path ) -def check_bigwig( file_path ): - return BigWig().sniff( file_path ) -def check_bigbed( file_path ): - return BigBed().sniff( file_path ) def parse_outputs( args ): rval = {} for arg in args: @@ -122,21 +112,11 @@ data_type = 'multi-byte char' ext = sniff.guess_ext( dataset.path, is_multi_byte=True ) # Is dataset content supported sniffable binary? - elif check_bam( dataset.path ): - ext = 'bam' - data_type = 'bam' - elif check_sff( dataset.path ): - ext = 'sff' - data_type = 'sff' - elif check_pdf( dataset.path ): - ext = 'pdf' - data_type = 'pdf' - elif check_bigwig( dataset.path ): - ext = 'bigwig' - data_type = 'bigwig' - elif check_bigbed( dataset.path ): - ext = 'bigbed' - data_type = 'bigbed' + else: + type_info = Binary.is_sniffable_binary( dataset.path ) + if type_info: + data_type = type_info[0] + ext = type_info[1] if not data_type: # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress is_gzipped, is_valid = check_gzip( dataset.path ) @@ -268,10 +248,10 @@ parts = dataset.name.split( "." ) if len( parts ) > 1: ext = parts[1].strip().lower() - if ext not in unsniffable_binary_formats: + if not Binary.is_ext_unsniffable(ext): file_err( 'The uploaded binary file contains inappropriate content', dataset, json_file ) return - elif ext in unsniffable_binary_formats and dataset.file_type != ext: + elif Binary.is_ext_unsniffable(ext) and dataset.file_type != ext: err_msg = "You must manually set the 'File Format' to '%s' when uploading %s files." % ( ext.capitalize(), ext ) file_err( err_msg, dataset, json_file ) 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.

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commit/galaxy-central: inithello: Fixed error in solid2fasta.xml preventing help text from displaying.
by Bitbucket 04 Sep '12

04 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/83434eb47d58/ changeset: 83434eb47d58 user: inithello date: 2012-09-04 16:15:18 summary: Fixed error in solid2fasta.xml preventing help text from displaying. affected #: 1 file diff -r b31863f9408d082a8dbd209af1eb4b8609faa9ac -r 83434eb47d587fe729252fe9d7ef6e34e499afb8 tools/next_gen_conversion/solid2fastq.xml --- a/tools/next_gen_conversion/solid2fastq.xml +++ b/tools/next_gen_conversion/solid2fastq.xml @@ -66,7 +66,6 @@ </test></tests><help> - **What it does** Converts output of SOLiD instrument (versions 3.5 and earlier) to fastq format suitable for bowtie, bwa, and PerM mappers. @@ -79,22 +78,22 @@ Reads:: - >1831_573_1004_F3 + >1831_573_1004_F3 T00030133312212111300011021310132222 - >1831_573_1567_F3 + >1831_573_1567_F3 T03330322230322112131010221102122113 Quality scores:: - >1831_573_1004_F3 + >1831_573_1004_F3 4 29 34 34 32 32 24 24 20 17 10 34 29 20 34 13 30 34 22 24 11 28 19 17 34 17 24 17 25 34 7 24 14 12 22 - >1831_573_1567_F3 + >1831_573_1567_F3 8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 32 10 13 6 32 10 6 16 11 **Mate pairs** -If your data is from a mate-paired run, you will have additional read and quality datasets that will look similar to the ones above with one exception: the names of reads will be ending with "_R3". +If your data is from a mate-paired run, you will have additional read and quality datasets that will look similar to the ones above with one exception: the names of reads will be ending with "_R3". In this case choose **Yes** from the *Is this a mate-pair run?* drop down and you will be able to select R reads. When processing mate pairs this tool generates two output files: one for F3 reads and the other for R3 reads. The reads are guaranteed to be paired -- mated reads will be in the same position in F3 and R3 fastq file. However, because pairing is verified it may take a while to process an entire SOLiD run (several hours). @@ -104,11 +103,11 @@ **Remove reads containing color qualities below this value** - any read that contains as least one color call with quality lower than the specified value **will not** be reported. -**Trim trailing "_F3" and "_R3"?** - does just that. Not necessary for bowtie. Required for BWA. +**Trim trailing "_F3" and "_R3"?** - does just that. Not necessary for bowtie. Required for BWA. **Trim first base?** - SOLiD reads contain an adapter base such as the first T in this read:: - >1831_573_1004_F3 + >1831_573_1004_F3 T00030133312212111300011021310132222 this option removes this base leaving only color calls. Not necessary for bowtie. Required for BWA. @@ -119,42 +118,37 @@ **Examples of output** -When all parameters are left "as-is" you will get this (using reads and qualities shown above):: +When all parameters are left "as-is" you will get this (using reads and qualities shown above):: @1831_573_1004 T00030133312212111300011021310132222 + - %>CCAA9952+C>5C.?C79,=42C292:C(9/-7 + %%>CCAA9952+C>5C.?C79,=42C292:C(9/-7 @1831_573_1004 T03330322230322112131010221102122113 + - );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1, + );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1, Setting *Trim first base from reads* to **Yes** will produce this:: @1831_573_1004 00030133312212111300011021310132222 + - %>CCAA9952+C>5C.?C79,=42C292:C(9/-7 + %%>CCAA9952+C>5C.?C79,=42C292:C(9/-7 @1831_573_1004 03330322230322112131010221102122113 + - );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1, + );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1, Finally, setting *Double encode* to **Yes** will yield:: @1831_573_1004 TAAATACTTTCGGCGCCCTAAACCAGCTCACTGGGG + - %>CCAA9952+C>5C.?C79,=42C292:C(9/-7 + %%>CCAA9952+C>5C.?C79,=42C292:C(9/-7 @1831_573_1004 TATTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT + - );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1, - - - - - + );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1, </help></tool> 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: inithello: Improve display of job status, migration script to accomodate same
by Bitbucket 04 Sep '12

04 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b31863f9408d/ changeset: b31863f9408d user: inithello date: 2012-09-04 15:42:54 summary: Improve display of job status, migration script to accomodate same affected #: 5 files diff -r f7775cff6f6c8b3527557cae16151c9c38945679 -r b31863f9408d082a8dbd209af1eb4b8609faa9ac lib/galaxy/jobs/deferred/liftover_transfer.py --- a/lib/galaxy/jobs/deferred/liftover_transfer.py +++ b/lib/galaxy/jobs/deferred/liftover_transfer.py @@ -40,7 +40,7 @@ deferred = trans.app.model.DeferredJob( state = self.app.model.DeferredJob.states.NEW, plugin = 'LiftOverTransferPlugin', params = params ) self.sa_session.add( deferred ) self.sa_session.flush() - return job.id + return deferred.id def check_job( self, job ): if job.params['type'] == 'init_transfer': diff -r f7775cff6f6c8b3527557cae16151c9c38945679 -r b31863f9408d082a8dbd209af1eb4b8609faa9ac lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1539,7 +1539,7 @@ properties=dict( job = relation( Job ), history = relation( History ) ) ) assign_mapper( context, GenomeIndexToolData, GenomeIndexToolData.table, - properties=dict( job = relation( Job ), + properties=dict( job = relation( Job, backref='job' ), dataset = relation( Dataset ), user = relation( User ), deferred = relation( DeferredJob, backref='deferred_job' ), diff -r f7775cff6f6c8b3527557cae16151c9c38945679 -r b31863f9408d082a8dbd209af1eb4b8609faa9ac lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py @@ -0,0 +1,82 @@ +""" +Migration script to update the deferred job parameters for liftover transfer jobs. +""" + +from sqlalchemy import * +from migrate import * +from sqlalchemy.orm import * + +import datetime +now = datetime.datetime.utcnow + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * +from galaxy.model.orm.ext.assignmapper import assign_mapper + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +context = scoped_session( sessionmaker( autoflush=False, autocommit=True ) ) + +metadata = MetaData( migrate_engine ) + +class DeferredJob( object ): + states = Bunch( NEW = 'new', + WAITING = 'waiting', + QUEUED = 'queued', + RUNNING = 'running', + OK = 'ok', + ERROR = 'error' ) + def __init__( self, state=None, plugin=None, params=None ): + self.state = state + self.plugin = plugin + self.params = params + +DeferredJob.table = Table( "deferred_job", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "state", String( 64 ), index=True ), + Column( "plugin", String( 128 ), index=True ), + Column( "params", JSONType ) ) + +assign_mapper( context, DeferredJob, DeferredJob.table, properties = {} ) + +def upgrade(): + print __doc__ + liftoverjobs = dict() + + jobs = context.query( DeferredJob ).filter_by( plugin='LiftOverTransferPlugin' ).all() + + for job in jobs: + if job.params[ 'parentjob' ] not in liftoverjobs: + liftoverjobs[ job.params[ 'parentjob' ] ] = [] + liftoverjobs[ job.params[ 'parentjob'] ].append( job.id ) + + for parent in liftoverjobs: + lifts = liftoverjobs[ parent ] + deferred = context.query( DeferredJob ).filter_by( id=parent ).first() + deferred.params[ 'liftover' ] = lifts + + context.flush() + +def downgrade(): + + jobs = context.query( DeferredJob ).filter_by( plugin='GenomeTransferPlugin' ).all() + + for job in jobs: + if len( job.params[ 'liftover' ] ) == 0: + continue + transfers = [] + for lift in job.params[ 'liftover' ]: + liftoverjob = context.query( DeferredJob ).filter_by( id=lift ).first() + transfers.append( liftoverjob.params[ 'transfer_job_id' ] ) + job.params[ 'liftover' ] = transfers + + context.flush() diff -r f7775cff6f6c8b3527557cae16151c9c38945679 -r b31863f9408d082a8dbd209af1eb4b8609faa9ac lib/galaxy/tools/actions/index_genome.py --- a/lib/galaxy/tools/actions/index_genome.py +++ b/lib/galaxy/tools/actions/index_genome.py @@ -37,7 +37,7 @@ # Setup job and job wrapper. # - # Add association for keeping track of job, history, archive relationship. + # Add association for keeping track of index jobs, transfer jobs, and so on. user = trans.sa_session.query( trans.app.model.User ).get( int( incoming['user'] ) ) assoc = trans.app.model.GenomeIndexToolData( job=job, dataset=temp_dataset, fasta_path=incoming['path'], \ indexer=incoming['indexer'], user=user, \ @@ -46,11 +46,10 @@ job_wrapper = GenomeIndexToolWrapper( job ) cmd_line = job_wrapper.setup_job( assoc ) + # # Add parameters to job_parameter table. # - - # Set additional parameters. incoming[ '__GENOME_INDEX_COMMAND__' ] = cmd_line for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): job.add_parameter( name, value ) diff -r f7775cff6f6c8b3527557cae16151c9c38945679 -r b31863f9408d082a8dbd209af1eb4b8609faa9ac lib/galaxy/web/controllers/data_admin.py --- a/lib/galaxy/web/controllers/data_admin.py +++ b/lib/galaxy/web/controllers/data_admin.py @@ -116,99 +116,22 @@ def download_build( self, trans, **kwd ): """Download a genome from a remote source and add it to the library.""" params = util.Params( kwd ) - source = params.get('source', '') - longname = params.get('longname', None) - if not isinstance( params.get( 'indexers', None ), list ): - indexers = [ params.get( 'indexers', None ) ] - else: - indexers = params.get( 'indexers', None ) - if indexers is not None: - if indexers == [None]: - indexers = None - url = None - liftover = None - newlift = [] - dbkey = params.get( 'dbkey', None ) + paramdict = build_param_dict( params, trans ) + if paramdict[ 'status' ] == 'error': + return trans.fill_template( '/admin/data_admin/generic_error.mako', message=paramdict[ 'message' ] ) + url = paramdict[ 'url' ] + liftover = paramdict[ 'liftover' ] + dbkey = paramdict[ 'dbkey' ] + indexers = paramdict[ 'indexers' ] + longname = paramdict[ 'longname' ] dbkeys = dict() protocol = 'http' - - if source == 'NCBI': - build = params.get('ncbi_name', '') - dbkey = build.split( ': ' )[0] - longname = build.split( ': ' )[-1] - url = 'http://togows.dbcls.jp/entry/ncbi-nucleotide/%s.fasta' % dbkey - elif source == 'URL': - dbkey = params.get( 'url_dbkey', '' ) - url = params.get( 'url', None ) - longname = params.get( 'longname', None ) - elif source == 'UCSC': - longname = None - for build in trans.ucsc_builds: - if dbkey == build[0]: - dbkey = build[0] - longname = build[1] - break - if dbkey == '?': - return trans.fill_template( '/admin/data_admin/generic_error.mako', message='An invalid build was specified.' ) - ftp = ftplib.FTP('hgdownload.cse.ucsc.edu') - ftp.login('anonymous', trans.get_user().email) - checker = [] - liftover = [] - newlift = [] - try: - ftp.retrlines('NLST /goldenPath/%s/liftOver/*.chain.gz' % dbkey, liftover.append) - for chain in liftover: - fname = chain.split( '/' )[-1] - target = fname.replace( '.over.chain.gz', '' ).split( 'To' )[1] - target = target[0].lower() + target[1:] - if not os.path.exists( os.path.join( trans.app.config.get( 'genome_data_path', 'tool-data/genome' ), dbkey, 'liftOver', fname ) ): - newlift.append( [ chain, dbkey, target ] ) - current = dbkey[0].upper() + dbkey[1:] - targetfile = '%sTo%s.over.chain.gz' % ( target, current ) - if not os.path.exists( os.path.join( trans.app.config.get( 'genome_data_path', 'tool-data/genome' ), target, 'liftOver', targetfile ) ): - newlift.append( [ '/goldenPath/%s/liftOver/%s' % ( target, targetfile ), target, dbkey ] ) - except: - newlift = None - pass - ftp.retrlines('NLST /goldenPath/%s/bigZips/' % dbkey, checker.append) - ftp.quit() - for filename in [ dbkey, 'chromFa' ]: - for extension in [ '.tar.gz', '.tar.bz2', '.zip', '.fa.gz', '.fa.bz2' ]: - testfile = '/goldenPath/%s/bigZips/%s%s' % ( dbkey, filename, extension ) - if testfile in checker: - url = 'ftp://hgdownload.cse.ucsc.edu%s' % testfile - break; - else: - continue - if url is None: - message = u'The genome %s was not found on the UCSC server.' % dbkey - status = u'error' - return trans.fill_template( '/admin/data_admin/data_form.mako', - message=message, - status=status, - ensembls=trans.ensembl_builds, - dbkeys=trans.ucsc_builds ) - elif source == 'Ensembl': - dbkey = params.get( 'ensembl_dbkey', None ) - if dbkey == '?': - return trans.fill_template( '/admin/data_admin/generic_error.mako', message='An invalid build was specified.' ) - for build in trans.ensembl_builds: - if build[ 'dbkey' ] == dbkey: - dbkey = build[ 'dbkey' ] - release = build[ 'release' ] - pathname = '_'.join( build[ 'name' ].split(' ')[0:2] ) - longname = build[ 'name' ].replace('_', ' ') - break - url = 'ftp://ftp.ensembl.org/pub/release-%s/fasta/%s/dna/%s.%s.%s.dna.toplevel.fa.…' % ( release, pathname.lower(), pathname, dbkey, release ) - else: - return trans.fill_template( '/admin/data_admin/generic_error.mako', message='An invalid data source was specified.' ) if url is None: return trans.fill_template( '/admin/data_admin/generic_error.mako', message='Unable to generate a valid URL with the specified parameters.' ) - params = dict( protocol='http', name=dbkey, datatype='fasta', url=url, user=trans.user.id ) jobid = trans.app.job_manager.deferred_job_queue.plugins['GenomeTransferPlugin'].create_job( trans, url, dbkey, longname, indexers ) chainjob = [] - if newlift is not None: - for chain in newlift: + if liftover is not None: + for chain in liftover: liftover_url = u'ftp://hgdownload.cse.ucsc.edu%s' % chain[0] from_genome = chain[1] to_genome = chain[2] @@ -228,11 +151,10 @@ def monitor_status( self, trans, **kwd ): params = util.Params( kwd ) jobid = params.get( 'job', '' ) - gname = params.get( 'intname', '' ) deferred = trans.app.model.context.current.query( model.DeferredJob ).filter_by( id=jobid ).first() gname = deferred.params[ 'intname' ] indexers = ', '.join( deferred.params[ 'indexes' ] ) - jobs = self._get_jobs( jobid, trans ) + jobs = self._get_jobs( deferred, trans ) jsonjobs = json.dumps( jobs ) return trans.fill_template( '/admin/data_admin/download_status.mako', name=gname, indexers=indexers, mainjob=jobid, jobs=jobs, jsonjobs=jsonjobs ) @@ -243,15 +165,16 @@ jobs = [] params = util.Params( kwd ) jobid = params.get( 'jobid', '' ) - jobs = self._get_jobs( jobid, trans ) + job = sa_session.query( model.DeferredJob ).filter_by( id=jobid ).first() + jobs = self._get_jobs( job, trans ) return trans.fill_template( '/admin/data_admin/ajax_status.mako', json=json.dumps( jobs ) ) def _get_job( self, jobid, jobtype, trans ): sa = trans.app.model.context.current if jobtype == 'liftover': - job = sa.query( model.TransferJob ).filter_by( id=jobid ).first() - liftover = trans.app.job_manager.deferred_job_queue.plugins['LiftOverTransferPlugin'].get_job_status( jobid ) - joblabel = 'Download liftOver (%s to %s)' % ( liftover.params[ 'from_genome' ], liftover.params[ 'to_genome' ] ) + liftoverjob = sa.query( model.DeferredJob ).filter_by( id=jobid ).first() + job = sa.query( model.TransferJob ).filter_by( id=liftoverjob.params[ 'transfer_job_id' ] ).first() + joblabel = 'Download liftOver (%s to %s)' % ( liftoverjob.params[ 'from_genome' ], liftoverjob.params[ 'to_genome' ] ) elif jobtype == 'transfer': job = sa.query( model.TransferJob ).filter_by( id=jobid ).first() joblabel = 'Download Genome' @@ -259,21 +182,111 @@ job = sa.query( model.DeferredJob ).filter_by( id=jobid ).first() joblabel = 'Main Controller' elif jobtype == 'index': - job = sa.query( model.Job ).filter_by( id=jobid ).first() - joblabel = 'Index Genome' + job = sa.query( model.Job ).filter_by( id=jobid.job_id ).first() + joblabel = 'Index Genome (%s)' % jobid.indexer return dict( status=job.state, jobid=job.id, style=self.jobstyles[job.state], type=jobtype, label=joblabel ) - def _get_jobs( self, jobid, trans ): + def _get_jobs( self, deferredjob, trans ): jobs = [] - job = trans.app.job_manager.deferred_job_queue.plugins['GenomeTransferPlugin'].get_job_status( jobid ) + idxjobs = [] sa_session = trans.app.model.context.current - jobs.append( self._get_job( job.id, 'deferred', trans ) ) - if hasattr( job, 'transfer_job' ): # This is a transfer job, check for indexers - jobs.append( self._get_job( job.transfer_job.id, 'transfer', trans ) ) - idxjobs = sa_session.query( model.GenomeIndexToolData ).filter_by( deferred_job_id=job.id, transfer_job_id=job.transfer_job.id ).all() - if job.params.has_key( 'liftover' ) and job.params[ 'liftover' ] is not None: - for jobid in job.params[ 'liftover' ]: - jobs.append( self._get_job( jobid, 'liftover', trans ) ) - for idxjob in idxjobs: - jobs.append( self._get_job( idxjob.job_id, 'index', trans ) ) + job = sa_session.query( model.GenomeIndexToolData ).filter_by( deferred=deferredjob ).first() + jobs.append( self._get_job( deferredjob.id, 'deferred', trans ) ) + if 'transfer_job_id' in deferredjob.params: #hasattr( job, 'transfer' ) and job.transfer is not None: # This is a transfer job, check for indexers + jobs.append( self._get_job( deferredjob.params[ 'transfer_job_id' ], 'transfer', trans ) ) + if hasattr( job, 'deferred' ): + idxjobs = sa_session.query( model.GenomeIndexToolData ).filter_by( deferred=job.deferred, transfer=job.transfer ).all() + if deferredjob.params.has_key( 'liftover' ) and deferredjob.params[ 'liftover' ] is not None: + for jobid in deferredjob.params[ 'liftover' ]: + jobs.append( self._get_job( jobid, 'liftover', trans ) ) + for idxjob in idxjobs: + jobs.append( self._get_job( idxjob, 'index', trans ) ) return jobs + +def build_param_dict( params, trans ): + + source = params.get('source', '') + longname = params.get('longname', None) + if not isinstance( params.get( 'indexers', None ), list ): + indexers = [ params.get( 'indexers', None ) ] + else: + indexers = params.get( 'indexers', None ) + if indexers is not None: + if indexers == [None]: + indexers = None + url = None + liftover = None + newlift = [] + dbkey = params.get( 'dbkey', None ) + dbkeys = dict() + protocol = 'http' + + if source == 'NCBI': + build = params.get('ncbi_name', '') + dbkey = build.split( ': ' )[0] + longname = build.split( ': ' )[-1] + url = 'http://togows.dbcls.jp/entry/ncbi-nucleotide/%s.fasta' % dbkey + elif source == 'URL': + dbkey = params.get( 'url_dbkey', '' ) + url = params.get( 'url', None ) + longname = params.get( 'longname', None ) + elif source == 'UCSC': + longname = None + for build in trans.ucsc_builds: + if dbkey == build[0]: + dbkey = build[0] + longname = build[1] + break + if dbkey == '?': + return dict( status='error', message='An invalid build was specified.' ) + ftp = ftplib.FTP('hgdownload.cse.ucsc.edu') + ftp.login('anonymous', trans.get_user().email) + checker = [] + liftover = [] + newlift = [] + try: + ftp.retrlines('NLST /goldenPath/%s/liftOver/*.chain.gz' % dbkey, liftover.append) + for chain in liftover: + fname = chain.split( '/' )[-1] + target = fname.replace( '.over.chain.gz', '' ).split( 'To' )[1] + target = target[0].lower() + target[1:] + if not os.path.exists( os.path.join( trans.app.config.get( 'genome_data_path', 'tool-data/genome' ), dbkey, 'liftOver', fname ) ): + newlift.append( [ chain, dbkey, target ] ) + current = dbkey[0].upper() + dbkey[1:] + targetfile = '%sTo%s.over.chain.gz' % ( target, current ) + if not os.path.exists( os.path.join( trans.app.config.get( 'genome_data_path', 'tool-data/genome' ), target, 'liftOver', targetfile ) ): + newlift.append( [ '/goldenPath/%s/liftOver/%s' % ( target, targetfile ), target, dbkey ] ) + except: + newlift = None + pass + ftp.retrlines('NLST /goldenPath/%s/bigZips/' % dbkey, checker.append) + ftp.quit() + for filename in [ dbkey, 'chromFa' ]: + for extension in [ '.tar.gz', '.tar.bz2', '.zip', '.fa.gz', '.fa.bz2' ]: + testfile = '/goldenPath/%s/bigZips/%s%s' % ( dbkey, filename, extension ) + if testfile in checker: + url = 'ftp://hgdownload.cse.ucsc.edu%s' % testfile + break; + else: + continue + if url is None: + message = 'The genome %s was not found on the UCSC server.' % dbkey + status = 'error' + return dict( status=status, message=message ) + + elif source == 'Ensembl': + dbkey = params.get( 'ensembl_dbkey', None ) + if dbkey == '?': + return dict( status='error', message='An invalid build was specified.' ) + for build in trans.ensembl_builds: + if build[ 'dbkey' ] == dbkey: + dbkey = build[ 'dbkey' ] + release = build[ 'release' ] + pathname = '_'.join( build[ 'name' ].split(' ')[0:2] ) + longname = build[ 'name' ].replace('_', ' ') + break + url = 'ftp://ftp.ensembl.org/pub/release-%s/fasta/%s/dna/%s.%s.%s.dna.toplevel.fa.…' % ( release, pathname.lower(), pathname, dbkey, release ) + + params = dict( status='ok', dbkey=dbkey, datatype='fasta', url=url, user=trans.user.id, liftover=newlift, longname=longname, indexers=indexers ) + + return params \ 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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