- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Trackster: make overview its own track, add icons for showing/hiding overview, and make track header optional.
by Bitbucket 23 Oct '11

23 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/32af86dbaf9a/ changeset: 32af86dbaf9a user: jgoecks date: 2011-10-23 22:32:04 summary: Trackster: make overview its own track, add icons for showing/hiding overview, and make track header optional. affected #: 9 files diff -r 35887d54b5a0b62bc7b03dfc603755edb3d86849 -r 32af86dbaf9a962eaea12a04df817c6f282331df static/images/fugue/application-dock-270-bw.png Binary file static/images/fugue/application-dock-270-bw.png has changed diff -r 35887d54b5a0b62bc7b03dfc603755edb3d86849 -r 32af86dbaf9a962eaea12a04df817c6f282331df static/images/fugue/application-dock-270.png Binary file static/images/fugue/application-dock-270.png has changed diff -r 35887d54b5a0b62bc7b03dfc603755edb3d86849 -r 32af86dbaf9a962eaea12a04df817c6f282331df static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -7,14 +7,16 @@ #zoom-in,#zoom-out{display:inline-block;height:16px;width:16px;margin-bottom:-3px;cursor:pointer;} #zoom-out{background:transparent url(../images/fugue/magnifier-zoom-out.png) center center no-repeat;} #zoom-in{margin-left:10px;background:transparent url(../images/fugue/magnifier-zoom.png) center center no-repeat;} +.overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;} +.overview-icon:hover{background:transparent url(../images/fugue/application-dock-270.png) no-repeat;} .settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;} .settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;} .tools-icon{background:transparent url(../images/fugue/toolbox-bw.png) no-repeat;} .tools-icon:hover{background:transparent url(../images/fugue/toolbox.png) no-repeat;} .filters-icon{background:transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat;} .filters-icon:hover{background:transparent url(../images/fugue/ui-slider-050.png) no-repeat;} -.remove-icon{background:transparent url(../images/fugue/cross-small-bw.png) no-repeat;} -.remove-icon:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} +.remove-icon,.overview-close{background:transparent url(../images/fugue/cross-small-bw.png) no-repeat;} +.remove-icon:hover,.overview-close:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} #close-icon{background:transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px;} #close-icon:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} #add-tracks-icon{background:transparent url(../images/fugue/plus-button-bw.png) no-repeat;} diff -r 35887d54b5a0b62bc7b03dfc603755edb3d86849 -r 32af86dbaf9a962eaea12a04df817c6f282331df static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -303,6 +303,13 @@ .settings-icon:hover { background: transparent url(../images/fugue/gear.png) no-repeat; } +.overview-icon { + background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat; +} +.overview-icon:hover { + background:transparent url(../images/fugue/application-dock-270.png) no-repeat; +} + .tools-icon { background: transparent url(../images/fugue/toolbox-bw.png) no-repeat; } @@ -315,10 +322,10 @@ .filters-icon:hover { background: transparent url(../images/fugue/ui-slider-050.png) no-repeat; } -.remove-icon { +.remove-icon, .overview-close { background: transparent url(../images/fugue/cross-small-bw.png) no-repeat; } -.remove-icon:hover { +.remove-icon:hover, .overview-close:hover { background: transparent url(../images/fugue/cross-circle.png) no-repeat; } #close-icon { diff -r 35887d54b5a0b62bc7b03dfc603755edb3d86849 -r 32af86dbaf9a962eaea12a04df817c6f282331df static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};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 trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(ah,ak,al,ai,aj){if(ai>1){return{data:null}}return T.prototype.load_data.call(this,ah,ak,al,ai,aj)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};q(R.prototype,r.prototype,z.prototype,{update_track_icons:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;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 ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+" ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){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(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ar,al,at,aj,ai){r.call(this,ak,ar,al,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ai?ai:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.id=j.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var am=this;this.header_div.dblclick(function(au){au.stopPropagation()});this.settings_icon.click(function(){var aw=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(){am.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(ax){if((ax.keyCode||ax.which)===27){aw()}else{if((ax.keyCode||ax.which)===13){au()}}};$(window).bind("keypress.check_enter_esc",av);show_modal("Configure Track",am.config.build_form(),{Cancel:aw,OK:au})});this.filters_icon.click(function(){am.filters_div.toggle();am.filters_manager.reset_filters()});this.tools_icon.click(function(){am.dynamic_tool_div.toggle();if(am.dynamic_tool_div.is(":visible")){am.set_name(am.name+am.tool_region_and_parameters_str())}else{am.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();am.remove()});if(am.display_modes!==undefined){if(am.mode_div===undefined){am.mode_div=$("<div class='right-float menubutton popup' />").appendTo(am.header_div);var an=(am.config&&am.config.values.mode?am.config.values.mode:am.display_modes[0]);am.mode=an;am.mode_div.text(an);var ah={};for(var ao=0,aq=am.display_modes.length;ao<aq;ao++){var ap=am.display_modes[ao];ah[ap]=function(au){return function(){am.change_mode(au)}}(ap)}make_popupmenu(am.mode_div,ah)}else{am.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){am.icons_div.show()},function(){am.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.update_track_icons()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){},});var O=function(ak,aj){var ai=this,ah=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ak!==undefined?ak:{}));this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new s(this,aj):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},update_track_icons:function(){var ah=this;if(ah.filters_available>0){ah.filters_icon.show()}else{ah.filters_icon.hide()}if(ah.tool){ah.tools_icon.show()}else{ah.tools_icon.hide()}},set_is_overview:function(ah){this.is_overview=ah;this.update_track_icons()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.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:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.update_track_icons()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,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=N.ReadPainter;this.update_track_icons()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=(A?A.data:null)};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(W,R,N,ab,C,V,K,H,G){W.textAlign="center";var U=this,B=[ab,C],Q=0,X=0,T=0,z=W.canvas.manager.char_width_px;var ag=[];if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){T=Math.round(N/2)}if(!K){K=[[0,H.length]]}for(var O=0,Z=K.length;O<Z;O++){var L=K[O],D="MIDNSHP=X"[L[0]],P=L[1];if(D==="H"||D==="S"){Q-=P}var I=V+Q,af=Math.floor(Math.max(0,(I-ab)*N)),J=Math.floor(Math.max(0,(I+P-ab)*N));if(af===J){J+=1}switch(D){case"H":break;case"S":case"M":case"=":if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(T>0){W.fillStyle=this.prefs.block_color;W.fillRect(af-T,G+1,J-af,9);W.fillStyle=h;for(var ad=0,A=S.length;ad<A;ad++){if(this.prefs.show_differences&&this.ref_seq){var M=this.ref_seq[I-ab+ad];if(!M||M.toLowerCase()===S[ad].toLowerCase()){continue}}if(I+ad>=ab&&I+ad<=C){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae,G+9)}}}else{W.fillStyle=this.prefs.block_color;W.fillRect(af,G+4,J-af,f)}}X+=P;Q+=P;break;case"N":W.fillStyle=h;W.fillRect(af-T,G+5,J-af,1);Q+=P;break;case"D":W.fillStyle="red";W.fillRect(af-T,G+4,J-af,3);Q+=P;break;case"P":break;case"I":var aa=af-T;if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(this.prefs.show_insertions){var F=af-(J-af)/2;if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){W.fillStyle="yellow";W.fillRect(F-T,G-9,J-af,9);ag[ag.length]={type:"triangle",data:[aa,G+4,5]};W.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):S=S.slice(ab-I);break;case (OVERLAP_END):S=S.slice(0,I-C);break;case (CONTAINED_BY):break;case (CONTAINS):S=S.slice(ab-I,I-C);break}for(var ad=0,A=S.length;ad<A;ad++){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae-(J-af)/2,G)}}else{W.fillStyle="yellow";W.fillRect(F,G+(this.mode!=="Dense"?2:5),J-af,(R!=="Dense"?f:t))}}else{if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){ag[ag.length]={type:"text",data:[S.length,aa,G+9]}}else{}}}X+=P;break;case"X":X+=P;break}}W.fillStyle="yellow";var ac,E,ah;for(var Y=0;Y<ag.length;Y++){ac=ag[Y];E=ac.type;ah=ac.data;if(E==="text"){W.save();W.font="bold "+W.font;W.fillText(ah[0],ah[1],ah[2]);W.restore()}else{if(E=="triangle"){r(W,ah[0],ah[1],ah[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(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 f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};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 trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(ah,ak,al,ai,aj){if(ai>1){return{data:null}}return T.prototype.load_data.call(this,ah,ak,al,ai,aj)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=al;this.is_overview=false};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};q(R.prototype,r.prototype,z.prototype,{update_track_icons:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;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 ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("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 ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(aj){if(this.overview_drawable){if(this.overview_drawable.dataset_id===aj.dataset_id){return}this.overview_viewport.find(".track").remove()}var ai=aj.copy({content_div:this.overview_viewport}),ah=this;ai.header_div.hide();ai.is_overview=true;ah.overview_drawable=ai;this.overview_drawable.postdraw_actions=function(){ah.overview_highlight.show().height(ah.overview_drawable.content_div.height());ah.overview_viewport.height(ah.overview_drawable.content_div.height()+ah.overview_box.outerHeight());ah.overview_close.show();ah.resize_window()};this.overview_drawable.init();ah.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+" ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){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(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,at,al,ao,au,aj,ai){r.call(this,ak,at,al,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ai?ai:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.id=j.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(ao){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var am=this;this.header_div.dblclick(function(av){av.stopPropagation()});this.settings_icon.click(function(){var ax=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(){am.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},aw=function(ay){if((ay.keyCode||ay.which)===27){ax()}else{if((ay.keyCode||ay.which)===13){av()}}};$(window).bind("keypress.check_enter_esc",aw);show_modal("Configure Track",am.config.build_form(),{Cancel:ax,OK:av})});this.overview_icon.click(function(){am.view.set_overview(am)});this.filters_icon.click(function(){am.filters_div.toggle();am.filters_manager.reset_filters()});this.tools_icon.click(function(){am.dynamic_tool_div.toggle();if(am.dynamic_tool_div.is(":visible")){am.set_name(am.name+am.tool_region_and_parameters_str())}else{am.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();am.remove()});if(am.display_modes!==undefined){if(am.mode_div===undefined){am.mode_div=$("<div class='right-float menubutton popup' />").appendTo(am.header_div);var an=(am.config&&am.config.values.mode?am.config.values.mode:am.display_modes[0]);am.mode=an;am.mode_div.text(an);var ah={};for(var ap=0,ar=am.display_modes.length;ap<ar;ap++){var aq=am.display_modes[ap];ah[aq]=function(av){return function(){am.change_mode(av)}}(aq)}make_popupmenu(am.mode_div,ah)}else{am.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){am.icons_div.show()},function(){am.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.update_track_icons()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var O=function(ak,aj){var ai=this,ah=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ak!==undefined?ak:{}));this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new s(this,aj):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};q(O.prototype,r.prototype,j.prototype,{copy:function(ah){return new this.constructor(this.name,this.view,ah,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json: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,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},update_track_icons:function(){var ah=this;if(ah.filters_available>0){ah.filters_icon.show()}else{ah.filters_icon.hide()}if(ah.tool){ah.tools_icon.show()}else{ah.tools_icon.hide()}},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(this.is_overview){aq=this.view.max_low;an=this.view.max_high;am=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D)));av=ak/(view.max_high-view.max_low)}if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw(false,false,false,al)});return null},show_tile:function(an,ap,aq){var aj=this,ai=an.canvas,am=ai;if(an.message){var ar=$("<div/>"),ao=$("<div/>").addClass("tile-message").text(an.message).css({height:F-1,width:an.canvas.width}).appendTo(ar),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ao),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ao);ar.append(ai);am=ar;al.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()});ah.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()})}an.predisplay_actions();var ak=(an.low-(this.is_overview?this.view.max_low:this.view.low))*aq;if(this.left_offset){ak-=this.left_offset}am.css({position:"absolute",top:0,left:ak,height:""});ap.append(am);aj.max_height=Math.max(aj.max_height,am.height());aj.content_div.css("height",aj.max_height+"px");ap.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){j.call(this,"label",ai,ah,false,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){j.call(this,"reference",ah,{content_div:ah.top_labeltrack},false,{});O.call(this);ah.reference_track=this;this.left_offset=200;this.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:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar.data===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,true,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.update_track_icons()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"||aA.is_overview){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,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=N.ReadPainter;this.update_track_icons()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=(A?A.data:null)};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(W,R,N,ab,C,V,K,H,G){W.textAlign="center";var U=this,B=[ab,C],Q=0,X=0,T=0,z=W.canvas.manager.char_width_px;var ag=[];if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){T=Math.round(N/2)}if(!K){K=[[0,H.length]]}for(var O=0,Z=K.length;O<Z;O++){var L=K[O],D="MIDNSHP=X"[L[0]],P=L[1];if(D==="H"||D==="S"){Q-=P}var I=V+Q,af=Math.floor(Math.max(0,(I-ab)*N)),J=Math.floor(Math.max(0,(I+P-ab)*N));if(af===J){J+=1}switch(D){case"H":break;case"S":case"M":case"=":if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(T>0){W.fillStyle=this.prefs.block_color;W.fillRect(af-T,G+1,J-af,9);W.fillStyle=h;for(var ad=0,A=S.length;ad<A;ad++){if(this.prefs.show_differences&&this.ref_seq){var M=this.ref_seq[I-ab+ad];if(!M||M.toLowerCase()===S[ad].toLowerCase()){continue}}if(I+ad>=ab&&I+ad<=C){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae,G+9)}}}else{W.fillStyle=this.prefs.block_color;W.fillRect(af,G+4,J-af,f)}}X+=P;Q+=P;break;case"N":W.fillStyle=h;W.fillRect(af-T,G+5,J-af,1);Q+=P;break;case"D":W.fillStyle="red";W.fillRect(af-T,G+4,J-af,3);Q+=P;break;case"P":break;case"I":var aa=af-T;if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(this.prefs.show_insertions){var F=af-(J-af)/2;if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){W.fillStyle="yellow";W.fillRect(F-T,G-9,J-af,9);ag[ag.length]={type:"triangle",data:[aa,G+4,5]};W.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):S=S.slice(ab-I);break;case (OVERLAP_END):S=S.slice(0,I-C);break;case (CONTAINED_BY):break;case (CONTAINS):S=S.slice(ab-I,I-C);break}for(var ad=0,A=S.length;ad<A;ad++){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae-(J-af)/2,G)}}else{W.fillStyle="yellow";W.fillRect(F,G+(this.mode!=="Dense"?2:5),J-af,(R!=="Dense"?f:t))}}else{if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){ag[ag.length]={type:"text",data:[S.length,aa,G+9]}}else{}}}X+=P;break;case"X":X+=P;break}}W.fillStyle="yellow";var ac,E,ah;for(var Y=0;Y<ag.length;Y++){ac=ag[Y];E=ac.type;ah=ac.data;if(E==="text"){W.save();W.font="bold "+W.font;W.fillText(ah[0],ah[1],ah[2]);W.restore()}else{if(E=="triangle"){r(W,ah[0],ah[1],ah[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(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 35887d54b5a0b62bc7b03dfc603755edb3d86849 -r 32af86dbaf9a962eaea12a04df817c6f282331df static/scripts/packed/trackster_ui.js --- a/static/scripts/packed/trackster_ui.js +++ b/static/scripts/packed/trackster_ui.js @@ -1,1 +1,1 @@ -var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name==m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file +var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file diff -r 35887d54b5a0b62bc7b03dfc603755edb3d86849 -r 32af86dbaf9a962eaea12a04df817c6f282331df static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -589,7 +589,6 @@ this.name = name; this.view = view; this.container = container; - this.drag_handle_class = drag_handle_class; this.config = new DrawableConfig({ track: this, params: [ @@ -601,6 +600,8 @@ } }); this.prefs = this.config.values; + this.drag_handle_class = drag_handle_class; + this.is_overview = false; }; extend(Drawable.prototype, { @@ -852,7 +853,7 @@ // Overview (scrollbar and overview plot) at bottom this.overview = $("<div/>").addClass("overview").appendTo(this.bottom_container); this.overview_viewport = $("<div/>").addClass("overview-viewport").appendTo(this.overview); - this.overview_close = $("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport); + 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); @@ -1195,13 +1196,14 @@ /** * Request that view redraw some or all tracks. If a track is not specificied, redraw all tracks. */ + // FIXME: change method call so that track is first and additional parameters are optional. request_redraw: function(nodraw, force, clear_after, track) { var view = this, - // Either redrawing a single track or all view's tracks. + // Either redrawing a single drawable or all view's drawables. track_list = (track ? [track] : view.drawables), track_index; - + // Add/update tracks in track list to redraw list. var track; for (var i = 0; i < track_list.length; i++) { @@ -1318,42 +1320,44 @@ this.nav_container.width( this.container.width() ); this.request_redraw(); }, - /** Show a track in the overview. */ - set_overview: function(track) { - // Get data and draw tile. - $.when(track.get_overview_tile()).then(function(tile) { - // Update UI. - view.overview_viewport.find(".track-tile").remove(); + /** Show a Drawable in the overview. */ + set_overview: function(drawable) { + if (this.overview_drawable) { + // If drawable to be set as overview is already in overview, do nothing. + // Otherwise, remove overview. + if (this.overview_drawable.dataset_id === drawable.dataset_id) { + return; + } + this.overview_viewport.find(".track").remove(); + } + + // Set new overview. + var + overview_drawable = drawable.copy( { content_div: this.overview_viewport } ), + view = this; + overview_drawable.header_div.hide(); + overview_drawable.is_overview = true; + view.overview_drawable = overview_drawable; + this.overview_drawable.postdraw_actions = function() { + view.overview_highlight.show().height(view.overview_drawable.content_div.height()); + view.overview_viewport.height(view.overview_drawable.content_div.height() + view.overview_box.outerHeight()); view.overview_close.show(); - view.overview_viewport.append(tile.canvas); - view.overview_highlight.show().height(tile.canvas.height()); - view.overview_viewport.height(tile.canvas.height() + view.overview_box.outerHeight()); view.resize_window(); - - // Update view, track states. - if (view.overview_track) { - view.overview_track.set_is_overview(false); - } - view.overview_track = track; - track.set_is_overview(true); - }); + }; + this.overview_drawable.init(); view.has_changes = true; }, /** Close and reset overview. */ reset_overview: function() { // Update UI. + $(".tipsy").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(); - - // Update view, track states. - if (view.overview_track) { - view.overview_track.set_is_overview(false); - } - view.overview_track = null; + view.overview_drawable = null; } }); @@ -2243,7 +2247,7 @@ * -------> ToolDataFeatureTrack * -------> VcfTrack */ -var Track = function(name, view, container, prefs, data_url, data_query_wait) { +var Track = function(name, view, container, show_header, prefs, data_url, data_query_wait) { // For now, track's container is always view. Drawable.call(this, name, view, container, {}, "draghandle"); @@ -2263,8 +2267,8 @@ // this.container_div = $("<div />").addClass('track').attr("id", "track_" + this.id).css("position", "relative"); - // Create and initialize track header and icons. Only non-hidden tracks have headers. - if (!this.hidden) { + // Create and initialize track header and icons. + if (show_header) { this.header_div = $("<div class='track-header' />").appendTo(this.container_div); if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); } this.name_div = $("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name) @@ -2275,6 +2279,9 @@ this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings") .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) .appendTo(this.icons_div); + this.overview_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set as overview") + .addClass("icon-button overview-icon").tipsy( {gravity: 's'} ) + .appendTo(this.icons_div); this.filters_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Filters") .addClass("icon-button filters-icon").tipsy( {gravity: 's'} ) .appendTo(this.icons_div).hide(); @@ -2312,18 +2319,10 @@ }); }); - // FIXME: old code for overview. - /* - track_dropdown[(this.is_overview ? "Hide overview" : "Set as overview")] = function() { - if (track.is_overview) { - track.view.reset_overview(); - } - else { - track.view.set_overview(track); - } - }; - */ - + this.overview_icon.click( function() { + track.view.set_overview(track); + }); + this.filters_icon.click( function() { // TODO: update tipsy text. track.filters_div.toggle(); @@ -2488,7 +2487,7 @@ /** * Additional initialization required before drawing track for the first time. */ - predraw_init: function() {}, + predraw_init: function() {} }); var TiledTrack = function(filters_list, tool_dict) { @@ -2504,28 +2503,33 @@ this.filters_available = false; this.filters_visible = false; this.tool = (tool_dict !== undefined && obj_length(tool_dict) > 0 ? new Tool(this, tool_dict) : undefined); - this.is_overview = false; - if (track.hidden) { return; } + if (this.header_div) { + // + // Create filters div. + // + if (this.filters_manager) { + this.filters_div = this.filters_manager.parent_div + this.header_div.after(this.filters_div); + } - // - // Create filters div. - // - if (this.filters_manager) { - this.filters_div = this.filters_manager.parent_div - this.header_div.after(this.filters_div); - } - - // - // Create dynamic tool div. - // - if (this.tool) { - this.dynamic_tool_div = this.tool.parent_div; - this.header_div.after(this.dynamic_tool_div); + // + // Create dynamic tool div. + // + if (this.tool) { + this.dynamic_tool_div = this.tool.parent_div; + this.header_div.after(this.dynamic_tool_div); + } } }; extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { /** + * Returns a copy of the track. + */ + copy: function(container) { + return new this.constructor(this.name, this.view, container, this.hda_ldda, this.dataset_id, this.prefs, this.filters, this.tool); + }, + /** * Convert track to JSON object. */ to_json: function() { @@ -2589,52 +2593,6 @@ */ }, /** - * Set track's overview status. - */ - set_is_overview: function(is_overview) { - this.is_overview = is_overview; - this.update_track_icons(); - }, - /** - * Returns a jQuery Deferred object that resolves to a Tile with track's overview. - * TODO: this should be the approach used when drawing any tile so that tile drawing is not blocking. - */ - get_overview_tile: function() { - var - track = this; - view = track.view, - resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / DENSITY ) / Math.log(RESOLUTION) )), - view_width = view.container.width(), - // w_scale units are pixels per base. - w_scale = view_width / (view.max_high - view.max_low), - overview_tile = $.Deferred(); - $.when(track.data_manager.get_data(view.max_low, view.max_high, "Auto", resolution, track.data_url_extra_params)).then(function(overview_data) { - var - key = track._gen_tile_cache_key(view_width, w_scale, 0), - tile = track.tile_cache.get(key); - - // Draw tile if necessary. - if (!tile) { - tile = track.draw_tile(overview_data, "Auto", resolution, 0, w_scale); - track.tile_cache.set(key, tile); - } - - // Always copy tile because it may need to be used in viz. - var - src_canvas = $(tile.canvas.find("canvas")), - new_canvas = src_canvas.clone(), - src_ctx = src_canvas.get(0).getContext("2d"), - tgt_ctx = new_canvas.get(0).getContext("2d"), - data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height); - // Need to undo offsets when placing image data. - tgt_ctx.putImageData(data, -track.left_offset, (tile.data.dataset_type === "summary_tree" ? SUMMARY_TREE_TOP_PADDING : 0)); - new_tile = new Tile(track, -1, resolution, new_canvas); - overview_tile.resolve(new_tile); - }); - - return overview_tile; - }, - /** * Generate a key for the tile cache. * TODO: create a TileCache object (like DataCache) and generate key internally. */ @@ -2667,6 +2625,14 @@ w_scale = width / range, resolution = this.view.resolution, parent_element = $("<div style='position: relative;'></div>"); + + // For overview, adjust high, low, resolution, and w_scale. + if (this.is_overview) { + low = this.view.max_low; + high = this.view.max_high; + resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / DENSITY ) / Math.log(RESOLUTION) )); + w_scale = width / (view.max_high - view.max_low); + } if (!clear_after) { this.content_div.children().remove(); } this.content_div.append( parent_element ); @@ -2777,7 +2743,7 @@ // Can't draw now, so trigger another redraw when the data is ready $.when( tile_data, seq_data ).then( function() { - view.request_redraw(); + view.request_redraw(false, false, false, track); }); // Indicate to caller that this tile could not be drawn @@ -2837,8 +2803,7 @@ tile.predisplay_actions(); // Position tile element, recalculate left position at display time - var range = this.view.high - this.view.low, - left = (tile.low - this.view.low) * w_scale; + var left = ( tile.low - (this.is_overview? this.view.max_low : this.view.low) ) * w_scale; if (this.left_offset) { left -= this.left_offset; } @@ -2875,8 +2840,7 @@ }); var LabelTrack = function (view, container) { - this.hidden = true; - Track.call(this, "label", view, container, {} ); + Track.call(this, "label", view, container, false, {} ); this.container_div.addClass( "label-track" ); }; extend(LabelTrack.prototype, Track.prototype, { @@ -2906,8 +2870,7 @@ }); var ReferenceTrack = function (view) { - this.hidden = true; - Track.call(this, "reference", view, { content_div: view.top_labeltrack }, {}); + Track.call(this, "reference", view, { content_div: view.top_labeltrack }, false, {}); TiledTrack.call(this); view.reference_track = this; @@ -3109,7 +3072,7 @@ // // FIXME: cleaner init needed; should just be able to call TiledTrack() - Track.call(this, name, view, container, prefs); + Track.call(this, name, view, container, true, prefs); TiledTrack.call(this, filters, tool); // Define and restore track configuration. @@ -3371,9 +3334,12 @@ if (mode === "Auto") { if (result.dataset_type === "summary_tree") { mode = result.dataset_type; - } else if (result.extra_info === "no_detail") { + } + // HACK: use no_detail mode track is in overview to prevent overview from being too large. + else if (result.extra_info === "no_detail" || track.is_overview) { mode = "no_detail"; - } else { + } + else { // Choose b/t Squish and Pack. // Proxy measures for using Squish: // (a) error message re: limiting number of features shown; diff -r 35887d54b5a0b62bc7b03dfc603755edb3d86849 -r 32af86dbaf9a962eaea12a04df817c6f282331df static/scripts/trackster_ui.js --- a/static/scripts/trackster_ui.js +++ b/static/scripts/trackster_ui.js @@ -114,7 +114,7 @@ // Set overview. var overview_track; for (var i = 0; i < view.drawables.length; i++) { - if (view.drawables[i].name == overview_track_name) { + if (view.drawables[i].name === overview_track_name) { view.set_overview(view.drawables[i]); break; } diff -r 35887d54b5a0b62bc7b03dfc603755edb3d86849 -r 32af86dbaf9a962eaea12a04df817c6f282331df templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -195,7 +195,8 @@ }; }); - var overview_track_name = (view.overview_track ? view.overview_track.name : null); + // FIXME: give unique IDs to Drawables and save overview as ID. + var overview_track_name = (view.overview_drawable ? view.overview_drawable.name : null); var payload = { 'view': view.to_json(), 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Trackster: fix bug in drawing reference track.
by Bitbucket 23 Oct '11

23 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/35887d54b5a0/ changeset: 35887d54b5a0 user: jgoecks date: 2011-10-23 17:13:40 summary: Trackster: fix bug in drawing reference track. affected #: 1 file (-1 bytes) --- a/static/scripts/trackster.js Sat Oct 22 21:22:43 2011 -0400 +++ b/static/scripts/trackster.js Sun Oct 23 11:13:40 2011 -0400 @@ -463,7 +463,7 @@ // data is ready, it then replaces itself with the actual data entry = this.load_data(low, high, mode, resolution, extra_params); this.set_data(low, high, mode, entry); - return entry + return entry; }, /** "Deep" data request; used as a parameter for DataManager.get_more_data() */ DEEP_DATA_REQ: "deep", @@ -2935,7 +2935,7 @@ tile_length = DENSITY * resolution; if (w_scale > this.view.canvas_manager.char_width_px) { - if (seq === null) { + if (seq.data === null) { track.content_div.css("height", "0px"); return; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Fix bug in saving trackster bookmarks.
by Bitbucket 22 Oct '11

22 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cc266981f0d0/ changeset: cc266981f0d0 user: jgoecks date: 2011-10-23 03:22:43 summary: Fix bug in saving trackster bookmarks. affected #: 1 file diff -r 41fd9b7734a150f086998da216190bb8bfcd0046 -r cc266981f0d08167251fa2e42383ecf503c19acf lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -646,7 +646,7 @@ # TODO: unpack and validate bookmarks: def unpack_bookmarks( bookmarks_json ): - return + return bookmarks_json # Unpack and validate view content. view_content = unpack_collection( decoded_payload[ 'view' ] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Trackster: replace menus with icons + tooltips. Overview is not yet implemented.
by Bitbucket 21 Oct '11

21 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/41fd9b7734a1/ changeset: 41fd9b7734a1 user: jgoecks date: 2011-10-22 02:00:27 summary: Trackster: replace menus with icons + tooltips. Overview is not yet implemented. affected #: 23 files (-1 bytes) --- a/static/june_2007_style/blue/trackster.css Fri Oct 21 13:48:24 2011 -0400 +++ b/static/june_2007_style/blue/trackster.css Fri Oct 21 20:00:27 2011 -0400 @@ -3,9 +3,28 @@ .content{font:10px verdana;} .nav-controls{text-align:center;padding:1px 0;} .nav-controls input{margin:0 5px;} +.menu-button{padding: 0px 4px 0px 4px;} #zoom-in,#zoom-out{display:inline-block;height:16px;width:16px;margin-bottom:-3px;cursor:pointer;} #zoom-out{background:transparent url(../images/fugue/magnifier-zoom-out.png) center center no-repeat;} #zoom-in{margin-left:10px;background:transparent url(../images/fugue/magnifier-zoom.png) center center no-repeat;} +.settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;} +.settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;} +.tools-icon{background:transparent url(../images/fugue/toolbox-bw.png) no-repeat;} +.tools-icon:hover{background:transparent url(../images/fugue/toolbox.png) no-repeat;} +.filters-icon{background:transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat;} +.filters-icon:hover{background:transparent url(../images/fugue/ui-slider-050.png) no-repeat;} +.remove-icon{background:transparent url(../images/fugue/cross-small-bw.png) no-repeat;} +.remove-icon:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} +#close-icon{background:transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px;} +#close-icon:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} +#add-tracks-icon{background:transparent url(../images/fugue/plus-button-bw.png) no-repeat;} +#add-tracks-icon:hover{background:transparent url(../images/fugue/plus-button.png) no-repeat;} +#add-group-icon{background:transparent url(../images/fugue/block--plus-bw.png) no-repeat;} +#add-group-icon:hover{background:transparent url(../images/fugue/block--plus.png) no-repeat;} +#bookmarks-icon{background:transparent url(../images/fugue/bookmarks-bw.png) no-repeat;} +#bookmarks-icon:hover{background:transparent url(../images/fugue/bookmarks.png) no-repeat;} +#save-icon{background:transparent url(../images/fugue/disk--arrow-bw.png) no-repeat;} +#save-icon:hover{background:transparent url(../images/fugue/disk--arrow.png) no-repeat;} .nav-input{font-size:12px;width:30em;z-index:1000;} .location{display:inline-block;width:15em;margin:0 10px;} .draghandle{margin-top:2px;cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px;} @@ -19,12 +38,13 @@ .viewport-canvas{width:100%;height:100px;} .yaxislabel{color:#777;z-index:100;} .line-track .track-content{border-top:1px solid #eee;border-bottom:1px solid #eee;} -.group-handle{cursor:move;float:left;background:#eee url('/static/images/tracks/block.png');width:12px;height:12px;} +.group-handle{cursor:move;float:left;background:#eee url('../images/tracks/block.png');width:12px;height:12px;} .group{min-height:20px;border-top:2px solid #888;border-bottom:2px solid #888;} .track{background:white;} .track-header{text-align:left;padding:4px 0px;color:#666;} .track-header .menubutton{margin-left:0px;} -.track-content{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;} +.track-content{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('../images/tracks/diag_bg.gif');min-height:16px;} +.track-name{float:left;margin-top:2px;height:16px;} .label-track .track-content{background:white;} .track-tile{background:white;} .track-tile canvas{position:relative;z-index:100;} --- a/static/june_2007_style/trackster.css.tmpl Fri Oct 21 13:48:24 2011 -0400 +++ b/static/june_2007_style/trackster.css.tmpl Fri Oct 21 20:00:27 2011 -0400 @@ -130,7 +130,7 @@ .group-handle { cursor: move; float: left; - background: #eee url('/static/images/tracks/block.png'); + background: #eee url('../images/tracks/block.png'); width: 12px; height: 12px; } @@ -159,10 +159,16 @@ text-align: center; border-top: 1px solid #eee; border-bottom: 2px solid #eee; - background: #eee url('/static/images/tracks/diag_bg.gif'); + background: #eee url('../images/tracks/diag_bg.gif'); min-height: 16px; } +.track-name { + float: left; + margin-top: 2px; + height: 16px; +} + .label-track .track-content { background: white; } @@ -288,6 +294,63 @@ font-weight: bold; padding-top: 0.2em; } +.menu-button { + padding: 0px 4px 0px 4px; +} +.settings-icon { + background: transparent url(../images/fugue/gear-bw.png) no-repeat; +} +.settings-icon:hover { + background: transparent url(../images/fugue/gear.png) no-repeat; +} +.tools-icon { + background: transparent url(../images/fugue/toolbox-bw.png) no-repeat; +} +.tools-icon:hover { + background: transparent url(../images/fugue/toolbox.png) no-repeat; +} +.filters-icon { + background: transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat; +} +.filters-icon:hover { + background: transparent url(../images/fugue/ui-slider-050.png) no-repeat; +} +.remove-icon { + background: transparent url(../images/fugue/cross-small-bw.png) no-repeat; +} +.remove-icon:hover { + background: transparent url(../images/fugue/cross-circle.png) no-repeat; +} +#close-icon { + background: transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px; +} +#close-icon:hover { + background: transparent url(../images/fugue/cross-circle.png) no-repeat; +} +#add-tracks-icon { + background: transparent url(../images/fugue/plus-button-bw.png) no-repeat; +} +#add-tracks-icon:hover { + background: transparent url(../images/fugue/plus-button.png) no-repeat; +} +#add-group-icon { + background: transparent url(../images/fugue/block--plus-bw.png) no-repeat; +} +#add-group-icon:hover { + background: transparent url(../images/fugue/block--plus.png) no-repeat; +} +#bookmarks-icon { + background: transparent url(../images/fugue/bookmarks-bw.png) no-repeat; +} +#bookmarks-icon:hover { + background: transparent url(../images/fugue/bookmarks.png) no-repeat; +} +#save-icon { + background: transparent url(../images/fugue/disk--arrow-bw.png) no-repeat; +} +#save-icon:hover { + background: transparent url(../images/fugue/disk--arrow.png) no-repeat; +} .child-track-icon { background:url('../images/fugue/arrow-000-small-bw.png') no-repeat; width: 30px; @@ -317,7 +380,6 @@ .delete-icon-container { float:right; } - .icon { display:inline-block; width:16px; --- a/static/scripts/galaxy.base.js Fri Oct 21 13:48:24 2011 -0400 +++ b/static/scripts/galaxy.base.js Fri Oct 21 20:00:27 2011 -0400 @@ -698,6 +698,8 @@ }); // Tooltips if ( $.fn.tipsy ) { + // FIXME: tipsy gravity cannot be updated, so need classes that specify N/S gravity and + // initialize each separately. $(".tooltip").tipsy( { gravity: 's' } ); } // Make popup menus. --- a/static/scripts/packed/trackster.js Fri Oct 21 13:48:24 2011 -0400 +++ b/static/scripts/packed/trackster.js Fri Oct 21 20:00:27 2011 -0400 @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};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 trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(R.prototype,r.prototype,z.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;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 ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+" ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){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(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.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:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,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=N.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=A};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq.data,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,f)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?f:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(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 f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};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 trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(ah,ak,al,ai,aj){if(ai>1){return{data:null}}return T.prototype.load_data.call(this,ah,ak,al,ai,aj)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};q(R.prototype,r.prototype,z.prototype,{update_track_icons:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;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 ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+" ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){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(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ar,al,at,aj,ai){r.call(this,ak,ar,al,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ai?ai:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.id=j.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var am=this;this.header_div.dblclick(function(au){au.stopPropagation()});this.settings_icon.click(function(){var aw=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(){am.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(ax){if((ax.keyCode||ax.which)===27){aw()}else{if((ax.keyCode||ax.which)===13){au()}}};$(window).bind("keypress.check_enter_esc",av);show_modal("Configure Track",am.config.build_form(),{Cancel:aw,OK:au})});this.filters_icon.click(function(){am.filters_div.toggle();am.filters_manager.reset_filters()});this.tools_icon.click(function(){am.dynamic_tool_div.toggle();if(am.dynamic_tool_div.is(":visible")){am.set_name(am.name+am.tool_region_and_parameters_str())}else{am.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();am.remove()});if(am.display_modes!==undefined){if(am.mode_div===undefined){am.mode_div=$("<div class='right-float menubutton popup' />").appendTo(am.header_div);var an=(am.config&&am.config.values.mode?am.config.values.mode:am.display_modes[0]);am.mode=an;am.mode_div.text(an);var ah={};for(var ao=0,aq=am.display_modes.length;ao<aq;ao++){var ap=am.display_modes[ao];ah[ap]=function(au){return function(){am.change_mode(au)}}(ap)}make_popupmenu(am.mode_div,ah)}else{am.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){am.icons_div.show()},function(){am.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.update_track_icons()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){},});var O=function(ak,aj){var ai=this,ah=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ak!==undefined?ak:{}));this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new s(this,aj):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},update_track_icons:function(){var ah=this;if(ah.filters_available>0){ah.filters_icon.show()}else{ah.filters_icon.hide()}if(ah.tool){ah.tools_icon.show()}else{ah.tools_icon.hide()}},set_is_overview:function(ah){this.is_overview=ah;this.update_track_icons()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.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:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.update_track_icons()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,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=N.ReadPainter;this.update_track_icons()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=(A?A.data:null)};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(W,R,N,ab,C,V,K,H,G){W.textAlign="center";var U=this,B=[ab,C],Q=0,X=0,T=0,z=W.canvas.manager.char_width_px;var ag=[];if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){T=Math.round(N/2)}if(!K){K=[[0,H.length]]}for(var O=0,Z=K.length;O<Z;O++){var L=K[O],D="MIDNSHP=X"[L[0]],P=L[1];if(D==="H"||D==="S"){Q-=P}var I=V+Q,af=Math.floor(Math.max(0,(I-ab)*N)),J=Math.floor(Math.max(0,(I+P-ab)*N));if(af===J){J+=1}switch(D){case"H":break;case"S":case"M":case"=":if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(T>0){W.fillStyle=this.prefs.block_color;W.fillRect(af-T,G+1,J-af,9);W.fillStyle=h;for(var ad=0,A=S.length;ad<A;ad++){if(this.prefs.show_differences&&this.ref_seq){var M=this.ref_seq[I-ab+ad];if(!M||M.toLowerCase()===S[ad].toLowerCase()){continue}}if(I+ad>=ab&&I+ad<=C){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae,G+9)}}}else{W.fillStyle=this.prefs.block_color;W.fillRect(af,G+4,J-af,f)}}X+=P;Q+=P;break;case"N":W.fillStyle=h;W.fillRect(af-T,G+5,J-af,1);Q+=P;break;case"D":W.fillStyle="red";W.fillRect(af-T,G+4,J-af,3);Q+=P;break;case"P":break;case"I":var aa=af-T;if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(this.prefs.show_insertions){var F=af-(J-af)/2;if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){W.fillStyle="yellow";W.fillRect(F-T,G-9,J-af,9);ag[ag.length]={type:"triangle",data:[aa,G+4,5]};W.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):S=S.slice(ab-I);break;case (OVERLAP_END):S=S.slice(0,I-C);break;case (CONTAINED_BY):break;case (CONTAINS):S=S.slice(ab-I,I-C);break}for(var ad=0,A=S.length;ad<A;ad++){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae-(J-af)/2,G)}}else{W.fillStyle="yellow";W.fillRect(F,G+(this.mode!=="Dense"?2:5),J-af,(R!=="Dense"?f:t))}}else{if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){ag[ag.length]={type:"text",data:[S.length,aa,G+9]}}else{}}}X+=P;break;case"X":X+=P;break}}W.fillStyle="yellow";var ac,E,ah;for(var Y=0;Y<ag.length;Y++){ac=ag[Y];E=ac.type;ah=ac.data;if(E==="text"){W.save();W.font="bold "+W.font;W.fillText(ah[0],ah[1],ah[2]);W.restore()}else{if(E=="triangle"){r(W,ah[0],ah[1],ah[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(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 --- a/static/scripts/trackster.js Fri Oct 21 13:48:24 2011 -0400 +++ b/static/scripts/trackster.js Fri Oct 21 20:00:27 2011 -0400 @@ -608,7 +608,7 @@ request_draw: function() {}, _draw: function() {}, to_json: function() {}, - make_name_popup_menu: function() {}, + update_track_icons: function() {}, /** * Set drawable name. */ @@ -750,14 +750,14 @@ is_container(this.content_div, this); moveable(this.container_div, this.drag_handle_class, ".group", this); - this.make_name_popup_menu(); + this.update_track_icons(); }; extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, { /** * Make popup menu for group. */ - make_name_popup_menu: function() { + update_track_icons: function() { var group = this; var group_dropdown = {}; @@ -2254,18 +2254,133 @@ this.data_url_extra_params = {} this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT); this.dataset_check_url = converted_datasets_state_url; + + if (!Track.id_counter) { Track.id_counter = 0; } + this.id = Track.id_counter++; // // Create HTML element structure for track. // - if (!Track.id_counter) { Track.id_counter = 0; } - this.container_div = $("<div />").addClass('track').attr("id", "track_" + Track.id_counter++).css("position", "relative"); + this.container_div = $("<div />").addClass('track').attr("id", "track_" + this.id).css("position", "relative"); + + // Create and initialize track header and icons. Only non-hidden tracks have headers. if (!this.hidden) { this.header_div = $("<div class='track-header' />").appendTo(this.container_div); if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); } - this.name_div = $("<div class='menubutton popup' />").appendTo(this.header_div); - this.name_div.text(this.name); - this.name_div.attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() ); + this.name_div = $("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name) + .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() ); + this.icons_div = $("<div/>").css("float", "left").appendTo(this.header_div).hide(); + + // Track icons. + this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings") + .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) + .appendTo(this.icons_div); + this.filters_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Filters") + .addClass("icon-button filters-icon").tipsy( {gravity: 's'} ) + .appendTo(this.icons_div).hide(); + this.tools_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Tools") + .addClass("icon-button tools-icon").tipsy( {gravity: 's'} ) + .appendTo(this.icons_div).hide(); + this.remove_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Remove") + .addClass("icon-button remove-icon").tipsy( {gravity: 's'} ) + .appendTo(this.icons_div); + var track = this; + + // Suppress double clicks in header so that they do not impact viz. + this.header_div.dblclick( function(e) { e.stopPropagation(); } ); + + // Clicking on settings icon opens track config. + this.settings_icon.click( function() { + var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, + ok_fn = function() { + track.config.update_from_form( $(".dialog-box") ); + hide_modal(); + $(window).unbind("keypress.check_enter_esc"); + }, + check_enter_esc = function(e) { + if ((e.keyCode || e.which) === 27) { // Escape key + cancel_fn(); + } else if ((e.keyCode || e.which) === 13) { // Enter key + ok_fn(); + } + }; + + $(window).bind("keypress.check_enter_esc", check_enter_esc); + show_modal("Configure Track", track.config.build_form(), { + "Cancel": cancel_fn, + "OK": ok_fn + }); + }); + + // FIXME: old code for overview. + /* + track_dropdown[(this.is_overview ? "Hide overview" : "Set as overview")] = function() { + if (track.is_overview) { + track.view.reset_overview(); + } + else { + track.view.set_overview(track); + } + }; + */ + + this.filters_icon.click( function() { + // TODO: update tipsy text. + track.filters_div.toggle(); + track.filters_manager.reset_filters(); + }); + + this.tools_icon.click( function() { + // TODO: update tipsy text. + + track.dynamic_tool_div.toggle(); + + // Update track name. + if (track.dynamic_tool_div.is(":visible")) { + track.set_name(track.name + track.tool_region_and_parameters_str()); + } + else { + track.revert_name(); + } + // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed. + $(".tipsy").remove(); + }); + + // Clicking on remove icon removes track. + this.remove_icon.click( function() { + // Tipsy for remove icon must be deleted when track is deleted. + $(".tipsy").remove(); + track.remove(); + }); + + // Set up behavior for modes popup. + if (track.display_modes !== undefined) { + if (track.mode_div === undefined) { + track.mode_div = $("<div class='right-float menubutton popup' />").appendTo(track.header_div); + var init_mode = (track.config && track.config.values['mode'] ? + track.config.values['mode'] : track.display_modes[0]); + track.mode = init_mode; + track.mode_div.text(init_mode); + + var mode_mapping = {}; + for (var i = 0, len = track.display_modes.length; i < len; i++) { + var mode = track.display_modes[i]; + mode_mapping[mode] = function(mode) { + return function() { track.change_mode(mode); }; + }(mode); + } + make_popupmenu(track.mode_div, mode_mapping); + } else { + track.mode_div.hide(); + } + + this.header_div.append( $("<div/>").css("clear", "both") ); + + // Set up config icon. + + // Show icons when users is hovering over track. + this.container_div.hover( function() { track.icons_div.show(); }, function() { track.icons_div.hide(); } ); + } } // @@ -2352,7 +2467,7 @@ } else if (result['status'] === "data") { if (result['valid_chroms']) { track.valid_chroms = result['valid_chroms']; - track.make_name_popup_menu(); + track.update_track_icons(); } track.content_div.text(DATA_OK); if (track.view.chrom) { @@ -2367,6 +2482,8 @@ } } }); + + this.update_track_icons(); }, /** * Additional initialization required before drawing track for the first time. @@ -2405,33 +2522,7 @@ if (this.tool) { this.dynamic_tool_div = this.tool.parent_div; this.header_div.after(this.dynamic_tool_div); - } - - // - // Create modes control. - // - if (track.display_modes !== undefined) { - if (track.mode_div === undefined) { - track.mode_div = $("<div class='right-float menubutton popup' />").appendTo(track.header_div); - var init_mode = (track.config && track.config.values['mode'] ? - track.config.values['mode'] : track.display_modes[0]); - track.mode = init_mode; - track.mode_div.text(init_mode); - - var mode_mapping = {}; - for (var i = 0, len = track.display_modes.length; i < len; i++) { - var mode = track.display_modes[i]; - mode_mapping[mode] = function(mode) { - return function() { track.change_mode(mode); }; - }(mode); - } - make_popupmenu(track.mode_div, mode_mapping); - } else { - track.mode_div.hide(); - } } - - this.make_name_popup_menu(); }; extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { /** @@ -2461,87 +2552,31 @@ return track; }, /** - * Make popup menu for track name. + * Update track's buttons. */ - make_name_popup_menu: function() { + update_track_icons: function() { var track = this; - var track_dropdown = {}; - // - // Make track overview option. - // - track_dropdown[(this.is_overview ? "Hide overview" : "Set as overview")] = function() { - if (track.is_overview) { - track.view.reset_overview(); - } - else { - track.view.set_overview(track); - } - }; - - // - // Edit config option. - // - track_dropdown["Edit configuration"] = function() { - var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, - ok_fn = function() { - track.config.update_from_form( $(".dialog-box") ); - hide_modal(); - $(window).unbind("keypress.check_enter_esc"); - }, - check_enter_esc = function(e) { - if ((e.keyCode || e.which) === 27) { // Escape key - cancel_fn(); - } else if ((e.keyCode || e.which) === 13) { // Enter key - ok_fn(); - } - }; - - $(window).bind("keypress.check_enter_esc", check_enter_esc); - show_modal("Configure Track", track.config.build_form(), { - "Cancel": cancel_fn, - "OK": ok_fn - }); - }; - - // - // Show/hide filters option. + // Show/hide filter icon. // if (track.filters_available > 0) { - // Show/hide filters menu item. - var text = (track.filters_div.is(":visible") ? "Hide filters" : "Show filters"); - track_dropdown[text] = function() { - // Toggle filtering div, reset filters, and remake menu. - track.filters_visible = (track.filters_div.is(":visible")); - if (track.filters_visible) { - track.filters_manager.reset_filters(); - } - track.filters_div.toggle(); - track.make_name_popup_menu(); - }; + track.filters_icon.show(); + } + else { + track.filters_icon.hide(); } // - // Show/hide tool option. + // Show/hide tool icon. // if (track.tool) { - // Show/hide dynamic tool menu item. - var text = (track.dynamic_tool_div.is(":visible") ? "Hide tool" : "Show tool"); - track_dropdown[text] = function() { - // Set track name, toggle tool div, and remake menu. - if (!track.dynamic_tool_div.is(":visible")) { - track.set_name(track.name + track.tool_region_and_parameters_str()); - } - else { - menu_option_text = "Show dynamic tool"; - track.revert_name(); - } - track.dynamic_tool_div.toggle(); - track.make_name_popup_menu(); - }; + track.tools_icon.show(); } - + else { + track.tools_icon.hide(); + } + // // List chrom/contigs with data option. // @@ -2552,22 +2587,13 @@ }; } */ - - // - // Remove option. - // - track_dropdown.Remove = function() { - track.remove(); - }; - - make_popupmenu(track.name_div, track_dropdown); }, /** * Set track's overview status. */ set_is_overview: function(is_overview) { this.is_overview = is_overview; - this.make_name_popup_menu(); + this.update_track_icons(); }, /** * Returns a jQuery Deferred object that resolves to a Tile with track's overview. @@ -3203,7 +3229,7 @@ if (!track.filters_available) { track.filters_div.hide(); } - track.make_name_popup_menu(); + track.update_track_icons(); } } }, @@ -3495,7 +3521,7 @@ this.prefs = this.config.values; this.painter = painters.ReadPainter; - this.make_name_popup_menu(); + this.update_track_icons(); }; extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); --- a/templates/tracks/browser.mako Fri Oct 21 13:48:24 2011 -0400 +++ b/templates/tracks/browser.mako Fri Oct 21 20:00:27 2011 -0400 @@ -42,10 +42,9 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]--> -${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic" )} +${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic", "jquery.tipsy" )} <script type="text/javascript"> - // // Place URLs here so that url_for can be used to generate them. // @@ -113,6 +112,9 @@ }; $(function() { + // Manual tipsy config because default gravity is S and cannot be changed. + $(".menu-button").tipsy( {gravity: 'n'} ); + // Hide bookmarks by default right now. parent.force_right_panel("hide"); @@ -172,59 +174,61 @@ %endif // - // Make actions menu. + // Initialize icons. // - $("#viz-actions-button").css( "position", "relative" ); - make_popupmenu( $("#viz-actions-button"), { - "Add Tracks": add_tracks, - "Add Group": function() { - var group = new DrawableGroup("New Group", view, view); - view.add_drawable(group); - }, - "Save": function() { - // Show saving dialog box - show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>"); - - // Save bookmarks. - var bookmarks = []; - $(".bookmark").each(function() { - bookmarks[bookmarks.length] = { - position: $(this).children(".position").text(), - annotation: $(this).children(".annotation").text() - }; - }); - - var overview_track_name = (view.overview_track ? view.overview_track.name : null); - var payload = { - 'view': view.to_json(), - 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, - 'bookmarks': bookmarks - }; - - $.ajax({ - url: "${h.url_for( action='save' )}", - type: "POST", - data: { - 'vis_id': view.vis_id, - 'vis_title': view.title, - 'dbkey': view.dbkey, - 'payload': JSON.stringify(payload) - }, - success: function(vis_id) { - view.vis_id = vis_id; - view.has_changes = false; - hide_modal(); - }, - error: function() { alert("Could not save visualization"); } - }); - }, - "Bookmarks": function() { - // HACK -- use style to determine if panel is hidden and hide/show accordingly. - parent.force_right_panel(($("div#right").css("right") == "0px" ? "hide" : "show")); - }, - "Close": function() { window.location = "${h.url_for( controller='visualization', action='list' )}"; } + $("#add-tracks-icon").click( function() { add_tracks(); } ); + + $("#add-group-icon").click( function() { + view.add_drawable( new DrawableGroup("New Group", view, view) ); }); + $("#save-icon").click( function() { + // Show saving dialog box + show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>"); + + // Save bookmarks. + var bookmarks = []; + $(".bookmark").each(function() { + bookmarks[bookmarks.length] = { + position: $(this).children(".position").text(), + annotation: $(this).children(".annotation").text() + }; + }); + + var overview_track_name = (view.overview_track ? view.overview_track.name : null); + var payload = { + 'view': view.to_json(), + 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, + 'bookmarks': bookmarks + }; + + $.ajax({ + url: "${h.url_for( action='save' )}", + type: "POST", + data: { + 'vis_id': view.vis_id, + 'vis_title': view.title, + 'dbkey': view.dbkey, + 'payload': JSON.stringify(payload) + }, + success: function(vis_id) { + view.vis_id = vis_id; + view.has_changes = false; + hide_modal(); + }, + error: function() { alert("Could not save visualization"); } + }); + }); + + $("#bookmarks-icon").click( function() { + // HACK -- use style to determine if panel is hidden and hide/show accordingly. + parent.force_right_panel(($("div#right").css("right") == "0px" ? "hide" : "show")); + }); + + $("#close-icon").click( function() { + window.location = "${h.url_for( controller='visualization', action='list' )}"; + }); + $("#add-bookmark-button").click(function() { // Add new bookmark. var position = view.chrom + ":" + view.low + "-" + view.high, @@ -245,9 +249,14 @@ <div class="unified-panel-header-inner"><div style="float:left;" id="title"></div><div style="float: right"> - <a id="viz-actions-button" class='panel-header-button popup' href="javascript:void(0)" target="galaxy_main">${_('Actions')}</a> + <a id="add-tracks-icon" class='icon-button menu-button' href="javascript:void(0);" title="Add tracks"></a> + <a id="add-group-icon" class='icon-button menu-button' href="javascript:void(0);" title="Add new group"></a> + <a id="bookmarks-icon" class='icon-button menu-button' href="javascript:void(0);" title="Bookmarks"></a> + <a id="save-icon" class='icon-button menu-button' href="javascript:void(0);" title="Save"></a> + <a id="close-icon" class='icon-button menu-button' href="javascript:void(0);" title="Close"></a></div></div> + <div style="clear: both"></div></div><div id="browser-container" class="unified-panel-body"></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Update generic GATK command line options.
by Bitbucket 21 Oct '11

21 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e494ac4c1e47/ changeset: e494ac4c1e47 user: dan date: 2011-10-21 19:48:24 summary: Update generic GATK command line options. affected #: 12 files (-1 bytes) --- a/tools/gatk/count_covariates.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/count_covariates.xml Fri Oct 21 13:48:24 2011 -0400 @@ -59,14 +59,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -78,11 +80,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -202,7 +211,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -218,12 +227,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -240,7 +255,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -254,7 +269,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -267,19 +282,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + </param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> --- a/tools/gatk/indel_realigner.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/indel_realigner.xml Fri Oct 21 13:48:24 2011 -0400 @@ -165,7 +165,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -181,12 +181,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -203,7 +209,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -217,7 +223,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -230,19 +236,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + </param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> --- a/tools/gatk/realigner_target_creator.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/realigner_target_creator.xml Fri Oct 21 13:48:24 2011 -0400 @@ -47,12 +47,13 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' @@ -67,11 +68,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if $reference_source.reference_source_selector == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -151,7 +159,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -167,8 +175,12 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat><param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option> @@ -191,7 +203,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -205,7 +217,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -218,19 +230,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + </param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> --- a/tools/gatk/table_recalibration.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/table_recalibration.xml Fri Oct 21 13:48:24 2011 -0400 @@ -35,29 +35,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if - #set $rod_binding_names = dict() - #for $rod_binding in $gatk_param_type.rod_bind: - #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': - #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name - #else - #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector - #end if - #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 - -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" - #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ): - -p '--rodToIntervalTrackName "${rod_bind_name}"' - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' - #if str( $gatk_param_type.input_dbsnp_rod ) != "None": - -d "-D" "${gatk_param_type.input_dbsnp_rod}" "${gatk_param_type.input_dbsnp_rod.ext}" "dbsnp_rod" - #end if + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -69,11 +56,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -147,7 +141,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -163,35 +157,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> - <repeat name="rod_bind" title="Binding for reference-ordered data"> - <conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="snps" selected="True">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> - <when value="snps"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="indels"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="custom"> - <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - </conditional> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> - <param name="input_dbsnp_rod" type="data" format="gatk_dbsnp" optional="True" label="dbSNP reference ordered data (ROD)" /> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -208,7 +185,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -222,7 +199,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -235,19 +212,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + </param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> --- a/tools/gatk/unified_genotyper.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/unified_genotyper.xml Fri Oct 21 13:48:24 2011 -0400 @@ -56,12 +56,13 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' @@ -76,11 +77,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if $reference_source.reference_source_selector == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -194,7 +202,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -210,8 +218,12 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat><param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option> @@ -234,7 +246,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -248,7 +260,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -261,19 +273,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + </param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> --- a/tools/gatk/variant_annotator.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variant_annotator.xml Fri Oct 21 13:48:24 2011 -0400 @@ -89,14 +89,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -108,10 +110,16 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" @@ -252,28 +260,34 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> - </param> - <when value="ZeroMappingQualityRead"> -  - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> + </param> + <when value="ZeroMappingQualityRead"> +  + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -281,55 +295,74 @@ <option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when></conditional><param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + </param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> --- a/tools/gatk/variant_apply_recalibration.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variant_apply_recalibration.xml Fri Oct 21 13:48:24 2011 -0400 @@ -37,14 +37,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -56,11 +58,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -118,28 +127,34 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> - </param> - <when value="ZeroMappingQualityRead"> -  - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> + </param> + <when value="ZeroMappingQualityRead"> +  + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -147,55 +162,74 @@ <option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when></conditional><param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + </param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> --- a/tools/gatk/variant_combine.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variant_combine.xml Fri Oct 21 13:48:24 2011 -0400 @@ -28,7 +28,6 @@ --rod_priority_list "${ ','.join( $priority_order ) }" ' - ##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": #for $sample_metadata in $gatk_param_type.sample_metadata: @@ -44,13 +43,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -62,11 +64,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if $reference_source.reference_source_selector == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -138,7 +147,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -154,12 +163,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -176,7 +191,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -190,7 +205,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -203,19 +218,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + </param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> --- a/tools/gatk/variant_eval.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variant_eval.xml Fri Oct 21 13:48:24 2011 -0400 @@ -56,13 +56,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -74,11 +77,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if $reference_source.reference_source_selector == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -195,7 +205,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -211,12 +221,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -233,7 +249,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -247,7 +263,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -260,19 +276,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + </param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> --- a/tools/gatk/variant_filtration.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variant_filtration.xml Fri Oct 21 13:48:24 2011 -0400 @@ -50,14 +50,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -69,11 +71,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -152,7 +161,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -168,12 +177,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -190,7 +205,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -204,7 +219,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -217,19 +232,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + </param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> --- a/tools/gatk/variant_recalibrator.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variant_recalibrator.xml Fri Oct 21 13:48:24 2011 -0400 @@ -58,14 +58,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -77,11 +79,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -382,28 +391,34 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> - </param> - <when value="ZeroMappingQualityRead"> -  - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> + </param> + <when value="ZeroMappingQualityRead"> +  + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -411,55 +426,74 @@ <option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when></conditional><param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + </param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> --- a/tools/gatk/variants_validate.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variants_validate.xml Fri Oct 21 13:48:24 2011 -0400 @@ -42,13 +42,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -60,11 +63,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if $reference_source.reference_source_selector == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -120,7 +130,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -136,12 +146,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -158,7 +174,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -172,7 +188,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -185,19 +201,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + </param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 21 Oct '11

21 Oct '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2b683b63de2e/ changeset: 2b683b63de2e user: John Duddy date: 2011-10-14 23:03:56 summary: Fix API code errors, add ability to set ldda associations, fixed misc error in util affected #: 4 files (-1 bytes) --- a/lib/galaxy/util/__init__.py Fri Oct 14 15:20:12 2011 -0400 +++ b/lib/galaxy/util/__init__.py Fri Oct 14 14:03:56 2011 -0700 @@ -133,6 +133,8 @@ def restore_text(text): """Restores sanitized text""" + if not text: + return text for key, value in mapped_chars.items(): text = text.replace(value, key) return text --- a/lib/galaxy/web/api/histories.py Fri Oct 14 15:20:12 2011 -0400 +++ b/lib/galaxy/web/api/histories.py Fri Oct 14 14:03:56 2011 -0700 @@ -88,9 +88,10 @@ state = states.QUEUED elif summary[states.OK] == num_sets: state = states.OK + item['state_details'] = summary item['contents_url'] = url_for( 'history_contents', history_id=history_id ) + item['state'] = state - item['state_details'] = summary except Exception, e: item = "Error in history API at showing history detail" log.error(item + ": %s" % str(e)) --- a/lib/galaxy/web/api/history_contents.py Fri Oct 14 15:20:12 2011 -0400 +++ b/lib/galaxy/web/api/history_contents.py Fri Oct 14 14:03:56 2011 -0700 @@ -14,7 +14,7 @@ log = logging.getLogger( __name__ ) -class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociation, UsesHistory ): +class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociation, UsesHistory, UsesLibrary, UsesLibraryItems ): @web.expose_api def index( self, trans, history_id, **kwd ): @@ -85,7 +85,7 @@ if from_ld_id: try: - ld = get_library_content_for_access( trans, from_ld_id ) + ld = self.get_library_dataset( trans, from_ld_id, check_ownership=False, check_accessible=False ) assert type( ld ) is trans.app.model.LibraryDataset, "Library content id ( %s ) is not a dataset" % from_ld_id except AssertionError, e: trans.response.status = 400 --- a/lib/galaxy/web/api/library_contents.py Fri Oct 14 15:20:12 2011 -0400 +++ b/lib/galaxy/web/api/library_contents.py Fri Oct 14 14:03:56 2011 -0700 @@ -75,9 +75,9 @@ """ class_name, content_id = self.__decode_library_content_id( trans, id ) if class_name == 'LibraryFolder': - content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessibility=True ) + content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessible=True ) else: - content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessibility=True ) + content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessible=True ) return self.encode_all_ids( trans, content.get_api_value( view='element' ) ) @web.expose_api @@ -100,9 +100,10 @@ return "Missing requred 'folder_id' parameter." else: folder_id = payload.pop( 'folder_id' ) + class_name, folder_id = self.__decode_library_content_id( trans, folder_id ) try: # security is checked in the downstream controller - parent = self.get_library_folder( trans, folder_id, check_ownership=False, check_accessibility=False ) + parent = self.get_library_folder( trans, folder_id, check_ownership=False, check_accessible=False ) except Exception, e: return str( e ) # The rest of the security happens in the library_common controller. @@ -128,6 +129,23 @@ url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) return rval + @web.expose_api + def update( self, trans, id, library_id, payload, **kwd ): + """ + PUT /api/libraries/{encoded_library_id}/contents/{encoded_content_type_and_id} + Sets relationships among items + """ + if 'converted_dataset_id' in payload: + converted_id = payload.pop( 'converted_dataset_id' ) + content = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=False ) + content_conv = self.get_library_dataset( trans, converted_id, check_ownership=False, check_accessible=False ) + assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = content.library_dataset_dataset_association, + dataset = content_conv.library_dataset_dataset_association, + file_type = content_conv.library_dataset_dataset_association.extension, + metadata_safe = True ) + trans.sa_session.add( assoc ) + trans.sa_session.flush() + def __decode_library_content_id( self, trans, content_id ): if ( len( content_id ) % 16 == 0 ): return 'LibraryDataset', content_id http://bitbucket.org/galaxy/galaxy-central/changeset/91d5661608b9/ changeset: 91d5661608b9 user: John Duddy date: 2011-10-14 23:05:15 summary: Correct indentation, only access summary if it is set! affected #: 1 file (-1 bytes) --- a/lib/galaxy/web/api/histories.py Fri Oct 14 14:03:56 2011 -0700 +++ b/lib/galaxy/web/api/histories.py Fri Oct 14 14:05:15 2011 -0700 @@ -88,9 +88,8 @@ state = states.QUEUED elif summary[states.OK] == num_sets: state = states.OK - item['state_details'] = summary + item['state_details'] = summary item['contents_url'] = url_for( 'history_contents', history_id=history_id ) - item['state'] = state except Exception, e: item = "Error in history API at showing history detail" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fixes for searching for and installing tools from a tool shed. The value of the webapp request parameter is heavily used throughout this process, and has been added to all grid forms that include operation buttons.
by Bitbucket 20 Oct '11

20 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3d1dafee5c62/ changeset: 3d1dafee5c62 user: greg date: 2011-10-20 22:57:09 summary: Fixes for searching for and installing tools from a tool shed. The value of the webapp request parameter is heavily used throughout this process, and has been added to all grid forms that include operation buttons. affected #: 9 files (-1 bytes) --- a/lib/galaxy/web/controllers/admin.py Thu Oct 20 16:38:14 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Thu Oct 20 16:57:09 2011 -0400 @@ -708,7 +708,7 @@ def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = trans.request.host - url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) + url = '%s/repository/browse_valid_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Oct 20 16:38:14 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Oct 20 16:57:09 2011 -0400 @@ -183,7 +183,7 @@ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table ) -class DownloadableRepositoryListGrid( RepositoryListGrid ): +class ValidRepositoryListGrid( RepositoryListGrid ): class RevisionColumn( grids.GridColumn ): def __init__( self, col_name ): grids.GridColumn.__init__( self, col_name ) @@ -196,7 +196,7 @@ if len( select_field.options ) > 1: return select_field.get_html() return repository.revision - title = "Downloadable repositories" + title = "Valid repositories" columns = [ RepositoryListGrid.NameColumn( "Name", key="name", @@ -210,11 +210,6 @@ attach_popup=False, key="User.username" ) ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) operations = [] def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( self.model_class ) \ @@ -237,7 +232,7 @@ return repository_metadata.repository.user.username return 'no user' # Grid definition - title = "Matched repositories" + title = "Repositories with matching tools" model_class = model.RepositoryMetadata template='/webapps/community/repository/grid.mako' default_sort_key = "Repository.name" @@ -282,21 +277,19 @@ .filter( self.model_class.table.c.repository_id == 0 ) class InstallMatchedRepositoryListGrid( MatchedRepositoryListGrid ): - # Grid definition - title = "Repositories that contain tools matching search criteria" columns = [ col for col in MatchedRepositoryListGrid.columns ] # Override the NameColumn columns[ 0 ] = MatchedRepositoryListGrid.NameColumn( "Name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id, webapp="galaxy" ) ), - attach_popup=True ) + attach_popup=False ) class RepositoryController( BaseUIController, ItemRatings ): install_matched_repository_list_grid = InstallMatchedRepositoryListGrid() matched_repository_list_grid = MatchedRepositoryListGrid() - downloadable_repository_list_grid = DownloadableRepositoryListGrid() + valid_repository_list_grid = ValidRepositoryListGrid() repository_list_grid = RepositoryListGrid() category_list_grid = CategoryListGrid() @@ -340,7 +333,7 @@ # Render the list view return self.category_list_grid( trans, **kwd ) @web.expose - def browse_downloadable_repositories( self, trans, **kwd ): + def browse_valid_repositories( self, trans, **kwd ): webapp = kwd.get( 'webapp', 'community' ) galaxy_url = kwd.get( 'galaxy_url', None ) if galaxy_url: @@ -352,6 +345,7 @@ repository = get_repository( trans, repository_id ) return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', + webapp=webapp, repository_id=repository_id, changeset_revision=repository.tip ) ) # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change @@ -371,16 +365,16 @@ webapp=webapp, repository_id=trans.security.encode_id( repository.id ), changeset_revision=v ) ) - url_args = dict( action='browse_downloadable_repositories', + url_args = dict( action='browse_valid_repositories', operation='preview_tools_in_changeset', webapp=webapp, repository_id=repository_id ) - self.downloadable_repository_list_grid.operations = [ grids.GridOperation( "Preview and install", - url_args=url_args, - allow_multiple=False, - async_compatible=False ) ] + self.valid_repository_list_grid.operations = [ grids.GridOperation( "Preview and install", + url_args=url_args, + allow_multiple=False, + async_compatible=False ) ] # Render the list view - return self.downloadable_repository_list_grid( trans, **kwd ) + return self.valid_repository_list_grid( trans, **kwd ) @web.expose def find_tools( self, trans, **kwd ): params = util.Params( kwd ) @@ -391,38 +385,35 @@ if galaxy_url: trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) if 'operation' in kwd: - operation = kwd[ 'operation' ].lower() - is_admin = trans.user_is_admin() - if operation == "view_or_manage_repository": - # The received id is a RepositoryMetadata id, so we have to get the repository id. - repository_metadata = get_repository_metadata_by_id( trans, kwd[ 'id' ] ) - repository_id = trans.security.encode_id( repository_metadata.repository.id ) - repository = get_repository( trans, repository_id ) - kwd[ 'id' ] = repository_id - kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision - if webapp == 'community' and ( is_admin or repository.user == trans.user ): - a = 'manage_repository' - else: - a = 'view_repository' - return trans.response.send_redirect( web.url_for( controller='repository', - action=a, - **kwd ) ) - if operation == "install": - repo_info_dict = {} - galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - # TODO: support https in the following url. - url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s' % ( galaxy_url, trans.request.host, webapp ) - repository_metadata_ids = util.listify( kwd[ 'id' ] ) - for repository_metadata_id in repository_metadata_ids: - repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) - repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) - repository_id = trans.security.encode_id( repository.id ) - changeset_revision = repository_metadata.changeset_revision - repository_clone_url = generate_clone_url( trans, repository_id ) - repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) - encoded_repo_info_dict = self.__encode( repo_info_dict ) - url += '&repo_info_dict=%s' % encoded_repo_info_dict - return trans.response.send_redirect( url ) + item_id = kwd.get( 'id', '' ) + if item_id: + operation = kwd[ 'operation' ].lower() + is_admin = trans.user_is_admin() + if operation == "view_or_manage_repository": + # The received id is a RepositoryMetadata id, so we have to get the repository id. + repository_metadata = get_repository_metadata_by_id( trans, item_id ) + repository_id = trans.security.encode_id( repository_metadata.repository.id ) + repository = get_repository( trans, repository_id ) + kwd[ 'id' ] = repository_id + kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision + if webapp == 'community' and ( is_admin or repository.user == trans.user ): + a = 'manage_repository' + else: + a = 'view_repository' + return trans.response.send_redirect( web.url_for( controller='repository', + action=a, + **kwd ) ) + if operation == "install": + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) + # TODO: support https in the following url. + url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \ + ( galaxy_url, trans.request.host, webapp, encoded_repo_info_dict ) + return trans.response.send_redirect( url ) + else: + # This can only occur when there is a multi-select grid with check boxes and an operation, + # and the user clicked the operation button without checking any of the check boxes. + return trans.show_error_message( "No items were selected." ) tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ] tool_names = [ item.lower() for item in util.listify( kwd.get( 'tool_name', '' ) ) ] tool_versions = [ item.lower() for item in util.listify( kwd.get( 'tool_version', '' ) ) ] @@ -436,7 +427,12 @@ kwd[ 'match_tuples' ] = match_tuples # Render the list view if webapp == 'galaxy': - # Our request originated from a Galaxy instance. + # Our initial request originated from a Galaxy instance. + global_actions = [ grids.GridAction( "Browse valid repositories", + dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ), + grids.GridAction( "Search for valid tools", + dict( controller='repository', action='find_tools', webapp=webapp ) ) ] + self.install_matched_repository_list_grid.global_actions = global_actions install_url_args = dict( controller='repository', action='find_tools', webapp=webapp ) operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] self.install_matched_repository_list_grid.operations = operations @@ -583,8 +579,21 @@ if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) return match_tuples - def __encode( self, repo_info_dict ): - value = simplejson.dumps( repo_info_dict ) + def __encode_repo_info_dict( self, trans, webapp, repository_metadata_ids ): + repo_info_dict = {} + for repository_metadata_id in repository_metadata_ids: + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) + repository_id = trans.security.encode_id( repository.id ) + changeset_revision = repository_metadata.changeset_revision + repository_clone_url = generate_clone_url( trans, repository_id ) + repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) + return self.__encode( repo_info_dict ) + def __encode( self, val ): + if isinstance( val, dict ): + value = simplejson.dumps( val ) + else: + value = val a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) b = binascii.hexlify( value ) return "%s:%s" % ( a, b ) @@ -620,14 +629,18 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + repository_clone_url = generate_clone_url( trans, repository_id ) repository = get_repository( trans, repository_id ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) + repo_info_dict = {} + repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) + encoded_repo_info_dict = self.__encode( repo_info_dict ) # Redirect back to local Galaxy to perform install. - repository_clone_url = generate_clone_url( trans, repository_id ) # TODO: support https in the following url. - url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&name=%s&description=%s&repository_clone_url=%s&changeset_revision=%s' % \ - ( galaxy_url, trans.request.host, repository.name, repository.description, repository_clone_url, changeset_revision ) + url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&repo_info_dict=%s' % \ + ( galaxy_url, trans.request.host, encoded_repo_info_dict ) return trans.response.send_redirect( url ) @web.expose def check_for_updates( self, trans, **kwd ): --- a/templates/grid_base.mako Thu Oct 20 16:38:14 2011 -0400 +++ b/templates/grid_base.mako Thu Oct 20 16:57:09 2011 -0400 @@ -777,6 +777,7 @@ show_item_checkboxes = True %><form action="${url()}" method="post" onsubmit="return false;"> + <input type="hidden" name="webapp" value="${webapp}"/><table id="grid-table" class="grid"><thead id="grid-table-header"><tr> --- a/templates/webapps/community/repository/find_tools.mako Thu Oct 20 16:38:14 2011 -0400 +++ b/templates/webapps/community/repository/find_tools.mako Thu Oct 20 16:57:09 2011 -0400 @@ -10,6 +10,13 @@ %><%inherit file="${inherit(context)}"/> +%if webapp == 'galaxy': + <br/><br/> + <ul class="manage-table-actions"> + <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a></li> + </ul> +%endif + %if message: ${render_msg( message, status )} %endif --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako Thu Oct 20 16:38:14 2011 -0400 +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako Thu Oct 20 16:57:09 2011 -0400 @@ -64,7 +64,12 @@ <br/><br/><ul class="manage-table-actions"> - <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + </div></ul> %if message: --- a/templates/webapps/community/repository/tool_form.mako Thu Oct 20 16:38:14 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Thu Oct 20 16:57:09 2011 -0400 @@ -111,7 +111,12 @@ <br/><br/><ul class="manage-table-actions"> %if webapp == 'galaxy': - <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + </div> %else: %if is_new: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> --- a/templates/webapps/community/repository/view_repository.mako Thu Oct 20 16:38:14 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Thu Oct 20 16:57:09 2011 -0400 @@ -94,7 +94,12 @@ </div> %endif %else: - <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + </div> %endif </ul> --- a/templates/webapps/community/repository/view_tool_metadata.mako Thu Oct 20 16:38:14 2011 -0400 +++ b/templates/webapps/community/repository/view_tool_metadata.mako Thu Oct 20 16:57:09 2011 -0400 @@ -34,7 +34,12 @@ <br/><br/><ul class="manage-table-actions"> %if webapp == 'galaxy': - <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + </div> %else: %if is_new: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> --- a/templates/webapps/galaxy/admin/tool_sheds.mako Thu Oct 20 16:38:14 2011 -0400 +++ b/templates/webapps/galaxy/admin/tool_sheds.mako Thu Oct 20 16:57:09 2011 -0400 @@ -16,7 +16,7 @@ <div class="toolFormTitle">Accessible Galaxy tool sheds</div><div class="toolFormBody"><div class="form-row"> - <table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid"> + <table class="grid"><% shed_id = 0 %> %for name, url in trans.app.tool_shed_registry.tool_sheds.items(): <tr class="libraryTitle"> @@ -25,7 +25,7 @@ <a class="view-info" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">${name}</a></div><div popupmenu="dataset-${shed_id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">Browse downloadable repositories</a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='admin', action='find_tools_in_tool_shed', tool_shed_url=url )}">Search for valid tools</a></div></td> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Update sff extractor to version 0.2.10.
by Bitbucket 20 Oct '11

20 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8227055957e5/ changeset: 8227055957e5 user: dan date: 2011-10-20 22:38:14 summary: Update sff extractor to version 0.2.10. affected #: 2 files (-1 bytes) --- a/tools/filters/sff_extract.py Thu Oct 20 10:24:19 2011 -0400 +++ b/tools/filters/sff_extract.py Thu Oct 20 16:38:14 2011 -0400 @@ -27,7 +27,7 @@ __author__ = 'Jose Blanca and Bastien Chevreux' __copyright__ = 'Copyright 2008, Jose Blanca, COMAV, and Bastien Chevreux' __license__ = 'GPLv3 or later' -__version__ = '0.2.8' +__version__ = '0.2.10' __email__ = 'jblanca(a)btc.upv.es' __status__ = 'beta' @@ -298,7 +298,8 @@ #we check that we're removing the asked tag if tag is not None and tag != last_tag: - raise RuntimeError("The given xml tag wasn't the last one in the file") + etxt=join('The given xml tag (',tag,') was not the last one in the file'); + raise RuntimeError(etxt) # while we are at it: also remove all white spaces in that line :-) i -= 1 @@ -843,7 +844,7 @@ if len(boundaries) == 3: # case: mask char on both sides of sequence #print "bounds3" - data['clip_adapter_left']=1+boundaries[0][1] + data['clip_adapter_left']=boundaries[0][1] data['clip_adapter_right']=boundaries[2][0] elif len(boundaries) == 2: # case: mask char left or right of sequence @@ -851,7 +852,7 @@ if maskedseq[0] == maskchar : # case: mask char left #print "left" - data['clip_adapter_left']=1+boundaries[0][1] + data['clip_adapter_left']=boundaries[0][1] else: # case: mask char right #print "right" @@ -1192,7 +1193,11 @@ ''' left, right = return_merged_clips(data) seq = data['bases'] - new_seq = ''.join((seq[:left-1].lower(), seq[left-1:right], seq[right:].lower())) + if left >= right: + new_seq = seq.lower() + else: + new_seq = ''.join((seq[:left-1].lower(), seq[left-1:right], seq[right:].lower())) + return new_seq def clip_read(data): @@ -1209,14 +1214,14 @@ -def tests_for_ssaha(linker_fname): +def tests_for_ssaha(): '''Tests whether SSAHA2 can be successfully called.''' try: print "Testing whether SSAHA2 is installed and can be launched ... ", sys.stdout.flush() fh = open('/dev/null', 'w') - retcode = subprocess.call(["ssaha2", "-v"], stdout = fh) + retcode = subprocess.call(["ssaha2"], stdout = fh) fh.close() print "ok." except : @@ -1247,6 +1252,8 @@ '''Launches SSAHA2 on the linker and query file, string SSAHA2 output into the output filehandle''' + tests_for_ssaha() + try: print "Searching linker sequences with SSAHA2 (this may take a while) ... ", sys.stdout.flush() --- a/tools/filters/sff_extractor.xml Thu Oct 20 10:24:19 2011 -0400 +++ b/tools/filters/sff_extractor.xml Thu Oct 20 16:38:14 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="Sff_extractor" name="SFF converter" version="1.0.0"> +<tool id="Sff_extractor" name="SFF converter" version="1.0.1"><description></description><command interpreter="python"> #if str($fastq_output) == "fastq_false" #sff_extract.py $clip --seq_file=$out_file3 --qual_file=$out_file4 --xml_file=$out_file2 $input Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: First pass at updating GATK tools to version 1.2. Changes are not backwards compatible with workflows. Still considered BETA, and so future changes are like to also not be backwards compatible.
by Bitbucket 20 Oct '11

20 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/070513d25b63/ changeset: 070513d25b63 user: dan date: 2011-10-20 16:24:19 summary: First pass at updating GATK tools to version 1.2. Changes are not backwards compatible with workflows. Still considered BETA, and so future changes are like to also not be backwards compatible. affected #: 20 files (-1 bytes) --- a/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains Thu Oct 20 10:03:28 2011 -0400 +++ b/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains Thu Oct 20 10:24:19 2011 -0400 @@ -10,4 +10,4 @@ UnifiedGenotyper - % confidently called bases of callable loci 100.000 UnifiedGenotyper - Actual calls made 1 TraversalEngine - Total runtime -TraversalEngine - 0 reads were filtered out during traversal out of 10 total (0.00%) \ No newline at end of file +TraversalEngine - 0 reads were filtered out during traversal out of 20 total (0.00%) --- a/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf Thu Oct 20 10:03:28 2011 -0400 +++ b/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf Thu Oct 20 10:24:19 2011 -0400 @@ -21,7 +21,8 @@ ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> -##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> -##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpXqIddV/gatk_input_0.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpXqIddV/gatk_input.fasta rodBind=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpXqIddV/input_dbsnp_0.bed] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_CONFIDENT_SITES standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=-1.0 min_indel_count_for_genotyping=2 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=3.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[]" +##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input_0.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_CONFIDENT_SITES standard_min_confidence_threshold_for_calling=0.0 standard_min_confidence_threshold_for_emitting=4.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=-1.0 min_indel_count_for_genotyping=2 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=3.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/input_dbsnp_0.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null annotation=[]" +##contig=<ID=phiX174,length=5386> +##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . 37.27 . AC=0;AF=0.00;AN=2;DP=10;MQ=37.74;MQ0=0 GT:DP:GQ:PL 0/0:7:0:0,0,0 +phiX174 1443 . AC . 0 . DB;DP=10;MQ=37.74;MQ0=0;QD=0.00 GT:DP:PL ./.:10:0,0,0 --- a/test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf Thu Oct 20 10:03:28 2011 -0400 +++ b/test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf Thu Oct 20 10:24:19 2011 -0400 @@ -22,8 +22,10 @@ ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> -##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> -##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpXqIddV/gatk_input_0.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpXqIddV/gatk_input.fasta rodBind=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpXqIddV/input_dbsnp_0.bed] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_CONFIDENT_SITES standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=-1.0 min_indel_count_for_genotyping=2 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=3.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[]" -##VariantAnnotator="analysis_type=VariantAnnotator input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpYvqW3G/gatk_input.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpYvqW3G/gatk_input.fasta rodBind=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpYvqW3G/input_variant.vcf, /var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpYvqW3G/input_dbsnp_0.bed] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sampleName=null annotation=[AlleleBalance, BaseQualityRankSumTest, DepthOfCoverage, HomopolymerRun, MappingQualityRankSumTest, MappingQualityZero, QualByDepth, RMSMappingQuality, SpanningDeletions, HaplotypeScore] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false" +##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input_0.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_CONFIDENT_SITES standard_min_confidence_threshold_for_calling=0.0 standard_min_confidence_threshold_for_emitting=4.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=-1.0 min_indel_count_for_genotyping=2 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=3.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/input_dbsnp_0.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null annotation=[]" +##VariantAnnotator="analysis_type=VariantAnnotator input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_variant.vcf) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_dbsnp_dbsnp.vcf) comp=[] resource=[] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub annotation=[SpanningDeletions, MappingQualityZero, AlleleBalance, RMSMappingQuality, HaplotypeScore, HomopolymerRun, DepthOfCoverage, MappingQualityRankSumTest, BaseQualityRankSumTest, QualByDepth] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false" +##contig=<ID=phiX174,length=5386> +##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta +##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . 37.27 . AC=0;AF=0.00;AN=2;DP=10;MQ=37.74;MQ0=0 GT:DP:GQ:PL 0/0:7:0:0,0,0 +phiX174 1443 . AC . 0 . DB;DP=10;MQ=37.74;MQ0=0;QD=0.00 GT:DP:PL ./.:10:0,0,0 --- a/test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf Thu Oct 20 10:03:28 2011 -0400 +++ b/test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf Thu Oct 20 10:24:19 2011 -0400 @@ -1,5 +1,5 @@ ##fileformat=VCFv4.1 -##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpNWtPhs/gatk_input.fasta rodBind=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpNWtPhs/input_variant_from_variant_annotator.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=from_variant_annotator printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 masterMerge=false mergeInfoWithMaxAC=false" +##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-bFIpbp/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false variant=[(RodBinding name=from_variant_annotator source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-bFIpbp/input_variant_from_variant_annotator.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=from_variant_annotator printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 mergeInfoWithMaxAC=false" ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)"> ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality"> @@ -23,9 +23,11 @@ ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> -##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> ##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants"> -##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpXqIddV/gatk_input_0.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpXqIddV/gatk_input.fasta rodBind=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpXqIddV/input_dbsnp_0.bed] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_CONFIDENT_SITES standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=-1.0 min_indel_count_for_genotyping=2 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=3.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[]" -##VariantAnnotator="analysis_type=VariantAnnotator input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpYvqW3G/gatk_input.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpYvqW3G/gatk_input.fasta rodBind=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpYvqW3G/input_variant.vcf, /var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmpYvqW3G/input_dbsnp_0.bed] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sampleName=null annotation=[AlleleBalance, BaseQualityRankSumTest, DepthOfCoverage, HomopolymerRun, MappingQualityRankSumTest, MappingQualityZero, QualByDepth, RMSMappingQuality, SpanningDeletions, HaplotypeScore] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false" +##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input_0.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_CONFIDENT_SITES standard_min_confidence_threshold_for_calling=0.0 standard_min_confidence_threshold_for_emitting=4.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=-1.0 min_indel_count_for_genotyping=2 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=3.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/input_dbsnp_0.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null annotation=[]" +##VariantAnnotator="analysis_type=VariantAnnotator input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_variant.vcf) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_dbsnp_dbsnp.vcf) comp=[] resource=[] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub annotation=[SpanningDeletions, MappingQualityZero, AlleleBalance, RMSMappingQuality, HaplotypeScore, HomopolymerRun, DepthOfCoverage, MappingQualityRankSumTest, BaseQualityRankSumTest, QualByDepth] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false" +##contig=<ID=phiX174,length=5386> +##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta +##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-bFIpbp/gatk_input.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . . PASS AC=0;AF=0.00;AN=2;DP=10;MQ=37.74;MQ0=0;set=ReferenceInAll GT:DP:GQ:PL 0/0:7:0:0,0,0 +phiX174 1443 . AC . . PASS AC=0;AF=0.00;AN=0;DB;DP=10;MQ=37.74;MQ0=0;QD=0.00;set=ReferenceInAll GT:DP:PL ./.:10:0,0,0 --- a/test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular Thu Oct 20 10:03:28 2011 -0400 +++ b/test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular Thu Oct 20 10:24:19 2011 -0400 @@ -1,36 +1,36 @@ -##:GATKReport.v0.1 CompOverlap : The overlap between eval and comp sites -CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants nCompVariants novelSites nVariantsAtComp compRate nConcordant concordantRate -CompOverlap dbsnp eval none all 0 0 0 0 0.00000000 0 0.00000000 -CompOverlap dbsnp eval none known 0 0 0 0 0.00000000 0 0.00000000 -CompOverlap dbsnp eval none novel 0 0 0 0 0.00000000 0 0.00000000 +##:GATKReport.v0.2 CompOverlap : The overlap between eval and comp sites +CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants novelSites nVariantsAtComp compRate nConcordant concordantRate +CompOverlap dbsnp input_0 none all 0 0 0 0.00000000 0 0.00000000 +CompOverlap dbsnp input_0 none known 0 0 0 0.00000000 0 0.00000000 +CompOverlap dbsnp input_0 none novel 0 0 0 0.00000000 0 0.00000000 -##:GATKReport.v0.1 CountVariants : Counts different classes of variants in the sample -CountVariants CompRod EvalRod JexlExpression Novelty nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp deletionInsertionRatio -CountVariants dbsnp eval none all 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -CountVariants dbsnp eval none known 5386 0 0 0 0.00000000 0.00000000 0 0 0 0 0 0 0 0 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -CountVariants dbsnp eval none novel 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 +##:GATKReport.v0.2 CountVariants : Counts different classes of variants in the sample +CountVariants CompRod EvalRod JexlExpression Novelty nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nMixed nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp deletionInsertionRatio +CountVariants dbsnp input_0 none all 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 1 0 0 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 +CountVariants dbsnp input_0 none known 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 1 0 0 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 +CountVariants dbsnp input_0 none novel 5386 0 0 0 0.00000000 0.00000000 0 0 0 0 0 0 0 0 0 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -##:GATKReport.v0.1 SimpleMetricsByAC.metrics : TiTv by allele count +##:GATKReport.v0.2 SimpleMetricsByAC.metrics : TiTv by allele count SimpleMetricsByAC.metrics CompRod EvalRod JexlExpression Novelty row AC nTi nTv n TiTv -SimpleMetricsByAC.metrics dbsnp eval none all ac0 0 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp eval none all ac1 1 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp eval none all ac2 2 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp eval none known ac0 0 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp eval none known ac1 1 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp eval none known ac2 2 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp eval none novel ac0 0 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp eval none novel ac1 1 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp eval none novel ac2 2 0 0 0 0.0 +SimpleMetricsByAC.metrics dbsnp input_0 none all ac0 0 0 0 0 0.0 +SimpleMetricsByAC.metrics dbsnp input_0 none all ac1 1 0 0 0 0.0 +SimpleMetricsByAC.metrics dbsnp input_0 none all ac2 2 0 0 0 0.0 +SimpleMetricsByAC.metrics dbsnp input_0 none known ac0 0 0 0 0 0.0 +SimpleMetricsByAC.metrics dbsnp input_0 none known ac1 1 0 0 0 0.0 +SimpleMetricsByAC.metrics dbsnp input_0 none known ac2 2 0 0 0 0.0 +SimpleMetricsByAC.metrics dbsnp input_0 none novel ac0 0 0 0 0 0.0 +SimpleMetricsByAC.metrics dbsnp input_0 none novel ac1 1 0 0 0 0.0 +SimpleMetricsByAC.metrics dbsnp input_0 none novel ac2 2 0 0 0 0.0 -##:GATKReport.v0.1 TiTvVariantEvaluator : Ti/Tv Variant Evaluator -TiTvVariantEvaluator CompRod EvalRod JexlExpression Novelty nTi nTv tiTvRatio nTiInComp nTvInComp TiTvRatioStandard nTiDerived nTvDerived tiTvDerivedRatio -TiTvVariantEvaluator dbsnp eval none all 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000 -TiTvVariantEvaluator dbsnp eval none known 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000 -TiTvVariantEvaluator dbsnp eval none novel 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000 +##:GATKReport.v0.2 TiTvVariantEvaluator : Ti/Tv Variant Evaluator +TiTvVariantEvaluator CompRod EvalRod JexlExpression Novelty nTi nTv tiTvRatio nTiInComp nTvInComp TiTvRatioStandard nTiDerived nTvDerived tiTvDerivedRatio +TiTvVariantEvaluator dbsnp input_0 none all 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000 +TiTvVariantEvaluator dbsnp input_0 none known 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000 +TiTvVariantEvaluator dbsnp input_0 none novel 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000 -##:GATKReport.v0.1 ValidationReport : Assess site accuracy and sensitivity of callset against follow-up validation assay -ValidationReport CompRod EvalRod JexlExpression Novelty nComp TP FP FN TN sensitivity specificity PPV FDR CompMonoEvalNoCall CompMonoEvalFiltered CompMonoEvalMono CompMonoEvalPoly CompPolyEvalNoCall CompPolyEvalFiltered CompPolyEvalMono CompPolyEvalPoly CompFiltered nDifferentAlleleSites -ValidationReport dbsnp eval none all 0 0 0 0 0 NaN 100.00000000 NaN NaN 0 0 0 0 0 0 0 0 0 0 -ValidationReport dbsnp eval none known 0 0 0 0 0 NaN 100.00000000 NaN NaN 0 0 0 0 0 0 0 0 0 0 -ValidationReport dbsnp eval none novel 0 0 0 0 0 NaN 100.00000000 NaN NaN 0 0 0 0 0 0 0 0 0 0 +##:GATKReport.v0.2 ValidationReport : Assess site accuracy and sensitivity of callset against follow-up validation assay +ValidationReport CompRod EvalRod JexlExpression Novelty nComp TP FP FN TN sensitivity specificity PPV FDR CompMonoEvalNoCall CompMonoEvalFiltered CompMonoEvalMono CompMonoEvalPoly CompPolyEvalNoCall CompPolyEvalFiltered CompPolyEvalMono CompPolyEvalPoly CompFiltered nDifferentAlleleSites +ValidationReport dbsnp input_0 none all 43 0 0 0 43 NaN 100.00000000 NaN NaN 42 0 1 0 0 0 0 0 0 0 +ValidationReport dbsnp input_0 none known 1 0 0 0 1 NaN 100.00000000 NaN NaN 0 0 1 0 0 0 0 0 0 0 +ValidationReport dbsnp input_0 none novel 42 0 0 0 42 NaN 100.00000000 NaN NaN 42 0 0 0 0 0 0 0 0 0 --- a/tools/gatk/analyze_covariates.xml Thu Oct 20 10:03:28 2011 -0400 +++ b/tools/gatk/analyze_covariates.xml Thu Oct 20 10:24:19 2011 -0400 @@ -1,7 +1,10 @@ -<tool id="gatk_analyze_covariates" name="Analyze Covariates" version="0.0.2"> +<tool id="gatk_analyze_covariates" name="Analyze Covariates" version="0.0.3"><description>- draw plots</description> -<command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "2" + <requirements> + <requirement type="package" version="1.2">gatk</requirement> + </requirements> + <command interpreter="python">gatk_wrapper.py + --max_jvm_heap_fraction "1" --stdout "${output_log}" --html_report_from_directory "${output_html}" "${output_html.files_path}" -p 'java --- a/tools/gatk/count_covariates.xml Thu Oct 20 10:03:28 2011 -0400 +++ b/tools/gatk/count_covariates.xml Thu Oct 20 10:24:19 2011 -0400 @@ -1,7 +1,10 @@ -<tool id="gatk_count_covariates" name="Count Covariates" version="0.0.2"> +<tool id="gatk_count_covariates" name="Count Covariates" version="0.0.3"><description>on BAM files</description> + <requirements> + <requirement type="package" version="1.2">gatk</requirement> + </requirements><command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "2" + --max_jvm_heap_fraction "1" --stdout "${output_log}" -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index @@ -35,7 +38,7 @@ #set $snp_dataset_provided = True #end if #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 - -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" + -d "--knownSites:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ): -p '--rodToIntervalTrackName "${rod_bind_name}"' #end if --- a/tools/gatk/indel_realigner.xml Thu Oct 20 10:03:28 2011 -0400 +++ b/tools/gatk/indel_realigner.xml Thu Oct 20 10:24:19 2011 -0400 @@ -1,7 +1,10 @@ -<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.2"> +<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.3"><description>- perform local realignment</description> + <requirements> + <requirement type="package" version="1.2">gatk</requirement> + </requirements><command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "2" + --max_jvm_heap_fraction "1" --stdout "${output_log}" -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index @@ -26,7 +29,7 @@ #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector #end if #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 - -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" + -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ): -p '--rodToIntervalTrackName "${rod_bind_name}"' #end if @@ -104,7 +107,7 @@ <when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /></param><param name="ref_file" type="select" label="Using reference genome"><options from_data_table="picard_indexes"> @@ -114,7 +117,11 @@ </when><when value="history"><param name="input_bam" type="data" format="bam" label="BAM file" /> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file"> + <options> + <filter type="data_meta" key="dbkey" ref="input_bam" /> + </options> + </param></when></conditional><param name="target_intervals" type="data" format="gatk_interval,bed,picard_interval_list" label="Restrict realignment to provided intervals" /> @@ -277,7 +284,7 @@ <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" /><param name="rod_bind_type_selector" value="snps" /><param name="rodToIntervalTrackName" /> - <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> + <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /><param name="lod_threshold" value="5.0" /><param name="knowns_only" /><param name="gatk_param_type_selector" value="basic" /> --- a/tools/gatk/realigner_target_creator.xml Thu Oct 20 10:03:28 2011 -0400 +++ b/tools/gatk/realigner_target_creator.xml Thu Oct 20 10:24:19 2011 -0400 @@ -1,7 +1,10 @@ -<tool id="gatk_realigner_target_creator" name="Realigner Target Creator" version="0.0.2"> +<tool id="gatk_realigner_target_creator" name="Realigner Target Creator" version="0.0.3"><description>for use in local realignment</description> + <requirements> + <requirement type="package" version="1.2">gatk</requirement> + </requirements><command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "2" + --max_jvm_heap_fraction "1" --stdout "${output_log}" -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index @@ -23,7 +26,7 @@ #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector #end if #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 - -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" + -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ): -p '--rodToIntervalTrackName "${rod_bind_name}"' #end if @@ -92,7 +95,7 @@ <when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /></param><param name="ref_file" type="select" label="Using reference genome"><options from_data_table="picard_indexes"> @@ -100,9 +103,13 @@ </options></param></when> - <when value="history"> + <when value="history"><param name="input_bam" type="data" format="bam" label="BAM file" /> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file"> + <options> + <filter type="data_meta" key="dbkey" ref="input_bam" /> + </options> + </param></when></conditional> @@ -115,20 +122,20 @@ <option value="custom">Custom</option></param><when value="dbsnp"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="snps"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="indels"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="custom"><param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when></conditional> @@ -254,9 +261,13 @@ <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" /><param name="rod_bind_type_selector" value="dbsnp" /><param name="rodToIntervalTrackName" /> - <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> + <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /><param name="gatk_param_type_selector" value="basic" /> - <param name="analysis_param_type_selector" value="basic" /> + <param name="analysis_param_type_selector" value="advanced" /> + <param name="windowSize" value="10" /> + <param name="mismatchFraction" value="0.15" /> + <param name="minReadsAtLocus" value="4" /> + <param name="maxIntervalSize" value="500" /><output name="output_interval" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" /><output name="output_log" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains" compare="contains"/></test> --- a/tools/gatk/table_recalibration.xml Thu Oct 20 10:03:28 2011 -0400 +++ b/tools/gatk/table_recalibration.xml Thu Oct 20 10:24:19 2011 -0400 @@ -1,7 +1,10 @@ -<tool id="gatk_table_recalibration" name="Table Recalibration" version="0.0.2"> +<tool id="gatk_table_recalibration" name="Table Recalibration" version="0.0.3"><description>on BAM files</description> + <requirements> + <requirement type="package" version="1.2">gatk</requirement> + </requirements><command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "2" + --max_jvm_heap_fraction "1" --stdout "${output_log}" -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index @@ -120,7 +123,7 @@ <when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /></param><param name="ref_file" type="select" label="Using reference genome"><options from_data_table="picard_indexes"> --- a/tools/gatk/unified_genotyper.xml Thu Oct 20 10:03:28 2011 -0400 +++ b/tools/gatk/unified_genotyper.xml Thu Oct 20 10:24:19 2011 -0400 @@ -1,9 +1,14 @@ -<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.2"> +<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.3"><description>SNP and indel caller</description> + <requirements> + <requirement type="package" version="1.2">gatk</requirement> + </requirements><command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "2" + --max_jvm_heap_fraction "1" --stdout "${output_log}" #for $i, $input_bam in enumerate( $reference_source.input_bams ): + ${dir( $input_bam.input_bam )} + ${dir( $input_bam.input_bam.dataset )} -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}" -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index #end for @@ -11,12 +16,14 @@ -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" --num_threads 4 ##hard coded, for now - -o "${output_vcf}" + --out "${output_vcf}" + --metrics_file "${output_metrics}" -et "NO_ET" ##ET no phone home ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" #end if + --genotype_likelihoods_model "${genotype_likelihoods_model}" --standard_min_confidence_threshold_for_calling "${standard_min_confidence_threshold_for_calling}" --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}" ' @@ -28,7 +35,7 @@ #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector #end if #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 - -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" + -d "--dbsnp:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ): -p '--rodToIntervalTrackName "${rod_bind_name}"' #end if @@ -81,13 +88,15 @@ ##start analysis specific options #if $analysis_param_type.analysis_param_type_selector == "advanced": -p ' - --genotype_likelihoods_model "${analysis_param_type.genotype_likelihoods_model}" --p_nonref_model "${analysis_param_type.p_nonref_model}" --heterozygosity "${analysis_param_type.heterozygosity}" --pcr_error_rate "${analysis_param_type.pcr_error_rate}" - --genotyping_mode "${analysis_param_type.genotyping_mode}" + --genotyping_mode "${analysis_param_type.genotyping_mode_type.genotyping_mode}" + #if str( $analysis_param_type.genotyping_mode_type.genotyping_mode ) == 'GENOTYPE_GIVEN_ALLELES': + --alleles "${analysis_param_type.genotyping_mode_type.input_alleles_rod}" + #end if --output_mode "${analysis_param_type.output_mode}" - ${analysis_param_type.noSLOD} + ${analysis_param_type.compute_SLOD} --min_base_quality_score "${analysis_param_type.min_base_quality_score}" --min_mapping_quality_score "${analysis_param_type.min_mapping_quality_score}" --max_deletion_fraction "${analysis_param_type.max_deletion_fraction}" @@ -120,7 +129,7 @@ <repeat name="input_bams" title="Sample BAM file" min="1"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /></param></repeat><param name="ref_file" type="select" label="Using reference genome"> @@ -146,25 +155,31 @@ <option value="custom">Custom</option></param><when value="dbsnp"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="snps"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="indels"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="custom"><param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when></conditional></repeat> + <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ"> + <option value="BOTH" selected="True">BOTH</option> + <option value="SNP">SNP</option> + <option value="INDEL">INDEL</option> + </param> + <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" /><param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" /> @@ -271,27 +286,30 @@ </when><when value="advanced"> - <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ"> - <option value="BOTH" selected="True">BOTH</option> - <option value="SNP">SNP</option> - <option value="INDEL">INDEL</option> - </param><param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ"><option value="EXACT" selected="True">EXACT</option><option value="GRID_SEARCH">GRID_SEARCH</option></param><param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" /><param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" /> - <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping"> - <option value="DISCOVERY" selected="True">DISCOVERY</option> - <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option> - </param> + <conditional name="genotyping_mode_type"> + <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping"> + <option value="DISCOVERY" selected="True">DISCOVERY</option> + <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option> + </param> + <when value="DISCOVERY"> +  + </when> + <when value="GENOTYPE_GIVEN_ALLELES"> + <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" /> + </when> + </conditional><param name="output_mode" type="select" label="Should we output confident genotypes (i.e. including ref calls) or just the variants?"><option value="EMIT_VARIANTS_ONLY" selected="True">EMIT_VARIANTS_ONLY</option><option value="EMIT_ALL_CONFIDENT_SITES">EMIT_ALL_CONFIDENT_SITES</option><option value="EMIT_ALL_SITES">EMIT_ALL_SITES</option></param> - <param name="noSLOD" type="boolean" truevalue="--noSLOD" falsevalue="" label="Do not calculate the SLOD" /> + <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" /><param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" /><param name="min_mapping_quality_score" type="integer" value="20" label="Minimum read mapping quality required to consider a read for calling" /><param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to < 0 or > 1" /> @@ -302,16 +320,35 @@ <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" /><param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" /><param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types"> - <option value="AlleleBalance">AlleleBalance</option> - <option value="BaseQualityRankSumTest">BaseQualityRankSumTest</option> - <option value="DepthOfCoverage">DepthOfCoverage</option> - <option value="HomopolymerRun">HomopolymerRun</option> - <option value="MappingQualityRankSumTest">MappingQualityRankSumTest</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="QualByDepth">QualByDepth</option> - <option value="RMSMappingQuality">RMSMappingQuality</option> - <option value="SpanningDeletions">SpanningDeletions</option> - <option value="HaplotypeScore">HaplotypeScore</option> + <option value="ChromosomeCounts"/> + <option value="IndelType"/> + <option value="SpanningDeletions"/> + <option value="HardyWeinberg"/> + <option value="NBaseCount"/> + <option value="MappingQualityZero"/> + <option value="AlleleBalance"/> + <option value="BaseCounts"/> + <option value="LowMQ"/> + <option value="InbreedingCoeff"/> + <option value="RMSMappingQuality"/> + <option value="HaplotypeScore"/> + <option value="TechnologyComposition"/> + <option value="SampleList"/> + <option value="FisherStrand"/> + <option value="HomopolymerRun"/> + <option value="DepthOfCoverage"/> + <option value="SnpEff"/> + <option value="MappingQualityZeroFraction"/> + <option value="GCContent"/> + <option value="MappingQualityRankSumTest"/> + <option value="ReadPosRankSumTest"/> + <option value="BaseQualityRankSumTest"/> + <option value="QualByDepth"/> + <option value="SBByDepth"/> + <option value="ReadDepthAndAllelicFractionBySample"/> + <option value="AlleleBalanceBySample"/> + <option value="DepthPerAlleleBySample"/> + <option value="MappingQualityZeroBySample"/></param><param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups"><option value="Standard">Standard</option> @@ -324,6 +361,7 @@ </inputs><outputs><data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" /> + <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" /><data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /></outputs> @@ -333,9 +371,9 @@ <param name="ref_file" value="phiX.fasta" ftype="fasta" /><param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /><param name="rod_bind_type_selector" value="dbsnp" /> - <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> + <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /><param name="rodToIntervalTrackName" /> - <param name="standard_min_confidence_threshold_for_calling" value="4" /> + <param name="standard_min_confidence_threshold_for_calling" value="0" /><param name="standard_min_confidence_threshold_for_emitting" value="4" /><param name="gatk_param_type_selector" value="basic" /><param name="analysis_param_type_selector" value="advanced" /> @@ -345,7 +383,7 @@ <param name="pcr_error_rate" value="0.0001" /><param name="genotyping_mode" value="DISCOVERY" /><param name="output_mode" value="EMIT_ALL_CONFIDENT_SITES" /> - <param name="noSLOD" /> + <param name="compute_SLOD" /><param name="min_base_quality_score" value="17" /><param name="min_mapping_quality_score" value="20" /><param name="max_deletion_fraction" value="-1" /> @@ -357,8 +395,9 @@ <param name="doContextDependentGapPenalties" /> - <output name="output_vcf" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="2"/> - <output name="output_log" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains" compare="contains"/> + <output name="output_vcf" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="4" /> + <output name="output_metrics" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics" /> + <output name="output_log" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains" compare="contains" /></test></tests><help> --- a/tools/gatk/variant_annotator.xml Thu Oct 20 10:03:28 2011 -0400 +++ b/tools/gatk/variant_annotator.xml Thu Oct 20 10:24:19 2011 -0400 @@ -1,13 +1,16 @@ -<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.1"> +<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.2"><description></description> + <requirements> + <requirement type="package" version="1.2">gatk</requirement> + </requirements><command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "2" + --max_jvm_heap_fraction "1" --stdout "${output_log}" #if str( $reference_source.input_bam ) != "None": -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index #end if - -d "-B:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" + -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "VariantAnnotator" @@ -35,26 +38,40 @@ ## #end if ## #end for ## #end for - #if str( $reference_source.input_variant_name ): - --sampleName "${reference_source.input_variant_name}" - #end if ${reference_source.input_variant_bti} ' - #set $rod_binding_names = dict() - #for $rod_binding in $rod_bind: - #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': - #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name - #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp': - #set $rod_bind_name = "comp" + str( $rod_binding.rod_bind_type.custom_rod_name ) - #else - #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector + #for $rod_binding in $comp_rod_bind: + -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}" + #if str( $rod_binding.comp_rodToIntervalTrackName ): + -p '--rodToIntervalTrackName "${rod_binding.comp_rod_name}"' #end if - #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 - -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" - #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ): - -p '--rodToIntervalTrackName "${rod_bind_name}"' + #end for + + #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp': + -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}" + #if str( $dbsnp_rod_bind_type.dbsnp_rodToIntervalTrackName ): + -p '--rodToIntervalTrackName "${dbsnp_rod_bind_type.dbsnp_rod_name}"' #end if + #end if + + + #for $rod_binding in $resource_rod_bind: + -d "--resource:${rod_binding.resource_rod_name},%(file_type)s" "${rod_binding.resource_input_rod}" "${rod_binding.resource_input_rod.ext}" "input_resource_${rod_binding.resource_rod_name}" + #if str( $rod_binding.resource_rodToIntervalTrackName ): + -p '--rodToIntervalTrackName "${rod_binding.resource_rod_name}"' + #end if + #end for + + #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': + -d "--snpEff:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}" + #if str( $snpEff_rod_bind_type.snpEff_rodToIntervalTrackName ): + -p '--rodToIntervalTrackName "${snpEff_rod_bind_type.snpEff_rod_name}"' + #end if + #end if + + #for $expression in $expressions: + -p '--expression "${expression.expression}"' #end for ##start standard gatk options @@ -101,16 +118,13 @@ #end if ##end standard gatk options - ##start analysis specific options - #if $analysis_param_type.analysis_param_type_selector == "advanced": - -p ' - #if $analysis_param_type.group.value: - #for $annotation_group in str( $analysis_param_type.group ).split( ',' ): - --group "${annotation_group}" - #end for - #end if + -p ' + #if $annotation_group.value: + #for $group in str( $annotation_group ).split( ',' ): + --group "${group}" + #end for + #end if ' - #end if </command><inputs><conditional name="reference_source"> @@ -119,12 +133,11 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_variant" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" /> - <param name="input_variant_name" type="text" value="" label="Variant Name" help="Not needed for VCF inputs."/> + <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /><param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." /><param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." ><validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /></param><param name="ref_file" type="select" label="Using reference genome"><options from_data_table="picard_indexes"> @@ -133,8 +146,7 @@ </param></when><when value="history"> - <param name="input_variant" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" /> - <param name="input_variant_name" type="text" value="" label="Variant Name" help="Not needed for VCF inputs."/> + <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /><param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." /><param name="input_bam" type="data" format="bam" label="BAM file" optional="True" /><param name="ref_file" type="data" format="fasta" label="Using reference file" /> @@ -151,90 +163,83 @@ <when value="choose"><param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" > - <option value="AlleleBalance" /> - <option value="BaseQualityRankSumTest" /> - <option value="DepthOfCoverage" /> - <option value="HomopolymerRun" /> - <option value="MappingQualityRankSumTest" /> - <option value="MappingQualityZero" /> - <option value="QualByDepth" /> - <option value="RMSMappingQuality" /> - <option value="SpanningDeletions" /> - <option value="HaplotypeScore" /> -  - <option value="ChromosomeCounts" /> - <option value="IndelType" /> - <option value="HardyWeinberg" /> - <option value="BaseCounts" /> - <option value="LowMQ" /> - <option value="FisherStrand" /> - <option value="GenomicAnnotation" /> - <option value="GCContent" /> - <option value="ReadPosRankSumTest" /> - <option value="SBByDepth" /> - <option value="ReadDepthAndAllelicFractionBySample" /> - <option value="AlleleBalanceBySample" /> - <option value="DepthPerAlleleBySample" /> - <option value="MappingQualityZeroBySample" /> - <option value="NBaseCount" /> - <option value="GLstats" /> - <option value="SampleList" /> - <option value="MappingQualityZeroFraction" /> + <option value="ChromosomeCounts"/> + <option value="IndelType"/> + <option value="SpanningDeletions"/> + <option value="HardyWeinberg"/> + <option value="NBaseCount"/> + <option value="MappingQualityZero"/> + <option value="AlleleBalance"/> + <option value="BaseCounts"/> + <option value="LowMQ"/> + <option value="InbreedingCoeff"/> + <option value="RMSMappingQuality"/> + <option value="HaplotypeScore"/> + <option value="TechnologyComposition"/> + <option value="SampleList"/> + <option value="FisherStrand"/> + <option value="HomopolymerRun"/> + <option value="DepthOfCoverage"/> + <option value="SnpEff"/> + <option value="MappingQualityZeroFraction"/> + <option value="GCContent"/> + <option value="MappingQualityRankSumTest"/> + <option value="ReadPosRankSumTest"/> + <option value="BaseQualityRankSumTest"/> + <option value="QualByDepth"/> + <option value="SBByDepth"/> + <option value="ReadDepthAndAllelicFractionBySample"/> + <option value="AlleleBalanceBySample"/> + <option value="DepthPerAlleleBySample"/> + <option value="MappingQualityZeroBySample"/></param></when></conditional> -  - <repeat name="rod_bind" title="Binding for reference-ordered data"> - <conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="variant">Variants</option> - <option value="dbsnp">dbSNP</option> - <option value="snps">SNPs</option> - <option value="comp" selected="True">Comps</option> - <option value="indels">INDELs</option> - <option value="mask">Mask</option> - <option value="custom">Custom</option> - </param> - <when value="variant"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="Variant ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="comp"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp" label="ROD file" /> - <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="dbsnp"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="snps"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="indels"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="mask"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="custom"> - <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - </conditional> + + <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data"> + <param name="comp_input_rod" type="data" format="vcf" label="ROD file" /> + <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/> + <param name="comp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> + </repeat> + + <conditional name="dbsnp_rod_bind_type"> + <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file"> + <option value="set_dbsnp" selected="True">Set dbSNP</option> + <option value="exclude_dbsnp">Don't set dbSNP</option> + </param> + <when value="exclude_dbsnp"> +  + </when> + <when value="set_dbsnp"> + <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" /> + <param name="dbsnp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> + <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/> + </when> + </conditional> + + <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data"> + <param name="resource_input_rod" type="data" format="vcf" label="ROD file" /> + <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/> + <param name="resource_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> + </repeat> + + <conditional name="snpEff_rod_bind_type"> + <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file"> + <option value="set_snpEff">Set snpEff</option> + <option value="exclude_snpEff" selected="True">Don't set snpEff</option> + </param> + <when value="exclude_snpEff"> +  + </when> + <when value="set_snpEff"> + <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" /> + <param name="snpEff_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> + <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/> + </when> + </conditional> + + <repeat name="expressions" title="Expression"> + <param name="expression" type="text" value="" label="Expression"/></repeat><conditional name="gatk_param_type"> @@ -328,23 +333,14 @@ </when></conditional> - <conditional name="analysis_param_type"> - <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> - <option value="basic" selected="True">Basic</option> - <option value="advanced">Advanced</option> - </param> - <when value="basic"> -  - </when> - <when value="advanced"> - <param name="group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls"> - <option value="Standard">Standard</option> - <option value="Experimental">Experimental</option> - <option value="WorkInProgress">WorkInProgress</option> - </param> - - </when> - </conditional> + <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls"> + <option value="RodRequiringAnnotation">RodRequiringAnnotation</option> + <option value="Standard">Standard</option> + <option value="Experimental">Experimental</option> + <option value="WorkInProgress">WorkInProgress</option> + <option value="RankSumTest">RankSumTest</option> + </param> + </inputs><outputs><data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> @@ -356,17 +352,20 @@ <param name="ref_file" value="phiX.fasta" ftype="fasta" /><param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /><param name="input_variant" value="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" ftype="vcf" /> + <param name="input_variant_bti" /><param name="annotations_type_selector" value="choose" /><param name="annotations" value="AlleleBalance,BaseQualityRankSumTest,DepthOfCoverage,HomopolymerRun,MappingQualityRankSumTest,MappingQualityZero,QualByDepth,RMSMappingQuality,SpanningDeletions,HaplotypeScore" /> -  - <param name="rod_bind_type_selector" value="dbsnp" /> - <param name="rodToIntervalTrackName" /> - <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> + <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" /> + <param name="dbsnp_rodToIntervalTrackName" /> + <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> + <param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" /><param name="gatk_param_type_selector" value="basic" /> - <param name="analysis_param_type_selector" value="basic" /> - <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="2" /> + <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" /><output name="output_log" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.log.contains" compare="contains" /> + <param name="comp_rod_bind" value="0" /> + <param name="resource_rod_bind" value="0" /> + <param name="expressions" value="0" /> + </test></tests><help> --- a/tools/gatk/variant_apply_recalibration.xml Thu Oct 20 10:03:28 2011 -0400 +++ b/tools/gatk/variant_apply_recalibration.xml Thu Oct 20 10:24:19 2011 -0400 @@ -1,9 +1,14 @@ -<tool id="gatk_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.1"> +<tool id="gatk_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.2"><description></description> + <requirements> + <requirement type="package" version="1.2">gatk</requirement> + </requirements><command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "2" + --max_jvm_heap_fraction "1" --stdout "${output_log}" - -d "-B:input,%(file_type)s" "${reference_source.input_variants}" "${reference_source.input_variants.ext}" "input_variants" + #for $var_count, $variant in enumerate( $reference_source.variants ): + -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}" + #end for -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "ApplyRecalibration" @@ -62,21 +67,18 @@ ##end standard gatk options ##start analysis specific options + -p ' + --mode "${mode}" - #if $analysis_param_type.analysis_param_type_selector == "advanced": - -p ' - --mode "${analysis_param_type.mode}" - - #for $ignore_filter in $analysis_param_type.ignore_filters: - #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector ) - #if $ignore_filter_name == "custom": - #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name ) - #end if - --ignore_filter "${ignore_filter_name}" - #end for - ' - #end if - -p '--ts_filter_level "${ts_filter_level}"' + #for $ignore_filter in $ignore_filters: + #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector ) + #if $ignore_filter_name == "custom": + #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name ) + #end if + --ignore_filter "${ignore_filter_name}" + #end for + --ts_filter_level "${ts_filter_level}" + ' </command><inputs><conditional name="reference_source"> @@ -85,17 +87,21 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_variants" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" /> + <repeat name="variants" title="Variant" min="1"> + <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" /> + </repeat><param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" /><param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" /><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> - <filter type="data_meta" key="dbkey" ref="input_variants" column="dbkey"/> - </options> + </param></when><when value="history"> - <param name="input_variants" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" /> + <repeat name="variants" title="Variant" min="1"> + <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" /> + </repeat><param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" /><param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" /><param name="ref_file" type="data" format="fasta" label="Using reference file" /> @@ -193,15 +199,6 @@ </when></conditional> - <conditional name="analysis_param_type"> - <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> - <option value="basic" selected="True">Basic</option> - <option value="advanced">Advanced</option> - </param> - <when value="basic"> -  - </when> - <when value="advanced"><param name="mode" type="select" label="Recalibration mode"><option value="SNP" selected="True">SNP</option><option value="INDEL">INDEL</option> @@ -219,8 +216,6 @@ </when></conditional></repeat> - </when> - </conditional><param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0"/></inputs><outputs> --- a/tools/gatk/variant_combine.xml Thu Oct 20 10:03:28 2011 -0400 +++ b/tools/gatk/variant_combine.xml Thu Oct 20 10:24:19 2011 -0400 @@ -1,12 +1,15 @@ -<tool id="gatk_variant_combine" name="Combine Variants" version="0.0.1"> +<tool id="gatk_variant_combine" name="Combine Variants" version="0.0.2"><description></description> + <requirements> + <requirement type="package" version="1.2">gatk</requirement> + </requirements><command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "2" + --max_jvm_heap_fraction "1" --stdout "${output_log}" #set $priority_order = [] #for $input_variant in $reference_source.input_variants: - -d "-B:${input_variant.input_variant_name},%(file_type)s" "${input_variant.input_variant}" "${input_variant.input_variant.ext}" "input_variant_${input_variant.input_variant_name}" + -d "--variant:${input_variant.input_variant_name},%(file_type)s" "${input_variant.input_variant}" "${input_variant.input_variant.ext}" "input_variant_${input_variant.input_variant_name}" #set $input_variant_name = str( $input_variant.input_variant_name ) #assert $input_variant_name not in $priority_order, "Variant Names must be unique" ##this should be handled by a validator #silent $priority_order.append( $input_variant_name ) @@ -21,6 +24,7 @@ #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" #end if + --genotypemergeoption "${genotype_merge_option}" --rod_priority_list "${ ','.join( $priority_order ) }" ' @@ -72,7 +76,6 @@ ##start analysis specific options #if $analysis_param_type.analysis_param_type_selector == "advanced": -p ' - --genotypemergeoption "${analysis_param_type.genotype_merge_option}" --filteredrecordsmergetype "${analysis_param_type.filtered_records_merge_type}" ${analysis_param_type.print_complex_merges} ${analysis_param_type.filtered_are_uncalled} @@ -95,7 +98,7 @@ <option value="history">History</option></param><when value="cached"> - <repeat min="1" name="input_variants" title="Variants to Merge"> + <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here."><param name="input_variant" type="data" format="vcf" label="Input variant file" /><param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique"><validator type="length" min="1" message="You must provide a unique name for this set of variants" /> @@ -108,7 +111,7 @@ </param></when><when value="history"> - <repeat min="1" name="input_variants" title="Variants to Merge"> + <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here."><param name="input_variant" type="data" format="vcf" label="Input variant file" /><param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique"><validator type="length" min="1" message="You must provide a unique name for this set of variants" /> @@ -117,7 +120,14 @@ <param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> - + + <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" > + <option value="UNIQUIFY" /> + <option value="PRIORITIZE" selected="true"/> + <option value="UNSORTED" /> + <option value="REQUIRE_UNIQUE" /> + </param> + <conditional name="gatk_param_type"><param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"><option value="basic" selected="True">Basic</option> @@ -219,16 +229,10 @@ </when><when value="advanced"> - <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" > - <option value="UNIQUIFY" /> - <option value="PRIORITIZE" selected="true"/> - <option value="UNSORTED" /> - <option value="REQUIRE_UNIQUE" /> - </param><param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields? " ><option value="KEEP_IF_ANY_UNFILTERED" selected="true"/><option value="KEEP_IF_ALL_UNFILTERED" /> - </param> + </param><param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" /><param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" /> @@ -253,9 +257,10 @@ <param name="ref_file" value="phiX.fasta" ftype="fasta" /><param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /><param name="input_variant_name" value="from_variant_annotator" /> + <param name="genotype_merge_option" value="PRIORITIZE" /><param name="gatk_param_type_selector" value="basic" /><param name="analysis_param_type_selector" value="basic" /> - <output name="output_variants" file="gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf" lines_diff="2" /> + <output name="output_variants" file="gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf" lines_diff="4" /><output name="output_log" file="gatk/gatk_variant_combine/gatk_variant_combine_out_1.log.contains" compare="contains" /></test></tests> --- a/tools/gatk/variant_eval.xml Thu Oct 20 10:03:28 2011 -0400 +++ b/tools/gatk/variant_eval.xml Thu Oct 20 10:24:19 2011 -0400 @@ -1,9 +1,14 @@ -<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.1"> +<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.2"><description></description> + <requirements> + <requirement type="package" version="1.2">gatk</requirement> + </requirements><command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "2" + --max_jvm_heap_fraction "1" --stdout "${output_log}" - -d "-B:eval,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" + #for $var_count, $variant in enumerate( $reference_source.variants ): + -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}" + #end for -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "VariantEval" @@ -16,23 +21,25 @@ #end if ' - #set $rod_binding_names = dict() - #for $rod_binding in $rod_bind: - #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': - #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name - #else - #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector + #for $rod_binding in $comp_rod_bind: + -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}" + #if str( $rod_binding.comp_rodToIntervalTrackName ): + -p '--rodToIntervalTrackName "${rod_binding.comp_rod_name}"' #end if - #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 - -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" - #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ): - -p '--rodToIntervalTrackName "${rod_bind_name}"' + #if str( $rod_binding.comp_known_names ): + -p '--known_names "${rod_binding.comp_rod_name}"' #end if - #if str( $rod_binding.rod_bind_type.known_names ): - -p '--known_names "${rod_bind_name}"' + #end for + + #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp': + -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}" + #if str( $dbsnp_rod_bind_type.dbsnp_rodToIntervalTrackName ): + -p '--rodToIntervalTrackName "${dbsnp_rod_bind_type.dbsnp_rod_name}"' + #if str( $dbsnp_rod_bind_type.dbsnp_known_names ): + -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"' + #end if #end if - - #end for + #end if ##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": @@ -138,51 +145,46 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_variant" type="data" format="vcf" label="Input variant file" /> + <repeat name="variants" title="Variant" min="1"> + <param name="input_variant" type="data" format="vcf" label="Input variant file" /> + </repeat><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + </param></when><when value="history"> - <param name="input_variant" type="data" format="vcf" label="Input variant file" /> + <repeat name="variants" title="Variant" min="1"> + <param name="input_variant" type="data" format="vcf" label="Input variant file" /> + </repeat><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> - <repeat name="rod_bind" title="Binding for reference-ordered data"> - <conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> - <when value="dbsnp"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - <param name="known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Treat ROD as known when splitting eval rods into known and novel subsets" /> - </when> - <when value="snps"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - <param name="known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Treat ROD as known when splitting eval rods into known and novel subsets" /> - </when> - <when value="indels"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - <param name="known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Treat ROD as known when splitting eval rods into known and novel subsets" /> - </when> - <when value="custom"> - <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - <param name="known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Treat ROD as known when splitting eval rods into known and novel subsets" /> - </when> - </conditional> + <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data"> + <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" /> + <param name="comp_rod_name" type="text" value="Unnamed" label="Comparison ROD Name"/> + <param name="comp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use Comparison ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> + <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" /></repeat> + <conditional name="dbsnp_rod_bind_type"> + <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file"> + <option value="set_dbsnp" selected="True">Set dbSNP</option> + <option value="exclude_dbsnp">Don't set dbSNP</option> + </param> + <when value="exclude_dbsnp"> +  + </when> + <when value="set_dbsnp"> + <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" /> + <param name="dbsnp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use dbSNP ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> + <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="dbSNP ROD Name"/> + <param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" /> + </when> + </conditional> + <conditional name="gatk_param_type"><param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"><option value="basic" selected="True">Basic</option> @@ -293,7 +295,7 @@ <param name="sample" value="" type="text" label="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context"/></repeat> - <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" > + <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the w track(s)" ><option value="AlleleFrequency" /><option value="AlleleCount" /> @@ -356,10 +358,11 @@ <param name="reference_source_selector" value="history" /><param name="ref_file" value="phiX.fasta" ftype="fasta" /><param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> - <param name="rod_bind_type_selector" value="dbsnp" /> - <param name="rodToIntervalTrackName" /> - <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> - <param name="known_names" value="True"/> + <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" /> + <param name="dbsnp_rodToIntervalTrackName" /> + <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> + <param name="dbsnp_known_names" value="True"/> + <param name="comp_rod_bind" value="0" /><param name="gatk_param_type_selector" value="basic" /><param name="analysis_param_type_selector" value="basic" /><output name="output_table" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular" /> --- a/tools/gatk/variant_filtration.xml Thu Oct 20 10:03:28 2011 -0400 +++ b/tools/gatk/variant_filtration.xml Thu Oct 20 10:24:19 2011 -0400 @@ -1,9 +1,12 @@ -<tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.1"> +<tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.2"><description>on VCF files</description> + <requirements> + <requirement type="package" version="1.2">gatk</requirement> + </requirements><command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "2" + --max_jvm_heap_fraction "1" --stdout "${output_log}" - -d "-B:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" + -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "VariantFiltration" @@ -20,22 +23,17 @@ #end for ' - #set $rod_binding_names = dict() - #for $rod_binding in $rod_bind: - #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': - #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name - #else - #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector + + #if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask': + -d "--mask:${mask_rod_bind_type.mask_rod_name},%(file_type)s" "${mask_rod_bind_type.input_mask_rod}" "${mask_rod_bind_type.input_mask_rod.ext}" "input_mask_${mask_rod_bind_type.mask_rod_name}" + -p ' + --maskExtension "${mask_rod_bind_type.mask_extension}" + --maskName "${mask_rod_bind_type.mask_rod_name}" + ' + #if str( $mask_rod_bind_type.mask_rodToIntervalTrackName ): + -p '--rodToIntervalTrackName "${mask_rod_bind_type.mask_rod_name}"' #end if - #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 - -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" - #if $rod_binding.rod_bind_type.rod_bind_type_selector == "mask": - --maskName "${rod_binding.rod_bind_type.mask_rod_name}" - #end if - #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ): - -p '--rodToIntervalTrackName "${rod_bind_name}"' - #end if - #end for + #end if ##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": @@ -97,7 +95,7 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_variant" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" /> + <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /><param name="ref_file" type="select" label="Using reference genome"><options from_data_table="picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> @@ -105,7 +103,7 @@ </param></when><when value="history"> - <param name="input_variant" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" /> + <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> @@ -125,39 +123,24 @@ <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" /></repeat> - <repeat name="rod_bind" title="Binding for reference-ordered data"> - <conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="mask" selected="True">Mask</option> - <option value="custom">Custom</option> - </param> - <when value="dbsnp"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="snps"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="indels"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="custom"> - <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="mask"> - <param name="mask_rod_name" type="text" value="Unknown" label="Mask Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - </conditional> - </repeat> + + + <conditional name="mask_rod_bind_type"> + <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file"> + <option value="set_mask" selected="True">Set maskP</option> + <option value="exclude_mask">Don't set mask</option> + </param> + <when value="exclude_mask"> +  + </when> + <when value="set_mask"> + <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" /> + <param name="mask_rod_name" type="text" value="Mask" label="Mask Name"/> + <param name="mask_extension" type="integer" value="0" label="Mask Extension"/> + <param name="mask_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use Mask ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> + </when> + </conditional> + <conditional name="gatk_param_type"><param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"> @@ -279,9 +262,11 @@ <param name="filter_expression" value="MQ < 37.74 || MQ0 > 50" /><param name="filter_name" value="Galaxy_filter" /><param name="is_genotype_filter" /> - <param name="rod_bind_type_selector" value="dbsnp" /> - <param name="rodToIntervalTrackName" /> - <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> + <param name="mask_rod_bind_type_selector" value="set_mask" /> + <param name="mask_rodToIntervalTrackName" /> + <param name="input_mask_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> + <param name="mask_rod_name" value="." /> + <param name="mask_extension" value="0" /><param name="gatk_param_type_selector" value="basic" /><param name="cluster_snp_type_selector" value="do_not_cluster_snp" /><param name="missing_values_in_expressions_should_evaluate_as_failing" /> --- a/tools/gatk/variant_recalibrator.xml Thu Oct 20 10:03:28 2011 -0400 +++ b/tools/gatk/variant_recalibrator.xml Thu Oct 20 10:24:19 2011 -0400 @@ -1,9 +1,14 @@ -<tool id="gatk_variant_recalibrator" name="Variant Recalibrator" version="0.0.1"> +<tool id="gatk_variant_recalibrator" name="Variant Recalibrator" version="0.0.2"><description></description> + <requirements> + <requirement type="package" version="1.2">gatk</requirement> + </requirements><command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "2" + --max_jvm_heap_fraction "1" --stdout "${output_log}" - -d "-B:input,%(file_type)s" "${reference_source.input_variants}" "${reference_source.input_variants.ext}" "input_variants" + #for $var_count, $variant in enumerate( $reference_source.variants ): + -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}" + #end for -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "VariantRecalibrator" @@ -29,9 +34,9 @@ #end if #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known": - -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" + -d "--resource:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" #else: - -d "-B:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" + -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" #end if #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ): -p '--rodToIntervalTrackName "${rod_bind_name}"' @@ -89,11 +94,11 @@ --use_annotation "${annotation}" #end for #end if + --mode "${mode}" ' #if $analysis_param_type.analysis_param_type_selector == "advanced": -p ' - --mode "${analysis_param_type.mode}" --maxGaussians "${analysis_param_type.max_gaussians}" --maxIterations "${analysis_param_type.max_iterations}" --numKMeans "${analysis_param_type.num_k_means}" @@ -102,8 +107,11 @@ --shrinkage "${analysis_param_type.shrinkage}" --dirichlet "${analysis_param_type.dirichlet}" --priorCounts "${analysis_param_type.prior_counts}" - --percentBadVariants "${analysis_param_type.percent_bad_variants}" - --minNumBadVariants "${analysis_param_type.min_num_bad_variants}" + #if str( $analysis_param_type.bad_variant_selector.bad_variant_selector_type ) == 'percent': + --percentBadVariants "${analysis_param_type.bad_variant_selector.percent_bad_variants}" + #else: + --minNumBadVariants "${analysis_param_type.bad_variant_selector.min_num_bad_variants}" + #end if --target_titv "${analysis_param_type.target_titv}" #for $tranche in [ $tranche.strip() for $tranche in str( $analysis_param_type.ts_tranche ).split( ',' ) if $tranche.strip() ] --TStranche "${tranche}" @@ -131,15 +139,19 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_variants" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" /> + <repeat name="variants" title="Variant" min="1"> + <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /> + </repeat><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> - <filter type="data_meta" key="dbkey" ref="input_variants" column="dbkey"/> - </options> + </param></when><when value="history"> - <param name="input_variants" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" /> + <repeat name="variants" title="Variant" min="1"> + <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /> + </repeat><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> @@ -323,37 +335,42 @@ <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations"> - <option value="AlleleBalance" /> - <option value="BaseQualityRankSumTest" /> - <option value="DepthOfCoverage" /> - <option value="HomopolymerRun" /> - <option value="MappingQualityRankSumTest" /> - <option value="MappingQualityZero" /> - <option value="QualByDepth" /> - <option value="RMSMappingQuality" /> - <option value="SpanningDeletions" /> - <option value="HaplotypeScore" /> -  - <option value="ChromosomeCounts" /> - <option value="IndelType" /> - <option value="HardyWeinberg" /> - <option value="BaseCounts" /> - <option value="LowMQ" /> - <option value="FisherStrand" /> - <option value="GenomicAnnotation" /> - <option value="GCContent" /> - <option value="ReadPosRankSumTest" /> - <option value="SBByDepth" /> - <option value="ReadDepthAndAllelicFractionBySample" /> - <option value="AlleleBalanceBySample" /> - <option value="DepthPerAlleleBySample" /> - <option value="MappingQualityZeroBySample" /> - <option value="NBaseCount" /> - <option value="GLstats" /> - <option value="SampleList" /> - <option value="MappingQualityZeroFraction" /> + <option value="ChromosomeCounts"/> + <option value="IndelType"/> + <option value="SpanningDeletions"/> + <option value="HardyWeinberg"/> + <option value="NBaseCount"/> + <option value="MappingQualityZero"/> + <option value="AlleleBalance"/> + <option value="BaseCounts"/> + <option value="LowMQ"/> + <option value="InbreedingCoeff"/> + <option value="RMSMappingQuality"/> + <option value="HaplotypeScore"/> + <option value="TechnologyComposition"/> + <option value="SampleList"/> + <option value="FisherStrand"/> + <option value="HomopolymerRun"/> + <option value="DepthOfCoverage"/> + <option value="SnpEff"/> + <option value="MappingQualityZeroFraction"/> + <option value="GCContent"/> + <option value="MappingQualityRankSumTest"/> + <option value="ReadPosRankSumTest"/> + <option value="BaseQualityRankSumTest"/> + <option value="QualByDepth"/> + <option value="SBByDepth"/> + <option value="ReadDepthAndAllelicFractionBySample"/> + <option value="AlleleBalanceBySample"/> + <option value="DepthPerAlleleBySample"/> + <option value="MappingQualityZeroBySample"/></param> + <param name="mode" type="select" label="Recalibration mode"> + <option value="SNP" selected="True">SNP</option> + <option value="INDEL">INDEL</option> + <option value="BOTH">BOTH</option> + </param><conditional name="gatk_param_type"><param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"> @@ -455,11 +472,6 @@ </when><when value="advanced"> - <param name="mode" type="select" label="Recalibration mode"> - <option value="SNP" selected="True">SNP</option> - <option value="INDEL">INDEL</option> - <option value="BOTH">BOTH</option> - </param><param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10"/><param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="100"/><param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="30"/> @@ -468,8 +480,18 @@ <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0"/><param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001"/><param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0"/> - <param name="percent_bad_variants" type="float" label="percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent." value="0.03"/> - <param name="min_num_bad_variants" type="integer" label="minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary" value="2000"/> + <conditional name="bad_variant_selector"> + <param name="bad_variant_selector_type" type="select" label="Basic or Advanced Analysis options"> + <option value="percent" selected="True">Percent</option> + <option value="min_num">Number</option> + </param> + <when value="percent"> + <param name="percent_bad_variants" type="float" label="percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent." value="0.03"/> + </when> + <when value="min_num"> + <param name="min_num_bad_variants" type="integer" label="minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary" value="2000"/> + </when> + </conditional><param name="target_titv" type="float" label="expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!" value="2.15"/><param name="ts_tranche" type="text" label="levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)" value="100.0, 99.9, 99.0, 90.0"/><repeat name="ignore_filters" title="Ignore Filter"> --- a/tools/gatk/variants_validate.xml Thu Oct 20 10:03:28 2011 -0400 +++ b/tools/gatk/variants_validate.xml Thu Oct 20 10:24:19 2011 -0400 @@ -1,9 +1,12 @@ -<tool id="gatk_validate_variants" name="Validate Variants" version="0.0.1"> +<tool id="gatk_validate_variants" name="Validate Variants" version="0.0.2"><description></description> + <requirements> + <requirement type="package" version="1.2">gatk</requirement> + </requirements><command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "2" + --max_jvm_heap_fraction "1" --stdout "${output_log}" - -d "-B:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" + -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "ValidateVariants" @@ -17,19 +20,12 @@ ${do_not_validate_filtered_records} ' - #set $rod_binding_names = dict() - #for $rod_binding in $rod_bind: - #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': - #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name - #else - #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector + #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp': + -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}" + #if str( $dbsnp_rod_bind_type.dbsnp_rodToIntervalTrackName ): + -p '--rodToIntervalTrackName "${dbsnp_rod_bind_type.dbsnp_rod_name}"' #end if - #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 - -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" - #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ): - -p '--rodToIntervalTrackName "${rod_bind_name}"' - #end if - #end for + #end if ##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": @@ -96,38 +92,21 @@ </when></conditional> - <repeat name="rod_bind" title="Binding for reference-ordered data"> - <conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> -  - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> -  - </param> - <when value="variant"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="dbsnp"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="snps"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="indels"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="custom"> - <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - </conditional> - </repeat> + <conditional name="dbsnp_rod_bind_type"> + <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file"> + <option value="set_dbsnp" selected="True">Set dbSNP</option> + <option value="exclude_dbsnp">Don't set dbSNP</option> + </param> + <when value="exclude_dbsnp"> +  + </when> + <when value="set_dbsnp"> + <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" /> + <param name="dbsnp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> + <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/> + </when> + </conditional> + <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen. "/><param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed. "/> @@ -231,9 +210,9 @@ <param name="reference_source_selector" value="history" /><param name="ref_file" value="phiX.fasta" ftype="fasta" /><param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> - <param name="rod_bind_type_selector" value="dbsnp" /> - <param name="rodToIntervalTrackName" /> - <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> + <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" /> + <param name="dbsnp_rodToIntervalTrackName" /> + <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /><param name="warn_on_errors" value="True"/><param name="do_not_validate_filtered_records" /><param name="gatk_param_type_selector" value="basic" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Allow toolbox tests to test 0 instances of a repeat.
by Bitbucket 20 Oct '11

20 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2ed732bca4f6/ changeset: 2ed732bca4f6 user: dan date: 2011-10-20 16:03:28 summary: Allow toolbox tests to test 0 instances of a repeat. affected #: 1 file (-1 bytes) --- a/test/functional/test_toolbox.py Thu Oct 20 09:37:02 2011 -0400 +++ b/test/functional/test_toolbox.py Thu Oct 20 10:03:28 2011 -0400 @@ -59,7 +59,7 @@ # See if we have a grouping.Repeat element repeat_name = None for input_name, input_value in testdef.tool.inputs_by_page[0].items(): - if isinstance( input_value, grouping.Repeat ): + if isinstance( input_value, grouping.Repeat ) and all_inputs.get( input_name, 1 ) not in [ 0, "0" ]: #default behavior is to test 1 repeat, for backwards compatibility repeat_name = input_name break #check if we need to verify number of outputs created dynamically by 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.

1 0

commit/galaxy-central: dan: Allow specifying a help attribute for repeat parameter grouping.
by Bitbucket 20 Oct '11

20 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/93e463402081/ changeset: 93e463402081 user: dan date: 2011-10-20 15:37:02 summary: Allow specifying a help attribute for repeat parameter grouping. affected #: 3 files (-1 bytes) --- a/lib/galaxy/tools/__init__.py Wed Oct 19 16:47:25 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Thu Oct 20 09:37:02 2011 -0400 @@ -814,7 +814,8 @@ if elem.tag == "repeat": group = Repeat() group.name = elem.get( "name" ) - group.title = elem.get( "title" ) + group.title = elem.get( "title" ) + group.help = elem.get( "help", None ) group.inputs = self.parse_input_elem( elem, enctypes, context ) group.default = int( elem.get( "default", 0 ) ) group.min = int( elem.get( "min", 0 ) ) --- a/lib/galaxy/tools/parameters/grouping.py Wed Oct 19 16:47:25 2011 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Thu Oct 20 09:37:02 2011 -0400 @@ -45,6 +45,7 @@ Group.__init__( self ) self.title = None self.inputs = None + self.help = None self.default = 0 self.min = None self.max = None --- a/templates/tool_form.mako Wed Oct 19 16:47:25 2011 -0400 +++ b/templates/tool_form.mako Thu Oct 20 09:37:02 2011 -0400 @@ -120,7 +120,13 @@ <% pass %> %elif input.type == "repeat": <div class="repeat-group"> - <div class="form-title-row"><strong>${input.title_plural}</strong></div> + <div class="form-title-row"><strong>${input.title_plural}</strong> + %if input.help: + <div class="toolParamHelp" style="clear: both;"> + ${input.help} + </div> + %endif + </div><% repeat_state = tool_state[input.name] %> %for i in range( len( repeat_state ) ): <div class="repeat-group-item"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Enhanced Galaxy instance <=> Galaxy tool shed integration:
by Bitbucket 19 Oct '11

19 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6c8695c2a949/ changeset: 6c8695c2a949 user: greg date: 2011-10-19 22:47:25 summary: Enhanced Galaxy instance <=> Galaxy tool shed integration: 1. All accessible tool sheds are now displayed in a mako template in teh Admin view rather than the left tool panel 2. From Galaxy you can now search for tools by id, name, version in a selected Galaxy tool shed. 3. Tools found using the above search can now be installed in the local Galaxy instance. affected #: 18 files (-1 bytes) --- a/lib/galaxy/web/controllers/admin.py Wed Oct 19 10:14:51 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Wed Oct 19 16:47:25 2011 -0400 @@ -688,20 +688,28 @@ return self.repository_list_grid( trans, **kwd ) @web.expose @web.require_admin + def browse_tool_sheds( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + return trans.fill_template( '/webapps/galaxy/admin/tool_sheds.mako', + webapp='galaxy', + message=message, + status='error' ) + @web.expose + @web.require_admin + def find_tools_in_tool_shed( self, trans, **kwd ): + tool_shed_url = kwd[ 'tool_shed_url' ] + galaxy_url = trans.request.host + url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) + return trans.response.send_redirect( url ) + @web.expose + @web.require_admin def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = trans.request.host - url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url ) + url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) - def _decode( self, value ): - # Extract and verify hash - a, b = value.split( ":" ) - value = binascii.unhexlify( b ) - test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) - assert a == test - # Restore from string - values = json_fix( simplejson.loads( value ) ) - return values @web.expose @web.require_admin def install_tool_shed_repository( self, trans, **kwd ): @@ -728,7 +736,7 @@ section_key = 'section_%s' % kwd[ 'tool_panel_section' ] tool_section = trans.app.toolbox.tool_panel[ section_key ] # Decode the encoded repo_info_dict param value. - repo_info_dict = self._decode( repo_info_dict ) + repo_info_dict = self.__decode( repo_info_dict ) # Clone the repository to the configured location. current_working_dir = os.getcwd() for name, repo_info_tuple in repo_info_dict.items(): @@ -846,7 +854,7 @@ galaxy_url = trans.request.host # Send a request to the relevant tool shed to see if there are any updates. # TODO: support https in the following url. - url = 'http://%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=community' % \ + url = 'http://%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ ( repository.tool_shed, galaxy_url, repository.name, repository.owner, repository.changeset_revision ) return trans.response.send_redirect( url ) @web.expose @@ -1149,6 +1157,15 @@ section_str += ' </tool>\n' section_str += ' </section>\n' return section_str + def __decode( self, value ): + # Extract and verify hash + a, b = value.split( ":" ) + value = binascii.unhexlify( b ) + test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) + assert a == test + # Restore from string + values = json_fix( simplejson.loads( value ) ) + return values ## ---- Utility methods ------------------------------------------------------- --- a/lib/galaxy/webapps/community/controllers/repository.py Wed Oct 19 10:14:51 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Wed Oct 19 16:47:25 2011 -0400 @@ -283,13 +283,14 @@ class InstallMatchedRepositoryListGrid( MatchedRepositoryListGrid ): # Grid definition - title = "Repositories with required tools" - operations = [ grids.GridOperation( "Install tools", - url_args = dict( controller='repository', - action='find_tools', - webapp='community' ), - allow_multiple=True, - async_compatible=False ) ] + title = "Repositories that contain tools matching search criteria" + columns = [ col for col in MatchedRepositoryListGrid.columns ] + # Override the NameColumn + columns[ 0 ] = MatchedRepositoryListGrid.NameColumn( "Name", + link=( lambda item: dict( operation="view_or_manage_repository", + id=item.id, + webapp="galaxy" ) ), + attach_popup=True ) class RepositoryController( BaseUIController, ItemRatings ): @@ -340,6 +341,7 @@ return self.category_list_grid( trans, **kwd ) @web.expose def browse_downloadable_repositories( self, trans, **kwd ): + webapp = kwd.get( 'webapp', 'community' ) galaxy_url = kwd.get( 'galaxy_url', None ) if galaxy_url: trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) @@ -366,12 +368,14 @@ if repository.tip != v: return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', + webapp=webapp, repository_id=trans.security.encode_id( repository.id ), changeset_revision=v ) ) url_args = dict( action='browse_downloadable_repositories', operation='preview_tools_in_changeset', + webapp=webapp, repository_id=repository_id ) - self.downloadable_repository_list_grid.operations = [ grids.GridOperation( "Preview and install tools", + self.downloadable_repository_list_grid.operations = [ grids.GridOperation( "Preview and install", url_args=url_args, allow_multiple=False, async_compatible=False ) ] @@ -396,18 +400,18 @@ repository = get_repository( trans, repository_id ) kwd[ 'id' ] = repository_id kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision - if is_admin or repository.user == trans.user: + if webapp == 'community' and ( is_admin or repository.user == trans.user ): a = 'manage_repository' else: a = 'view_repository' return trans.response.send_redirect( web.url_for( controller='repository', action=a, **kwd ) ) - if operation == "install tools": + if operation == "install": repo_info_dict = {} galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) # TODO: support https in the following url. - url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s' % ( galaxy_url, trans.request.host ) + url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s' % ( galaxy_url, trans.request.host, webapp ) repository_metadata_ids = util.listify( kwd[ 'id' ] ) for repository_metadata_id in repository_metadata_ids: repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) @@ -416,7 +420,7 @@ changeset_revision = repository_metadata.changeset_revision repository_clone_url = generate_clone_url( trans, repository_id ) repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) - encoded_repo_info_dict = self._encode( repo_info_dict ) + encoded_repo_info_dict = self.__encode( repo_info_dict ) url += '&repo_info_dict=%s' % encoded_repo_info_dict return trans.response.send_redirect( url ) tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ] @@ -427,17 +431,19 @@ match_tuples = [] ok = True if tool_ids or tool_names or tool_versions: - ok, match_tuples = self._search_repository_metadata( trans, tool_ids, tool_names, tool_versions, exact_matches_checked ) + ok, match_tuples = self.__search_repository_metadata( trans, tool_ids, tool_names, tool_versions, exact_matches_checked ) if ok: kwd[ 'match_tuples' ] = match_tuples # Render the list view - if galaxy_url: - # Our request originated from a Galaxy instance, so we're listing tools - # that have been found for a workflow in Galaxy. + if webapp == 'galaxy': + # Our request originated from a Galaxy instance. + install_url_args = dict( controller='repository', action='find_tools', webapp=webapp ) + operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] + self.install_matched_repository_list_grid.operations = operations return self.install_matched_repository_list_grid( trans, **kwd ) else: kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ - ( self._stringify( tool_ids ), self._stringify( tool_names ), self._stringify( tool_versions ), str( exact_matches_checked ) ) + ( self.__stringify( tool_ids ), self.__stringify( tool_names ), self.__stringify( tool_versions ), str( exact_matches_checked ) ) return self.matched_repository_list_grid( trans, **kwd ) else: message = "No search performed - each field must contain the same number of comma-separated items." @@ -445,13 +451,13 @@ exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) return trans.fill_template( '/webapps/community/repository/find_tools.mako', webapp=webapp, - tool_id=self._stringify( tool_ids ), - tool_name=self._stringify( tool_names ), - tool_version=self._stringify( tool_versions ), + tool_id=self.__stringify( tool_ids ), + tool_name=self.__stringify( tool_names ), + tool_version=self.__stringify( tool_versions ), exact_matches_check_box=exact_matches_check_box, message=message, status=status ) - def _search_repository_metadata( self, trans, tool_ids, tool_names, tool_versions, exact_matches_checked ): + def __search_repository_metadata( self, trans, tool_ids, tool_names, tool_versions, exact_matches_checked ): match_tuples = [] ok = True for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): @@ -460,38 +466,38 @@ for tool_dict in tools: if tool_ids and not tool_names and not tool_versions: for tool_id in tool_ids: - if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) elif tool_names and not tool_ids and not tool_versions: for tool_name in tool_names: - if self._in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) elif tool_versions and not tool_ids and not tool_names: for tool_version in tool_versions: - if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) elif tool_ids and tool_names and not tool_versions: if len( tool_ids ) == len( tool_names ): - match_tuples = self._search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) elif len( tool_ids ) == 1 or len( tool_names ) == 1: - tool_ids, tool_names = self._make_same_length( tool_ids, tool_names ) - match_tuples = self._search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) else: ok = False elif tool_ids and tool_versions and not tool_names: if len( tool_ids ) == len( tool_versions ): - match_tuples = self._search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) elif len( tool_ids ) == 1 or len( tool_versions ) == 1: - tool_ids, tool_versions = self._make_same_length( tool_ids, tool_versions ) - match_tuples = self._search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) else: ok = False elif tool_versions and tool_names and not tool_ids: if len( tool_versions ) == len( tool_names ): - match_tuples = self._search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) elif len( tool_versions ) == 1 or len( tool_names ) == 1: - tool_versions, tool_names = self._make_same_length( tool_versions, tool_names ) - match_tuples = self._search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) else: ok = False elif tool_versions and tool_names and tool_ids: @@ -499,12 +505,12 @@ for i, tool_version in enumerate( tool_versions ): tool_name = tool_names[ i ] tool_id = tool_ids[ i ] - if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) else: ok = False return ok, match_tuples - def _in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): + def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): found = False if tool_id and not tool_name and not tool_version: tool_dict_tool_id = tool_dict[ 'id' ].lower() @@ -545,13 +551,13 @@ tool_dict_tool_name.find( tool_name ) >= 0 and \ tool_dict_tool_id.find( tool_id ) >= 0 ) return found - def _stringify( self, list ): + def __stringify( self, list ): if list: return ','.join( list ) return '' - def _make_same_length( self, list1, list2 ): + def __make_same_length( self, list1, list2 ): # If either list is 1 item, we'll append to it until its - #length is the same as the other. + # length is the same as the other. if len( list1 ) == 1: for i in range( 1, len( list2 ) ): list1.append( list1[ 0 ] ) @@ -559,25 +565,25 @@ for i in range( 1, len( list1 ) ): list2.append( list2[ 0 ] ) return list1, list2 - def _search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ): + def __search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ): for i, tool_id in enumerate( tool_ids ): tool_name = tool_names[ i ] - if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ): + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) return match_tuples - def _search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ): + def __search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ): for i, tool_id in enumerate( tool_ids ): tool_version = tool_versions[ i ] - if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ): + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) return match_tuples - def _search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ): + def __search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ): for i, tool_name in enumerate( tool_names ): tool_version = tool_versions[ i ] - if self._in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ): + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) return match_tuples - def _encode( self, repo_info_dict ): + def __encode( self, repo_info_dict ): value = simplejson.dumps( repo_info_dict ) a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) b = binascii.hexlify( value ) @@ -587,6 +593,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) repository = get_repository( trans, repository_id ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) @@ -605,7 +612,7 @@ revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, metadata=metadata, - display_for_install=True, + webapp=webapp, message=message, status=status ) @web.expose @@ -631,7 +638,7 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - webapp = params.get( 'webapp', None ) + webapp = params.get( 'webapp', 'community' ) # Start building up the url to redirect back to the calling Galaxy instance. # TODO: support https in the following url. url = 'http://%s/admin/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, trans.request.host ) @@ -713,6 +720,8 @@ # We add params to the keyword dict in this method in order to rename the param # with an "f-" prefix, simulating filtering by clicking a search link. We have # to take this approach because the "-" character is illegal in HTTP requests. + if 'webapp' not in kwd: + kwd[ 'webapp' ] = 'community' if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "view_or_manage_repository": @@ -855,6 +864,7 @@ message = "Repository '%s' has been created." % repository.name trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', + webapp='community', message=message, id=trans.security.encode_id( repository.id ) ) ) return trans.fill_template( '/webapps/community/repository/create_repository.mako', @@ -945,6 +955,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) repository = get_repository( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) @@ -957,6 +968,7 @@ repository=repository, commit_message=commit_message, is_malicious=is_malicious, + webapp=webapp, message=message, status=status ) @web.expose @@ -1098,6 +1110,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) + webapp = params.get( 'webapp', 'community' ) repo = hg.repository( get_configured_ui(), repository.repo_path ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) @@ -1155,6 +1168,7 @@ changeset_revision_select_field=changeset_revision_select_field, revision_label=revision_label, is_malicious=is_malicious, + webapp=webapp, message=message, status=status ) @web.expose @@ -1191,6 +1205,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', id=id, + webapp='community', message=message, status=status ) ) if repo_name != repository.name: @@ -1482,7 +1497,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - display_for_install = util.string_as_bool( params.get( 'display_for_install', False ) ) + webapp = params.get( 'webapp', 'community' ) repository = get_repository( trans, repository_id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) try: @@ -1523,12 +1538,12 @@ tool=tool, tool_state=tool_state, is_malicious=is_malicious, - display_for_install=display_for_install, + webapp=webapp, message=message, status=status ) except Exception, e: message = "Error loading tool: %s. Click <b>Reset metadata</b> to correct this error." % str( e ) - if display_for_install: + if webapp == 'galaxy': return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=repository_id, @@ -1558,7 +1573,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - display_for_install = util.string_as_bool( params.get( 'display_for_install', False ) ) + webapp = params.get( 'webapp', 'community' ) repository = get_repository( trans, repository_id ) metadata = {} tool = None @@ -1587,7 +1602,7 @@ revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, is_malicious=is_malicious, - display_for_install=display_for_install, + webapp=webapp, message=message, status=status ) @web.expose --- a/lib/galaxy/webapps/community/controllers/upload.py Wed Oct 19 10:14:51 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Wed Oct 19 16:47:25 2011 -0400 @@ -138,6 +138,7 @@ action='browse_repository', id=repository_id, commit_message='Deleted selected files', + webapp='community', message=message, status=status ) ) else: --- a/templates/webapps/community/repository/browse_repository.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/community/repository/browse_repository.mako Wed Oct 19 16:47:25 2011 -0400 @@ -71,13 +71,13 @@ %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> --- a/templates/webapps/community/repository/common.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/community/repository/common.mako Wed Oct 19 16:47:25 2011 -0400 @@ -83,7 +83,7 @@ hg clone <a href="${clone_str}">${clone_str}</a></%def> -<%def name="render_repository_tools_and_workflows( metadata, can_set_metadata=False, display_for_install=False )"> +<%def name="render_repository_tools_and_workflows( metadata, can_set_metadata=False, webapp='community' )"> %if metadata or can_set_metadata: <p/><div class="toolForm"> @@ -111,12 +111,12 @@ <tr><td><div style="float: left; margin-left: 1px;" class="menubutton split popup" id="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision, display_for_install=display_for_install )}"> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}"> ${tool_dict[ 'name' ]} </a></div><div popupmenu="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ], display_for_install=display_for_install )}">View tool metadata</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ], webapp=webapp )}">View tool metadata</a></div></td><td>${tool_dict[ 'description' ]}</td> --- a/templates/webapps/community/repository/contact_owner.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/community/repository/contact_owner.mako Wed Oct 19 16:47:25 2011 -0400 @@ -37,16 +37,16 @@ %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> --- a/templates/webapps/community/repository/find_tools.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/community/repository/find_tools.mako Wed Oct 19 16:47:25 2011 -0400 @@ -18,9 +18,10 @@ <div class="toolFormTitle">Search repositories for valid tools</div><div class="toolFormBody"><div class="form-row"> - Valid tools are those that properly load in Galaxy. Enter any combination of the following tool attributes to locate matching valid tools. + Valid tools are those that properly load in Galaxy. Enter any combination of the following tool attributes to find repositories that contain + valid tools matching the search criteria.<br/><br/> Comma-separated strings may be entered in each field to expand search criteria. Each field must contain the same number of comma-separated - strings if these types of strings are entered in more than one field. + strings if these types of search strings are entered in more than one field. </div><div style="clear: both"></div><form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}" method="post" > --- a/templates/webapps/community/repository/manage_repository.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Wed Oct 19 16:47:25 2011 -0400 @@ -77,13 +77,13 @@ <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> %endif %if can_contact_owner: <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> @@ -290,7 +290,7 @@ <div class="toolFormBody"> %if display_reviews: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False )}"><label>Hide Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False, webapp='community' )}"><label>Hide Reviews</label></a></div><table class="grid"><thead> @@ -317,7 +317,7 @@ </table> %else: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True )}"><label>Display Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True, webapp='community' )}"><label>Display Reviews</label></a></div> %endif </div> --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako Wed Oct 19 16:47:25 2011 -0400 @@ -64,7 +64,7 @@ <br/><br/><ul class="manage-table-actions"> - <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp='community', changeset_revision=changeset_revision )}">Install to local Galaxy</a> + <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></ul> %if message: @@ -98,4 +98,4 @@ </div></div><p/> -${render_repository_tools_and_workflows( metadata, display_for_install=display_for_install )} +${render_repository_tools_and_workflows( metadata, webapp=webapp )} --- a/templates/webapps/community/repository/rate_repository.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/community/repository/rate_repository.mako Wed Oct 19 16:47:25 2011 -0400 @@ -78,16 +78,16 @@ %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> %endif %if can_contact_owner: <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> --- a/templates/webapps/community/repository/tool_form.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Wed Oct 19 16:47:25 2011 -0400 @@ -110,33 +110,33 @@ <br/><br/><ul class="manage-table-actions"> - %if display_for_install: - <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp='community', changeset_revision=changeset_revision )}">Install to local Galaxy</a> + %if webapp == 'galaxy': + <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a> %else: %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> --- a/templates/webapps/community/repository/upload.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/community/repository/upload.mako Wed Oct 19 16:47:25 2011 -0400 @@ -50,13 +50,13 @@ %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">Browse or delete repository files</a> %endif </div></ul> --- a/templates/webapps/community/repository/view_changelog.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/community/repository/view_changelog.mako Wed Oct 19 16:47:25 2011 -0400 @@ -49,13 +49,13 @@ %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> %endif %if can_contact_owner: <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> --- a/templates/webapps/community/repository/view_changeset.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/community/repository/view_changeset.mako Wed Oct 19 16:47:25 2011 -0400 @@ -50,16 +50,16 @@ %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> %endif %if can_contact_owner: <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> --- a/templates/webapps/community/repository/view_repository.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Wed Oct 19 16:47:25 2011 -0400 @@ -11,8 +11,8 @@ can_rate = not is_new and trans.user and repository.user != trans.user can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) - can_browse_contents = not is_new - can_view_change_log = not is_new + can_browse_contents = webapp == 'community' and not is_new + can_view_change_log = webapp == 'community' and not is_new if can_push: browse_label = 'Browse or delete repository files' else: @@ -65,32 +65,36 @@ <br/><br/><ul class="manage-table-actions"> - %if is_new and can_upload: - <li><a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a></li> + %if webapp == 'community': + %if is_new and can_upload: + <li><a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a></li> + %else: + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + %if can_upload: + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + %endif + %if can_view_change_log: + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> + %endif + %if can_rate: + <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">Rate repository</a> + %endif + %if can_browse_contents: + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> + %endif + %if can_contact_owner: + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> + %endif + %if can_download: + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz', webapp=webapp )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2', webapp=webapp )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip', webapp=webapp )}">Download as a zip file</a> + %endif + </div> + %endif %else: - <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> - <div popupmenu="repository-${repository.id}-popup"> - %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> - %endif - %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> - %endif - %if can_rate: - <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> - %endif - %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> - %endif - %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> - %endif - %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> - %endif - </div> + <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a> %endif </ul> @@ -102,7 +106,7 @@ <div class="toolForm"><div class="toolFormTitle">Repository revision</div><div class="toolFormBody"> - <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), webapp=webapp )}" method="post" ><div class="form-row"><% if changeset_revision == repository.tip: @@ -132,7 +136,7 @@ <div class="form-row"><label>Name:</label> %if can_browse_contents: - <a href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${repository.name}</a> + <a href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${repository.name}</a> %else: ${repository.name} %endif @@ -151,7 +155,7 @@ <div class="form-row"><label>Revision:</label> %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a> + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${revision_label}</a> %else: ${revision_label} %endif @@ -176,7 +180,7 @@ %endif </div></div> -${render_repository_tools_and_workflows( metadata )} +${render_repository_tools_and_workflows( metadata, webapp=webapp )} %if repository.categories: <p/><div class="toolForm"> @@ -191,12 +195,12 @@ </div></div> %endif -%if trans.user and trans.app.config.smtp_server: +%if webapp == 'community' and trans.user and trans.app.config.smtp_server: <p/><div class="toolForm"><div class="toolFormTitle">Notification on update</div><div class="toolFormBody"> - <form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), webapp=webapp )}" method="post" ><div class="form-row"><label>Receive email alerts:</label> ${alerts_check_box.get_html()} @@ -233,7 +237,7 @@ <div class="toolFormBody"> %if display_reviews: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False )}"><label>Hide Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False, webapp=webapp )}"><label>Hide Reviews</label></a></div><table class="grid"><thead> @@ -260,7 +264,7 @@ </table> %else: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True )}"><label>Display Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True, webapp=webapp )}"><label>Display Reviews</label></a></div> %endif </div> --- a/templates/webapps/community/repository/view_tool_metadata.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/community/repository/view_tool_metadata.mako Wed Oct 19 16:47:25 2011 -0400 @@ -12,10 +12,10 @@ can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) - can_browse_contents = not is_new + can_browse_contents = webapp == 'community' and not is_new can_rate = repository.user != trans.user can_manage = is_admin or repository.user == trans.user - can_view_change_log = not is_new + can_view_change_log = webapp == 'community' and not is_new if can_push: browse_label = 'Browse or delete repository files' else: @@ -33,30 +33,30 @@ <br/><br/><ul class="manage-table-actions"> - %if display_for_install: - <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp='community', changeset_revision=changeset_revision )}">Install to local Galaxy</a> + %if webapp == 'galaxy': + <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a> %else: %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> @@ -76,7 +76,7 @@ <div class="toolFormTitle">Repository revision</div><div class="toolFormBody"> %if len( changeset_revision_select_field.options ) > 1: - <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=metadata[ 'id' ], display_for_install=display_for_install )}" method="post" > + <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=metadata[ 'id' ], webapp=webapp )}" method="post" ><div class="form-row"><% if changeset_revision == repository.tip: @@ -124,7 +124,7 @@ <div class="toolFormBody"><div class="form-row"><label>Name:</label> - <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=metadata[ 'tool_config' ], changeset_revision=changeset_revision )}">${metadata[ 'name' ]}</a> + <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=metadata[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}">${metadata[ 'name' ]}</a><div style="clear: both"></div></div> %if 'description' in metadata: --- a/templates/webapps/galaxy/admin/index.mako Wed Oct 19 10:14:51 2011 -0400 +++ b/templates/webapps/galaxy/admin/index.mako Wed Oct 19 16:47:25 2011 -0400 @@ -73,10 +73,7 @@ <div class="toolSectionTitle">Tool sheds</div><div class="toolSectionBody"><div class="toolSectionBg"> - %for name, url in trans.app.tool_shed_registry.tool_sheds.items(): - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}" target="galaxy_main">${name}</a></div> - %endfor - </div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_sheds' )}" target="galaxy_main">Browse tool sheds</a></div></div></div> %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Add dataset_metadata_in_data_table validator. Mimics behavior of dataset_metadata_in_file, but uses data tables.
by Bitbucket 19 Oct '11

19 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/150069a23aad/ changeset: 150069a23aad user: dan date: 2011-10-19 16:14:51 summary: Add dataset_metadata_in_data_table validator. Mimics behavior of dataset_metadata_in_file, but uses data tables. affected #: 1 file (-1 bytes) --- a/lib/galaxy/tools/parameters/validation.py Tue Oct 18 16:57:45 2011 -0400 +++ b/lib/galaxy/tools/parameters/validation.py Wed Oct 19 10:14:51 2011 -0400 @@ -189,7 +189,7 @@ class UnspecifiedBuildValidator( Validator ): """ - Validator that checks for missing metadata + Validator that checks for dbkey not equal to '?' """ def __init__( self, message=None ): if message is None: @@ -268,6 +268,45 @@ return raise ValueError( self.message ) +class MetadataInDataTableColumnValidator( Validator ): + """ + Validator that checks if the value for a dataset's metadata item exists in a file. + """ + @classmethod + def from_element( cls, param, elem ): + table_name = elem.get( "table_name", None ) + assert table_name, 'You must specify a table_name.' + tool_data_table = param.tool.app.tool_data_tables[ table_name ] + metadata_name = elem.get( "metadata_name", None ) + if metadata_name: + metadata_name = metadata_name.strip() + metadata_column = elem.get( "metadata_column", 0 ) + try: + metadata_column = int( metadata_column ) + except: + pass + message = elem.get( "message", "Value for metadata %s was not found in %s." % ( metadata_name, table_name ) ) + line_startswith = elem.get( "line_startswith", None ) + if line_startswith: + line_startswith = line_startswith.strip() + return cls( tool_data_table, metadata_name, metadata_column, message, line_startswith ) + def __init__( self, tool_data_table, metadata_name, metadata_column, message="Value for metadata not found.", line_startswith=None ): + self.metadata_name = metadata_name + self.message = message + self.valid_values = [] + if isinstance( metadata_column, basestring ): + metadata_column = tool_data_table.columns[ metadata_column ] + for fields in tool_data_table.get_fields(): + if metadata_column < len( fields ): + self.valid_values.append( fields[ metadata_column ] ) + def validate( self, value, history = None ): + if not value: return + if hasattr( value, "metadata" ): + if value.metadata.spec[self.metadata_name].param.to_string( value.metadata.get( self.metadata_name ) ) in self.valid_values: + return + raise ValueError( self.message ) + + validator_types = dict( expression=ExpressionValidator, regex=RegexValidator, in_range=InRangeValidator, @@ -277,6 +316,7 @@ no_options=NoOptionsValidator, empty_field=EmptyTextfieldValidator, dataset_metadata_in_file=MetadataInFileColumnValidator, + dataset_metadata_in_data_table=MetadataInDataTableColumnValidator, dataset_ok_validator=DatasetOkValidator ) def get_suite(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fixes and code cleanup for searching for tools in tool shed repositories.
by Bitbucket 18 Oct '11

18 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e810fd94b4ed/ changeset: e810fd94b4ed user: greg date: 2011-10-18 22:57:45 summary: Fixes and code cleanup for searching for tools in tool shed repositories. affected #: 1 file (-1 bytes) --- a/lib/galaxy/webapps/community/controllers/repository.py Tue Oct 18 11:41:08 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Oct 18 16:57:45 2011 -0400 @@ -340,8 +340,6 @@ return self.category_list_grid( trans, **kwd ) @web.expose def browse_downloadable_repositories( self, trans, **kwd ): - # Set the toolshedgalaxyurl cookie so we can get back - # to the calling local Galaxy instance. galaxy_url = kwd.get( 'galaxy_url', None ) if galaxy_url: trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) @@ -354,7 +352,6 @@ action='preview_tools_in_changeset', repository_id=repository_id, changeset_revision=repository.tip ) ) - # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change # which sends in request parameters like changeset_revison_1, changeset_revision_2, etc. One # of the many select fields on the grid performed the refresh_on_change, so we loop through @@ -385,9 +382,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = params.get( 'webapp', 'galaxy' ) - # Set the toolshedgalaxyurl cookie so we can get back - # to the calling local Galaxy instance. + webapp = params.get( 'webapp', 'community' ) galaxy_url = kwd.get( 'galaxy_url', None ) if galaxy_url: trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) @@ -395,20 +390,19 @@ operation = kwd[ 'operation' ].lower() is_admin = trans.user_is_admin() if operation == "view_or_manage_repository": + # The received id is a RepositoryMetadata id, so we have to get the repository id. repository_metadata = get_repository_metadata_by_id( trans, kwd[ 'id' ] ) repository_id = trans.security.encode_id( repository_metadata.repository.id ) repository = get_repository( trans, repository_id ) - # The received id is a RepositoryMetadata.id, so we have to get the repository id. kwd[ 'id' ] = repository_id kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision if is_admin or repository.user == trans.user: - return trans.response.send_redirect( web.url_for( controller='repository', - action='manage_repository', - **kwd ) ) + a = 'manage_repository' else: - return trans.response.send_redirect( web.url_for( controller='repository', - action='view_repository', - **kwd ) ) + a = 'view_repository' + return trans.response.send_redirect( web.url_for( controller='repository', + action=a, + **kwd ) ) if operation == "install tools": repo_info_dict = {} galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) @@ -416,7 +410,6 @@ url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s' % ( galaxy_url, trans.request.host ) repository_metadata_ids = util.listify( kwd[ 'id' ] ) for repository_metadata_id in repository_metadata_ids: - #self._set_clone_repository_cookie( trans, index, repository_metadata_id ) repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) repository_id = trans.security.encode_id( repository.id ) @@ -426,60 +419,15 @@ encoded_repo_info_dict = self._encode( repo_info_dict ) url += '&repo_info_dict=%s' % encoded_repo_info_dict return trans.response.send_redirect( url ) - tool_ids = [ tid.lower() for tid in util.listify( kwd.get( 'tool_id', '' ) ) ] - tool_names = [ tn.lower() for tn in util.listify( kwd.get( 'tool_name', '' ) ) ] - tool_versions = [ tv.lower() for tv in util.listify( kwd.get( 'tool_version', '' ) ) ] + tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ] + tool_names = [ item.lower() for item in util.listify( kwd.get( 'tool_name', '' ) ) ] + tool_versions = [ item.lower() for item in util.listify( kwd.get( 'tool_version', '' ) ) ] exact_matches = params.get( 'exact_matches', '' ) exact_matches_checked = CheckboxField.is_checked( exact_matches ) match_tuples = [] ok = True if tool_ids or tool_names or tool_versions: - for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): - metadata = repository_metadata.metadata - tools = metadata[ 'tools' ] - for tool_dict in tools: - if tool_ids and not tool_names and not tool_versions: - for tool_id in tool_ids: - if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_names and not tool_ids and not tool_versions: - for tool_name in tool_names: - if self._in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_versions and not tool_ids and not tool_names: - for tool_version in tool_versions: - if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_ids and tool_names and not tool_versions: - if len( tool_ids ) == len( tool_names ): - for i, tool_id in enumerate( tool_ids ): - tool_name = tool_names[ i ] - if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - else: - message = "No search performed - each field must contain the same number of comma-separated items." - status = "error" - ok = False - elif tool_ids and tool_versions and not tool_names: - if len( tool_ids ) == len( tool_versions ): - for i, tool_id in enumerate( tool_ids ): - tool_version = tool_versions[ i ] - if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - else: - message = "No search performed - each field must contain the same number of comma-separated items." - status = "error" - ok = False - elif tool_versions and tool_names and not tool_ids: - if len( tool_versions ) == len( tool_names ): - for i, tool_version in enumerate( tool_versions ): - tool_name = tool_names[ i ] - if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version, tool_name=tool_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - else: - message = "No search performed - each field must contain the same number of comma-separated items." - status = "error" - ok = False + ok, match_tuples = self._search_repository_metadata( trans, tool_ids, tool_names, tool_versions, exact_matches_checked ) if ok: kwd[ 'match_tuples' ] = match_tuples # Render the list view @@ -488,42 +436,74 @@ # that have been found for a workflow in Galaxy. return self.install_matched_repository_list_grid( trans, **kwd ) else: - if tool_ids: - tool_id_str = ','.join( tool_ids ) - else: - tool_id_str = '' - if tool_names: - tool_name_str = ','.join( tool_names ) - else: - tool_name_str = '' - if tool_versions: - tool_version_str = ','.join( tool_versions ) - else: - tool_version_str = '' kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ - ( tool_id_str, tool_name_str, tool_version_str, str( exact_matches_checked ) ) + ( self._stringify( tool_ids ), self._stringify( tool_names ), self._stringify( tool_versions ), str( exact_matches_checked ) ) return self.matched_repository_list_grid( trans, **kwd ) + else: + message = "No search performed - each field must contain the same number of comma-separated items." + status = "error" exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) - if tool_ids: - tool_id = ','.join( tool_ids ) - else: - tool_id = '' - if tool_names: - tool_name = ','.join( tool_names ) - else: - tool_name = '' - if tool_versions: - tool_version = ','.join( tool_versions ) - else: - tool_version = '' return trans.fill_template( '/webapps/community/repository/find_tools.mako', webapp=webapp, - tool_id=tool_id, - tool_name=tool_name, - tool_version=tool_version, + tool_id=self._stringify( tool_ids ), + tool_name=self._stringify( tool_names ), + tool_version=self._stringify( tool_versions ), exact_matches_check_box=exact_matches_check_box, message=message, status=status ) + def _search_repository_metadata( self, trans, tool_ids, tool_names, tool_versions, exact_matches_checked ): + match_tuples = [] + ok = True + for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): + metadata = repository_metadata.metadata + tools = metadata[ 'tools' ] + for tool_dict in tools: + if tool_ids and not tool_names and not tool_versions: + for tool_id in tool_ids: + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_names and not tool_ids and not tool_versions: + for tool_name in tool_names: + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_versions and not tool_ids and not tool_names: + for tool_version in tool_versions: + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_ids and tool_names and not tool_versions: + if len( tool_ids ) == len( tool_names ): + match_tuples = self._search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + elif len( tool_ids ) == 1 or len( tool_names ) == 1: + tool_ids, tool_names = self._make_same_length( tool_ids, tool_names ) + match_tuples = self._search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + else: + ok = False + elif tool_ids and tool_versions and not tool_names: + if len( tool_ids ) == len( tool_versions ): + match_tuples = self._search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + elif len( tool_ids ) == 1 or len( tool_versions ) == 1: + tool_ids, tool_versions = self._make_same_length( tool_ids, tool_versions ) + match_tuples = self._search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and not tool_ids: + if len( tool_versions ) == len( tool_names ): + match_tuples = self._search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + elif len( tool_versions ) == 1 or len( tool_names ) == 1: + tool_versions, tool_names = self._make_same_length( tool_versions, tool_names ) + match_tuples = self._search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and tool_ids: + if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): + for i, tool_version in enumerate( tool_versions ): + tool_name = tool_names[ i ] + tool_id = tool_ids[ i ] + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + ok = False + return ok, match_tuples def _in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): found = False if tool_id and not tool_name and not tool_version: @@ -553,7 +533,50 @@ tool_dict_tool_name = tool_dict[ 'name' ].lower() found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \ ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) + elif tool_version and tool_name and tool_id: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + tool_dict_tool_id = tool_dict[ 'id' ].lower() + found = ( tool_version == tool_dict_tool_version and \ + tool_name == tool_dict_tool_name and \ + tool_id == tool_dict_tool_id ) or \ + ( not exact_matches_checked and \ + tool_dict_tool_version.find( tool_version ) >= 0 and \ + tool_dict_tool_name.find( tool_name ) >= 0 and \ + tool_dict_tool_id.find( tool_id ) >= 0 ) return found + def _stringify( self, list ): + if list: + return ','.join( list ) + return '' + def _make_same_length( self, list1, list2 ): + # If either list is 1 item, we'll append to it until its + #length is the same as the other. + if len( list1 ) == 1: + for i in range( 1, len( list2 ) ): + list1.append( list1[ 0 ] ) + elif len( list2 ) == 1: + for i in range( 1, len( list1 ) ): + list2.append( list2[ 0 ] ) + return list1, list2 + def _search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ): + for i, tool_id in enumerate( tool_ids ): + tool_name = tool_names[ i ] + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return match_tuples + def _search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ): + for i, tool_id in enumerate( tool_ids ): + tool_version = tool_versions[ i ] + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return match_tuples + def _search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ): + for i, tool_name in enumerate( tool_names ): + tool_version = tool_versions[ i ] + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return match_tuples def _encode( self, repo_info_dict ): value = simplejson.dumps( repo_info_dict ) a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Add new tool attributes to hold information about tools installed from a Galaxy tool shed. Enhance the toolbox's <tool> tag parser to handle these new tool attributes for installed tools. Enhance the Workflow import and load functions to search these new attributes when looking for required tools in the Galaxy instance.
by Bitbucket 18 Oct '11

18 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/fcaf6ec8e51b/ changeset: fcaf6ec8e51b user: greg date: 2011-10-18 17:41:08 summary: Add new tool attributes to hold information about tools installed from a Galaxy tool shed. Enhance the toolbox's <tool> tag parser to handle these new tool attributes for installed tools. Enhance the Workflow import and load functions to search these new attributes when looking for required tools in the Galaxy instance. affected #: 2 files (-1 bytes) --- a/lib/galaxy/tools/__init__.py Tue Oct 18 10:50:16 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Tue Oct 18 11:41:08 2011 -0400 @@ -104,6 +104,14 @@ try: path = elem.get( "file" ) tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) + if guid is not None: + # Tool was installed from a Galaxy tool shed. + tool.tool_shed = elem.find( "tool_shed" ).text + tool.repository_name = elem.find( "repository_name" ).text + tool.repository_owner = elem.find( "repository_owner" ).text + tool.changeset_revision = elem.find( "changeset_revision" ).text + tool.old_id = elem.find( "id" ).text + tool.version = elem.find( "version" ).text if self.app.config.get_bool( 'enable_tool_tags', False ): tag_names = elem.get( "tags", "" ).split( "," ) for tag_name in tag_names: @@ -364,9 +372,7 @@ # legacy basic mode - provide compatible defaults self.attributes['split_size'] = 20 self.attributes['split_mode'] = 'number_of_parts' - - - + class Tool: """ Represents a computational tool that can be executed through Galaxy. @@ -387,6 +393,13 @@ # easily ensure that parameter dependencies like index files or # tool_data_table_conf.xml entries exist. self.input_params = [] + # Attributes of tools installed from Galaxy tool sheds. + self.tool_shed = None + self.repository_name = None + self.repository_owner = None + self.changeset_revision = None + self.old_id = None + self.version = None # Parse XML element containing configuration self.parse( root, guid=guid ) @@ -407,14 +420,14 @@ raise Exception, "Missing tool 'name'" # Get the UNIQUE id for the tool # TODO: can this be generated automatically? - if guid is not None: + if guid is None: + self.id = root.get( "id" ) + self.version = root.get( "version" ) + else: self.id = guid - else: - self.id = root.get( "id" ) if not self.id: - raise Exception, "Missing tool 'id'" - self.version = root.get( "version" ) - if not self.version: + raise Exception, "Missing tool 'id'" + if not self.version: # For backward compatibility, some tools may not have versions yet. self.version = "1.0.0" # Support multi-byte tools --- a/lib/galaxy/workflow/modules.py Tue Oct 18 10:50:16 2011 -0400 +++ b/lib/galaxy/workflow/modules.py Tue Oct 18 11:41:08 2011 -0400 @@ -171,15 +171,10 @@ except KeyError, e: # Handle the case where the workflow requires a tool not available in the local Galaxy instance. self.tool = None - # TODO: Instead of parsing the guid, get the tool_id and version from the shed_tool_conf.xml, - # which requires enhancements to the tool loading process. + # The id value of tools installed from a Galaxy tool shed is a guid, but + # these tool's old_id attribute should contain what we're looking for. for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): - if available_tool_id.find( tool_id ) >=0: - # We're attempting to match tool id against a tool guid. - # TODO: match by tool_id (and version if we attempt that, but - # workflows will break) is not good enough because - # 2 tools installed from a tool shed could both match this. We - # need to present a select list here. + if tool_id == available_tool.old_id: self.tool = available_tool break self.post_job_actions = {} @@ -211,13 +206,10 @@ tool_id = step.tool_id install_tool_id = None if tool_id not in trans.app.toolbox.tools_by_id: + # The id value of tools installed from a Galaxy tool shed is a guid, but + # these tool's old_id attribute should contain what we're looking for. for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): - if available_tool_id.find( tool_id ) >=0: - # We're attempting to match tool id against a tool guid. - # TODO: match by tool_id (and version if we attempt that, but - # workflows will break) is not good enough because - # 2 tools installed from a tool shed could both match this. We - # need to present a select list here. + if tool_id == available_tool.old_id: install_tool_id = available_tool_id break if tool_id in trans.app.toolbox.tools_by_id or install_tool_id: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Bug fixes to Trackster ReferenceDataManager.
by Bitbucket 18 Oct '11

18 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8cbd9e1a9bee/ changeset: 8cbd9e1a9bee user: jgoecks date: 2011-10-18 16:50:16 summary: Bug fixes to Trackster ReferenceDataManager. affected #: 1 file (-1 bytes) --- a/static/scripts/trackster.js Tue Oct 18 09:51:39 2011 -0400 +++ b/static/scripts/trackster.js Tue Oct 18 10:50:16 2011 -0400 @@ -561,13 +561,13 @@ DataManager.call(this, num_elements, track, subset); }; extend(ReferenceTrackDataManager.prototype, DataManager.prototype, Cache.prototype, { - load_data: function(chrom, low, high, mode, resolution, extra_params) { + load_data: function(low, high, mode, resolution, extra_params) { if (resolution > 1) { // Now that data is pre-fetched before draw, we don't load reference tracks - // unless it's at the bottom level - return; + // unless it's at the bottom level. + return { data: null }; } - return DataManager.prototype.load_data.call(this, chrom, low, high, mode, resolution, extra_params); + return DataManager.prototype.load_data.call(this, low, high, mode, resolution, extra_params); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Make sure the same key is used in encoding and decoding between Galaxy and the tool sheds.
by Bitbucket 18 Oct '11

18 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0cb44cddd40d/ changeset: 0cb44cddd40d user: greg date: 2011-10-18 14:43:30 summary: Make sure the same key is used in encoding and decoding between Galaxy and the tool sheds. affected #: 2 files (-1 bytes) --- a/lib/galaxy/web/controllers/admin.py Mon Oct 17 19:57:54 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Tue Oct 18 08:43:30 2011 -0400 @@ -693,13 +693,12 @@ galaxy_url = trans.request.host url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) - def _decode( self, trans, value, secure=True ): - if secure: - # Extract and verify hash - a, b = value.split( ":" ) - value = binascii.unhexlify( b ) - test = hmac_new( trans.app.config.tool_secret, value ) - assert a == test + def _decode( self, value ): + # Extract and verify hash + a, b = value.split( ":" ) + value = binascii.unhexlify( b ) + test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) + assert a == test # Restore from string values = json_fix( simplejson.loads( value ) ) return values @@ -729,7 +728,7 @@ section_key = 'section_%s' % kwd[ 'tool_panel_section' ] tool_section = trans.app.toolbox.tool_panel[ section_key ] # Decode the encoded repo_info_dict param value. - repo_info_dict = self._decode( trans, repo_info_dict ) + repo_info_dict = self._decode( repo_info_dict ) # Clone the repository to the configured location. current_working_dir = os.getcwd() for name, repo_info_tuple in repo_info_dict.items(): --- a/lib/galaxy/webapps/community/controllers/repository.py Mon Oct 17 19:57:54 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Oct 18 08:43:30 2011 -0400 @@ -423,7 +423,7 @@ changeset_revision = repository_metadata.changeset_revision repository_clone_url = generate_clone_url( trans, repository_id ) repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) - encoded_repo_info_dict = self._encode( trans, repo_info_dict, secure=True ) + encoded_repo_info_dict = self._encode( repo_info_dict ) url += '&repo_info_dict=%s' % encoded_repo_info_dict return trans.response.send_redirect( url ) tool_ids = [ tid.lower() for tid in util.listify( kwd.get( 'tool_id', '' ) ) ] @@ -554,15 +554,11 @@ found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \ ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) return found - def _encode( self, trans, repo_info_dict, secure=True ): + def _encode( self, repo_info_dict ): value = simplejson.dumps( repo_info_dict ) - # Make it secure - if secure: - a = hmac_new( trans.app.config.tool_secret, value ) - b = binascii.hexlify( value ) - return "%s:%s" % ( a, b ) - else: - return value + a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) + b = binascii.hexlify( value ) + return "%s:%s" % ( a, b ) @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): params = util.Params( kwd ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Better handling of reference data in Trackster read tracks.
by Bitbucket 17 Oct '11

17 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5c7333bb427f/ changeset: 5c7333bb427f user: jgoecks date: 2011-10-18 01:57:54 summary: Better handling of reference data in Trackster read tracks. affected #: 1 file (-1 bytes) --- a/static/scripts/trackster.js Mon Oct 17 17:41:10 2011 -0400 +++ b/static/scripts/trackster.js Mon Oct 17 19:57:54 2011 -0400 @@ -4375,7 +4375,7 @@ 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; + this.ref_seq = (ref_seq ? ref_seq.data : null); }; ReadPainter.prototype.default_prefs = extend({}, FeaturePainter.prototype.default_prefs, { show_insertions: false }); @@ -4410,8 +4410,7 @@ tile_region = [tile_low, tile_high], base_offset = 0, seq_offset = 0, - gap = 0 - ref_seq = this.ref_seq.data, + gap = 0, char_width_px = ctx.canvas.manager.char_width_px; // Keep list of items that need to be drawn on top of initial drawing layer. @@ -4465,8 +4464,8 @@ // TODO: this can be made much more efficient by computing the complete sequence // to draw and then drawing it. for (var c = 0, str_len = seq.length; c < str_len; c++) { - if (this.prefs.show_differences && ref_seq) { - var ref_char = ref_seq[seq_start - tile_low + c]; + if (this.prefs.show_differences && this.ref_seq) { + var ref_char = this.ref_seq[seq_start - tile_low + c]; if (!ref_char || ref_char.toLowerCase() === seq[c].toLowerCase()) { continue; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Encode the tool shed repository information and include in the request when installing into local Galaxy instances rather than using cookies.
by Bitbucket 17 Oct '11

17 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1748b377cd2f/ changeset: 1748b377cd2f user: greg date: 2011-10-17 23:41:10 summary: Encode the tool shed repository information and include in the request when installing into local Galaxy instances rather than using cookies. affected #: 4 files (-1 bytes) --- a/lib/galaxy/web/controllers/admin.py Mon Oct 17 16:03:47 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon Oct 17 17:41:10 2011 -0400 @@ -3,7 +3,9 @@ from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.tools.search import ToolBoxSearch -import logging +from galaxy.tools import json_fix +from galaxy.util.hash_util import * +import simplejson, binascii, logging log = logging.getLogger( __name__ ) from galaxy.actions.admin import AdminActions @@ -688,9 +690,19 @@ @web.require_admin def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] - trans.set_cookie( trans.request.host, name='toolshedgalaxyurl' ) - url = '%s/repository/browse_downloadable_repositories?webapp=galaxy' % tool_shed_url + galaxy_url = trans.request.host + url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) + def _decode( self, trans, value, secure=True ): + if secure: + # Extract and verify hash + a, b = value.split( ":" ) + value = binascii.unhexlify( b ) + test = hmac_new( trans.app.config.tool_secret, value ) + assert a == test + # Restore from string + values = json_fix( simplejson.loads( value ) ) + return values @web.expose @web.require_admin def install_tool_shed_repository( self, trans, **kwd ): @@ -703,10 +715,10 @@ message += 'target=_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the ' message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed" target="_blank">Galaxy tool shed wiki</a> for all of the details.' return trans.show_error_message( message ) - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - tool_shed_url = trans.get_cookie( name='galaxytoolshedurl' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + tool_shed_url = kwd[ 'tool_shed_url' ] + repo_info_dict = kwd[ 'repo_info_dict' ] if kwd.get( 'select_tool_panel_section_button', False ): shed_tool_conf = kwd[ 'shed_tool_conf' ] # Get the tool path. @@ -716,18 +728,12 @@ if 'tool_panel_section' in kwd: section_key = 'section_%s' % kwd[ 'tool_panel_section' ] tool_section = trans.app.toolbox.tool_panel[ section_key ] - # Get the number of repositories to clone from a cookie. - num_repos_to_clone = int( trans.get_cookie( name='numrepostoclone' ) ) + # Decode the encoded repo_info_dict param value. + repo_info_dict = self._decode( trans, repo_info_dict ) # Clone the repository to the configured location. current_working_dir = os.getcwd() - for index in range( 0, num_repos_to_clone ): - cookie_name = 'toolshedrepository%i' % index - clone_repo_info_str = trans.get_cookie( name=cookie_name ) - clone_repo_info_items = clone_repo_info_str.split( '&' ) - name = clone_repo_info_items[ 0 ] - description = clone_repo_info_items[ 1 ] - repository_clone_url = clone_repo_info_items[ 2 ] - changeset_revision = clone_repo_info_items[ 3 ] + for name, repo_info_tuple in repo_info_dict.items(): + description, repository_clone_url, changeset_revision = repo_info_tuple clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) ) if os.path.exists( clone_dir ): # Repository and revision has already been cloned. @@ -825,6 +831,8 @@ shed_tool_conf_select_field = None tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) return trans.fill_template( '/admin/select_tool_panel_section.mako', + tool_shed_url=tool_shed_url, + repo_info_dict=repo_info_dict, shed_tool_conf=shed_tool_conf, shed_tool_conf_select_field=shed_tool_conf_select_field, tool_panel_section_select_field=tool_panel_section_select_field, @@ -836,12 +844,11 @@ params = util.Params( kwd ) repository_id = params.get( 'id', None ) repository = get_repository( trans, repository_id ) - trans.set_cookie( trans.request.host, name='toolshedgalaxyurl' ) + galaxy_url = trans.request.host # Send a request to the relevant tool shed to see if there are any updates. # TODO: support https in the following url. - # TODO: Set cookies for name, owner, changeset-revision instead of sending in request - url = 'http://%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&webapp=community' % \ - ( repository.tool_shed, repository.name, repository.owner, repository.changeset_revision ) + url = 'http://%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=community' % \ + ( repository.tool_shed, galaxy_url, repository.name, repository.owner, repository.changeset_revision ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -1087,10 +1094,10 @@ # http://test@bx.psu.edu:9009/repos/some_username/column items = repository_clone_url.split( '@' ) tmp_url = items[ 1 ] - elif repository_clone_url.find( '\/\/' ) > 0: + elif repository_clone_url.find( '//' ) > 0: # We have an url that includes only a protocol, something like: # http://bx.psu.edu:9009/repos/some_username/column - items = repository_clone_url.split( '\/\/' ) + items = repository_clone_url.split( '//' ) tmp_url = items[ 1 ] else: tmp_url = repository_clone_url --- a/lib/galaxy/web/controllers/workflow.py Mon Oct 17 16:03:47 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Mon Oct 17 17:41:10 2011 -0400 @@ -1156,14 +1156,12 @@ # involved in workflow development needs to figure out what it will take to be able to switch # back and forth between Galaxy (with panels ) and the workflow view (without panels ), having # the Galaxy panels displayed whenever in Galaxy. - trans.set_cookie( trans.request.host, name='toolshedgalaxyurl' ) - galaxy_url = trans.request.host message += "The workflow requires the following tools that are not available in this Galaxy instance." message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>" for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items(): if tool_shed_url.endswith( '/' ): tool_shed_url = tool_shed_url.rstrip( '/' ) - url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) + url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, trans.request.host ) for missing_tool_tup in missing_tool_tups: missing_tool_id = missing_tool_tup[0] url += '&tool_id=%s' % missing_tool_id --- a/lib/galaxy/webapps/community/controllers/repository.py Mon Oct 17 16:03:47 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Mon Oct 17 17:41:10 2011 -0400 @@ -9,6 +9,7 @@ from galaxy.webapps.community.model import directory_hash_id from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.hash_util import * from galaxy.model.orm import * from common import * from mercurial import hg, ui, patch, commands @@ -283,7 +284,7 @@ class InstallMatchedRepositoryListGrid( MatchedRepositoryListGrid ): # Grid definition title = "Repositories with required tools" - operations = [ grids.GridOperation( "Preview and install tools", + operations = [ grids.GridOperation( "Install tools", url_args = dict( controller='repository', action='find_tools', webapp='community' ), @@ -408,17 +409,22 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', **kwd ) ) - if operation == "preview and install tools": + if operation == "install tools": + repo_info_dict = {} galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - trans.set_cookie( trans.request.host, name='galaxytoolshedurl' ) # TODO: support https in the following url. - url = 'http://%s/admin/install_tool_shed_repository' % ( galaxy_url ) - repos_to_clone = util.listify( kwd[ 'id' ] ) - num_repos_to_clone = len( repos_to_clone ) - trans.set_cookie( num_repos_to_clone, name='numrepostoclone' ) - for index in range( 0, num_repos_to_clone ): - repository_metadata_id = repos_to_clone[ index ] - self._set_clone_repository_cookie( trans, index, repository_metadata_id ) + url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s' % ( galaxy_url, trans.request.host ) + repository_metadata_ids = util.listify( kwd[ 'id' ] ) + for repository_metadata_id in repository_metadata_ids: + #self._set_clone_repository_cookie( trans, index, repository_metadata_id ) + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) + repository_id = trans.security.encode_id( repository.id ) + changeset_revision = repository_metadata.changeset_revision + repository_clone_url = generate_clone_url( trans, repository_id ) + repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) + encoded_repo_info_dict = self._encode( trans, repo_info_dict, secure=True ) + url += '&repo_info_dict=%s' % encoded_repo_info_dict return trans.response.send_redirect( url ) tool_ids = [ tid.lower() for tid in util.listify( kwd.get( 'tool_id', '' ) ) ] tool_names = [ tn.lower() for tn in util.listify( kwd.get( 'tool_name', '' ) ) ] @@ -548,16 +554,15 @@ found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \ ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) return found - def _set_clone_repository_cookie( self, trans, index, repository_metadata_id ): - cookie_name = 'toolshedrepository%i' % index - repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) - repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) - repository_id = trans.security.encode_id( repository.id ) - changeset_revision = repository_metadata.changeset_revision - # Redirect back to local Galaxy to perform install. - repository_clone_url = generate_clone_url( trans, repository_id ) - cookie_value = '%s&%s&%s&%s' % ( repository.name, repository.description, repository_clone_url, changeset_revision ) - trans.set_cookie( cookie_value, name=cookie_name ) + def _encode( self, trans, repo_info_dict, secure=True ): + value = simplejson.dumps( repo_info_dict ) + # Make it secure + if secure: + a = hmac_new( trans.app.config.tool_secret, value ) + b = binascii.hexlify( value ) + return "%s:%s" % ( a, b ) + else: + return value @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): params = util.Params( kwd ) @@ -593,28 +598,24 @@ repository = get_repository( trans, repository_id ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) # Redirect back to local Galaxy to perform install. - trans.set_cookie( trans.request.host, name='galaxytoolshedurl' ) repository_clone_url = generate_clone_url( trans, repository_id ) # TODO: support https in the following url. - url = 'http://%s/admin/install_tool_shed_repository?name=%s&description=%s&repository_clone_url=%s&changeset_revision=%s' % \ - ( galaxy_url, repository.name, repository.description, repository_clone_url, changeset_revision ) + url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&name=%s&description=%s&repository_clone_url=%s&changeset_revision=%s' % \ + ( galaxy_url, trans.request.host, repository.name, repository.description, repository_clone_url, changeset_revision ) return trans.response.send_redirect( url ) @web.expose def check_for_updates( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - # The sender didn't store galaxy_url in a cookie since - # this method immediately redirects back to the caller. galaxy_url = kwd[ 'galaxy_url' ] name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) webapp = params.get( 'webapp', None ) - trans.set_cookie( trans.request.host, name='galaxytoolshedurl' ) # Start building up the url to redirect back to the calling Galaxy instance. # TODO: support https in the following url. - url = 'http://%s/admin/update_to_changeset_revision' % galaxy_url + url = 'http://%s/admin/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, trans.request.host ) repository = get_repository_by_name_and_owner( trans, name, owner ) url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ ( repository.name, repository.user.username, changeset_revision ) --- a/templates/admin/select_tool_panel_section.mako Mon Oct 17 16:03:47 2011 -0400 +++ b/templates/admin/select_tool_panel_section.mako Mon Oct 17 17:41:10 2011 -0400 @@ -25,7 +25,7 @@ <div class="toolForm"><div class="toolFormTitle">Load tools into tool panel</div><div class="toolFormBody"> - <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository' )}" method="post" > + <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict )}" method="post" > %if shed_tool_conf_select_field: <div class="form-row"><label>Shed tool configuration file:</label> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Fix Trackster bug that prevented differences from being displayed in mapped reads.
by Bitbucket 17 Oct '11

17 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/07d6165f4fd8/ changeset: 07d6165f4fd8 user: jgoecks date: 2011-10-17 22:03:47 summary: Fix Trackster bug that prevented differences from being displayed in mapped reads. affected #: 2 files (-1 bytes) --- a/static/scripts/packed/trackster.js Mon Oct 17 15:50:10 2011 -0400 +++ b/static/scripts/packed/trackster.js Mon Oct 17 16:03:47 2011 -0400 @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};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 trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(R.prototype,r.prototype,z.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;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 ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+" ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){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(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.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:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,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=N.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=A};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,f)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?f:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(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 f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};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 trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(R.prototype,r.prototype,z.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;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 ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+" ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){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(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.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:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,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=N.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=A};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq.data,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,f)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?f:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(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 --- a/static/scripts/trackster.js Mon Oct 17 15:50:10 2011 -0400 +++ b/static/scripts/trackster.js Mon Oct 17 16:03:47 2011 -0400 @@ -4411,7 +4411,7 @@ base_offset = 0, seq_offset = 0, gap = 0 - ref_seq = this.ref_seq, + ref_seq = this.ref_seq.data, char_width_px = ctx.canvas.manager.char_width_px; // Keep list of items that need to be drawn on top of initial drawing layer. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Improvements to Trackster filters: (a) scaler framework replaces generator framework; (b) addition of height scaler to set feature height based on attributes; and (c) no transparency for feature labels.
by Bitbucket 17 Oct '11

17 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/cc1f050c1515/ changeset: cc1f050c1515 user: jgoecks date: 2011-10-17 21:50:10 summary: Improvements to Trackster filters: (a) scaler framework replaces generator framework; (b) addition of height scaler to set feature height based on attributes; and (c) no transparency for feature labels. affected #: 4 files (-1 bytes) --- a/static/june_2007_style/blue/trackster.css Mon Oct 17 14:19:34 2011 -0400 +++ b/static/june_2007_style/blue/trackster.css Mon Oct 17 15:50:10 2011 -0400 @@ -46,7 +46,8 @@ .filters>.sliders,.display-controls{float:left;margin:1em;} .sliders{width:410px;} .display-controls{border-left:solid 2px #DDDDDD;padding-left:1em} -.slider-row{margin-top:0.4em;margin-left:1em;} +.filter-row{margin-top:0.4em;} +.slider-row{margin-left:1em;} .elt-label{float:left;font-weight:bold;margin-right:1em;} .slider{float:right;width:200px;position:relative;} .tool-name{font-size:110%;font-weight:bold;} --- a/static/june_2007_style/trackster.css.tmpl Mon Oct 17 14:19:34 2011 -0400 +++ b/static/june_2007_style/trackster.css.tmpl Mon Oct 17 15:50:10 2011 -0400 @@ -255,12 +255,14 @@ .sliders{ width: 410px; } -.display-controls{ +.display-controls { border-left: solid 2px #DDDDDD; padding-left: 1em } +.filter-row { + margin-top:0.4em; +} .slider-row { - margin-top: 0.4em; margin-left: 1em; } .elt-label { --- a/static/scripts/packed/trackster.js Mon Oct 17 14:19:34 2011 -0400 +++ b/static/scripts/packed/trackster.js Mon Oct 17 15:50:10 2011 -0400 @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};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 trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),M=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,H=9,E=20,U=H+2,A=100,J=12000,S=200,D=5,w=10,L=5000,x=100,p="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var I=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(I.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(R.prototype,r.prototype,z.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;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 ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new O(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(K)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var O=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){O.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new X(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var P=function(ai,ah){M.AlphaGenerator.call(this,ah);this.filter=ai};P.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(G.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:L);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(F)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var N=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(N.prototype,r.prototype,j.prototype,{to_json: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,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:E-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});N.call(this);ah.reference_track=this;this.left_offset=200;this.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:ah.dbkey};this.data_manager=new I(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);N.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,N.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new M.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);N.call(this,ak,al);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};q(e.prototype,r.prototype,N.prototype,{postdraw_actions:function(ax,ah,ay,aw){N.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aL=am[0],ai=am[1],ay=ai-aL,aC=Math.ceil(ay*ar),aP=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aO=aw.data;if(this.view.high-this.view.low>J){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aL,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new M.SummaryTreePainter(aw,aL,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,U);aM.draw(aD,aC,an);return new l(aB,aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aK=0,aN=au.length;aK<aN;aK++){av=au[aK];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new P(this.filters_manager.alpha_filter):null);var aM=new (this.painter)(aq,aL,ai,this.prefs,az,aA,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aJ=null;aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aJ=aM.draw(aD,aC,an,ax);aJ.translation=-al}return new Q(aB,aI,aE,aj,aw.data,az,aw.message,aJ)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=M.VariantPainter};q(V.prototype,r.prototype,N.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,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=M.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,N.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,N.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=L;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var g=function(z){this.default_alpha=(z?z:1)};g.prototype.gen_alpha=function(z){return this.default_alpha};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(C,E,z,B,D,A){n.call(this,C,E,z,B,D);this.alpha_generator=(A?A:new g())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,f=1,t=3,e=3,a=9,l=2,h="#ccc";var s=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(L,E,T,G,N,ae,ai,ak,z){var Q=T[0],ag=T[1],Y=T[2],O=T[3],Z=Math.floor(Math.max(0,(ag-N)*ai)),M=Math.ceil(Math.min(z,Math.max(0,(Y-N)*ai))),X=Z,aj=M,W=(E==="Dense"?0:(0+G))*ak,K,ac,P=null,al=null,C=this.prefs.block_color,ab=this.prefs.label_color;L.globalAlpha=this.alpha_generator.gen_alpha(T);if(E=="Dense"){G=1}if(E==="no_detail"){L.fillStyle=C;L.fillRect(Z,W+5,M-Z,f)}else{var J=T[4],V=T[5],aa=T[6],D=T[7];if(V&&aa){P=Math.floor(Math.max(0,(V-N)*ai));al=Math.ceil(Math.min(z,Math.max(0,(aa-N)*ai)))}var ah,R;if(E==="Squish"||E==="Dense"){ah=1;R=e}else{ah=5;R=a}if(!D){if(T.strand){if(T.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(T.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=C}L.fillRect(Z,W,M-Z,R)}else{var I,S;if(E==="Squish"||E==="Dense"){L.fillStyle=h;I=W+Math.floor(e/2)+1;S=1}else{if(J){var I=W;var S=R;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=h;I+=(e/2)+1;S=1}}L.fillRect(Z,I,M-Z,S);for(var af=0,B=D.length;af<B;af++){var F=D[af],A=Math.floor(Math.max(0,(F[0]-N)*ai)),U=Math.ceil(Math.min(z,Math.max((F[1]-N)*ai)));if(A>U){continue}L.fillStyle=C;L.fillRect(A,W+(R-ah)/2+1,U-A,ah);if(P!==undefined&&aa>V&&!(A>al||U<P)){var ad=Math.max(A,P),H=Math.min(U,al);L.fillRect(ad,W+1,H-ad,R);if(D.length==1&&E=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ad+14<H){ad+=2;H-=2}L.fillRect(ad,W+1,H-ad,R)}}}}if(E==="Pack"&&ag>N){L.fillStyle=ab;if(N===0&&Z-L.measureText(O).width<0){L.textAlign="left";L.fillText(O,M+l,W+8);aj+=L.measureText(O).width+l}else{L.textAlign="right";L.fillText(O,Z-l,W+8);X-=L.measureText(O).width+l}}}L.globalAlpha=1;return[X,aj]}});var b=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(D,F,z,C,E,A,B){p.call(this,D,F,z,C,E,A);this.ref_seq=B};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,e)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?e:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.AlphaGenerator=g;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(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 f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};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 trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(R.prototype,r.prototype,z.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;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 ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+" ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){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(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.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:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,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=N.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=A};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,f)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?f:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(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 --- a/static/scripts/trackster.js Mon Oct 17 14:19:34 2011 -0400 +++ b/static/scripts/trackster.js Mon Oct 17 15:50:10 2011 -0400 @@ -1804,7 +1804,7 @@ var sliders_div = $("<div/>").addClass("sliders").appendTo(this.parent_div); var manager = this; $.each(this.filters, function(index, filter) { - filter.container = $("<div/>").addClass("slider-row").appendTo(sliders_div); + filter.container = $("<div/>").addClass("filter-row slider-row").appendTo(sliders_div); // Set up filter label (name, values). var filter_label = $("<div/>").addClass("elt-label").appendTo(filter.container) @@ -1860,25 +1860,39 @@ // var display_controls_div = $("<div/>").addClass("display-controls").appendTo(this.parent_div), - header_text = $("<span/>").addClass("elt-label").text("Transparency:").appendTo(display_controls_div), - alpha_select = $("<select/>").attr("name", "alpha_dropdown").appendTo(display_controls_div); - - // Dropdown for selecting attribute to use for alpha channel manipulation. - this.alpha_filter = null; - $("<option/>").attr("value", -1).text("== None ==").appendTo(alpha_select); - for (var i = 0; i < this.filters.length; i++) { - $("<option/>").attr("value", i).text(this.filters[i].name).appendTo(alpha_select); - } - alpha_select.change(function() { - $(this).children("option:selected").each(function() { - var filterIndex = parseInt($(this).val()); - manager.alpha_filter = (filterIndex >= 0 ? manager.filters[filterIndex] : null); - manager.track.request_draw(true, true); - }) + formatting_div, + header_text, + select, + // TODO: find better way to specify and change control filters. + filter_controls_dict = { + "Transparency": function(new_filter) { manager.alpha_filter = new_filter; }, + "Height" : function(new_filter) { manager.height_filter = new_filter; } + }; + + $.each(filter_controls_dict, function(control_name, filter) { + // Display name and select option. + formatting_div = $("<div/>").addClass("filter-row").appendTo(display_controls_div), + header_text = $("<span/>").addClass("elt-label").text(control_name + ":").appendTo(formatting_div), + select = $("<select/>").attr("name", control_name + "_dropdown").css("float", "right").appendTo(formatting_div); + + // Dropdown for selecting filter. + $("<option/>").attr("value", -1).text("== None ==").appendTo(select); + for (var i = 0; i < manager.filters.length; i++) { + $("<option/>").attr("value", i).text(manager.filters[i].name).appendTo(select); + } + select.change(function() { + $(this).children("option:selected").each(function() { + var filterIndex = parseInt($(this).val()); + filter_controls_dict[control_name]( (filterIndex >= 0 ? manager.filters[filterIndex] : null) ); + manager.track.request_draw(true, true); + }) + }); + + // Clear floating. + $("<div style='clear: both;'/>").appendTo(formatting_div); }); // Clear floating. - // Add to clear floating layout. $("<div style='clear: both;'/>").appendTo(this.parent_div); }; @@ -1892,6 +1906,7 @@ filter.slider.slider("option", "values", [filter.min, filter.max]); } this.alpha_filter = null; + this.height_filter = null; }, run_on_dataset: function() { // Get or create dictionary item. @@ -1979,20 +1994,20 @@ }); /** - * Generates alpha values based on filter and feature's value for filter. + * Generates scale values based on filter and feature's value for filter. */ -var FilterAlphaGenerator = function(filter, default_alpha) { - painters.AlphaGenerator.call(this, default_alpha); +var FilterScaler = function(filter, default_val) { + painters.Scaler.call(this, default_val); this.filter = filter; }; -FilterAlphaGenerator.prototype.gen_alpha = function(feature_data) { - // If filter is not initalized yet, return default alpha. +FilterScaler.prototype.gen_val = function(feature_data) { + // If filter is not initalized yet, return default val. if (this.filter.high === Number.MAX_VALUE || this.filter.low === -Number.MAX_VALUE || this.filter.low === this.filter.high) { - return this.default_alpha; + return this.default_val; } - // Alpha value is ratio of (filter's value compared to low) to (complete filter range). + // Scaling value is ratio of (filter's value compared to low) to (complete filter range). return ( ( parseFloat(feature_data[this.filter.index]) - this.filter.low ) / ( this.filter.high - this.filter.low ) ); }; @@ -3419,9 +3434,10 @@ } // Create painter, and canvas of sufficient size to contain all features. - var filter_alpha_generator = (this.filters_manager.alpha_filter ? new FilterAlphaGenerator(this.filters_manager.alpha_filter) : null); + var filter_alpha_scaler = (this.filters_manager.alpha_filter ? new FilterScaler(this.filters_manager.alpha_filter) : null); + var filter_height_scaler = (this.filters_manager.height_filter ? new FilterScaler(this.filters_manager.height_filter) : null); // HACK: ref_seq will only be defined for ReadTracks, and only the ReadPainter accepts that argument - var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_generator, ref_seq); + var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_scaler, filter_height_scaler, ref_seq); var required_height = Math.max(MIN_TRACK_HEIGHT, painter.get_required_height(slots_required)); var canvas = this.view.canvas_manager.new_canvas(); var feature_mapper = null; @@ -3755,17 +3771,17 @@ }; /** - * Base class for all alpha generators. + * Base class for all scalers. Scalers produce values that are used to change (scale) drawing attributes. */ -var AlphaGenerator = function(default_alpha) { - this.default_alpha = (default_alpha ? default_alpha : 1); +var Scaler = function(default_val) { + this.default_val = (default_val ? default_val : 1); }; /** - * Base method for generating an alpha channel value; returns default alpha if not implemented. + * Produce a scaling value. */ -AlphaGenerator.prototype.gen_alpha = function(data) { - return this.default_alpha; +Scaler.prototype.gen_val = function(input) { + return this.default_val; }; /** @@ -4008,9 +4024,10 @@ /** * Abstract object for painting feature tracks. Subclasses must implement draw_element() for painting to work. */ -var FeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_generator) { +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_generator = (alpha_generator ? alpha_generator : new AlphaGenerator()); + 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" }; @@ -4085,8 +4102,8 @@ LABEL_SPACING = 2, CONNECTOR_COLOR = "#ccc"; -var LinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_generator) { - FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_generator); +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); }; extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, { @@ -4131,8 +4148,8 @@ label_color = this.prefs.label_color; // Set global alpha. - ctx.globalAlpha = this.alpha_generator.gen_alpha(feature); - + ctx.globalAlpha = this.alpha_scaler.gen_val(feature); + // In dense mode, put all data in top slot. if (mode == "Dense") { slot = 1; @@ -4141,7 +4158,6 @@ if (mode === "no_detail") { // No details for feature, so only one way to display. ctx.fillStyle = block_color; - // TODO: what should width be here? ctx.fillRect(f_start, y_center + 5, f_end - f_start, NO_DETAIL_FEATURE_HEIGHT); } else { // Mode is either Squish or Pack: @@ -4181,6 +4197,7 @@ } ctx.fillRect(f_start, y_center, f_end - f_start, thick_height); } else { + // // There are feature blocks and mode is either Squish or Pack. // // Approach: (a) draw whole feature as connector/intron and (b) draw blocks as @@ -4213,6 +4230,8 @@ } ctx.fillRect(f_start, cur_y_center, f_end - f_start, cur_height); + // Draw blocks. + 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) ), @@ -4223,17 +4242,16 @@ // Draw thin block. ctx.fillStyle = block_color; - ctx.fillRect(block_start, y_center + (thick_height-thin_height)/2 + 1, - block_end - block_start, thin_height); + ctx.fillRect(block_start, y_center + (thick_height-thin_height)/2 + 1, block_end - block_start, thin_height ); // If block intersects with thick region, draw block as thick. // - No thick is sometimes encoded as thick_start == thick_end, so don't draw in that case 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); + 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") { - // Exactly one block means we have no introns, but do have a distinct "thick" region, + // Exactly one block means we have no introns, but do have a distinct "thick" region, // draw arrows over it if in pack mode if (feature_strand === "+") { ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand_inv' ); @@ -4245,12 +4263,33 @@ block_thick_start += 2; block_thick_end -= 2; } - ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height); + ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height ); } } } + + // FIXME: Height scaling only works in Pack mode right now. + if (mode === "Pack") { + // Reset alpha so height scaling is not impacted by alpha scaling. + ctx.globalAlpha = 1; + + // Height scaling: draw white lines to reduce height according to height scale factor. + ctx.fillStyle = "white"; // TODO: set this to background color. + var + hscale_factor = this.height_scaler.gen_val(feature), + // Ceil ensures that min height is >= 1. + 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); + } + } } + // Reset alpha so that label is not transparent. + ctx.globalAlpha = 1; + // Draw label for Pack mode. if (mode === "Pack" && feature_start > tile_low) { ctx.fillStyle = label_color; @@ -4276,8 +4315,8 @@ }); -var VariantPainter = function(data, view_start, view_end, prefs, mode, alpha_generator) { - FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_generator); +var VariantPainter = 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); } extend(VariantPainter.prototype, FeaturePainter.prototype, { @@ -4334,8 +4373,8 @@ } }); -var ReadPainter = function(data, view_start, view_end, prefs, mode, alpha_generator, ref_seq) { - FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_generator); +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; }; @@ -4624,7 +4663,7 @@ } }); -exports.AlphaGenerator = AlphaGenerator; +exports.Scaler = Scaler; exports.SummaryTreePainter = SummaryTreePainter; exports.LinePainter = LinePainter; exports.LinkedFeaturePainter = LinkedFeaturePainter; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: PBS cluster error user messages now suggest retrying the job.
by Bitbucket 17 Oct '11

17 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2fed8f8737cd/ changeset: 2fed8f8737cd user: natefoo date: 2011-10-17 20:19:34 summary: PBS cluster error user messages now suggest retrying the job. affected #: 1 file (-1 bytes) --- a/lib/galaxy/jobs/runners/pbs.py Mon Oct 17 13:49:06 2011 -0400 +++ b/lib/galaxy/jobs/runners/pbs.py Mon Oct 17 14:19:34 2011 -0400 @@ -292,7 +292,7 @@ if not job_id: errno, text = pbs.error() log.debug( "(%s) pbs_submit failed, PBS error %d: %s" % (galaxy_job_id, errno, text) ) - job_wrapper.fail( "Unable to run this job due to a cluster error" ) + job_wrapper.fail( "Unable to run this job due to a cluster error, please retry it later" ) return if pbs_queue_name is None: @@ -419,7 +419,7 @@ assert int( status.exit_status ) == 0 log.debug("(%s/%s) PBS job has completed successfully" % ( galaxy_job_id, job_id ) ) except AssertionError: - pbs_job_state.fail_message = 'Job cannot be completed due to a cluster error. Please retry or' + pbs_job_state.fail_message = 'Job cannot be completed due to a cluster error, please retry it later' log.error( '(%s/%s) PBS job failed: %s' % ( galaxy_job_id, job_id, JOB_EXIT_STATUS.get( int( status.exit_status ), 'Unknown error: %s' % status.exit_status ) ) ) self.work_queue.put( ( 'fail', pbs_job_state ) ) continue Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix for loading a workflow that contains tools whose tools ids are the old version of tools ids, but whose available tools use the new tool guids as the tool id because the tools were installed from a Galaxy tool shed.
by Bitbucket 17 Oct '11

17 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/be6c89c33639/ changeset: be6c89c33639 user: greg date: 2011-10-17 19:49:06 summary: Fix for loading a workflow that contains tools whose tools ids are the old version of tools ids, but whose available tools use the new tool guids as the tool id because the tools were installed from a Galaxy tool shed. affected #: 1 file (-1 bytes) --- a/lib/galaxy/workflow/modules.py Mon Oct 17 12:22:27 2011 -0400 +++ b/lib/galaxy/workflow/modules.py Mon Oct 17 13:49:06 2011 -0400 @@ -209,9 +209,18 @@ @classmethod def from_workflow_step( Class, trans, step ): tool_id = step.tool_id + install_tool_id = None if tool_id not in trans.app.toolbox.tools_by_id: - return None - else: + for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): + if available_tool_id.find( tool_id ) >=0: + # We're attempting to match tool id against a tool guid. + # TODO: match by tool_id (and version if we attempt that, but + # workflows will break) is not good enough because + # 2 tools installed from a tool shed could both match this. We + # need to present a select list here. + install_tool_id = available_tool_id + break + if tool_id in trans.app.toolbox.tools_by_id or install_tool_id: module = Class( trans, tool_id ) module.state = DefaultToolState() module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) @@ -223,6 +232,7 @@ pjadict[pja.action_type] = pja module.post_job_actions = pjadict return module + return None def save_to_step( self, step ): step.type = self.type step.tool_id = self.tool_id Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Enhance automatic tool shed repository installation to enable installation of multiple repositories using a multi-select frid layout instead of installing just a single repository at a time.
by Bitbucket 17 Oct '11

17 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a0f021288c57/ changeset: a0f021288c57 user: greg date: 2011-10-17 18:22:27 summary: Enhance automatic tool shed repository installation to enable installation of multiple repositories using a multi-select frid layout instead of installing just a single repository at a time. affected #: 5 files (-1 bytes) --- a/lib/galaxy/web/controllers/admin.py Fri Oct 14 15:20:12 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon Oct 17 12:22:27 2011 -0400 @@ -688,8 +688,8 @@ @web.require_admin def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] - galaxy_url = trans.request.host - url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url ) + trans.set_cookie( trans.request.host, name='toolshedgalaxyurl' ) + url = '%s/repository/browse_downloadable_repositories?webapp=galaxy' % tool_shed_url return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -706,11 +706,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - tool_shed_url = kwd[ 'tool_shed_url' ] - name = kwd[ 'name' ] - description = kwd[ 'description' ] - changeset_revision = kwd[ 'changeset_revision' ] - repository_clone_url = kwd[ 'repository_clone_url' ] + tool_shed_url = trans.get_cookie( name='galaxytoolshedurl' ) if kwd.get( 'select_tool_panel_section_button', False ): shed_tool_conf = kwd[ 'shed_tool_conf' ] # Get the tool path. @@ -720,94 +716,104 @@ if 'tool_panel_section' in kwd: section_key = 'section_%s' % kwd[ 'tool_panel_section' ] tool_section = trans.app.toolbox.tool_panel[ section_key ] + # Get the number of repositories to clone from a cookie. + num_repos_to_clone = int( trans.get_cookie( name='numrepostoclone' ) ) # Clone the repository to the configured location. current_working_dir = os.getcwd() - clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) ) - if os.path.exists( clone_dir ): - # Repository and revision has already been cloned. - # TODO: implement the ability to re-install or revert an existing repository. - message = 'Revision <b>%s</b> of repository <b>%s</b> has already been installed. Updating an existing repository is not yet supported.' % \ - ( changeset_revision, name ) - status = 'error' - else: - os.makedirs( clone_dir ) - log.debug( 'Cloning %s...' % repository_clone_url ) - cmd = 'hg clone %s' % repository_clone_url - tmp_name = tempfile.NamedTemporaryFile().name - tmp_stderr = open( tmp_name, 'wb' ) - os.chdir( clone_dir ) - proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - os.chdir( current_working_dir ) - tmp_stderr.close() - if returncode == 0: - # Add a new record to the tool_shed_repository table. - tool_shed_repository = self.__create_tool_shed_repository( trans, - name, - description, - changeset_revision, - repository_clone_url ) - # Update the cloned repository to changeset_revision. - repo_files_dir = os.path.join( clone_dir, name ) - log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision ) - cmd = 'hg update -r %s' % changeset_revision + for index in range( 0, num_repos_to_clone ): + cookie_name = 'toolshedrepository%i' % index + clone_repo_info_str = trans.get_cookie( name=cookie_name ) + clone_repo_info_items = clone_repo_info_str.split( '&' ) + name = clone_repo_info_items[ 0 ] + description = clone_repo_info_items[ 1 ] + repository_clone_url = clone_repo_info_items[ 2 ] + changeset_revision = clone_repo_info_items[ 3 ] + clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) ) + if os.path.exists( clone_dir ): + # Repository and revision has already been cloned. + # TODO: implement the ability to re-install or revert an existing repository. + message += 'Revision <b>%s</b> of repository <b>%s</b> has already been installed. Updating an existing repository is not yet supported.<br/>' % \ + ( changeset_revision, name ) + status = 'error' + else: + os.makedirs( clone_dir ) + log.debug( 'Cloning %s...' % repository_clone_url ) + cmd = 'hg clone %s' % repository_clone_url tmp_name = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_name, 'wb' ) - os.chdir( repo_files_dir ) - proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() ) + os.chdir( clone_dir ) + proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) returncode = proc.wait() os.chdir( current_working_dir ) tmp_stderr.close() if returncode == 0: - sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir ) - if repository_tools_tups: - # Handle missing data table entries for tool parameters that are dynamically generated select lists. - repository_tools_tups = self.__handle_missing_data_table_entry( trans, tool_path, sample_files, repository_tools_tups ) - # Handle missing index files for tool parameters that are dynamically generated select lists. - repository_tools_tups = self.__handle_missing_index_file( trans, tool_path, sample_files, repository_tools_tups ) - # Handle tools that use fabric scripts to install dependencies. - self.__handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups ) - # Generate an in-memory tool conf section that includes the new tools. - new_tool_section = self.__generate_tool_panel_section( name, - repository_clone_url, + # Add a new record to the tool_shed_repository table. + tool_shed_repository = self.__create_tool_shed_repository( trans, + name, + description, changeset_revision, - tool_section, - repository_tools_tups ) - # Create a temporary file to persist the in-memory tool section - # TODO: Figure out how to do this in-memory using xml.etree. - tmp_name = tempfile.NamedTemporaryFile().name - persisted_new_tool_section = open( tmp_name, 'wb' ) - persisted_new_tool_section.write( new_tool_section ) - persisted_new_tool_section.close() - # Parse the persisted tool panel section - tree = ElementTree.parse( tmp_name ) - root = tree.getroot() - ElementInclude.include( root ) - # Load the tools in the section into the tool panel. - trans.app.toolbox.load_section_tag_set( root, trans.app.toolbox.tool_panel, tool_path ) - # Remove the temporary file - try: - os.unlink( tmp_name ) - except: - pass - # Append the new section to the shed_tool_config file. - self.__add_shed_tool_conf_entry( trans, shed_tool_conf, new_tool_section ) - if trans.app.toolbox_search.enabled: - # If search support for tools is enabled, index the new installed tools. - trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox ) - message = 'Revision <b>%s</b> of repository <b>%s</b> has been installed in tool panel section <b>%s</b>.' % \ - ( changeset_revision, name, tool_section.name ) - return trans.show_ok_message( message ) + repository_clone_url ) + # Update the cloned repository to changeset_revision. + repo_files_dir = os.path.join( clone_dir, name ) + log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision ) + cmd = 'hg update -r %s' % changeset_revision + tmp_name = tempfile.NamedTemporaryFile().name + tmp_stderr = open( tmp_name, 'wb' ) + os.chdir( repo_files_dir ) + proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + os.chdir( current_working_dir ) + tmp_stderr.close() + if returncode == 0: + sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir ) + if repository_tools_tups: + # Handle missing data table entries for tool parameters that are dynamically generated select lists. + repository_tools_tups = self.__handle_missing_data_table_entry( trans, tool_path, sample_files, repository_tools_tups ) + # Handle missing index files for tool parameters that are dynamically generated select lists. + repository_tools_tups = self.__handle_missing_index_file( trans, tool_path, sample_files, repository_tools_tups ) + # Handle tools that use fabric scripts to install dependencies. + self.__handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups ) + # Generate an in-memory tool conf section that includes the new tools. + new_tool_section = self.__generate_tool_panel_section( name, + repository_clone_url, + changeset_revision, + tool_section, + repository_tools_tups ) + # Create a temporary file to persist the in-memory tool section + # TODO: Figure out how to do this in-memory using xml.etree. + tmp_name = tempfile.NamedTemporaryFile().name + persisted_new_tool_section = open( tmp_name, 'wb' ) + persisted_new_tool_section.write( new_tool_section ) + persisted_new_tool_section.close() + # Parse the persisted tool panel section + tree = ElementTree.parse( tmp_name ) + root = tree.getroot() + ElementInclude.include( root ) + # Load the tools in the section into the tool panel. + trans.app.toolbox.load_section_tag_set( root, trans.app.toolbox.tool_panel, tool_path ) + # Remove the temporary file + try: + os.unlink( tmp_name ) + except: + pass + # Append the new section to the shed_tool_config file. + self.__add_shed_tool_conf_entry( trans, shed_tool_conf, new_tool_section ) + if trans.app.toolbox_search.enabled: + # If search support for tools is enabled, index the new installed tools. + trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox ) + message += 'Revision <b>%s</b> of repository <b>%s</b> has been loaded into tool panel section <b>%s</b>.<br/>' % \ + ( changeset_revision, name, tool_section.name ) + #return trans.show_ok_message( message ) + else: + tmp_stderr = open( tmp_name, 'rb' ) + message += '%s<br/>' % tmp_stderr.read() + tmp_stderr.close() + status = 'error' else: tmp_stderr = open( tmp_name, 'rb' ) - message = tmp_stderr.read() + message += '%s<br/>' % tmp_stderr.read() tmp_stderr.close() status = 'error' - else: - tmp_stderr = open( tmp_name, 'rb' ) - message = tmp_stderr.read() - tmp_stderr.close() - status = 'error' else: message = 'Choose the section in your tool panel to contain the installed tools.' status = 'error' @@ -819,11 +825,6 @@ shed_tool_conf_select_field = None tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) return trans.fill_template( '/admin/select_tool_panel_section.mako', - tool_shed_url=tool_shed_url, - name=name, - description=description, - changeset_revision=changeset_revision, - repository_clone_url=repository_clone_url, shed_tool_conf=shed_tool_conf, shed_tool_conf_select_field=shed_tool_conf_select_field, tool_panel_section_select_field=tool_panel_section_select_field, @@ -835,11 +836,12 @@ params = util.Params( kwd ) repository_id = params.get( 'id', None ) repository = get_repository( trans, repository_id ) - galaxy_url = trans.request.host + trans.set_cookie( trans.request.host, name='toolshedgalaxyurl' ) # Send a request to the relevant tool shed to see if there are any updates. # TODO: support https in the following url. - url = 'http://%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=community' % \ - ( repository.tool_shed, galaxy_url, repository.name, repository.owner, repository.changeset_revision ) + # TODO: Set cookies for name, owner, changeset-revision instead of sending in request + url = 'http://%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&webapp=community' % \ + ( repository.tool_shed, repository.name, repository.owner, repository.changeset_revision ) return trans.response.send_redirect( url ) @web.expose @web.require_admin --- a/lib/galaxy/web/controllers/workflow.py Fri Oct 14 15:20:12 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Mon Oct 17 12:22:27 2011 -0400 @@ -1150,17 +1150,20 @@ if missing_tool_tups: if trans.user_is_admin(): # A required tool is not available in the local Galaxy instance. - # TODO: It would sure be nice to be able to redirec to a mako tempalte here that displays a nice - # page including the links to the configured tool shed instead of this stupd message, but trying + # TODO: It would sure be nice to be able to redirect to a mako template here that displays a nice + # page including the links to the configured tool sheds instead of this message, but trying # to get the panels back is a nightmare since workflow eliminates the Galaxy panels. Someone - #involved in workflow development needs to figure out what it will take to get the Galaxy panels back... + # involved in workflow development needs to figure out what it will take to be able to switch + # back and forth between Galaxy (with panels ) and the workflow view (without panels ), having + # the Galaxy panels displayed whenever in Galaxy. + trans.set_cookie( trans.request.host, name='toolshedgalaxyurl' ) galaxy_url = trans.request.host message += "The workflow requires the following tools that are not available in this Galaxy instance." message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>" for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items(): if tool_shed_url.endswith( '/' ): tool_shed_url = tool_shed_url.rstrip( '/' ) - url = '%s/repository/find_tools?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url ) + url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) for missing_tool_tup in missing_tool_tups: missing_tool_id = missing_tool_tup[0] url += '&tool_id=%s' % missing_tool_id --- a/lib/galaxy/webapps/community/controllers/repository.py Fri Oct 14 15:20:12 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Mon Oct 17 12:22:27 2011 -0400 @@ -284,8 +284,9 @@ # Grid definition title = "Repositories with required tools" operations = [ grids.GridOperation( "Preview and install tools", - url_args = dict( action='find_tools', - operation='install_tools' ), + url_args = dict( controller='repository', + action='find_tools', + webapp='community' ), allow_multiple=True, async_compatible=False ) ] @@ -383,6 +384,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'galaxy' ) # Set the toolshedgalaxyurl cookie so we can get back # to the calling local Galaxy instance. galaxy_url = kwd.get( 'galaxy_url', None ) @@ -390,11 +392,11 @@ trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() + is_admin = trans.user_is_admin() if operation == "view_or_manage_repository": repository_metadata = get_repository_metadata_by_id( trans, kwd[ 'id' ] ) repository_id = trans.security.encode_id( repository_metadata.repository.id ) repository = get_repository( trans, repository_id ) - is_admin = trans.user_is_admin() # The received id is a RepositoryMetadata.id, so we have to get the repository id. kwd[ 'id' ] = repository_id kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision @@ -407,7 +409,17 @@ action='view_repository', **kwd ) ) if operation == "preview and install tools": - pass + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + trans.set_cookie( trans.request.host, name='galaxytoolshedurl' ) + # TODO: support https in the following url. + url = 'http://%s/admin/install_tool_shed_repository' % ( galaxy_url ) + repos_to_clone = util.listify( kwd[ 'id' ] ) + num_repos_to_clone = len( repos_to_clone ) + trans.set_cookie( num_repos_to_clone, name='numrepostoclone' ) + for index in range( 0, num_repos_to_clone ): + repository_metadata_id = repos_to_clone[ index ] + self._set_clone_repository_cookie( trans, index, repository_metadata_id ) + return trans.response.send_redirect( url ) tool_ids = [ tid.lower() for tid in util.listify( kwd.get( 'tool_id', '' ) ) ] tool_names = [ tn.lower() for tn in util.listify( kwd.get( 'tool_name', '' ) ) ] tool_versions = [ tv.lower() for tv in util.listify( kwd.get( 'tool_version', '' ) ) ] @@ -499,6 +511,7 @@ else: tool_version = '' return trans.fill_template( '/webapps/community/repository/find_tools.mako', + webapp=webapp, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version, @@ -535,6 +548,16 @@ found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \ ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) return found + def _set_clone_repository_cookie( self, trans, index, repository_metadata_id ): + cookie_name = 'toolshedrepository%i' % index + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) + repository_id = trans.security.encode_id( repository.id ) + changeset_revision = repository_metadata.changeset_revision + # Redirect back to local Galaxy to perform install. + repository_clone_url = generate_clone_url( trans, repository_id ) + cookie_value = '%s&%s&%s&%s' % ( repository.name, repository.description, repository_clone_url, changeset_revision ) + trans.set_cookie( cookie_value, name=cookie_name ) @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): params = util.Params( kwd ) @@ -570,11 +593,11 @@ repository = get_repository( trans, repository_id ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) # Redirect back to local Galaxy to perform install. - tool_shed_url = trans.request.host + trans.set_cookie( trans.request.host, name='galaxytoolshedurl' ) repository_clone_url = generate_clone_url( trans, repository_id ) # TODO: support https in the following url. - url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&name=%s&description=%s&repository_clone_url=%s&changeset_revision=%s' % \ - ( galaxy_url, tool_shed_url, repository.name, repository.description, repository_clone_url, changeset_revision ) + url = 'http://%s/admin/install_tool_shed_repository?name=%s&description=%s&repository_clone_url=%s&changeset_revision=%s' % \ + ( galaxy_url, repository.name, repository.description, repository_clone_url, changeset_revision ) return trans.response.send_redirect( url ) @web.expose def check_for_updates( self, trans, **kwd ): @@ -588,14 +611,11 @@ owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) webapp = params.get( 'webapp', None ) - tool_shed_url = trans.request.host + trans.set_cookie( trans.request.host, name='galaxytoolshedurl' ) # Start building up the url to redirect back to the calling Galaxy instance. # TODO: support https in the following url. - url = 'http://%s/admin/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, tool_shed_url ) + url = 'http://%s/admin/update_to_changeset_revision' % galaxy_url repository = get_repository_by_name_and_owner( trans, name, owner ) - #if error: - # url += '&message=%s&status=error' % message - #else: url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ ( repository.name, repository.user.username, changeset_revision ) if changeset_revision == repository.tip: --- a/templates/admin/select_tool_panel_section.mako Fri Oct 14 15:20:12 2011 -0400 +++ b/templates/admin/select_tool_panel_section.mako Mon Oct 17 12:22:27 2011 -0400 @@ -23,9 +23,9 @@ <br/><div class="toolForm"> - <div class="toolFormTitle">Install tools from repository '${name}'</div> + <div class="toolFormTitle">Load tools into tool panel</div><div class="toolFormBody"> - <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository', tool_shed_url=tool_shed_url, name=name, description=description, changeset_revision=changeset_revision, repository_clone_url=repository_clone_url )}" method="post" > + <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository' )}" method="post" > %if shed_tool_conf_select_field: <div class="form-row"><label>Shed tool configuration file:</label> --- a/templates/webapps/community/repository/find_tools.mako Fri Oct 14 15:20:12 2011 -0400 +++ b/templates/webapps/community/repository/find_tools.mako Mon Oct 17 12:22:27 2011 -0400 @@ -23,7 +23,7 @@ strings if these types of strings are entered in more than one field. </div><div style="clear: both"></div> - <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools' )}" method="post" > + <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}" method="post" ><div class="form-row"><label>Tool id:</label><input name="tool_id" type="textfield" value="${tool_id}" size="40"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Enhance tool searching in tool shed repositories to enable multiple values in any of tool_id, tool_name, tool_version. In the tool shed search form, taking advantage of this feature requires comma-separated lists to be entered in the form fields.
by Bitbucket 14 Oct '11

14 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7d9bb95caaa7/ changeset: 7d9bb95caaa7 user: greg date: 2011-10-14 21:20:12 summary: Enhance tool searching in tool shed repositories to enable multiple values in any of tool_id, tool_name, tool_version. In the tool shed search form, taking advantage of this feature requires comma-separated lists to be entered in the form fields. affected #: 3 files (-1 bytes) --- a/lib/galaxy/web/controllers/workflow.py Fri Oct 14 15:12:45 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Fri Oct 14 15:20:12 2011 -0400 @@ -1157,14 +1157,15 @@ galaxy_url = trans.request.host message += "The workflow requires the following tools that are not available in this Galaxy instance." message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>" - for missing_tool_tup in missing_tool_tups: - missing_tool_id = missing_tool_tup[0] - for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items(): - if tool_shed_url.endswith( '/' ): - tool_shed_url = tool_shed_url.rstrip( '/' ) - url = '%s/repository/find_tools?tool_id=%s&galaxy_url=%s&webapp=community' % ( tool_shed_url, missing_tool_id, galaxy_url ) - message += '<a href="%s">%s</a><br/>' % ( url, tool_shed_name ) - status = 'error' + for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items(): + if tool_shed_url.endswith( '/' ): + tool_shed_url = tool_shed_url.rstrip( '/' ) + url = '%s/repository/find_tools?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url ) + for missing_tool_tup in missing_tool_tups: + missing_tool_id = missing_tool_tup[0] + url += '&tool_id=%s' % missing_tool_id + message += '<a href="%s">%s</a><br/>' % ( url, tool_shed_name ) + status = 'error' return trans.response.send_redirect( web.url_for( controller='admin', action='index', webapp='galaxy', --- a/lib/galaxy/webapps/community/controllers/repository.py Fri Oct 14 15:12:45 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Fri Oct 14 15:20:12 2011 -0400 @@ -280,8 +280,18 @@ .join( model.User.table ) \ .filter( self.model_class.table.c.repository_id == 0 ) +class InstallMatchedRepositoryListGrid( MatchedRepositoryListGrid ): + # Grid definition + title = "Repositories with required tools" + operations = [ grids.GridOperation( "Preview and install tools", + url_args = dict( action='find_tools', + operation='install_tools' ), + allow_multiple=True, + async_compatible=False ) ] + class RepositoryController( BaseUIController, ItemRatings ): + install_matched_repository_list_grid = InstallMatchedRepositoryListGrid() matched_repository_list_grid = MatchedRepositoryListGrid() downloadable_repository_list_grid = DownloadableRepositoryListGrid() repository_list_grid = RepositoryListGrid() @@ -366,11 +376,18 @@ url_args=url_args, allow_multiple=False, async_compatible=False ) ] - # Render the list view return self.downloadable_repository_list_grid( trans, **kwd ) @web.expose def find_tools( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + # Set the toolshedgalaxyurl cookie so we can get back + # to the calling local Galaxy instance. + galaxy_url = kwd.get( 'galaxy_url', None ) + if galaxy_url: + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if operation == "view_or_manage_repository": @@ -389,61 +406,98 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', **kwd ) ) - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - # Set the toolshedgalaxyurl cookie so we can get back - # to the calling local Galaxy instance. - galaxy_url = kwd.get( 'galaxy_url', None ) - if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) - tool_id = kwd.get( 'tool_id', '' ).lower() - tool_name = kwd.get( 'tool_name', '' ).lower() - tool_version = kwd.get( 'tool_version', '' ).lower() + if operation == "preview and install tools": + pass + tool_ids = [ tid.lower() for tid in util.listify( kwd.get( 'tool_id', '' ) ) ] + tool_names = [ tn.lower() for tn in util.listify( kwd.get( 'tool_name', '' ) ) ] + tool_versions = [ tv.lower() for tv in util.listify( kwd.get( 'tool_version', '' ) ) ] exact_matches = params.get( 'exact_matches', '' ) exact_matches_checked = CheckboxField.is_checked( exact_matches ) match_tuples = [] - if tool_id or tool_name or tool_version: + ok = True + if tool_ids or tool_names or tool_versions: for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): metadata = repository_metadata.metadata tools = metadata[ 'tools' ] - found = False for tool_dict in tools: - if tool_id and not tool_name and not tool_version: - tool_dict_tool_id = tool_dict[ 'id' ].lower() - found = ( tool_id == tool_dict_tool_id ) or \ - ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 ) - elif tool_name and not tool_id and not tool_version: - tool_dict_tool_name = tool_dict[ 'name' ].lower() - found = ( tool_name == tool_dict_tool_name ) or \ - ( not exact_matches_checked and tool_dict_tool_name.find( tool_name ) >= 0 ) - elif tool_version and not tool_id and not tool_name: - tool_dict_tool_version = tool_dict[ 'version' ].lower() - found = ( tool_version == tool_dict_tool_version ) or \ - ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 ) - elif tool_id and tool_name and not tool_version: - tool_dict_tool_id = tool_dict[ 'id' ].lower() - tool_dict_tool_name = tool_dict[ 'name' ].lower() - found = ( tool_id == tool_dict_tool_id and tool_name == tool_dict_tool_name ) or \ - ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) - elif tool_id and tool_version and not tool_name: - tool_dict_tool_id = tool_dict[ 'id' ].lower() - tool_dict_tool_version = tool_dict[ 'version' ].lower() - found = ( tool_id == tool_dict_tool_id and tool_version == tool_dict_tool_version ) or \ - ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_version.find( tool_version ) >= 0 ) - elif tool_version and tool_name and not tool_id: - tool_dict_tool_version = tool_dict[ 'version' ].lower() - tool_dict_tool_name = tool_dict[ 'name' ].lower() - found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \ - ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) - if found: - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - kwd[ 'match_tuples' ] = match_tuples - kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ - ( tool_id, tool_name, tool_version, str( exact_matches_checked ) ) - # Render the list view - return self.matched_repository_list_grid( trans, **kwd ) + if tool_ids and not tool_names and not tool_versions: + for tool_id in tool_ids: + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_names and not tool_ids and not tool_versions: + for tool_name in tool_names: + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_versions and not tool_ids and not tool_names: + for tool_version in tool_versions: + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_ids and tool_names and not tool_versions: + if len( tool_ids ) == len( tool_names ): + for i, tool_id in enumerate( tool_ids ): + tool_name = tool_names[ i ] + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + message = "No search performed - each field must contain the same number of comma-separated items." + status = "error" + ok = False + elif tool_ids and tool_versions and not tool_names: + if len( tool_ids ) == len( tool_versions ): + for i, tool_id in enumerate( tool_ids ): + tool_version = tool_versions[ i ] + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + message = "No search performed - each field must contain the same number of comma-separated items." + status = "error" + ok = False + elif tool_versions and tool_names and not tool_ids: + if len( tool_versions ) == len( tool_names ): + for i, tool_version in enumerate( tool_versions ): + tool_name = tool_names[ i ] + if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + message = "No search performed - each field must contain the same number of comma-separated items." + status = "error" + ok = False + if ok: + kwd[ 'match_tuples' ] = match_tuples + # Render the list view + if galaxy_url: + # Our request originated from a Galaxy instance, so we're listing tools + # that have been found for a workflow in Galaxy. + return self.install_matched_repository_list_grid( trans, **kwd ) + else: + if tool_ids: + tool_id_str = ','.join( tool_ids ) + else: + tool_id_str = '' + if tool_names: + tool_name_str = ','.join( tool_names ) + else: + tool_name_str = '' + if tool_versions: + tool_version_str = ','.join( tool_versions ) + else: + tool_version_str = '' + kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ + ( tool_id_str, tool_name_str, tool_version_str, str( exact_matches_checked ) ) + return self.matched_repository_list_grid( trans, **kwd ) exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) + if tool_ids: + tool_id = ','.join( tool_ids ) + else: + tool_id = '' + if tool_names: + tool_name = ','.join( tool_names ) + else: + tool_name = '' + if tool_versions: + tool_version = ','.join( tool_versions ) + else: + tool_version = '' return trans.fill_template( '/webapps/community/repository/find_tools.mako', tool_id=tool_id, tool_name=tool_name, @@ -451,6 +505,36 @@ exact_matches_check_box=exact_matches_check_box, message=message, status=status ) + def _in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): + found = False + if tool_id and not tool_name and not tool_version: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + found = ( tool_id == tool_dict_tool_id ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 ) + elif tool_name and not tool_id and not tool_version: + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_name.find( tool_name ) >= 0 ) + elif tool_version and not tool_id and not tool_name: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + found = ( tool_version == tool_dict_tool_version ) or \ + ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 ) + elif tool_id and tool_name and not tool_version: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_id == tool_dict_tool_id and tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) + elif tool_id and tool_version and not tool_name: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + tool_dict_tool_version = tool_dict[ 'version' ].lower() + found = ( tool_id == tool_dict_tool_id and tool_version == tool_dict_tool_version ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_version.find( tool_version ) >= 0 ) + elif tool_version and tool_name and not tool_id: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) + return found @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): params = util.Params( kwd ) --- a/templates/webapps/community/repository/find_tools.mako Fri Oct 14 15:12:45 2011 -0400 +++ b/templates/webapps/community/repository/find_tools.mako Fri Oct 14 15:20:12 2011 -0400 @@ -19,6 +19,8 @@ <div class="toolFormBody"><div class="form-row"> Valid tools are those that properly load in Galaxy. Enter any combination of the following tool attributes to locate matching valid tools. + Comma-separated strings may be entered in each field to expand search criteria. Each field must contain the same number of comma-separated + strings if these types of strings are entered in more than one field. </div><div style="clear: both"></div><form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools' )}" method="post" > Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0