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commit/galaxy-central: natefoo: It turns out that our old version of SQLAlchemy already has the Postgres/MySQL BIGINT types, it just needed the BigInteger SQLAlchemy type and SQLite BIGINT. And fix a bug found by Jack Zhu.
by Bitbucket 29 Aug '11

29 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/62d51750d7df/ changeset: 62d51750d7df user: natefoo date: 2011-08-29 15:32:26 summary: It turns out that our old version of SQLAlchemy already has the Postgres/MySQL BIGINT types, it just needed the BigInteger SQLAlchemy type and SQLite BIGINT. And fix a bug found by Jack Zhu. affected #: 1 file (946 bytes) --- a/lib/galaxy/model/custom_types.py Sun Aug 28 14:07:33 2011 -0400 +++ b/lib/galaxy/model/custom_types.py Mon Aug 29 09:32:26 2011 -0400 @@ -105,40 +105,12 @@ class BIGINT( BigInteger ): """The SQL BIGINT type.""" -class DBBigInteger( BigInteger ): +class SLBigInteger( BigInteger ): def get_col_spec( self ): return "BIGINT" -sqlalchemy.databases.postgres.PGBigInteger = DBBigInteger -sqlalchemy.databases.postgres.colspecs[BigInteger] = DBBigInteger -sqlalchemy.databases.sqlite.SLBigInteger = DBBigInteger -sqlalchemy.databases.sqlite.colspecs[BigInteger] = DBBigInteger - -class MSBigInteger( BigInteger, sqlalchemy.databases.mysql.MSInteger ): - """MySQL BIGINTEGER type.""" - - def __init__(self, display_width=None, **kw): - """Construct a BIGINTEGER. - - :param display_width: Optional, maximum display width for this number. - - :param unsigned: a boolean, optional. - - :param zerofill: Optional. If true, values will be stored as strings - left-padded with zeros. Note that this does not effect the values - returned by the underlying database API, which continue to be - numeric. - - """ - self.display_width = display_width - sqlalchemy.databases.mysql._NumericType.__init__(self, kw) - BigInteger.__init__(self, **kw) - - def get_col_spec(self): - if self.display_width is not None: - return self._extend("BIGINT(%(display_width)s)" % {'display_width': self.display_width}) - else: - return self._extend("BIGINT") - -sqlalchemy.databases.mysql.MSBigInteger = MSBigInteger -sqlalchemy.databases.mysql.colspecs[BigInteger] = MSBigInteger +sqlalchemy.databases.sqlite.SLBigInteger = SLBigInteger +sqlalchemy.databases.sqlite.colspecs[BigInteger] = SLBigInteger +sqlalchemy.databases.sqlite.ischema_names['BIGINT'] = SLBigInteger +sqlalchemy.databases.postgres.colspecs[BigInteger] = sqlalchemy.databases.postgres.PGBigInteger +sqlalchemy.databases.mysql.colspecs[BigInteger] = sqlalchemy.databases.mysql.MSBigInteger Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: add left_offset attribute to LineTrack so that line tracks can be set in overview.
by Bitbucket 28 Aug '11

28 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/434f99cdfd96/ changeset: 434f99cdfd96 user: jgoecks date: 2011-08-28 20:07:33 summary: Trackster: add left_offset attribute to LineTrack so that line tracks can be set in overview. affected #: 1 file (26 bytes) --- a/static/scripts/trackster.js Fri Aug 26 17:45:50 2011 -0400 +++ b/static/scripts/trackster.js Sun Aug 28 14:07:33 2011 -0400 @@ -2598,6 +2598,7 @@ this.original_dataset_id = dataset_id; this.data_manager = new DataManager(CACHED_DATA, this); this.tile_cache = new Cache(CACHED_TILES_LINE); + this.left_offset = 0; // Define track configuration this.track_config = new TrackConfig( { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: introduce collections of tracks. Track 'groups' can be created and tracks can be added or removed from groups. Currently groups do not have a dropdown menu and cannot be saved.
by Bitbucket 26 Aug '11

26 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/732ad7ebde0c/ changeset: 732ad7ebde0c user: jgoecks date: 2011-08-26 23:45:50 summary: Trackster: introduce collections of tracks. Track 'groups' can be created and tracks can be added or removed from groups. Currently groups do not have a dropdown menu and cannot be saved. affected #: 6 files (5.2 KB) --- a/static/june_2007_style/blue/trackster.css Fri Aug 26 16:04:53 2011 -0400 +++ b/static/june_2007_style/blue/trackster.css Fri Aug 26 17:45:50 2011 -0400 @@ -19,6 +19,8 @@ .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{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;} --- a/static/june_2007_style/trackster.css.tmpl Fri Aug 26 16:04:53 2011 -0400 +++ b/static/june_2007_style/trackster.css.tmpl Fri Aug 26 17:45:50 2011 -0400 @@ -126,7 +126,19 @@ 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 { + min-height: 20px; + border-top: 2px solid #888; + border-bottom: 2px solid #888; +} .track { /* border-top: solid #DDDDDD 1px; */ /* border-bottom: solid #DDDDDD 1px; */ --- a/static/scripts/packed/trackster.js Fri Aug 26 16:04:53 2011 -0400 +++ b/static/scripts/packed/trackster.js Fri Aug 26 17:45:50 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,U){var n=f("class").extend,p=f("slotting"),I=f("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"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")};n(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var C=function(ac,ad){ac.bind("drag",{handle:ad,relative:true},function(ah,ai){var ag=$(this).parent();var af=ag.children();var ae;for(ae=0;ae<af.length;ae++){if(ai.offsetY<$(af.get(ae)).position().top){break}}if(ae===af.length){if(this!==af.get(ae-1)){ag.append(this)}}else{if(this!==af.get(ae)){$(this).insertBefore(af.get(ae))}}}).bind("dragstart",function(){$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css("border","0px")})};U.sortable=C;var aa=16,D=9,A=20,P=D+2,w=100,F=12000,N=200,z=5,s=10,H=5000,t=100,m="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",q="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",d=10,r=5,y=5;function u(ac){return Math.round(ac*1000)/1000}var c=function(ac){this.num_elements=ac;this.clear()};n(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var O=function(ad,ac,ae){c.call(this,ad);this.track=ac;this.subset=(ae!==undefined?ae:true)};n(O.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am[am.length]=ac[ah].name}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,aj,an)})},get_data:function(ac,ag,ah,ad,af){var ae=this.get_data_from_cache(ac,ag,ah);if(ae){return ae}ae=this.load_data(ac,ag,ah,ad,af);this.set_data(ac,ag,ah,ae);return ae},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get_data_from_cache(ak,af,aj);if(!al){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=al.data[al.data.length-1][2]+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,aj,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,aj,am);new_data_available.resolve(am)});return new_data_available},get_data_from_cache:function(ac,ad,ae){return this.get(this.gen_key(ac,ad,ae))},set_data:function(ad,ae,af,ac){return this.set(this.gen_key(ad,ae,af),ac)},gen_key:function(ac,ae,af){var ad=ac+"_"+ae+"_"+af;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){O.call(this,ad,ac,ae)};n(E.prototype,O.prototype,c.prototype,{load_data:function(ae,ac,ag,ah,ad,af){if(ad>1){return}return O.prototype.load_data.call(this,ae,ac,ag,ah,ad,af)}});var Z=function(ac,af,ae,ad,ag){this.container=ac;this.chrom=null;this.vis_id=ae;this.dbkey=ad;this.title=af;this.tracks=[];this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ag);this.canvas_manager=new ab(ac.get(0).ownerDocument);this.reset()};n(Z.prototype,{init:function(ag){var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<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 ad=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ag);this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.content_div.click(function(ah){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ah){ac.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ai)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ac.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){var ak=Math.round(-ai/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ac.content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX),width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ac.container.offset().left,ah=Math.max(al.pageX,am.startX)-ac.container.offset().left,ak=(ac.high-ac.low),aj=ac.viewport_container.width();ac.update_location(Math.round(ai/aj*ak)+ac.low,Math.round(ah/aj*ak)+ac.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ac.high-ac.low),aj=ac.viewport_container.width(),al=ac.low;ac.low=Math.round(ai/aj*ak)+al;ac.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,this.top_labeltrack));this.add_label_track(new Y(this,this.nav_labeltrack));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ad,ae){ad.num=t;$.extend(ad,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ac=this;$.ajax({url:chrom_url,data:ad,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ad.chrom);return}if(ag.reference){ac.add_label_track(new x(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+t+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+t+"</option>"}ac.chrom_select.html(aj);if(ae){ae()}ac.chrom_start_index=ag.start_index},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}})},change_chrom:function(ag,ad,ai){if(!ag||ag==="None"){return}var af=this;if(ag==="previous"){af.load_chroms({low:this.chrom_start_index-t});return}if(ag==="next"){af.load_chroms({low:this.chrom_start_index+t});return}var ah=$.grep(af.chrom_data,function(ak,al){return ak.chrom===ag})[0];if(ah===undefined){af.load_chroms({chrom:ag},function(){af.change_chrom(ag,ad,ai)});return}else{if(ag!==af.chrom){af.chrom=ag;af.chrom_select.val(af.chrom);af.max_high=ah.len-1;af.reset();af.request_redraw(true);for(var aj=0,ac=af.tracks.length;aj<ac;aj++){var ae=af.tracks[aj];if(ae.init){ae.init()}}}if(ad!==undefined&&ai!==undefined){af.low=Math.max(ad,0);af.high=Math.min(ai,af.max_high)}af.reset_overview();af.request_redraw()}},go_to:function(ag){var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0].replace(/,/g,""),10);af=parseInt(ah[1].replace(/,/g,""),10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_track:function(ac){ac.view=this;ac.track_id=this.track_id_counter;this.tracks.push(ac);if(ac.init){ac.init()}ac.container_div.attr("id","track_"+ac.track_id);C(ac.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1;this.has_changes=true;this.update_intro_div()},add_label_track:function(ac){ac.view=this;this.label_tracks.push(ac)},remove_track:function(ad){this.has_changes=true;delete this.tracks[this.tracks.indexOf(ad)];this.num_tracks-=1;var ac=this;ad.container_div.fadeOut("slow",function(){$(this).remove();ac.update_intro_div()})},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.tracks),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}requestAnimationFrame(function(){ai._redraw(ak)})},_redraw:function(am){var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution=Math.pow(z,Math.ceil(Math.log((this.high-this.low)/N)/Math.log(z)));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae&&ae.enabled){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.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(ac){$.when(ac.get_overview_tile()).then(function(ad){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ad.canvas);view.overview_highlight.show().height(ad.canvas.height());view.overview_viewport.height(ad.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ac;ac.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 o=function(ae,ai){this.track=ae;this.name=ai.name;this.params=[];var ap=ai.params;for(var af=0;af<ap.length;af++){var ak=ap[af],ad=ak.name,ao=ak.label,ag=unescape(ak.html),aq=ak.value,am=ak.type;if(am==="number"){this.params[this.params.length]=new g(ad,ao,ag,aq,ak.min,ak.max)}else{if(am=="select"){this.params[this.params.length]=new K(ad,ao,ag,aq)}else{console.log("WARNING: unrecognized tool parameter type:",ad,am)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(at){at.stopPropagation()}).click(function(at){at.stopPropagation()}).bind("dblclick",function(at){at.stopPropagation()});var an=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var al=this.params;var aj=this;$.each(this.params,function(au,ax){var aw=$("<div>").addClass("param-row").appendTo(aj.parent_div);var at=$("<div>").addClass("param-label").text(ax.label).appendTo(aw);var av=$("<div/>").addClass("slider").html(ax.html).appendTo(aw);av.find(":input").val(ax.value);$("<div style='clear: both;'/>").appendTo(aw)});this.parent_div.find("input").click(function(){$(this).select()});var ar=$("<div>").addClass("param-row").appendTo(this.parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ar);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ar);var aj=this;ac.click(function(){aj.run_on_region()});ah.click(function(){aj.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ac={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ae=this.track,ad=ac.tool_id+ae.tool_region_and_parameters_str(ac.chrom,ac.low,ac.high),af;if(ae instanceof e){af=new R(ad,view,ae.hda_ldda,undefined,{},{},ae);af.change_mode(ae.mode)}this.track.add_track(af);af.content_div.text("Starting job.");this.run(ac,af,function(ag){af.dataset_id=ag.dataset_id;af.content_div.text("Running job.");af.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(G)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var K=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=ae;this.value=af};var g=function(ae,ad,ag,ah,af,ac){K.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};var h=function(ad,ac,ae,af){this.name=ad;this.index=ac;this.tool_id=ae;this.tool_exp_name=af};var S=function(ad,ac,ae,af){h.call(this,ad,ac,ae,af);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};n(S.prototype,{applies_to:function(ac){if(ac.length>this.index){return true}return false},keep:function(ac){if(!this.applies_to(ac)){return true}var ad=parseFloat(ac[this.index]);return(isNaN(ad)||(ad>=this.low&&ad<=this.high))},update_attrs:function(ad){var ac=false;if(!this.applies_to(ad)){return ac}if(ad[this.index]<this.min){this.min=Math.floor(ad[this.index]);ac=true}if(ad[this.index]>this.max){this.max=Math.ceil(ad[this.index]);ac=true}return ac},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ae=function(ah,af){var ag=af-ah;return(ag<=2?0.01:1)};var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ae(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(am,at){this.track=am;this.filters=[];for(var an=0;an<at.length;an++){var ao=at[an],au=ao.name,ac=ao.type,af=ao.index,ar=ao.tool_id,aq=ao.tool_exp_name;if(ac==="int"||ac==="float"){this.filters[an]=new S(au,af,ar,aq)}else{console.log("ERROR: unsupported filter: ",au,ac)}}var ag=function(av,aw,ax){av.click(function(){var ay=aw.text();max=parseFloat(ax.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ax.slider("option","values")){input_size=2*input_size+1;multi_value=true}aw.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ay).appendTo(aw).focus().select().click(function(az){az.stopPropagation()}).blur(function(){$(this).remove();aw.text(ay)}).keyup(function(aD){if(aD.keyCode===27){$(this).trigger("blur")}else{if(aD.keyCode===13){var aB=ax.slider("option","min"),az=ax.slider("option","max"),aC=function(aE){return(isNaN(aE)||aE>az||aE<aB)},aA=$(this).val();if(!multi_value){aA=parseFloat(aA);if(aC(aA)){alert("Parameter value must be in the range ["+aB+"-"+az+"]");return $(this)}}else{aA=aA.split("-");aA=[parseFloat(aA[0]),parseFloat(aA[1])];if(aC(aA[0])||aC(aA[1])){alert("Parameter value must be in the range ["+aB+"-"+az+"]");return $(this)}}ax.slider((multi_value?"values":"value"),aA)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(av){av.stopPropagation()}).click(function(av){av.stopPropagation()}).bind("dblclick",function(av){av.stopPropagation()}).bind("keydown",function(av){av.stopPropagation()});var ap=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ak=this;$.each(this.filters,function(ay,aA){aA.container=$("<div/>").addClass("slider-row").appendTo(ap);var az=$("<div/>").addClass("elt-label").appendTo(aA.container);var ax=$("<span/>").addClass("slider-name").text(aA.name+" ").appendTo(az);var aw=$("<span/>");var aC=$("<span/>").addClass("slider-value").appendTo(az).append("[").append(aw).append("]");var av=$("<div/>").addClass("slider").appendTo(aA.container);aA.control_element=$("<div/>").attr("id",aA.name+"-filter-control").appendTo(av);var aB=[0,0];aA.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aE,aF){var aD=aF.values;aw.text(aD[0]+"-"+aD[1]);aA.low=aD[0];aA.high=aD[1];ak.track.request_draw(true,true)},change:function(aD,aE){aA.control_element.slider("option","slide").call(aA.control_element,aD,aE)}});aA.slider=aA.control_element;aA.slider_label=aw;ag(aC,aw,aA.control_element);$("<div style='clear: both;'/>").appendTo(aA.container)});if(this.filters.length!==0){var ah=$("<div/>").addClass("param-row").appendTo(ap);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ah);var ae=this;aj.click(function(){ae.run_on_dataset()})}var al=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ai=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(al),ad=$("<select/>").attr("name","alpha_dropdown").appendTo(al);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ad);for(var an=0;an<this.filters.length;an++){$("<option/>").attr("value",an).text(this.filters[an].name).appendTo(ad)}ad.change(function(){$(this).children("option:selected").each(function(){var av=parseInt($(this).val());ak.alpha_filter=(av>=0?ak.filters[av]:null);ak.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};n(X.prototype,{reset_filters:function(){for(var ac=0;ac<this.filters.length;ac++){filter=this.filters[ac];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!=ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!=ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var L=function(ad,ac){I.AlphaGenerator.call(this,ac);this.filter=ad};L.prototype.gen_alpha=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var W=function(ac){this.track=ac.track;this.params=ac.params;this.values={};if(ac.saved_values){this.restore_values(ac.saved_values)}this.onchange=ac.onchange};n(W.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var ad=this;var ac=$("<div />");$.each(this.params,function(ah,af){if(!af.hidden){var ae="param_"+ah;var am=$("<div class='form-row' />").appendTo(ac);am.append($("<label />").attr("for",ae).text(af.label+":"));if(af.type==="bool"){am.append($('<input type="checkbox" />').attr("id",ae).attr("name",ae).attr("checked",ad.values[af.key]))}else{if(af.type==="color"){var aj=ad.values[af.key];var ai=$("<input />").attr("id",ae).attr("name",ae).val(aj);var ak=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ag=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ak);var al=$("<div/>").appendTo(ag).farbtastic({width:100,height:100,callback:ai,color:aj});$("<div />").append(ai).append(ak).appendTo(am).bind("click",function(an){ak.css({left:$(this).position().left+($(ai).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ak.hide();$(document).unbind("click.color-picker")});an.stopPropagation()})}else{am.append($("<input />").attr("id",ae).attr("name",ae).val(ad.values[af.key]))}}}});return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange()}}});var b=function(ae,ad,ac,af){this.index=ae;this.low=ae*N*ad;this.high=(ae+1)*N*ad;this.resolution=ad;this.canvas=$("<div class='track-tile'/>").append(ac);this.data=af;this.stale=false};var l=function(ae,ad,ac,af,ag){b.call(this,ae,ad,ac,af);this.max_val=ag};var M=function(ae,ad,ac,ag,af){b.call(this,ae,ad,ac,ag);this.message=af};var j=function(ad,ac,ag,ae,af){this.name=ad;this.view=ac;this.parent_element=ag;this.data_url=(ae?ae:default_data_url);this.data_url_extra_params={};this.data_query_wait=(af?af:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").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 class='draghandle' />").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.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"ToolDataFeatureTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.initial_canvas=undefined;ac.content_div.css("height","auto");ac.container_div.removeClass("nodata error pending");if(!ac.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id,chrom:ac.view.chrom},function(ad){if(!ad||ad==="error"||ad.kind==="error"){ac.container_div.addClass("error");ac.content_div.text(m);if(ad.message){var af=ac.view.tracks.indexOf(ac);var ae=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ad.message+"</pre>",{Close:hide_modal})});ac.content_div.append(ae)}}else{if(ad==="no converter"){ac.container_div.addClass("error");ac.content_div.text(G)}else{if(ad==="no data"||(ad.data!==undefined&&(ad.data===null||ad.data.length===0))){ac.container_div.addClass("nodata");ac.content_div.text(B)}else{if(ad==="pending"){ac.container_div.addClass("pending");ac.content_div.text(q);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(ad.status==="data"){if(ad.valid_chroms){ac.valid_chroms=ad.valid_chroms;ac.make_name_popup_menu()}ac.content_div.text(V);if(ac.view.chrom){ac.content_div.text("");ac.content_div.css("height",ac.height_px+"px");ac.enabled=true;$.when(ac.predraw_init()).done(function(){ac.container_div.removeClass("nodata error pending");ac.request_draw()})}}}}}}})},predraw_init:function(){},update_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(aj,ah,ak){var ad=this,al=ad.view;this.filters_manager=(aj!==undefined?new X(this,aj):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ah!==undefined&&obj_length(ah)>0?new o(this,ah):undefined);this.is_overview=false;this.parent_track=ak;this.child_tracks=[];if(ad.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ad.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();ad.container_div.append(ad.child_tracks_container);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(ad.display_modes!==undefined){if(ad.mode_div===undefined){ad.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ad.header_div);var ae=(ad.track_config&&ad.track_config.values.mode?ad.track_config.values.mode:ad.display_modes[0]);ad.mode=ae;ad.mode_div.text(ae);var ac={};for(var af=0,ai=ad.display_modes.length;af<ai;af++){var ag=ad.display_modes[af];ac[ag]=function(am){return function(){ad.change_mode(am)}}(ag)}make_popupmenu(ad.mode_div,ac)}else{ad.mode_div.hide()}}this.make_name_popup_menu()};n(J.prototype,j.prototype,{change_mode:function(ad){var ac=this;ac.mode_div.text(ad);ac.mode=ad;ac.track_config.values.mode=ad;ac.tile_cache.clear();ac.request_draw()},make_name_popup_menu:function(){var ad=this;var ac={};ac[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ad.is_overview){ad.view.reset_overview()}else{ad.view.set_overview(ad)}};ac["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ad.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Track",ad.track_config.build_form(),{Cancel:aj,OK:ah})};if(ad.filters_available>0){var ag=(ad.filters_div.is(":visible")?"Hide filters":"Show filters");ac[ag]=function(){ad.filters_visible=(ad.filters_div.is(":visible"));if(ad.filters_visible){ad.filters_manager.reset_filters()}ad.filters_div.toggle();ad.make_name_popup_menu()}}if(ad.tool){var ag=(ad.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ac[ag]=function(){if(!ad.dynamic_tool_div.is(":visible")){ad.update_name(ad.name+ad.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ad.revert_name()}ad.dynamic_tool_div.toggle();ad.make_name_popup_menu()}}if(ad.valid_chroms){ac["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ad.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ae=view;var af=function(){$("#no-tracks").show()};if(this.parent_track){ae=this.parent_track;af=function(){}}ac.Remove=function(){ae.remove_track(ad);if(ae.num_tracks===0){af()}};make_popupmenu(ad.name_div,ac)},set_is_overview:function(ac){this.is_overview=ac;this.make_name_popup_menu()},get_overview_tile:function(){var ac=this;view=ac.view,resolution=Math.pow(z,Math.ceil(Math.log((view.max_high-view.max_low)/N)/Math.log(z))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ac.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ac.data_url_extra_params)).then(function(ad){var af=ac._gen_tile_cache_key(view_width,w_scale,0),ah=ac.tile_cache.get(af);if(!ah){ah=ac.draw_tile(ad,resolution,0,w_scale);ac.tile_cache.set(af,ah)}var ak=$(ah.canvas.find("canvas")),ag=ak.clone(),aj=ak.get(0).getContext("2d"),ae=ag.get(0).getContext("2d"),ai=aj.getImageData(0,0,aj.canvas.width,aj.canvas.height);ae.putImageData(ai,-ac.left_offset,(ah.data.dataset_type==="summary_tree"?P:0));new_tile=new b(-1,resolution,ag);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},_draw:function(ae,an){if(!this.dataset_id){return}var am=this.view.low,ai=this.view.high,ak=ai-am,af=this.view.container.width(),aq=af/ak,ah=this.view.resolution,ap=$("<div style='position: relative;'></div>");if(!an){this.content_div.children().remove()}this.content_div.append(ap);this.max_height=0;var ad=Math.floor(am/ah/N);var al=true;var ao=[];var ac=0;while((ad*N*ah)<ai){tile=this.draw_helper(ae,af,ad,ah,ap,aq);if(tile){ao.push(tile)}else{al=false}ad+=1;ac++}var ag=this;if(al){ag.postdraw_actions(ao,af,aq,an)}for(var aj=0;aj<this.child_tracks.length;aj++){this.child_tracks[aj].request_draw(ae,an)}},postdraw_actions:function(ag,ah,ai,ac){var ae=this;var af=false;for(var ad=0;ad<ag.length;ad++){if(ag[ad].message){af=true;break}}if(af){for(var ad=0;ad<ag.length;ad++){tile=ag[ad];if(!tile.message){tile.canvas.css("padding-top",A)}}}},draw_helper:function(ad,ae,af,ai,ao,at,ap,aj){var ag=this,an=this._gen_tile_cache_key(ae,at,af),ak=af*N*ai,ar=ak+N*ai;var al=(ad?undefined:ag.tile_cache.get(an));if(al){ag.show_tile(al,ao,at);return al}var am=function(au){return("isResolved" in au)};var ah=true;var ac=ag.data_manager.get_data(ak,ar,ag.mode,ai,ag.data_url_extra_params);if(am(ac)){ah=false}var aq;if(view.reference_track&&at>view.canvas_manager.char_width_px){aq=view.reference_track.data_manager.get_data(ak,ar,ag.mode,ai,view.reference_track.data_url_extra_params);if(am(aq)){ah=false}}if(ah){n(ac,aj);var al=ag.draw_tile(ac,ai,af,at,aq);ag.tile_cache.set(an,al);if(al!==undefined){ag.show_tile(al,ao,at)}return al}$.when(ac,aq).then(function(){view.request_redraw()});return null},show_tile:function(aj,al,am){var ae=this,ad=aj.canvas,ai=ad;if(aj.message){var an=$("<div/>"),ak=$("<div/>").addClass("tile-message").text(aj.message).css({height:A-1,width:aj.canvas.width}).appendTo(an),ag=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ak),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ak);an.append(ad);ai=an;ag.click(function(){aj.stale=true;ae.data_manager.get_more_data(aj.low,aj.high,ae.mode,aj.resolution,{},ae.data_manager.DEEP_DATA_REQ);ae.request_draw()}).dblclick(function(ao){ao.stopPropagation()});ac.click(function(){aj.stale=true;ae.data_manager.get_more_data(aj.low,aj.high,ae.mode,aj.resolution,{},ae.data_manager.BROAD_DATA_REQ);ae.request_draw()}).dblclick(function(ao){ao.stopPropagation()})}var ah=this.view.high-this.view.low,af=(aj.low-this.view.low)*am;if(this.left_offset){af-=this.left_offset}ai.css({position:"absolute",top:0,left:af,height:""});al.append(ai);ae.max_height=Math.max(ae.max_height,ai.height());ae.content_div.css("height",ae.max_height+"px");al.children().css("height",ae.max_height+"px")},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},add_track:function(ac){ac.track_id=this.track_id+"_"+this.child_tracks.length;ac.container_div.attr("id","track_"+ac.track_id);this.child_tracks_container.append(ac.container_div);C(ac.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(ac);this.view.has_changes=true},remove_track:function(ac){ac.container_div.fadeOut("slow",function(){$(this).remove()})}});var Y=function(ac,ad){this.hidden=true;j.call(this,null,ac,ad);this.container_div.addClass("label-track")};n(Y.prototype,j.prototype,{_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var x=function(ac){this.hidden=true;j.call(this,null,ac,ac.top_labeltrack);J.call(this);ac.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:ac.dbkey};this.data_manager=new E(y,this,false);this.tile_cache=new c(r)};n(x.prototype,J.prototype,{draw_tile:function(ak,ah,ad,am){var ag=this,ae=N*ah;if(am>this.view.canvas_manager.char_width_px){if(ak===null){ag.content_div.css("height","0px");return}var af=this.view.canvas_manager.new_canvas();var al=af.getContext("2d");af.width=Math.ceil(ae*am+ag.left_offset);af.height=ag.height_px;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.round(ai*am);al.fillText(ak[ai],ac+ag.left_offset,10)}return new b(ad,ah,af,ak)}this.content_div.css("height","0px")}});var k=function(ag,ae,ah,ac,af){var ad=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ag,ae,ae.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ah;this.dataset_id=ac;this.original_dataset_id=ac;this.data_manager=new O(y,this);this.tile_cache=new c(r);this.track_config=new W({track:this,params:[{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:af,onchange:function(){ad.vertical_range=ad.prefs.max_value-ad.prefs.min_value;$("#linetrack_"+ad.track_id+"_minval").text(ad.prefs.min_value);$("#linetrack_"+ad.track_id+"_maxval").text(ad.prefs.max_value);ad.tile_cache.clear();ad.request_draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,J.prototype,{add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){af=true;ad.show()},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.content_div).css("height",ag);ac.height_px=ag;ac.request_draw(true)}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.track_config.values.height=ac.height_px}).appendTo(ac.container_div)},predraw_init:function(){var ac=this,ad=ac.view.tracks.indexOf(ac);ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ae){ac.container_div.addClass("line-track");var ag=ae.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){ac.prefs.min_value=ag.min;ac.prefs.max_value=ag.max;$("#track_"+ad+"_minval").val(ac.prefs.min_value);$("#track_"+ad+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ad+"_minval").text(u(ac.prefs.min_value));var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ad+"_maxval").text(u(ac.prefs.max_value));af.css({position:"absolute",top:"24px",left:"10px"});af.prependTo(ac.container_div);ah.css({position:"absolute",bottom:"2px",left:"10px"});ah.prependTo(ac.container_div)})},draw_tile:function(am,ag,ad,al){if(this.vertical_range===undefined){return}var ah=ad*N*ag,af=N*ag,ac=Math.ceil(af*al),aj=this.height_px;var ae=this.view.canvas_manager.new_canvas();ae.width=ac,ae.height=aj;var ak=ae.getContext("2d");var ai=new I.LinePainter(am.data,ah,ah+af,this.prefs,this.mode);ai.draw(ak,ac,aj);return new b(ad,ag,ae,am.data)}});var e=function(ac,ah,ag,ak,aj,ae,af,ai){var ad=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new W({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){ad.tile_cache.clear();ad.request_draw()}});this.prefs=this.track_config.values;j.call(this,ac,ah,ah.viewport_container);J.call(this,ae,af,ai);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ag;this.dataset_id=ak;this.original_dataset_id=ak;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new O(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{postdraw_actions:function(ar,ac,at,aq){J.prototype.postdraw_actions.call(this,ar,aq);var af=this;if(aq){var ah=af.content_div.children();var ai=false;for(var ag=ah.length-1,am=0;ag>=am;ag--){var ae=$(ah[ag]);if(ai){ae.remove()}else{if(ae.children().length!==0){ai=true}}}}if(af.mode=="Histogram"){var al=-1;for(var ag=0;ag<ar.length;ag++){var ap=ar[ag].max_val;if(ap>al){al=ap}}for(var ag=0;ag<ar.length;ag++){var ao=ar[ag];if(ao.max_val!==al){ao.canvas.remove();af.draw_helper(true,ac,ao.index,ao.resolution,ao.canvas.parent(),at,[],{max:al})}}}if(af.filters_manager){var ad=af.filters_manager.filters;for(var ak=0;ak<ad.length;ak++){ad[ak].update_ui_elt()}var aj=false,an;for(var ag=0;ag<ar.length;ag++){if(ar[ag].data.length){an=ar[ag].data[0];for(var ak=0;ak<ad.length;ak++){if(ad[ak].applies_to(an)){aj=true;break}}}}if(af.filters_available!==aj){af.filters_available=aj;if(!af.filters_available){af.filters_div.hide()}af.make_name_popup_menu()}}},update_auto_mode:function(ac){if(this.mode=="Auto"){if(ac=="no_detail"){ac="feature spans"}else{if(ac=="summary_tree"){ac="coverage histogram"}}this.mode_div.text("Auto ("+ac+")")}},incremental_slots:function(ag,ad,af){var ae=this.view.canvas_manager.dummy_context,ac=this.inc_slots[ag];if(!ac||(ac.mode!==af)){ac=new (p.FeatureSlotter)(ag,af==="Pack",w,function(ah){return ae.measureText(ah)});ac.mode=af;this.inc_slots[ag]=ac}return ac.slot_features(ad)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},draw_tile:function(ap,ay,aC,al,af){var av=this,aE=aC*N*ay,ad=(aC+1)*N*ay,ar=ad-aE,aw=Math.ceil(ar*al),at=this.mode,aI=25,ag=this.left_offset,aq,ah;if(at==="Auto"){if(ap.dataset_type==="summary_tree"){at=ap.dataset_type}else{if(ap.extra_info==="no_detail"){at="no_detail"}else{var aH=ap.data;if(this.view.high-this.view.low>F){at="Squish"}else{at="Pack"}}}this.update_auto_mode(at)}if(at==="summary_tree"||at==="Histogram"){ah=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ac=$("<div />").addClass("yaxislabel");ac.text(ap.max);ac.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ac.prependTo(this.container_div);var ae=this.view.canvas_manager.new_canvas();ae.width=aw+ag;ae.height=ah+P;if(ap.dataset_type!="summary_tree"){var am=this.get_summary_tree_data(ap.data,aE,ad,200);if(ap.max){am.max=ap.max}ap=am}var aF=new I.SummaryTreePainter(ap,aE,ad,this.prefs);var ax=ae.getContext("2d");ax.translate(ag,P);aF.draw(ax,aw,ah);return new l(aC,ay,ae,ap.data,ap.max)}var aq,aj=1;if(at==="no_detail"||at==="Squish"||at==="Pack"){aj=this.incremental_slots(al,ap.data,at);aq=this.inc_slots[al].slots}var ak=[];if(ap.data){var an=this.filters_manager.filters;for(var az=0,aB=ap.data.length;az<aB;az++){var ai=ap.data[az];var aA=false;var ao;for(var aD=0,aG=an.length;aD<aG;aD++){ao=an[aD];ao.update_attrs(ai);if(!ao.keep(ai)){aA=true;break}}if(!aA){ak.push(ai)}}}var au=(this.filters_manager.alpha_filter?new L(this.filters_manager.alpha_filter):null);var aF=new (this.painter)(ak,aE,ad,this.prefs,at,au,af);var ah=Math.max(aa,aF.get_required_height(aj));var ae=this.view.canvas_manager.new_canvas();ae.width=aw+ag;ae.height=ah;var ax=ae.getContext("2d");ax.fillStyle=this.prefs.block_color;ax.font=ax.canvas.manager.default_font;ax.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ap.data){ax.translate(ag,0);aF.draw(ax,aw,ah,aq)}return new M(aC,ay,ae,ap.data,ap.message)}});var Q=function(af,ad,ah,ac,ae,ag){e.call(this,af,ad,ah,ac,ae,ag);this.painter=I.VariantPainter};n(Q.prototype,J.prototype,e.prototype);var T=function(af,ad,ah,ac,ae,ag){e.call(this,af,ad,ah,ac,ae,ag);this.track_config=new W({track:this,params:[{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:ae,onchange:function(){this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.track_config.values;this.painter=I.ReadPainter;this.make_name_popup_menu()};n(T.prototype,J.prototype,e.prototype);var R=function(ag,ae,ai,ac,af,ah,ad){e.call(this,ag,ae,ai,ac,af,ah,{},ad);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(R.prototype,J.prototype,e.prototype,{predraw_init:function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=H;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}});U.View=Z;U.LineTrack=k;U.FeatureTrack=e;U.ReadTrack=T};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,x){var u=k("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=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(y){this.default_alpha=(y?y:1)};g.prototype.gen_alpha=function(y){return this.default_alpha};var n=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};n.prototype.default_prefs={};var v=function(A,C,y,z,B){n.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.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(y,C,E,F,A){n.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};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 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af=am;if(ai===this.DEEP_DATA_REQ){$.extend(ak,{start_val:an.data.length+1})}else{if(ai===this.BROAD_DATA_REQ){af=an.data[an.data.length-1][2]+1}}var ae=this,aj=this.load_data(af,ah,al,ag,ak);new_data_available=$.Deferred();this.set_data(am,ah,al,new_data_available);$.when(aj).then(function(ao){if(ao.data){ao.data=an.data.concat(ao.data);if(ao.message){ao.message=ao.message.replace(/[0-9]+/,ao.data.length)}}ae.set_data(am,ah,al,ao);new_data_available.resolve(ao)});return new_data_available},get_data_from_cache:function(ae,af,ag){return this.get(this.gen_key(ae,af,ag))},set_data:function(af,ag,ah,ae){return this.set(this.gen_key(af,ag,ah),ae)},gen_key:function(ae,ag,ah){var af=ae+"_"+ag+"_"+ah;return af},split_key:function(ae){return ae.split("_")}});var G=function(af,ae,ag){Q.call(this,af,ae,ag)};p(G.prototype,Q.prototype,c.prototype,{load_data:function(ag,ae,ai,aj,af,ah){if(af>1){return}return Q.prototype.load_data.call(this,ag,ae,ai,aj,af,ah)}});var ab=function(ae,ah,ag,af,ai){this.container=ae;this.chrom=null;this.vis_id=ag;this.dbkey=af;this.title=ah;this.tracks=[];this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ai);this.canvas_manager=new ad(ae.get(0).ownerDocument);this.reset()};p(ab.prototype,{init:function(ai){var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<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=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.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(){ae.zoom_out();ae.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ae.zoom_in();ae.request_redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ai);this.chrom_select.bind("change",function(){ae.change_chrom(ae.chrom_select.val())});this.content_div.click(function(aj){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(aj){ae.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/ae.viewport_container.width()*(ae.max_high-ae.max_low));ae.move_delta(-ak)});this.overview_close.click(function(){ae.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>ae.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=ae.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){var am=Math.round(-ak/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:ae.content_div.height()+ae.top_labeltrack.height()+ae.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-ae.container.offset().left,aj=Math.max(an.pageX,ao.startX)-ae.container.offset().left,am=(ae.high-ae.low),al=ae.viewport_container.width();ae.update_location(Math.round(ak/al*am)+ae.low,Math.round(aj/al*am)+ae.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(ae.high-ae.low),al=ae.viewport_container.width(),an=ae.low;ae.low=Math.round(ak/al*am)+an;ae.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();ae.request_redraw()});this.add_label_track(new aa(this,this.top_labeltrack));this.add_label_track(new aa(this,this.nav_labeltrack));$(window).bind("resize",function(){ae.resize_window()});$(document).bind("redraw",function(){ae.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ae,af){this.location_span.text(commatize(ae)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ae)+"-"+commatize(af))},load_chroms:function(af,ag){af.num=v;$.extend(af,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ae=this;$.ajax({url:chrom_url,data:af,dataType:"json",success:function(ai){if(ai.chrom_info.length===0){alert("Invalid chromosome: "+af.chrom);return}if(ai.reference){ae.add_label_track(new A(ae))}ae.chrom_data=ai.chrom_info;var al='<option value="">Select Chrom/Contig</option>';for(var ak=0,ah=ae.chrom_data.length;ak<ah;ak++){var aj=ae.chrom_data[ak].chrom;al+='<option value="'+aj+'">'+aj+"</option>"}if(ai.prev_chroms){al+='<option value="previous">Previous '+v+"</option>"}if(ai.next_chroms){al+='<option value="next">Next '+v+"</option>"}ae.chrom_select.html(al);if(ag){ag()}ae.chrom_start_index=ai.start_index},error:function(){alert("Could not load chroms for this dbkey:",ae.dbkey)}})},change_chrom:function(ai,af,ak){if(!ai||ai==="None"){return}var ah=this;if(ai==="previous"){ah.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){ah.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(ah.chrom_data,function(am,an){return am.chrom===ai})[0];if(aj===undefined){ah.load_chroms({chrom:ai},function(){ah.change_chrom(ai,af,ak)});return}else{if(ai!==ah.chrom){ah.chrom=ai;ah.chrom_select.val(ah.chrom);ah.max_high=aj.len-1;ah.reset();ah.request_redraw(true);for(var al=0,ae=ah.tracks.length;al<ae;al++){var ag=ah.tracks[al];if(ag.init){ag.init()}}}if(af!==undefined&&ak!==undefined){ah.low=Math.max(af,0);ah.high=Math.min(ak,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(ai){var am=this,ae,ah,af=ai.split(":"),ak=af[0],al=af[1];if(al!==undefined){try{var aj=al.split("-");ae=parseInt(aj[0].replace(/,/g,""),10);ah=parseInt(aj[1].replace(/,/g,""),10)}catch(ag){return false}}am.change_chrom(ak,ae,ah)},move_fraction:function(ag){var ae=this;var af=ae.high-ae.low;this.move_delta(ag*af)},move_delta:function(ag){var ae=this;var af=ae.high-ae.low;if(ae.low-ag<ae.max_low){ae.low=ae.max_low;ae.high=ae.max_low+af}else{if(ae.high-ag>ae.max_high){ae.high=ae.max_high;ae.low=ae.max_high-af}else{ae.high-=ag;ae.low-=ag}}ae.request_redraw()},add_track:function(ae){ae.view=this;ae.track_id=this.track_id_counter;this.tracks.push(ae);if(ae.init){ae.init()}ae.container_div.attr("id","track_"+ae.track_id);m(ae.container_div,ae.drag_handle);this.track_id_counter+=1;this.num_tracks+=1;this.has_changes=true;this.update_intro_div()},add_label_track:function(ae){ae.view=this;this.label_tracks.push(ae)},remove_track:function(af){this.has_changes=true;delete this.tracks[this.tracks.indexOf(af)];this.num_tracks-=1;var ae=this;af.container_div.fadeOut("slow",function(){$(this).remove();ae.update_intro_div()})},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(am,ae,al,af){var ak=this,ai=(af?[af]:ak.tracks),ag;var af;for(var aj=0;aj<ai.length;aj++){af=ai[aj];ag=-1;for(var ah=0;ah<ak.tracks_to_be_redrawn.length;ah++){if(ak.tracks_to_be_redrawn[ah][0]===af){ag=ah;break}}if(ag<0){ak.tracks_to_be_redrawn.push([af,ae,al])}else{ak.tracks_to_be_redrawn[aj][1]=ae;ak.tracks_to_be_redrawn[aj][2]=al}}requestAnimationFrame(function(){ak._redraw(am)})},_redraw:function(ao){var al=this.low,ah=this.high;if(al<this.max_low){al=this.max_low}if(ah>this.max_high){ah=this.max_high}var an=this.high-this.low;if(this.high!==0&&an<this.min_separation){ah=al+this.min_separation}this.low=Math.floor(al);this.high=Math.ceil(ah);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/P)/Math.log(C)));this.zoom_res=Math.pow(u,Math.max(0,Math.ceil(Math.log(this.resolution,u)/Math.log(u))));var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ap=13;this.overview_box.css({left:ae,width:Math.max(ap,ak)}).show();if(ak<ap){this.overview_box.css("left",ae-(ap-ak)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ak})}this.update_location(this.low,this.high);if(!ao){var ag,af,am;for(var ai=0,aj=this.tracks_to_be_redrawn.length;ai<aj;ai++){ag=this.tracks_to_be_redrawn[ai][0];af=this.tracks_to_be_redrawn[ai][1];am=this.tracks_to_be_redrawn[ai][2];if(ag&&ag.enabled){ag._draw(af,am)}}this.tracks_to_be_redrawn=[];for(ai=0,aj=this.label_tracks.length;ai<aj;ai++){this.label_tracks[ai]._draw()}}},zoom_in:function(af,ag){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ah=this.high-this.low,ai=ah/2+this.low,ae=(ah/this.zoom_factor)/2;if(af){ai=af/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ai-ae);this.high=Math.round(ai+ae);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);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(ae){$.when(ae.get_overview_tile()).then(function(af){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(af.canvas);view.overview_highlight.show().height(af.canvas.height());view.overview_viewport.height(af.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ae;ae.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 q=function(ag,ak){this.track=ag;this.name=ak.name;this.params=[];var ar=ak.params;for(var ah=0;ah<ar.length;ah++){var am=ar[ah],af=am.name,aq=am.label,ai=unescape(am.html),at=am.value,ao=am.type;if(ao==="number"){this.params[this.params.length]=new g(af,aq,ai,at,am.min,am.max)}else{if(ao=="select"){this.params[this.params.length]=new M(af,aq,ai,at)}else{console.log("WARNING: unrecognized tool parameter type:",af,ao)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(av){av.stopPropagation()}).click(function(av){av.stopPropagation()}).bind("dblclick",function(av){av.stopPropagation()});var ap=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var an=this.params;var al=this;$.each(this.params,function(aw,az){var ay=$("<div>").addClass("param-row").appendTo(al.parent_div);var av=$("<div>").addClass("param-label").text(az.label).appendTo(ay);var ax=$("<div/>").addClass("slider").html(az.html).appendTo(ay);ax.find(":input").val(az.value);$("<div style='clear: both;'/>").appendTo(ay)});this.parent_div.find("input").click(function(){$(this).select()});var au=$("<div>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(au);var ae=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(au);var al=this;ae.click(function(){al.run_on_region()});aj.click(function(){al.run_on_dataset()})};p(q.prototype,{get_param_values_dict:function(){var ae={};this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();ae[af]=JSON.stringify(ag)});return ae},get_param_values:function(){var af=[];var ae={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();if(ag){af[af.length]=ah}});return af},run_on_dataset:function(){var ae=this;ae.run({dataset_id:this.track.original_dataset_id,tool_id:ae.name},null,function(af){show_modal(ae.name+" is Running",ae.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ae={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ag=this.track,af=ae.tool_id+ag.tool_region_and_parameters_str(ae.chrom,ae.low,ae.high),ah;if(ag instanceof e){ah=new T(af,view,ag.hda_ldda,undefined,{},{},ag);ah.change_mode(ag.mode)}this.track.add_track(ah);ah.content_div.text("Starting job.");this.run(ae,ah,function(ai){ah.dataset_id=ai.dataset_id;ah.content_div.text("Running job.");ah.init()})},run:function(af,ag,ah){$.extend(af,this.get_param_values_dict());var ae=function(){$.getJSON(rerun_tool_url,af,function(ai){if(ai==="no converter"){ag.container_div.addClass("error");ag.content_div.text(I)}else{if(ai.error){ag.container_div.addClass("error");ag.content_div.text(x+ai.message)}else{if(ai==="pending"){ag.container_div.addClass("pending");ag.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ae,2000)}else{ah(ai)}}}})};ae()}});var M=function(af,ae,ag,ah){this.name=af;this.label=ae;this.html=ag;this.value=ah};var g=function(ag,af,ai,aj,ah,ae){M.call(this,ag,af,ai,aj);this.min=ah;this.max=ae};var h=function(af,ae,ag,ah){this.name=af;this.index=ae;this.tool_id=ag;this.tool_exp_name=ah};var U=function(af,ae,ag,ah){h.call(this,af,ae,ag,ah);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};p(U.prototype,{applies_to:function(ae){if(ae.length>this.index){return true}return false},keep:function(ae){if(!this.applies_to(ae)){return true}var af=parseFloat(ae[this.index]);return(isNaN(af)||(af>=this.low&&af<=this.high))},update_attrs:function(af){var ae=false;if(!this.applies_to(af)){return ae}if(af[this.index]<this.min){this.min=Math.floor(af[this.index]);ae=true}if(af[this.index]>this.max){this.max=Math.ceil(af[this.index]);ae=true}return ae},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ag=function(aj,ah){var ai=ah-aj;return(ai<=2?0.01:1)};var af=this.slider.slider("option","min"),ae=this.slider.slider("option","max");if(this.min<af||this.max>ae){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ag(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var Z=function(ao,av){this.track=ao;this.filters=[];for(var ap=0;ap<av.length;ap++){var aq=av[ap],aw=aq.name,ae=aq.type,ah=aq.index,au=aq.tool_id,at=aq.tool_exp_name;if(ae==="int"||ae==="float"){this.filters[ap]=new U(aw,ah,au,at)}else{console.log("ERROR: unsupported filter: ",aw,ae)}}var ai=function(ax,ay,az){ax.click(function(){var aA=ay.text();max=parseFloat(az.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(az.slider("option","values")){input_size=2*input_size+1;multi_value=true}ay.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aA).appendTo(ay).focus().select().click(function(aB){aB.stopPropagation()}).blur(function(){$(this).remove();ay.text(aA)}).keyup(function(aF){if(aF.keyCode===27){$(this).trigger("blur")}else{if(aF.keyCode===13){var aD=az.slider("option","min"),aB=az.slider("option","max"),aE=function(aG){return(isNaN(aG)||aG>aB||aG<aD)},aC=$(this).val();if(!multi_value){aC=parseFloat(aC);if(aE(aC)){alert("Parameter value must be in the range ["+aD+"-"+aB+"]");return $(this)}}else{aC=aC.split("-");aC=[parseFloat(aC[0]),parseFloat(aC[1])];if(aE(aC[0])||aE(aC[1])){alert("Parameter value must be in the range ["+aD+"-"+aB+"]");return $(this)}}az.slider((multi_value?"values":"value"),aC)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(ax){ax.stopPropagation()}).click(function(ax){ax.stopPropagation()}).bind("dblclick",function(ax){ax.stopPropagation()}).bind("keydown",function(ax){ax.stopPropagation()});var ar=$("<div/>").addClass("sliders").appendTo(this.parent_div);var am=this;$.each(this.filters,function(aA,aC){aC.container=$("<div/>").addClass("slider-row").appendTo(ar);var aB=$("<div/>").addClass("elt-label").appendTo(aC.container);var az=$("<span/>").addClass("slider-name").text(aC.name+" ").appendTo(aB);var ay=$("<span/>");var aE=$("<span/>").addClass("slider-value").appendTo(aB).append("[").append(ay).append("]");var ax=$("<div/>").addClass("slider").appendTo(aC.container);aC.control_element=$("<div/>").attr("id",aC.name+"-filter-control").appendTo(ax);var aD=[0,0];aC.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aG,aH){var aF=aH.values;ay.text(aF[0]+"-"+aF[1]);aC.low=aF[0];aC.high=aF[1];am.track.request_draw(true,true)},change:function(aF,aG){aC.control_element.slider("option","slide").call(aC.control_element,aF,aG)}});aC.slider=aC.control_element;aC.slider_label=ay;ai(aE,ay,aC.control_element);$("<div style='clear: both;'/>").appendTo(aC.container)});if(this.filters.length!==0){var aj=$("<div/>").addClass("param-row").appendTo(ar);var al=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(aj);var ag=this;al.click(function(){ag.run_on_dataset()})}var an=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ak=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(an),af=$("<select/>").attr("name","alpha_dropdown").appendTo(an);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(af);for(var ap=0;ap<this.filters.length;ap++){$("<option/>").attr("value",ap).text(this.filters[ap].name).appendTo(af)}af.change(function(){$(this).children("option:selected").each(function(){var ax=parseInt($(this).val());am.alpha_filter=(ax>=0?am.filters[ax]:null);am.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(Z.prototype,{reset_filters:function(){for(var ae=0;ae<this.filters.length;ae++){filter=this.filters[ae];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var am=function(aq,ao,ap){if(!(ao in aq)){aq[ao]=ap}return aq[ao]};var ag={},ae,af,ah;for(var ai=0;ai<this.filters.length;ai++){ae=this.filters[ai];if(ae.tool_id){if(ae.min!=ae.low){af=am(ag,ae.tool_id,[]);af[af.length]=ae.tool_exp_name+" >= "+ae.low}if(ae.max!=ae.high){af=am(ag,ae.tool_id,[]);af[af.length]=ae.tool_exp_name+" <= "+ae.high}}}var ak=[];for(var an in ag){ak[ak.length]=[an,ag[an]]}var al=ak.length;(function aj(av,ar){var ap=ar[0],aq=ap[0],au=ap[1],at="("+au.join(") and (")+")",ao={cond:at,input:av,target_dataset_id:av,tool_id:aq},ar=ar.slice(1);$.getJSON(run_tool_url,ao,function(aw){if(aw.error){show_modal("Filter Dataset","Error running tool "+aq,{Close:hide_modal})}else{if(ar.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{aj(aw.dataset_id,ar)}}})})(this.track.dataset_id,ak)}});var N=function(af,ae){K.AlphaGenerator.call(this,ae);this.filter=af};N.prototype.gen_alpha=function(ae){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ae[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var Y=function(ae){this.track=ae.track;this.params=ae.params;this.values={};if(ae.saved_values){this.restore_values(ae.saved_values)}this.onchange=ae.onchange};p(Y.prototype,{restore_values:function(ae){var af=this;$.each(this.params,function(ag,ah){if(ae[ah.key]!==undefined){af.values[ah.key]=ae[ah.key]}else{af.values[ah.key]=ah.default_value}})},build_form:function(){var af=this;var ae=$("<div />");$.each(this.params,function(aj,ah){if(!ah.hidden){var ag="param_"+aj;var ao=$("<div class='form-row' />").appendTo(ae);ao.append($("<label />").attr("for",ag).text(ah.label+":"));if(ah.type==="bool"){ao.append($('<input type="checkbox" />').attr("id",ag).attr("name",ag).attr("checked",af.values[ah.key]))}else{if(ah.type==="color"){var al=af.values[ah.key];var ak=$("<input />").attr("id",ag).attr("name",ag).val(al);var am=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(am);var an=$("<div/>").appendTo(ai).farbtastic({width:100,height:100,callback:ak,color:al});$("<div />").append(ak).append(am).appendTo(ao).bind("click",function(ap){am.css({left:$(this).position().left+($(ak).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){am.hide();$(document).unbind("click.color-picker")});ap.stopPropagation()})}else{ao.append($("<input />").attr("id",ag).attr("name",ag).val(af.values[ah.key]))}}}});return ae},update_from_form:function(ae){var ag=this;var af=false;$.each(this.params,function(ah,aj){if(!aj.hidden){var ak="param_"+ah;var ai=ae.find("#"+ak).val();if(aj.type==="float"){ai=parseFloat(ai)}else{if(aj.type==="int"){ai=parseInt(ai)}else{if(aj.type==="bool"){ai=ae.find("#"+ak).is(":checked")}}}if(ai!==ag.values[aj.key]){ag.values[aj.key]=ai;af=true}}});if(af){this.onchange()}}});var b=function(ag,af,ae,ah){this.index=ag;this.low=ag*P*af;this.high=(ag+1)*P*af;this.resolution=af;this.canvas=$("<div class='track-tile'/>").append(ae);this.data=ah;this.stale=false};var l=function(ag,af,ae,ah,ai){b.call(this,ag,af,ae,ah);this.max_val=ai};var O=function(ag,af,ae,ai,ah){b.call(this,ag,af,ae,ai);this.message=ah};var o=function(af,ae){this.name=af;this.view=ae;this.parent_element=ae.viewport_container};o.prototype.request_draw=function(){};o.prototype.draw=function(){};var y=function(af,ae){o.call(this,af,ae);this.members=[];this.drag_handle_class="group-handle";this.container_div=$("<div/>").addClass("group").appendTo(this.parent_element);this.container_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name").text(this.name).appendTo(this.container_div);this.content_div=$("<div/>").addClass("content-div").appendTo(this.container_div)};p(y.prototype,o.prototype,{request_draw:function(af,ae){},draw:function(){}});var j=function(af,ae,ai,ag,ah){this.name=af;this.view=ae;this.parent_element=ai;this.data_url=(ag?ag:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ah?ah:J);this.dataset_check_url=converted_datasets_state_url;this.drag_handle_class="draghandle";this.container_div=$("<div />").addClass("track").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.parent_element.append(this.container_div)};p(j.prototype,{get_type:function(){if(this instanceof aa){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof V){return"ReadTrack"}else{if(this instanceof T){return"ToolDataFeatureTrack"}else{if(this instanceof S){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.initial_canvas=undefined;ae.content_div.css("height","auto");ae.container_div.removeClass("nodata error pending");if(!ae.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ae.hda_ldda,dataset_id:ae.dataset_id,chrom:ae.view.chrom},function(af){if(!af||af==="error"||af.kind==="error"){ae.container_div.addClass("error");ae.content_div.text(n);if(af.message){var ah=ae.view.tracks.indexOf(ae);var ag=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+af.message+"</pre>",{Close:hide_modal})});ae.content_div.append(ag)}}else{if(af==="no converter"){ae.container_div.addClass("error");ae.content_div.text(I)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ae.container_div.addClass("nodata");ae.content_div.text(E)}else{if(af==="pending"){ae.container_div.addClass("pending");ae.content_div.text(s);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(af.status==="data"){if(af.valid_chroms){ae.valid_chroms=af.valid_chroms;ae.make_name_popup_menu()}ae.content_div.text(X);if(ae.view.chrom){ae.content_div.text("");ae.content_div.css("height",ae.height_px+"px");ae.enabled=true;$.when(ae.predraw_init()).done(function(){ae.container_div.removeClass("nodata error pending");ae.request_draw()})}}}}}}})},predraw_init:function(){},update_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var L=function(al,aj,am){var af=this,an=af.view;this.filters_manager=(al!==undefined?new Z(this,al):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new q(this,aj):undefined);this.is_overview=false;this.parent_track=am;this.child_tracks=[];if(af.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}af.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();af.container_div.append(af.child_tracks_container);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(af.display_modes!==undefined){if(af.mode_div===undefined){af.mode_div=$("<div class='right-float menubutton popup' />").appendTo(af.header_div);var ag=(af.track_config&&af.track_config.values.mode?af.track_config.values.mode:af.display_modes[0]);af.mode=ag;af.mode_div.text(ag);var ae={};for(var ah=0,ak=af.display_modes.length;ah<ak;ah++){var ai=af.display_modes[ah];ae[ai]=function(ao){return function(){af.change_mode(ao)}}(ai)}make_popupmenu(af.mode_div,ae)}else{af.mode_div.hide()}}this.make_name_popup_menu()};p(L.prototype,j.prototype,{change_mode:function(af){var ae=this;ae.mode_div.text(af);ae.mode=af;ae.track_config.values.mode=af;ae.tile_cache.clear();ae.request_draw()},make_name_popup_menu:function(){var af=this;var ae={};ae[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(af.is_overview){af.view.reset_overview()}else{af.view.set_overview(af)}};ae["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){af.track_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()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Track",af.track_config.build_form(),{Cancel:al,OK:aj})};if(af.filters_available>0){var ai=(af.filters_div.is(":visible")?"Hide filters":"Show filters");ae[ai]=function(){af.filters_visible=(af.filters_div.is(":visible"));if(af.filters_visible){af.filters_manager.reset_filters()}af.filters_div.toggle();af.make_name_popup_menu()}}if(af.tool){var ai=(af.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ae[ai]=function(){if(!af.dynamic_tool_div.is(":visible")){af.update_name(af.name+af.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";af.revert_name()}af.dynamic_tool_div.toggle();af.make_name_popup_menu()}}if(af.valid_chroms){ae["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+af.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ag=view;var ah=function(){$("#no-tracks").show()};if(this.parent_track){ag=this.parent_track;ah=function(){}}ae.Remove=function(){ag.remove_track(af);if(ag.num_tracks===0){ah()}};make_popupmenu(af.name_div,ae)},set_is_overview:function(ae){this.is_overview=ae;this.make_name_popup_menu()},get_overview_tile:function(){var ae=this;view=ae.view,resolution=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/P)/Math.log(C))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ae.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ae.data_url_extra_params)).then(function(af){var ah=ae._gen_tile_cache_key(view_width,w_scale,0),aj=ae.tile_cache.get(ah);if(!aj){aj=ae.draw_tile(af,resolution,0,w_scale);ae.tile_cache.set(ah,aj)}var am=$(aj.canvas.find("canvas")),ai=am.clone(),al=am.get(0).getContext("2d"),ag=ai.get(0).getContext("2d"),ak=al.getImageData(0,0,al.canvas.width,al.canvas.height);ag.putImageData(ak,-ae.left_offset,(aj.data.dataset_type==="summary_tree"?R:0));new_tile=new b(-1,resolution,ai);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(af,ag,ae){return af+"_"+ag+"_"+ae},request_draw:function(af,ae){this.view.request_redraw(false,af,ae,this)},_draw:function(ag,ap){if(!this.dataset_id){return}var ao=this.view.low,ak=this.view.high,am=ak-ao,ah=this.view.container.width(),at=ah/am,aj=this.view.resolution,ar=$("<div style='position: relative;'></div>");if(!ap){this.content_div.children().remove()}this.content_div.append(ar);this.max_height=0;var af=Math.floor(ao/aj/P);var an=true;var aq=[];var ae=0;while((af*P*aj)<ak){tile=this.draw_helper(ag,ah,af,aj,ar,at);if(tile){aq.push(tile)}else{an=false}af+=1;ae++}var ai=this;if(an){ai.postdraw_actions(aq,ah,at,ap)}for(var al=0;al<this.child_tracks.length;al++){this.child_tracks[al].request_draw(ag,ap)}},postdraw_actions:function(ai,aj,ak,ae){var ag=this;var ah=false;for(var af=0;af<ai.length;af++){if(ai[af].message){ah=true;break}}if(ah){for(var af=0;af<ai.length;af++){tile=ai[af];if(!tile.message){tile.canvas.css("padding-top",D)}}}},draw_helper:function(af,ag,ah,ak,aq,av,ar,al){var ai=this,ap=this._gen_tile_cache_key(ag,av,ah),am=ah*P*ak,au=am+P*ak;var an=(af?undefined:ai.tile_cache.get(ap));if(an){ai.show_tile(an,aq,av);return an}var ao=function(aw){return("isResolved" in aw)};var aj=true;var ae=ai.data_manager.get_data(am,au,ai.mode,ak,ai.data_url_extra_params);if(ao(ae)){aj=false}var at;if(view.reference_track&&av>view.canvas_manager.char_width_px){at=view.reference_track.data_manager.get_data(am,au,ai.mode,ak,view.reference_track.data_url_extra_params);if(ao(at)){aj=false}}if(aj){p(ae,al);var an=ai.draw_tile(ae,ak,ah,av,at);ai.tile_cache.set(ap,an);if(an!==undefined){ai.show_tile(an,aq,av)}return an}$.when(ae,at).then(function(){view.request_redraw()});return null},show_tile:function(al,an,ao){var ag=this,af=al.canvas,ak=af;if(al.message){var ap=$("<div/>"),am=$("<div/>").addClass("tile-message").text(al.message).css({height:D-1,width:al.canvas.width}).appendTo(ap),ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(am),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(am);ap.append(af);ak=ap;ai.click(function(){al.stale=true;ag.data_manager.get_more_data(al.low,al.high,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);ag.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ae.click(function(){al.stale=true;ag.data_manager.get_more_data(al.low,al.high,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);ag.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}var aj=this.view.high-this.view.low,ah=(al.low-this.view.low)*ao;if(this.left_offset){ah-=this.left_offset}ak.css({position:"absolute",top:0,left:ah,height:""});an.append(ak);ag.max_height=Math.max(ag.max_height,ak.height());ag.content_div.css("height",ag.max_height+"px");an.children().css("height",ag.max_height+"px")},tool_region_and_parameters_str:function(ag,ae,ah){var af=this,ai=(ag!==undefined&&ae!==undefined&&ah!==undefined?ag+":"+ae+"-"+ah:"all");return" - region=["+ai+"], parameters=["+af.tool.get_param_values().join(", ")+"]"},add_track:function(ae){ae.track_id=this.track_id+"_"+this.child_tracks.length;ae.container_div.attr("id","track_"+ae.track_id);this.child_tracks_container.append(ae.container_div);m(ae.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(ae);this.view.has_changes=true},remove_track:function(ae){ae.container_div.fadeOut("slow",function(){$(this).remove()})}});var aa=function(ae,af){this.hidden=true;j.call(this,null,ae,af);this.container_div.addClass("label-track")};p(aa.prototype,j.prototype,{_draw:function(){var ag=this.view,ah=ag.high-ag.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/ak)*ak,ai=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var aj=(ae-ag.low)/ah*ai;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:aj-1}));ae+=ak}this.content_div.children(":first").remove();this.content_div.append(af)}});var A=function(ae){this.hidden=true;j.call(this,null,ae,ae.top_labeltrack);L.call(this);ae.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:ae.dbkey};this.data_manager=new G(B,this,false);this.tile_cache=new c(t)};p(A.prototype,L.prototype,{draw_tile:function(am,aj,af,ao){var ai=this,ag=P*aj;if(ao>this.view.canvas_manager.char_width_px){if(am===null){ai.content_div.css("height","0px");return}var ah=this.view.canvas_manager.new_canvas();var an=ah.getContext("2d");ah.width=Math.ceil(ag*ao+ai.left_offset);ah.height=ai.height_px;an.font=an.canvas.manager.default_font;an.textAlign="center";for(var ak=0,al=am.length;ak<al;ak++){var ae=Math.round(ak*ao);an.fillText(am[ak],ae+ai.left_offset,10)}return new b(af,aj,ah,am)}this.content_div.css("height","0px")}});var k=function(ai,ag,aj,ae,ah){var af=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ai,ag,ag.viewport_container);L.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=aj;this.dataset_id=ae;this.original_dataset_id=ae;this.data_manager=new Q(B,this);this.tile_cache=new c(t);this.track_config=new Y({track:this,params:[{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:ah,onchange:function(){af.vertical_range=af.prefs.max_value-af.prefs.min_value;$("#linetrack_"+af.track_id+"_minval").text(af.prefs.min_value);$("#linetrack_"+af.track_id+"_maxval").text(af.prefs.max_value);af.tile_cache.clear();af.request_draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};p(k.prototype,L.prototype,{add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){ah=true;af.show()},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.content_div).css("height",ai);ae.height_px=ai;ae.request_draw(true)}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.track_config.values.height=ae.height_px}).appendTo(ae.container_div)},predraw_init:function(){var ae=this,af=ae.view.tracks.indexOf(ae);ae.vertical_range=undefined;return $.getJSON(ae.data_url,{stats:true,chrom:ae.view.chrom,low:null,high:null,hda_ldda:ae.hda_ldda,dataset_id:ae.dataset_id},function(ag){ae.container_div.addClass("line-track");var ai=ag.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){ae.prefs.min_value=ai.min;ae.prefs.max_value=ai.max;$("#track_"+af+"_minval").val(ae.prefs.min_value);$("#track_"+af+"_maxval").val(ae.prefs.max_value)}ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.total_frequency=ai.total_frequency;ae.container_div.find(".yaxislabel").remove();var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af+"_minval").text(w(ae.prefs.min_value));var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af+"_maxval").text(w(ae.prefs.max_value));ah.css({position:"absolute",top:"24px",left:"10px"});ah.prependTo(ae.container_div);aj.css({position:"absolute",bottom:"2px",left:"10px"});aj.prependTo(ae.container_div)})},draw_tile:function(ao,ai,af,an){if(this.vertical_range===undefined){return}var aj=af*P*ai,ah=P*ai,ae=Math.ceil(ah*an),al=this.height_px;var ag=this.view.canvas_manager.new_canvas();ag.width=ae,ag.height=al;var am=ag.getContext("2d");var ak=new K.LinePainter(ao.data,aj,aj+ah,this.prefs,this.mode);ak.draw(am,ae,al);return new b(af,ai,ag,ao.data)}});var e=function(ae,aj,ai,am,al,ag,ah,ak){var af=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new Y({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:al,onchange:function(){af.tile_cache.clear();af.request_draw()}});this.prefs=this.track_config.values;j.call(this,ae,aj,aj.viewport_container);L.call(this,ag,ah,ak);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ai;this.dataset_id=am;this.original_dataset_id=am;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new Q(20,this);this.left_offset=200;this.painter=K.LinkedFeaturePainter};p(e.prototype,L.prototype,{postdraw_actions:function(au,ae,av,at){L.prototype.postdraw_actions.call(this,au,at);var ah=this;if(at){var aj=ah.content_div.children();var ak=false;for(var ai=aj.length-1,ao=0;ai>=ao;ai--){var ag=$(aj[ai]);if(ak){ag.remove()}else{if(ag.children().length!==0){ak=true}}}}if(ah.mode=="Histogram"){var an=-1;for(var ai=0;ai<au.length;ai++){var ar=au[ai].max_val;if(ar>an){an=ar}}for(var ai=0;ai<au.length;ai++){var aq=au[ai];if(aq.max_val!==an){aq.canvas.remove();ah.draw_helper(true,ae,aq.index,aq.resolution,aq.canvas.parent(),av,[],{max:an})}}}if(ah.filters_manager){var af=ah.filters_manager.filters;for(var am=0;am<af.length;am++){af[am].update_ui_elt()}var al=false,ap;for(var ai=0;ai<au.length;ai++){if(au[ai].data.length){ap=au[ai].data[0];for(var am=0;am<af.length;am++){if(af[am].applies_to(ap)){al=true;break}}}}if(ah.filters_available!==al){ah.filters_available=al;if(!ah.filters_available){ah.filters_div.hide()}ah.make_name_popup_menu()}}},update_auto_mode:function(ae){if(this.mode=="Auto"){if(ae=="no_detail"){ae="feature spans"}else{if(ae=="summary_tree"){ae="coverage histogram"}}this.mode_div.text("Auto ("+ae+")")}},incremental_slots:function(ai,af,ah){var ag=this.view.canvas_manager.dummy_context,ae=this.inc_slots[ai];if(!ae||(ae.mode!==ah)){ae=new (r.FeatureSlotter)(ai,ah==="Pack",z,function(aj){return ag.measureText(aj)});ae.mode=ah;this.inc_slots[ai]=ae}return ae.slot_features(af)},get_summary_tree_data:function(ai,al,ag,au){if(au>ag-al){au=ag-al}var ap=Math.floor((ag-al)/au),at=[],ah=0;var aj=0,ak=0,ao,ar=0,am=[],aq,an;var af=function(ax,aw,ay,av){ax[0]=aw+ay*av;ax[1]=aw+(ay+1)*av};while(ar<au&&aj!==ai.length){var ae=false;for(;ar<au&&!ae;ar++){af(am,al,ar,ap);for(ak=aj;ak<ai.length;ak++){ao=ai[ak].slice(1,3);if(is_overlap(ao,am)){ae=true;break}}if(ae){break}}data_start_index=ak;at[at.length]=aq=[am[0],0];for(;ak<ai.length;ak++){ao=ai[ak].slice(1,3);if(is_overlap(ao,am)){aq[1]++}else{break}}if(aq[1]>ah){ah=aq[1]}ar++}return{max:ah,delta:ap,data:at}},draw_tile:function(ar,aA,aE,an,ah){var ax=this,aG=aE*P*aA,af=(aE+1)*P*aA,au=af-aG,ay=Math.ceil(au*an),av=this.mode,aK=25,ai=this.left_offset,at,aj;if(av==="Auto"){if(ar.dataset_type==="summary_tree"){av=ar.dataset_type}else{if(ar.extra_info==="no_detail"){av="no_detail"}else{var aJ=ar.data;if(this.view.high-this.view.low>H){av="Squish"}else{av="Pack"}}}this.update_auto_mode(av)}if(av==="summary_tree"||av==="Histogram"){aj=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ae=$("<div />").addClass("yaxislabel");ae.text(ar.max);ae.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ae.prependTo(this.container_div);var ag=this.view.canvas_manager.new_canvas();ag.width=ay+ai;ag.height=aj+R;if(ar.dataset_type!="summary_tree"){var ao=this.get_summary_tree_data(ar.data,aG,af,200);if(ar.max){ao.max=ar.max}ar=ao}var aH=new K.SummaryTreePainter(ar,aG,af,this.prefs);var az=ag.getContext("2d");az.translate(ai,R);aH.draw(az,ay,aj);return new l(aE,aA,ag,ar.data,ar.max)}var at,al=1;if(av==="no_detail"||av==="Squish"||av==="Pack"){al=this.incremental_slots(an,ar.data,av);at=this.inc_slots[an].slots}var am=[];if(ar.data){var ap=this.filters_manager.filters;for(var aB=0,aD=ar.data.length;aB<aD;aB++){var ak=ar.data[aB];var aC=false;var aq;for(var aF=0,aI=ap.length;aF<aI;aF++){aq=ap[aF];aq.update_attrs(ak);if(!aq.keep(ak)){aC=true;break}}if(!aC){am.push(ak)}}}var aw=(this.filters_manager.alpha_filter?new N(this.filters_manager.alpha_filter):null);var aH=new (this.painter)(am,aG,af,this.prefs,av,aw,ah);var aj=Math.max(ac,aH.get_required_height(al));var ag=this.view.canvas_manager.new_canvas();ag.width=ay+ai;ag.height=aj;var az=ag.getContext("2d");az.fillStyle=this.prefs.block_color;az.font=az.canvas.manager.default_font;az.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ar.data){az.translate(ai,0);aH.draw(az,ay,aj,at)}return new O(aE,aA,ag,ar.data,ar.message)}});var S=function(ah,af,aj,ae,ag,ai){e.call(this,ah,af,aj,ae,ag,ai);this.painter=K.VariantPainter};p(S.prototype,L.prototype,e.prototype);var V=function(ah,af,aj,ae,ag,ai){e.call(this,ah,af,aj,ae,ag,ai);this.track_config=new Y({track:this,params:[{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:ag,onchange:function(){this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.track_config.values;this.painter=K.ReadPainter;this.make_name_popup_menu()};p(V.prototype,L.prototype,e.prototype);var T=function(ai,ag,ak,ae,ah,aj,af){e.call(this,ai,ag,ak,ae,ah,aj,{},af);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};p(T.prototype,L.prototype,e.prototype,{predraw_init:function(){var af=this;var ae=function(){if(af.data_manager.size()===0){setTimeout(ae,300)}else{af.data_url=default_data_url;af.data_query_wait=J;af.dataset_state_url=converted_datasets_state_url;$.getJSON(af.dataset_state_url,{dataset_id:af.dataset_id,hda_ldda:af.hda_ldda},function(ag){})}};ae()}});W.View=ab;W.DrawableCollection=y;W.LineTrack=k;W.FeatureTrack=e;W.ReadTrack=V};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,x){var u=k("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=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(y){this.default_alpha=(y?y:1)};g.prototype.gen_alpha=function(y){return this.default_alpha};var n=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};n.prototype.default_prefs={};var v=function(A,C,y,z,B){n.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.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(y,C,E,F,A){n.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};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(B,D,y,A,C,z){n.call(this,B,D,y,A,C);this.alpha_generator=(z?z:new g())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(z){var y=y_scale=this.get_row_height(),A=this.mode;if(A==="no_detail"||A==="Squish"||A==="Pack"){y=z*y_scale}return y+Math.max(Math.round(y_scale/2),5)},draw:function(K,B,J,G){var E=this.data,H=this.view_start,L=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var O=this.view_end-this.view_start,N=B/O,A=this.get_row_height();for(var D=0,F=E.length;D<F;D++){var M=E[D],C=M[0],y=M[1],z=M[2],I=(G&&G[C]!==undefined?G[C]:null);if((y<L&&z>H)&&(this.mode=="Dense"||I!==null)){this.draw_element(K,this.mode,M,I,H,L,N,A,B)}}K.restore()},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.")}});var d=10,j=3,m=5,w=10,f=1,s=3,e=3,a=9,l=2,h="#ccc";var r=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=d}else{if(z==="no_detail"){y=j}else{if(z==="Squish"){y=m}else{y=w}}}return y},draw_element:function(K,D,S,F,M,ac,ag,ah,y){var P=S[0],ae=S[1],W=S[2],N=S[3],X=Math.floor(Math.max(0,(ae-M)*ag)),L=Math.ceil(Math.min(y,Math.max(0,(W-M)*ag))),V=(D==="Dense"?0:(0+F))*ah,J,aa,O=null,ai=null,B=this.prefs.block_color,Z=this.prefs.label_color;K.globalAlpha=this.alpha_generator.gen_alpha(S);if(D=="Dense"){F=1}if(D==="no_detail"){K.fillStyle=B;K.fillRect(X,V+5,L-X,f)}else{var I=S[4],U=S[5],Y=S[6],C=S[7];if(U&&Y){O=Math.floor(Math.max(0,(U-M)*ag));ai=Math.ceil(Math.min(y,Math.max(0,(Y-M)*ag)))}var af,Q;if(D==="Squish"||D==="Dense"){af=1;Q=e}else{af=5;Q=a}if(!C){if(S.strand){if(S.strand==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(S.strand==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}}else{K.fillStyle=B}K.fillRect(X,V,L-X,Q)}else{var H,R;if(D==="Squish"||D==="Dense"){K.fillStyle=h;H=V+Math.floor(e/2)+1;R=1}else{if(I){var H=V;var R=Q;if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand")}}}else{K.fillStyle=h;H+=(e/2)+1;R=1}}K.fillRect(X,H,L-X,R);for(var ad=0,A=C.length;ad<A;ad++){var E=C[ad],z=Math.floor(Math.max(0,(E[0]-M)*ag)),T=Math.ceil(Math.min(y,Math.max((E[1]-M)*ag)));if(z>T){continue}K.fillStyle=B;K.fillRect(z,V+(Q-af)/2+1,T-z,af);if(O!==undefined&&Y>U&&!(z>ai||T<O)){var 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T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+l-O,C+8)}else{R.textAlign="right";R.fillText(J,D-l-O,C+8)}R.fillStyle=V}}});x.AlphaGenerator=g;x.SummaryTreePainter=v;x.LinePainter=c;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.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 Aug 26 16:04:53 2011 -0400 +++ b/static/scripts/trackster.js Fri Aug 26 17:45:50 2011 -0400 @@ -143,13 +143,66 @@ // ---- Web UI specific utilities ---- /** - * Make `element` sortable in parent by dragging `handle` (a selector) + * Make `element` moveable within parent and sibling elements by dragging `handle` (a selector). */ -var sortable = function( element, handle ) { +var moveable = function( element, handle, container_selector ) { + // HACK: set default value for container selector. + container_selector = ".group"; + var css_border_props = {}; element.bind( "drag", { handle: handle, relative: true }, function ( e, d ) { - var parent = $(this).parent(); - var children = parent.children(); - var i; + var + parent = $(this).parent(), + children = parent.children(), + child, + container, + top, + bottom, + i; + + // + // Enable three types of dragging: (a) out of container; (b) into container; + // (c) sibling movement, aka sorting. Handle in this order for simplicity. + // + + // Handle dragging out of container. + container = $(this).parents(container_selector); + if (container.length !== 0) { + top = container.position().top; + bottom = top + container.outerHeight(); + if (d.offsetY < top) { + // Moving above container. + $(this).insertBefore(container); + return; + } + else if (d.offsetY > bottom) { + // Moving below container. + $(this).insertAfter(container); + return; + } + } + + // Handle dragging into container. + container = null; + for ( i = 0; i < children.length; i++ ) { + child = $(children.get(i)); + top = child.position().top; + bottom = top + child.outerHeight(); + // Dragging into container if child is a container and offset is inside container. + if ( child.is(container_selector) && this !== child.get(0) && + d.offsetY >= top && d.offsetY <= bottom ) { + // Append/prepend based on where offsetY is closest to and return. + if (d.offsetY - top < bottom - d.offsetY) { + child.find(".content-div").prepend(this); + } + else { + child.find(".content-div").append(this); + } + return; + } + } + + // Handle sibling movement, aka sorting. + // Determine new position for ( i = 0; i < children.length; i++ ) { if ( d.offsetY < $(children.get(i)).position().top ) { @@ -168,15 +221,19 @@ $(this).insertBefore( children.get(i) ); } }).bind("dragstart", function() { + css_border_props["border-top"] = element.css("border-top"); + css_border_props["border-bottom"] = element.css("border-bottom"); $(this).css({ "border-top": "1px solid blue", "border-bottom": "1px solid blue" }); }).bind("dragend", function() { - $(this).css("border", "0px"); + $(this).css(css_border_props); }); }; -exports.sortable = sortable; + +// TODO: do we need to export? +exports.moveable = moveable; /** * Init constants & functions used throughout trackster. @@ -823,7 +880,7 @@ this.tracks.push(track); if (track.init) { track.init(); } track.container_div.attr('id', 'track_' + track.track_id); - sortable( track.container_div, '.draghandle' ); + moveable(track.container_div, track.drag_handle); this.track_id_counter += 1; this.num_tracks += 1; this.has_changes = true; @@ -1756,6 +1813,44 @@ }; /** + * Base interface for all drawable objects. + * TODO: Tracks should use this interface. + */ +var Drawable = function(name, view) { + this.name = name; + this.view = view; + this.parent_element = view.viewport_container; +}; + +Drawable.prototype.request_draw = function() {}; +Drawable.prototype.draw = function() {}; + +/** + * A collection of drawable objects. + */ +var DrawableCollection = function(name, view) { + Drawable.call(this, name, view); + + // Attribute init. + this.members = []; + this.drag_handle_class = "group-handle"; + + // HTML elements. + this.container_div = $("<div/>").addClass("group").appendTo(this.parent_element); + this.container_div.append($("<div/>").addClass(this.drag_handle_class)); + this.name_div = $("<div/>").addClass("group-name").text(this.name).appendTo(this.container_div); + this.content_div = $("<div/>").addClass("content-div").appendTo(this.container_div); +}; +extend(DrawableCollection.prototype, Drawable.prototype, { + request_draw: function(force, clear_after) { + + }, + draw: function() { + + } +}); + +/** * Tracks are objects can be added to the View. * * Track object hierarchy: @@ -1780,6 +1875,7 @@ 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; + this.drag_handle_class = "draghandle"; // // Create HTML element structure for track. @@ -1787,7 +1883,7 @@ this.container_div = $("<div />").addClass('track').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 class='draghandle' />").appendTo(this.header_div); } + if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); } this.name_div = $("<div class='menubutton popup' />").appendTo(this.header_div); this.name_div.text(this.name); this.name_div.attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() ); @@ -2399,7 +2495,7 @@ child_track.track_id = this.track_id + "_" + this.child_tracks.length; child_track.container_div.attr('id', 'track_' + child_track.track_id); this.child_tracks_container.append(child_track.container_div); - sortable( child_track.container_div, '.child-track-icon' ); + moveable( child_track.container_div, '.child-track-icon' ); if (!$(this.child_tracks_container).is(":visible")) { this.child_tracks_container.show(); } @@ -3082,6 +3178,7 @@ // Exports exports.View = View; +exports.DrawableCollection = DrawableCollection; exports.LineTrack = LineTrack; exports.FeatureTrack = FeatureTrack; exports.ReadTrack = ReadTrack; --- a/templates/tracks/browser.mako Fri Aug 26 16:04:53 2011 -0400 +++ b/templates/tracks/browser.mako Fri Aug 26 17:45:50 2011 -0400 @@ -197,6 +197,10 @@ $("#viz-actions-button").css( "position", "relative" ); make_popupmenu( $("#viz-actions-button"), { "Add Tracks": add_tracks, + "Add Group": function() { + var group = new DrawableCollection("New Group", view); + view.add_track(group); + }, "Save": function() { // Show saving dialog box show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>"); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Eliminate the code for the long-unused tool shed datatypes.
by Bitbucket 26 Aug '11

26 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ef955e304925/ changeset: ef955e304925 user: greg date: 2011-08-26 22:04:53 summary: Eliminate the code for the long-unused tool shed datatypes. affected #: 3 files (247 bytes) --- a/lib/galaxy/webapps/community/app.py Fri Aug 26 15:59:29 2011 -0400 +++ b/lib/galaxy/webapps/community/app.py Fri Aug 26 16:04:53 2011 -0400 @@ -13,8 +13,6 @@ self.config = config.Configuration( **kwargs ) self.config.check() config.configure_logging( self.config ) - # Set up datatypes registry - self.datatypes_registry = galaxy.datatypes.registry.Registry( self.config.root, self.config.datatypes_config ) # Determine the database url if self.config.database_connection: db_url = self.config.database_connection --- a/lib/galaxy/webapps/community/config.py Fri Aug 26 15:59:29 2011 -0400 +++ b/lib/galaxy/webapps/community/config.py Fri Aug 26 16:04:53 2011 -0400 @@ -70,7 +70,6 @@ self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False self.cloud_controller_instance = False - self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) # Proxy features self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False ) self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) --- a/lib/galaxy/webapps/community/datatypes/__init__.py Fri Aug 26 15:59:29 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,196 +0,0 @@ -import sys, logging, tarfile -from galaxy.util import parse_xml -from galaxy.util.bunch import Bunch - -log = logging.getLogger( __name__ ) - -if sys.version_info[:2] == ( 2, 4 ): - from galaxy import eggs - eggs.require( 'ElementTree' ) - from elementtree import ElementTree -else: - from xml.etree import ElementTree - -class DatatypeVerificationError( Exception ): - pass - -class Registry( object ): - def __init__( self, root_dir=None, config=None ): - self.datatypes_by_extension = {} - if root_dir and config: - # Parse datatypes_conf.xml - tree = parse_xml( config ) - root = tree.getroot() - # Load datatypes and converters from config - log.debug( 'Loading datatypes from %s' % config ) - registration = root.find( 'registration' ) - for elem in registration.findall( 'datatype' ): - try: - extension = elem.get( 'extension', None ) - dtype = elem.get( 'type', None ) - model_object = elem.get( 'model', None ) - if extension and dtype: - fields = dtype.split( ':' ) - datatype_module = fields[0] - datatype_class = fields[1] - fields = datatype_module.split( '.' ) - module = __import__( fields.pop(0) ) - for mod in fields: - module = getattr( module, mod ) - self.datatypes_by_extension[extension] = getattr( module, datatype_class )() - log.debug( 'Loaded datatype: %s' % dtype ) - if model_object: - model_module, model_class = model_object.split( ':' ) - fields = model_module.split( '.' ) - module = __import__( fields.pop(0) ) - for mod in fields: - module = getattr( module, mod ) - self.datatypes_by_extension[extension].model_object = getattr( module, model_class ) - log.debug( 'Added model class: %s to datatype: %s' % ( model_class, dtype ) ) - except Exception, e: - log.warning( 'Error loading datatype "%s", problem: %s' % ( extension, str( e ) ) ) - def get_datatype_by_extension( self, ext ): - return self.datatypes_by_extension.get( ext, None ) - def get_datatype_extensions( self ): - rval = [] - for ext, datatype in self.datatypes_by_extension.items(): - rval.append( ext ) - return rval - -class Tool( object ): - def __init__( self, model_object=None ): - self.model_object = model_object - self.label = 'Tool' - def verify( self, f, xml_files=[], tool_tags={} ): - # xml_files and tool_tags will only be received if we're called from the ToolSuite.verify() method. - try: - tar = tarfile.open( f.name ) - except tarfile.ReadError, e: - raise DatatypeVerificationError( 'Error reading the archive, problem: %s' % str( e ) ) - if not xml_files: - # Make sure we're not uploading a tool suite - if filter( lambda x: x.lower().find( 'suite_config.xml' ) >= 0, tar.getnames() ): - raise DatatypeVerificationError( 'The archive includes a suite_config.xml file, so set the upload type to "Tool Suite".' ) - xml_files = filter( lambda x: x.lower().endswith( '.xml' ), tar.getnames() ) - if not xml_files: - raise DatatypeVerificationError( 'The archive does not contain any xml config files.' ) - for xml_file in xml_files: - try: - tree = ElementTree.parse( tar.extractfile( xml_file ) ) - root = tree.getroot() - except Exception, e: - raise DatatypeVerificationError( 'Error parsing file "%s", problem: %s' % ( str( xml_file ), str( e ) ) ) - if root.tag == 'tool': - if 'id' not in root.keys(): - raise DatatypeVerificationError( "Tool xml file (%s) does not include the required 'id' attribute in the <tool> tag" % str( xml_file ) ) - if 'name' not in root.keys(): - raise DatatypeVerificationError( "Tool xml file (%s) does not include the required 'name' attribute in the <tool> tag" % str( xml_file ) ) - if 'version' not in root.keys(): - raise DatatypeVerificationError( "Tool xml file (%s) does not include the required 'version' attribute in the <tool> tag" % str( xml_file ) ) - if tool_tags: - # We are verifying the tools inside a tool suite, so the current tag should have been found in the suite_config.xml - # file parsed in the ToolSuite verify() method. The tool_tags dictionary should include a key matching the current - # tool Id, and a tuple value matching the tool name and version. - if root.attrib[ 'id' ] not in tool_tags: - raise DatatypeVerificationError( 'Tool Id (%s) is not included in the suite_config.xml file.' % \ - ( str( root.attrib[ 'id' ] ) ) ) - tup = tool_tags[ root.attrib[ 'id' ] ] - if root.attrib[ 'name' ] != tup[ 0 ]: - raise DatatypeVerificationError( 'Tool name (%s) differs between suite_config.xml and the tool config file for tool Id (%s).' % \ - ( str( root.attrib[ 'name' ] ), str( root.attrib[ 'id' ] ) ) ) - if root.attrib[ 'version' ] != tup[ 1 ]: - raise DatatypeVerificationError( 'Tool version (%s) differs between suite_config.xml and the tool config file for tool Id (%s).' % \ - ( str( root.attrib[ 'version' ] ), str( root.attrib[ 'id' ] ) ) ) - else: - # We are not verifying a tool suite, so we'll create a bunch for returning to the caller. - tool_bunch = Bunch() - try: - tool_bunch.id = root.attrib['id'] - tool_bunch.name = root.attrib['name'] - tool_bunch.version = root.attrib['version'] - except KeyError, e: - raise DatatypeVerificationError( 'Tool XML file does not conform to the specification. Missing required <tool> tag attribute: %s' % str( e ) ) - tool_bunch.description = '' - desc_tag = root.find( 'description' ) - if desc_tag is not None: - description = desc_tag.text - if description: - tool_bunch.description = description.strip() - tool_bunch.message = 'Tool: %s %s, Version: %s, Id: %s' % \ - ( str( tool_bunch.name ), str( tool_bunch.description ), str( tool_bunch.version ), str( tool_bunch.id ) ) - return tool_bunch - else: - # TODO: should we verify files that are not tool configs? - log.debug( "The file named (%s) is not a tool config, so skipping verification." % str( xml_file ) ) - def create_model_object( self, datatype_bunch ): - if self.model_object is None: - raise Exception( 'No model object configured for %s, check the datatype configuration file' % self.__class__.__name__ ) - if datatype_bunch is None: - # TODO: do it automatically - raise Exception( 'Unable to create %s model object without passing in data' % self.__class__.__name__ ) - o = self.model_object() - o.create_from_datatype( datatype_bunch ) - return o - -class ToolSuite( Tool ): - def __init__( self, model_object=None ): - self.model_object = model_object - self.label = 'Tool Suite' - def verify( self, f ): - """ - A sample tool suite config: - <suite id="onto_toolkit" name="ONTO Toolkit" version="1.0"> - <description>ONTO-Toolkit is a collection of Galaxy tools which support the manipulation of bio-ontologies.</description> - <tool id="get_ancestor_terms" name="Get the ancestor terms of a given OBO term" version="1.0.0"> - <description>Collects the ancestor terms from a given term in the given OBO ontology</description> - </tool> - <tool id="get_child_terms" name="Get the child terms of a given OBO term" version="1.0.0"> - <description>Collects the child terms from a given term in the given OBO ontology</description> - </tool> - </suite> - """ - try: - tar = tarfile.open( f.name ) - except tarfile.ReadError: - raise DatatypeVerificationError( 'The archive is not a readable tar file.' ) - suite_config = filter( lambda x: x.lower().find( 'suite_config.xml' ) >=0, tar.getnames() ) - if not suite_config: - raise DatatypeVerificationError( 'The archive does not contain the required suite_config.xml config file. If you are uploading a single tool archive, set the upload type to "Tool".' ) - suite_config = suite_config[ 0 ] - # Parse and verify suite_config - archive_ok = False - try: - tree = ElementTree.parse( tar.extractfile( suite_config ) ) - root = tree.getroot() - archive_ok = True - except: - log.exception( 'fail:' ) - if archive_ok and root.tag == 'suite': - suite_bunch = Bunch() - try: - suite_bunch.id = root.attrib['id'] - suite_bunch.name = root.attrib['name'] - suite_bunch.version = root.attrib['version'] - except KeyError, e: - raise DatatypeVerificationError( 'The file named tool-suite.xml does not conform to the specification. Missing required <suite> tag attribute: %s' % str( e ) ) - suite_bunch.description = '' - desc_tag = root.find( 'description' ) - if desc_tag is not None: - description = desc_tag.text - if description: - suite_bunch.description = description.strip() - suite_bunch.message = 'Tool suite: %s %s, Version: %s, Id: %s' % \ - ( str( suite_bunch.name ), str( suite_bunch.description ), str( suite_bunch.version ), str( suite_bunch.id ) ) - # Create a dictionary of the tools in the suite where the keys are tool_ids and the - # values are tuples of tool name and version - tool_tags = {} - for elem in root.findall( 'tool' ): - tool_tags[ elem.attrib['id'] ] = ( elem.attrib['name'], elem.attrib['version'] ) - else: - raise DatatypeVerificationError( "The file named %s is not a valid tool suite config." % str( suite_config ) ) - # Verify all included tool config files - xml_files = filter( lambda x: x.lower().endswith( '.xml' ) and x.lower() != 'suite_config.xml', tar.getnames() ) - if not xml_files: - raise DatatypeVerificationError( 'The archive does not contain any tool config (xml) files.' ) - Tool.verify( self, f, xml_files=xml_files, tool_tags=tool_tags ) - return suite_bunch Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Fix uploading sorted BAMs to libraries when using the link method rather than copying.
by Bitbucket 26 Aug '11

26 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4b3fefa396cf/ changeset: 4b3fefa396cf user: natefoo date: 2011-08-26 21:59:29 summary: Fix uploading sorted BAMs to libraries when using the link method rather than copying. affected #: 1 file (36 bytes) --- a/tools/data_source/upload.py Fri Aug 26 15:53:16 2011 -0400 +++ b/tools/data_source/upload.py Fri Aug 26 15:59:29 2011 -0400 @@ -297,7 +297,7 @@ datatype = registry.get_datatype_by_extension( ext ) if dataset.type in ( 'server_dir', 'path_paste' ) and link_data_only == 'link_to_files': # Never alter a file that will not be copied to Galaxy's local file store. - if datatype.dataset_content_needs_grooming( output_path ): + if datatype.dataset_content_needs_grooming( dataset.path ): err_msg = 'The uploaded files need grooming, so change your <b>Copy data into Galaxy?</b> selection to be ' + \ '<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed.' file_err( err_msg, dataset, json_file ) @@ -324,7 +324,7 @@ name = dataset.name, line_count = line_count ) json_file.write( to_json_string( info ) + "\n" ) - if datatype.dataset_content_needs_grooming( output_path ): + if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): # Groom the dataset content if necessary datatype.groom_dataset_content( output_path ) def add_composite_file( dataset, registry, json_file, output_path, files_path ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add SICER peak caller.
by Bitbucket 26 Aug '11

26 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/de634a2c3ed0/ changeset: de634a2c3ed0 user: dan date: 2011-08-26 21:53:16 summary: Add SICER peak caller. affected #: 28 files (50 bytes) Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: API enhancements: Rename the 'contents' controller to 'library_contents', move (some) sanity and security checks to galaxy.web.api.util, add some enhancements to the histories code and some sample scripts for histories.
by Bitbucket 26 Aug '11

26 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b35bf6a8c11f/ changeset: b35bf6a8c11f user: natefoo date: 2011-08-26 19:55:08 summary: API enhancements: Rename the 'contents' controller to 'library_contents', move (some) sanity and security checks to galaxy.web.api.util, add some enhancements to the histories code and some sample scripts for histories. affected #: 9 files (2.6 KB) --- a/lib/galaxy/web/api/contents.py Fri Aug 26 10:39:34 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,154 +0,0 @@ -""" -API operations on the contents of a library. -""" -import logging, os, string, shutil, urllib, re, socket -from cgi import escape, FieldStorage -from galaxy import util, datatypes, jobs, web, util -from galaxy.web.base.controller import * -from galaxy.util.sanitize_html import sanitize_html -from galaxy.model.orm import * - -log = logging.getLogger( __name__ ) - -class ContentsController( BaseController ): - - @web.expose_api - def index( self, trans, library_id, **kwd ): - """ - GET /api/libraries/{encoded_library_id}/contents - Displays a collection (list) of library contents (files and folders). - """ - rval = [] - current_user_roles = trans.get_current_user_roles() - def traverse( folder ): - admin = trans.user_is_admin() - rval = [] - for subfolder in folder.active_folders: - if not admin: - can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) - if (admin or can_access) and not subfolder.deleted: - subfolder.api_path = folder.api_path + '/' + subfolder.name - subfolder.api_type = 'folder' - rval.append( subfolder ) - rval.extend( traverse( subfolder ) ) - for ld in folder.datasets: - if not admin: - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) - if (admin or can_access) and not ld.deleted: - ld.api_path = folder.api_path + '/' + ld.name - ld.api_type = 'file' - rval.append( ld ) - return rval - try: - decoded_library_id = trans.security.decode_id( library_id ) - except TypeError: - trans.response.status = 400 - return "Malformed library id ( %s ) specified, unable to decode." % str( library_id ) - try: - library = trans.sa_session.query( trans.app.model.Library ).get( decoded_library_id ) - except: - library = None - if not library or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( current_user_roles, library ) ): - trans.response.status = 400 - return "Invalid library id ( %s ) specified." % str( library_id ) - encoded_id = trans.security.encode_id( 'folder.%s' % library.root_folder.id ) - rval.append( dict( id = encoded_id, - type = 'folder', - name = '/', - url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) - library.root_folder.api_path = '' - for content in traverse( library.root_folder ): - encoded_id = trans.security.encode_id( '%s.%s' % ( content.api_type, content.id ) ) - rval.append( dict( id = encoded_id, - type = content.api_type, - name = content.api_path, - url = url_for( 'library_content', library_id=library_id, id=encoded_id, ) ) ) - return rval - - @web.expose_api - def show( self, trans, id, library_id, **kwd ): - """ - GET /api/libraries/{encoded_library_id}/contents/{encoded_content_type_and_id} - Displays information about a library content (file or folder). - """ - content_id = id - try: - decoded_type_and_id = trans.security.decode_string_id( content_id ) - content_type, decoded_content_id = decoded_type_and_id.split( '.' ) - except: - trans.response.status = 400 - return "Malformed content id ( %s ) specified, unable to decode." % str( content_id ) - if content_type == 'folder': - model_class = trans.app.model.LibraryFolder - elif content_type == 'file': - model_class = trans.app.model.LibraryDataset - else: - trans.response.status = 400 - return "Invalid type ( %s ) specified." % str( content_type ) - try: - content = trans.sa_session.query( model_class ).get( decoded_content_id ) - except: - content = None - if not content or ( not trans.user_is_admin() and not trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), content, trans.user ) ): - trans.response.status = 400 - return "Invalid %s id ( %s ) specified." % ( content_type, str( content_id ) ) - return content.get_api_value( view='element' ) - - @web.expose_api - def create( self, trans, library_id, payload, **kwd ): - """ - POST /api/libraries/{encoded_library_id}/contents - Creates a new library content item (file or folder). - """ - create_type = None - if 'create_type' not in payload: - trans.response.status = 400 - return "Missing required 'create_type' parameter. Please consult the API documentation for help." - else: - create_type = payload.pop( 'create_type' ) - if create_type not in ( 'file', 'folder' ): - trans.response.status = 400 - return "Invalid value for 'create_type' parameter ( %s ) specified. Please consult the API documentation for help." % create_type - try: - content_id = str( payload.pop( 'folder_id' ) ) - decoded_type_and_id = trans.security.decode_string_id( content_id ) - parent_type, decoded_parent_id = decoded_type_and_id.split( '.' ) - assert parent_type in ( 'folder', 'file' ) - except: - trans.response.status = 400 - return "Malformed parent id ( %s ) specified, unable to decode." % content_id - # "content" can be either a folder or a file, but the parent of new contents can only be folders. - if parent_type == 'file': - trans.response.status = 400 - try: - # With admins or people who can access the dataset provided as the parent, be descriptive. - dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( decoded_parent_id ).library_dataset_dataset_association.dataset - assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), dataset ) - return "The parent id ( %s ) points to a file, not a folder." % content_id - except: - # If you can't access the parent we don't want to reveal its existence. - return "Invalid parent folder id ( %s ) specified." % content_id - # The rest of the security happens in the library_common controller. - folder_id = trans.security.encode_id( decoded_parent_id ) - # Now create the desired content object, either file or folder. - if create_type == 'file': - status, output = trans.webapp.controllers['library_common'].upload_library_dataset( trans, 'api', library_id, folder_id, **payload ) - elif create_type == 'folder': - status, output = trans.webapp.controllers['library_common'].create_folder( trans, 'api', folder_id, library_id, **payload ) - if status != 200: - trans.response.status = status - # We don't want to reveal the encoded folder_id since it's invalid - # in the API context. Instead, return the content_id originally - # supplied by the client. - output = output.replace( folder_id, content_id ) - return output - else: - rval = [] - for k, v in output.items(): - if type( v ) == trans.app.model.LibraryDatasetDatasetAssociation: - v = v.library_dataset - encoded_id = trans.security.encode_id( create_type + '.' + str( v.id ) ) - rval.append( dict( id = encoded_id, - name = v.name, - url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) - return rval --- a/lib/galaxy/web/api/histories.py Fri Aug 26 10:39:34 2011 -0400 +++ b/lib/galaxy/web/api/histories.py Fri Aug 26 13:55:08 2011 -0400 @@ -7,9 +7,9 @@ from galaxy.web.base.controller import * from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * -from galaxy.model import Dataset import galaxy.datatypes from galaxy.util.bunch import Bunch +from galaxy.web.api.util import * log = logging.getLogger( __name__ ) @@ -21,21 +21,26 @@ GET /api/histories Displays a collection (list) of histories. """ + rval = [] + try: query = trans.sa_session.query( trans.app.model.History ).filter_by( user=trans.user, deleted=False ).order_by( desc(trans.app.model.History.table.c.update_time)).all() except Exception, e: - log.debug("Error in history API: %s" % str(e)) + rval = "Error in history API" + log.error( rval + ": %s" % str(e) ) + trans.response.status = 500 - rval = [] - try: - for history in query: - item = history.get_api_value(value_mapper={'id':trans.security.encode_id}) - item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) - # item['id'] = trans.security.encode_id( item['id'] ) - rval.append( item ) - except Exception, e: - log.debug("Error in history API at constructing return list: %s" % str(e)) + if not rval: + try: + for history in query: + item = history.get_api_value(value_mapper={'id':trans.security.encode_id}) + item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) + rval.append( item ) + except Exception, e: + rval = "Error in history API at constructing return list" + log.error( rval + ": %s" % str(e) ) + trans.response.status = 500 return rval @web.expose_api @@ -49,42 +54,29 @@ def traverse( datasets ): rval = {} - states = Dataset.states + states = trans.app.model.Dataset.states for key, state in states.items(): rval[state] = 0 - #log.debug("History API: Init rval %s" % rval) for dataset in datasets: item = dataset.get_api_value( view='element' ) - #log.debug("History API: Set rval %s" % item['state']) if not item['deleted']: rval[item['state']] = rval[item['state']] + 1 - return rval + return rval try: - decoded_history_id = trans.security.decode_id( history_id ) - except TypeError: - trans.response.status = 400 - return "Malformed history id ( %s ) specified, unable to decode." % str( history_id ) - try: - history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id) - if history.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0: - trans.response.status = 400 - return("History is not owned by or shared with current user") - except: - trans.response.status = 400 - return "That history does not exist." + history = get_history_for_access( trans, history_id ) + except Exception, e: + return str( e ) try: item = history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) num_sets = len( [hda.id for hda in history.datasets if not hda.deleted] ) - states = Dataset.states + states = trans.app.model.Dataset.states state = states.ERROR - if num_sets == 0: + if num_sets == 0: state = states.NEW else: summary = traverse(history.datasets) - #log.debug("History API: Status summary %s" % summary) if summary[states.ERROR] > 0 or summary[states.FAILED_METADATA] > 0: state = states.ERROR elif summary[states.RUNNING] > 0 or summary[states.SETTING_METADATA] > 0: @@ -93,13 +85,13 @@ state = states.QUEUED elif summary[states.OK] == num_sets: state = states.OK - #item['user'] = item['user'].username item['contents_url'] = url_for( 'history_contents', history_id=history_id ) - #item['datasets'] = len( item['datasets'] ) item['state'] = state - #log.debug("History API: State %s for %d datasets" % (state, num_sets)) + item['state_details'] = summary except Exception, e: - log.debug("Error in history API at showing history detail: %s" % str(e)) + item = "Error in history API at showing history detail" + log.error(item + ": %s" % str(e)) + trans.response.status = 500 return item @web.expose_api @@ -109,13 +101,16 @@ Creates a new history. """ params = util.Params( payload ) - hist_name = util.restore_text( params.get( 'name', None ) ) + hist_name = None + if payload.get( 'name', None ): + hist_name = util.restore_text( payload['name'] ) new_history = trans.app.model.History( user=trans.user, name=hist_name ) trans.sa_session.add( new_history ) trans.sa_session.flush() item = new_history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) return item + @web.expose_api def delete( self, trans, id, **kwd ): """ @@ -123,33 +118,31 @@ Deletes a history """ history_id = id - params = util.Params( kwd ) + # a request body is optional here + purge = False + if kwd.get( 'payload', None ): + purge = util.string_as_bool( kwd['payload'].get( 'purge', False ) ) try: - decoded_history_id = trans.security.decode_id( history_id ) - except TypeError: - trans.response.status = 400 - return "Malformed history id ( %s ) specified, unable to decode." % str( history_id ) - try: - history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id) - if history.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0: - trans.response.status = 400 - return("History is not owned by or shared with current user") - except: - trans.response.status = 400 - return "That history does not exist." + history = get_history_for_modification( trans, history_id ) + except Exception, e: + return str( e ) + history.deleted = True - # If deleting the current history, make a new current. - if history == trans.get_history(): - trans.new_history() - if trans.app.config.allow_user_dataset_purge: + if purge and trans.app.config.allow_user_dataset_purge: for hda in history.datasets: + if hda.purged: + continue hda.purged = True trans.sa_session.add( hda ) + trans.sa_session.flush() if hda.dataset.user_can_purge: try: hda.dataset.full_delete() trans.sa_session.add( hda.dataset ) except: - trans.sa_session.flush() + pass + trans.sa_session.flush() + + trans.sa_session.flush() + return 'OK' --- a/lib/galaxy/web/api/history_contents.py Fri Aug 26 10:39:34 2011 -0400 +++ b/lib/galaxy/web/api/history_contents.py Fri Aug 26 13:55:08 2011 -0400 @@ -7,6 +7,7 @@ from galaxy.web.base.controller import * from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * +from galaxy.web.api.util import * import pkg_resources pkg_resources.require( "Routes" ) @@ -23,63 +24,36 @@ Displays a collection (list) of history contents """ try: - decoded_history_id = trans.security.decode_id( history_id ) - except TypeError: - trans.response.status = 400 - return "Malformed history id ( %s ) specified, unable to decode." % str( history_id ) - try: - history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id) - if history.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0: - trans.response.status = 400 - return("History is not owned by or shared with current user") - except: - trans.response.status = 400 - return "That history does not exist." + history = get_history_for_access( trans, history_id ) + except Exception, e: + return str( e ) rval = [] try: for dataset in history.datasets: api_type = "file" encoded_id = trans.security.encode_id( '%s.%s' % (api_type, dataset.id) ) - #log.debug("History dataset %s" % str(encoded_id)) rval.append( dict( id = encoded_id, type = api_type, name = dataset.name, url = url_for( 'history_content', history_id=history_id, id=encoded_id, ) ) ) except Exception, e: - log.debug("Error in history API at listing contents: %s" % str(e)) + rval = "Error in history API at listing contents" + log.error( rval + ": %s" % str(e) ) + trans.response.status = 500 return rval @web.expose_api def show( self, trans, id, history_id, **kwd ): """ GET /api/histories/{encoded_history_id}/contents/{encoded_content_type_and_id} - Displays information about a history content dataset. + Displays information about a history content (dataset). """ - #log.debug("Entering Content API for history dataset with %s" % str(history_id)) try: - content_id = id - try: - decoded_type_and_id = trans.security.decode_string_id( content_id ) - content_type, decoded_content_id = decoded_type_and_id.split( '.' ) - except: - trans.response.status = 400 - return "Malformed content id ( %s ) specified, unable to decode." % str( content_id ) - if content_type == 'file': - model_class = trans.app.model.HistoryDatasetAssociation - else: - trans.response.status = 400 - return "Invalid type ( %s ) specified." % str( content_type ) - try: - content = trans.sa_session.query( model_class ).get( decoded_content_id ) - except: - trans.response.status = 400 - return "Invalid %s id ( %s ) specified." % ( content_type, str( content_id ) ) - if content.history.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0: - trans.response.status = 400 - return("History is not owned by or shared with current user") + content = get_history_content_for_access( trans, content_id ) + except Exception, e: + return str( e ) + try: item = content.get_api_value( view='element' ) if not item['deleted']: # Problem: Method url_for cannot use the dataset controller @@ -87,23 +61,41 @@ url = routes.URLGenerator(trans.webapp.mapper, trans.environ) # http://routes.groovie.org/generating.html # url_for is being phased out, so new applications should use url - item['download_url'] = url(controller='dataset', action='display', dataset_id=trans.security.encode_id(decoded_content_id), to_ext=content.ext) + item['download_url'] = url(controller='dataset', action='display', dataset_id=trans.security.encode_id(content.id), to_ext=content.ext) except Exception, e: - log.debug("Error in history API at listing dataset: %s" % str(e)) + item = "Error in history API at listing dataset" + log.error( item + ": %s" % str(e) ) + trans.response.status = 500 return item @web.expose_api def create( self, trans, history_id, payload, **kwd ): """ POST /api/libraries/{encoded_history_id}/contents - Creates a new history content item. """ + Creates a new history content item (file, aka HistoryDatasetAssociation). + """ params = util.Params( payload ) - history_id = util.restore_text( params.get( 'history_id', None ) ) - ldda_id = util.restore_text( params.get( 'ldda_id', None ) ) - add_to_history = True - decoded_history_id = trans.security.decode_id( history_id ) - ld_t, ld_id = trans.security.decode_string_id(ldda_id).split('.') - history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id) - ldda = trans.sa_session.query(self.app.model.LibraryDatasetDatasetAssociation).get(ld_id) - hda = ldda.to_history_dataset_association(history, add_to_history=add_to_history) - history.add_dataset(hda) + from_ld_id = payload.get( 'from_ld_id', None ) + + try: + history = get_history_for_modification( trans, history_id ) + except Exception, e: + return str( e ) + + if from_ld_id: + try: + ld = get_library_content_for_access( trans, from_ld_id ) + 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 + return str( e ) + except Exception, e: + return str( e ) + hda = ld.library_dataset_dataset_association.to_history_dataset_association( history, add_to_history=True ) + history.add_dataset( hda ) + trans.sa_session.flush() + return hda.get_api_value() + else: + # TODO: implement other "upload" methods here. + trans.response.status = 403 + return "Not implemented." --- a/lib/galaxy/web/buildapp.py Fri Aug 26 10:39:34 2011 -0400 +++ b/lib/galaxy/web/buildapp.py Fri Aug 26 13:55:08 2011 -0400 @@ -108,7 +108,7 @@ add_api_controllers( webapp, app ) webapp.api_mapper.resource( 'content', 'contents', - controller='contents', + controller='library_contents', name_prefix='library_', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Fix SOAPdenovo binary name
by Bitbucket 26 Aug '11

26 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/81ee8622a9b5/ changeset: 81ee8622a9b5 user: natefoo date: 2011-08-26 16:39:34 summary: Fix SOAPdenovo binary name affected #: 1 file (2 bytes) --- a/tools/ilmn_pacbio/soap_denovo.xml Thu Aug 25 11:37:07 2011 -0400 +++ b/tools/ilmn_pacbio/soap_denovo.xml Fri Aug 26 10:39:34 2011 -0400 @@ -1,12 +1,12 @@ <tool id="soap_denovo" name="SOAPdenovo" version="1.0.0"><description>Short-read de novo assembly</description><command> - SOAPdenovo127mer all -s ${soap_config} -o assembly -K ${k} -p 24 -d -D -R + SOAPdenovo-127mer all -s ${soap_config} -o assembly -K ${k} -p 24 -d -D -R </command><inputs><conditional name="inputs"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: treat numbers as floats when dynamically filtering. Pack scripts.
by Bitbucket 25 Aug '11

25 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4f992059bfeb/ changeset: 4f992059bfeb user: jgoecks date: 2011-08-25 17:37:07 summary: Trackster: treat numbers as floats when dynamically filtering. Pack scripts. affected #: 3 files (26 bytes) --- a/static/scripts/packed/trackster.js Thu Aug 25 11:28:01 2011 -0400 +++ b/static/scripts/packed/trackster.js Thu Aug 25 11:37:07 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,U){var n=f("class").extend,p=f("slotting"),I=f("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"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")};n(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var C=function(ac,ad){ac.bind("drag",{handle:ad,relative:true},function(ah,ai){var ag=$(this).parent();var af=ag.children();var ae;for(ae=0;ae<af.length;ae++){if(ai.offsetY<$(af.get(ae)).position().top){break}}if(ae===af.length){if(this!==af.get(ae-1)){ag.append(this)}}else{if(this!==af.get(ae)){$(this).insertBefore(af.get(ae))}}}).bind("dragstart",function(){$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css("border","0px")})};U.sortable=C;var aa=16,D=9,A=20,P=D+2,w=100,F=12000,N=200,z=5,s=10,H=5000,t=100,m="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",q="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",d=10,r=5,y=5;function u(ac){return Math.round(ac*1000)/1000}var c=function(ac){this.num_elements=ac;this.clear()};n(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var O=function(ad,ac,ae){c.call(this,ad);this.track=ac;this.subset=(ae!==undefined?ae:true)};n(O.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am[am.length]=ac[ah].name}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,aj,an)})},get_data:function(ac,ag,ah,ad,af){var ae=this.get_data_from_cache(ac,ag,ah);if(ae){return ae}ae=this.load_data(ac,ag,ah,ad,af);this.set_data(ac,ag,ah,ae);return ae},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get_data_from_cache(ak,af,aj);if(!al){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=al.data[al.data.length-1][2]+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,aj,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,aj,am);new_data_available.resolve(am)});return new_data_available},get_data_from_cache:function(ac,ad,ae){return this.get(this.gen_key(ac,ad,ae))},set_data:function(ad,ae,af,ac){return this.set(this.gen_key(ad,ae,af),ac)},gen_key:function(ac,ae,af){var ad=ac+"_"+ae+"_"+af;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){O.call(this,ad,ac,ae)};n(E.prototype,O.prototype,c.prototype,{load_data:function(ae,ac,ag,ah,ad,af){if(ad>1){return}return O.prototype.load_data.call(this,ae,ac,ag,ah,ad,af)}});var Z=function(ac,af,ae,ad,ag){this.container=ac;this.chrom=null;this.vis_id=ae;this.dbkey=ad;this.title=af;this.tracks=[];this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ag);this.canvas_manager=new ab(ac.get(0).ownerDocument);this.reset()};n(Z.prototype,{init:function(ag){var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<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 ad=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ag);this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.content_div.click(function(ah){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ah){ac.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ai)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ac.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){var ak=Math.round(-ai/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ac.content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX),width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ac.container.offset().left,ah=Math.max(al.pageX,am.startX)-ac.container.offset().left,ak=(ac.high-ac.low),aj=ac.viewport_container.width();ac.update_location(Math.round(ai/aj*ak)+ac.low,Math.round(ah/aj*ak)+ac.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ac.high-ac.low),aj=ac.viewport_container.width(),al=ac.low;ac.low=Math.round(ai/aj*ak)+al;ac.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,this.top_labeltrack));this.add_label_track(new Y(this,this.nav_labeltrack));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ad,ae){ad.num=t;$.extend(ad,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ac=this;$.ajax({url:chrom_url,data:ad,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ad.chrom);return}if(ag.reference){ac.add_label_track(new x(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+t+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+t+"</option>"}ac.chrom_select.html(aj);if(ae){ae()}ac.chrom_start_index=ag.start_index},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}})},change_chrom:function(ag,ad,ai){if(!ag||ag==="None"){return}var af=this;if(ag==="previous"){af.load_chroms({low:this.chrom_start_index-t});return}if(ag==="next"){af.load_chroms({low:this.chrom_start_index+t});return}var ah=$.grep(af.chrom_data,function(ak,al){return ak.chrom===ag})[0];if(ah===undefined){af.load_chroms({chrom:ag},function(){af.change_chrom(ag,ad,ai)});return}else{if(ag!==af.chrom){af.chrom=ag;af.chrom_select.val(af.chrom);af.max_high=ah.len-1;af.reset();af.request_redraw(true);for(var aj=0,ac=af.tracks.length;aj<ac;aj++){var ae=af.tracks[aj];if(ae.init){ae.init()}}}if(ad!==undefined&&ai!==undefined){af.low=Math.max(ad,0);af.high=Math.min(ai,af.max_high)}af.reset_overview();af.request_redraw()}},go_to:function(ag){var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0].replace(/,/g,""),10);af=parseInt(ah[1].replace(/,/g,""),10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_track:function(ac){ac.view=this;ac.track_id=this.track_id_counter;this.tracks.push(ac);if(ac.init){ac.init()}ac.container_div.attr("id","track_"+ac.track_id);C(ac.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1;this.update_intro_div()},add_label_track:function(ac){ac.view=this;this.label_tracks.push(ac)},remove_track:function(ad){this.has_changes=true;delete this.tracks[this.tracks.indexOf(ad)];this.num_tracks-=1;var ac=this;ad.container_div.fadeOut("slow",function(){$(this).remove();ac.update_intro_div()})},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.tracks),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}requestAnimationFrame(function(){ai._redraw(ak)})},_redraw:function(am){var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution=Math.pow(z,Math.ceil(Math.log((this.high-this.low)/N)/Math.log(z)));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae&&ae.enabled){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.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(ac){$.when(ac.get_overview_tile()).then(function(ad){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ad.canvas);view.overview_highlight.show().height(ad.canvas.height());view.overview_viewport.height(ad.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ac;view.has_changes=true;ac.set_is_overview(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 o=function(ae,ai){this.track=ae;this.name=ai.name;this.params=[];var ap=ai.params;for(var af=0;af<ap.length;af++){var ak=ap[af],ad=ak.name,ao=ak.label,ag=unescape(ak.html),aq=ak.value,am=ak.type;if(am==="number"){this.params[this.params.length]=new g(ad,ao,ag,aq,ak.min,ak.max)}else{if(am=="select"){this.params[this.params.length]=new K(ad,ao,ag,aq)}else{console.log("WARNING: unrecognized tool parameter type:",ad,am)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(at){at.stopPropagation()}).click(function(at){at.stopPropagation()}).bind("dblclick",function(at){at.stopPropagation()});var an=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var al=this.params;var aj=this;$.each(this.params,function(au,ax){var aw=$("<div>").addClass("param-row").appendTo(aj.parent_div);var at=$("<div>").addClass("param-label").text(ax.label).appendTo(aw);var av=$("<div/>").addClass("slider").html(ax.html).appendTo(aw);av.find(":input").val(ax.value);$("<div style='clear: both;'/>").appendTo(aw)});this.parent_div.find("input").click(function(){$(this).select()});var ar=$("<div>").addClass("param-row").appendTo(this.parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ar);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ar);var aj=this;ac.click(function(){aj.run_on_region()});ah.click(function(){aj.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ac={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ae=this.track,ad=ac.tool_id+ae.tool_region_and_parameters_str(ac.chrom,ac.low,ac.high),af;if(ae instanceof e){af=new R(ad,view,ae.hda_ldda,undefined,{},{},ae);af.change_mode(ae.mode)}this.track.add_track(af);af.content_div.text("Starting job.");this.run(ac,af,function(ag){af.dataset_id=ag.dataset_id;af.content_div.text("Running job.");af.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(G)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var K=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=ae;this.value=af};var g=function(ae,ad,ag,ah,af,ac){K.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};var h=function(ad,ac,ae,af){this.name=ad;this.index=ac;this.tool_id=ae;this.tool_exp_name=af};var S=function(ad,ac,ae,af){h.call(this,ad,ac,ae,af);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};n(S.prototype,{applies_to:function(ac){if(ac.length>this.index){return true}return false},keep:function(ac){if(!this.applies_to(ac)){return true}var ad=parseInt(ac[this.index]);return(isNaN(ad)||(ad>=this.low&&ad<=this.high))},update_attrs:function(ad){var ac=false;if(!this.applies_to(ad)){return ac}if(ad[this.index]<this.min){this.min=Math.floor(ad[this.index]);ac=true}if(ad[this.index]>this.max){this.max=Math.ceil(ad[this.index]);ac=true}return ac},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ae=function(ah,af){var ag=af-ah;return(ag<=2?0.01:1)};var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ae(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(am,at){this.track=am;this.filters=[];for(var an=0;an<at.length;an++){var ao=at[an],au=ao.name,ac=ao.type,af=ao.index,ar=ao.tool_id,aq=ao.tool_exp_name;if(ac==="int"||ac==="float"){this.filters[an]=new S(au,af,ar,aq)}else{console.log("ERROR: unsupported filter: ",au,ac)}}var ag=function(av,aw,ax){av.click(function(){var ay=aw.text();max=parseFloat(ax.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ax.slider("option","values")){input_size=2*input_size+1;multi_value=true}aw.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ay).appendTo(aw).focus().select().click(function(az){az.stopPropagation()}).blur(function(){$(this).remove();aw.text(ay)}).keyup(function(aD){if(aD.keyCode===27){$(this).trigger("blur")}else{if(aD.keyCode===13){var aB=ax.slider("option","min"),az=ax.slider("option","max"),aC=function(aE){return(isNaN(aE)||aE>az||aE<aB)},aA=$(this).val();if(!multi_value){aA=parseFloat(aA);if(aC(aA)){alert("Parameter value must be in the range ["+aB+"-"+az+"]");return $(this)}}else{aA=aA.split("-");aA=[parseFloat(aA[0]),parseFloat(aA[1])];if(aC(aA[0])||aC(aA[1])){alert("Parameter value must be in the range ["+aB+"-"+az+"]");return $(this)}}ax.slider((multi_value?"values":"value"),aA)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(av){av.stopPropagation()}).click(function(av){av.stopPropagation()}).bind("dblclick",function(av){av.stopPropagation()}).bind("keydown",function(av){av.stopPropagation()});var ap=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ak=this;$.each(this.filters,function(ay,aA){aA.container=$("<div/>").addClass("slider-row").appendTo(ap);var az=$("<div/>").addClass("elt-label").appendTo(aA.container);var ax=$("<span/>").addClass("slider-name").text(aA.name+" ").appendTo(az);var aw=$("<span/>");var aC=$("<span/>").addClass("slider-value").appendTo(az).append("[").append(aw).append("]");var av=$("<div/>").addClass("slider").appendTo(aA.container);aA.control_element=$("<div/>").attr("id",aA.name+"-filter-control").appendTo(av);var aB=[0,0];aA.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aE,aF){var aD=aF.values;aw.text(aD[0]+"-"+aD[1]);aA.low=aD[0];aA.high=aD[1];ak.track.request_draw(true,true)},change:function(aD,aE){aA.control_element.slider("option","slide").call(aA.control_element,aD,aE)}});aA.slider=aA.control_element;aA.slider_label=aw;ag(aC,aw,aA.control_element);$("<div style='clear: both;'/>").appendTo(aA.container)});if(this.filters.length!==0){var ah=$("<div/>").addClass("param-row").appendTo(ap);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ah);var ae=this;aj.click(function(){ae.run_on_dataset()})}var al=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ai=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(al),ad=$("<select/>").attr("name","alpha_dropdown").appendTo(al);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ad);for(var an=0;an<this.filters.length;an++){$("<option/>").attr("value",an).text(this.filters[an].name).appendTo(ad)}ad.change(function(){$(this).children("option:selected").each(function(){var av=parseInt($(this).val());ak.alpha_filter=(av>=0?ak.filters[av]:null);ak.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};n(X.prototype,{reset_filters:function(){for(var ac=0;ac<this.filters.length;ac++){filter=this.filters[ac];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!=ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!=ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var L=function(ad,ac){I.AlphaGenerator.call(this,ac);this.filter=ad};L.prototype.gen_alpha=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var W=function(ac){this.track=ac.track;this.params=ac.params;this.values={};if(ac.saved_values){this.restore_values(ac.saved_values)}this.onchange=ac.onchange};n(W.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var ad=this;var ac=$("<div />");$.each(this.params,function(ah,af){if(!af.hidden){var ae="param_"+ah;var am=$("<div class='form-row' />").appendTo(ac);am.append($("<label />").attr("for",ae).text(af.label+":"));if(af.type==="bool"){am.append($('<input type="checkbox" />').attr("id",ae).attr("name",ae).attr("checked",ad.values[af.key]))}else{if(af.type==="color"){var aj=ad.values[af.key];var ai=$("<input />").attr("id",ae).attr("name",ae).val(aj);var ak=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ag=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ak);var al=$("<div/>").appendTo(ag).farbtastic({width:100,height:100,callback:ai,color:aj});$("<div />").append(ai).append(ak).appendTo(am).bind("click",function(an){ak.css({left:$(this).position().left+($(ai).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ak.hide();$(document).unbind("click.color-picker")});an.stopPropagation()})}else{am.append($("<input />").attr("id",ae).attr("name",ae).val(ad.values[af.key]))}}}});return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange()}}});var b=function(ae,ad,ac,af){this.index=ae;this.low=ae*N*ad;this.high=(ae+1)*N*ad;this.resolution=ad;this.canvas=$("<div class='track-tile'/>").append(ac);this.data=af;this.stale=false};var l=function(ae,ad,ac,af,ag){b.call(this,ae,ad,ac,af);this.max_val=ag};var M=function(ae,ad,ac,ag,af){b.call(this,ae,ad,ac,ag);this.message=af};var j=function(ad,ac,ag,ae,af){this.name=ad;this.view=ac;this.parent_element=ag;this.data_url=(ae?ae:default_data_url);this.data_url_extra_params={};this.data_query_wait=(af?af:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").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 class='draghandle' />").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.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"ToolDataFeatureTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.initial_canvas=undefined;ac.content_div.css("height","auto");ac.container_div.removeClass("nodata error pending");if(!ac.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id,chrom:ac.view.chrom},function(ad){if(!ad||ad==="error"||ad.kind==="error"){ac.container_div.addClass("error");ac.content_div.text(m);if(ad.message){var af=ac.view.tracks.indexOf(ac);var ae=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ad.message+"</pre>",{Close:hide_modal})});ac.content_div.append(ae)}}else{if(ad==="no converter"){ac.container_div.addClass("error");ac.content_div.text(G)}else{if(ad==="no data"||(ad.data!==undefined&&(ad.data===null||ad.data.length===0))){ac.container_div.addClass("nodata");ac.content_div.text(B)}else{if(ad==="pending"){ac.container_div.addClass("pending");ac.content_div.text(q);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(ad.status==="data"){if(ad.valid_chroms){ac.valid_chroms=ad.valid_chroms;ac.make_name_popup_menu()}ac.content_div.text(V);if(ac.view.chrom){ac.content_div.text("");ac.content_div.css("height",ac.height_px+"px");ac.enabled=true;$.when(ac.predraw_init()).done(function(){ac.container_div.removeClass("nodata error pending");ac.request_draw()})}}}}}}})},predraw_init:function(){},update_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(aj,ah,ak){var ad=this,al=ad.view;this.filters_manager=(aj!==undefined?new X(this,aj):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ah!==undefined&&obj_length(ah)>0?new o(this,ah):undefined);this.is_overview=false;this.parent_track=ak;this.child_tracks=[];if(ad.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ad.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();ad.container_div.append(ad.child_tracks_container);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(ad.display_modes!==undefined){if(ad.mode_div===undefined){ad.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ad.header_div);var ae=(ad.track_config&&ad.track_config.values.mode?ad.track_config.values.mode:ad.display_modes[0]);ad.mode=ae;ad.mode_div.text(ae);var ac={};for(var af=0,ai=ad.display_modes.length;af<ai;af++){var ag=ad.display_modes[af];ac[ag]=function(am){return function(){ad.change_mode(am)}}(ag)}make_popupmenu(ad.mode_div,ac)}else{ad.mode_div.hide()}}this.make_name_popup_menu()};n(J.prototype,j.prototype,{change_mode:function(ad){var ac=this;ac.mode_div.text(ad);ac.mode=ad;ac.track_config.values.mode=ad;ac.tile_cache.clear();ac.request_draw()},make_name_popup_menu:function(){var ad=this;var ac={};ac[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ad.is_overview){ad.view.reset_overview()}else{ad.view.set_overview(ad)}};ac["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ad.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Track",ad.track_config.build_form(),{Cancel:aj,OK:ah})};if(ad.filters_available>0){var ag=(ad.filters_div.is(":visible")?"Hide filters":"Show filters");ac[ag]=function(){ad.filters_visible=(ad.filters_div.is(":visible"));if(ad.filters_visible){ad.filters_manager.reset_filters()}ad.filters_div.toggle();ad.make_name_popup_menu()}}if(ad.tool){var ag=(ad.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ac[ag]=function(){if(!ad.dynamic_tool_div.is(":visible")){ad.update_name(ad.name+ad.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ad.revert_name()}ad.dynamic_tool_div.toggle();ad.make_name_popup_menu()}}if(ad.valid_chroms){ac["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ad.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ae=view;var af=function(){$("#no-tracks").show()};if(this.parent_track){ae=this.parent_track;af=function(){}}ac.Remove=function(){ae.remove_track(ad);if(ae.num_tracks===0){af()}};make_popupmenu(ad.name_div,ac)},set_is_overview:function(ac){this.is_overview=ac;this.make_name_popup_menu()},get_overview_tile:function(){var ac=this;view=ac.view,resolution=Math.pow(z,Math.ceil(Math.log((view.max_high-view.max_low)/N)/Math.log(z))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ac.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ac.data_url_extra_params)).then(function(ad){var af=ac._gen_tile_cache_key(view_width,w_scale,0),ah=ac.tile_cache.get(af);if(!ah){ah=ac.draw_tile(ad,resolution,0,w_scale);ac.tile_cache.set(af,ah)}var ak=$(ah.canvas.find("canvas")),ag=ak.clone(),aj=ak.get(0).getContext("2d"),ae=ag.get(0).getContext("2d"),ai=aj.getImageData(0,0,aj.canvas.width,aj.canvas.height);ae.putImageData(ai,-ac.left_offset,(ah.data.dataset_type==="summary_tree"?P:0));new_tile=new b(-1,resolution,ag);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},_draw:function(ae,an){if(!this.dataset_id){return}var am=this.view.low,ai=this.view.high,ak=ai-am,af=this.view.container.width(),aq=af/ak,ah=this.view.resolution,ap=$("<div style='position: relative;'></div>");if(!an){this.content_div.children().remove()}this.content_div.append(ap);this.max_height=0;var ad=Math.floor(am/ah/N);var al=true;var ao=[];var ac=0;while((ad*N*ah)<ai){tile=this.draw_helper(ae,af,ad,ah,ap,aq);if(tile){ao.push(tile)}else{al=false}ad+=1;ac++}var ag=this;if(al){ag.postdraw_actions(ao,af,aq,an)}for(var aj=0;aj<this.child_tracks.length;aj++){this.child_tracks[aj].request_draw(ae,an)}},postdraw_actions:function(ag,ah,ai,ac){var ae=this;var af=false;for(var ad=0;ad<ag.length;ad++){if(ag[ad].message){af=true;break}}if(af){for(var ad=0;ad<ag.length;ad++){tile=ag[ad];if(!tile.message){tile.canvas.css("padding-top",A)}}}},draw_helper:function(ad,ae,af,ai,ao,at,ap,aj){var ag=this,an=this._gen_tile_cache_key(ae,at,af),ak=af*N*ai,ar=ak+N*ai;var al=(ad?undefined:ag.tile_cache.get(an));if(al){ag.show_tile(al,ao,at);return al}var am=function(au){return("isResolved" in au)};var ah=true;var ac=ag.data_manager.get_data(ak,ar,ag.mode,ai,ag.data_url_extra_params);if(am(ac)){ah=false}var aq;if(view.reference_track&&at>view.canvas_manager.char_width_px){aq=view.reference_track.data_manager.get_data(ak,ar,ag.mode,ai,view.reference_track.data_url_extra_params);if(am(aq)){ah=false}}if(ah){n(ac,aj);var al=ag.draw_tile(ac,ai,af,at,aq);ag.tile_cache.set(an,al);if(al!==undefined){ag.show_tile(al,ao,at)}return al}$.when(ac,aq).then(function(){view.request_redraw()});return null},show_tile:function(aj,al,am){var ae=this,ad=aj.canvas,ai=ad;if(aj.message){var an=$("<div/>"),ak=$("<div/>").addClass("tile-message").text(aj.message).css({height:A-1,width:aj.canvas.width}).appendTo(an),ag=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ak),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ak);an.append(ad);ai=an;ag.click(function(){aj.stale=true;ae.data_manager.get_more_data(aj.low,aj.high,ae.mode,aj.resolution,{},ae.data_manager.DEEP_DATA_REQ);ae.request_draw()}).dblclick(function(ao){ao.stopPropagation()});ac.click(function(){aj.stale=true;ae.data_manager.get_more_data(aj.low,aj.high,ae.mode,aj.resolution,{},ae.data_manager.BROAD_DATA_REQ);ae.request_draw()}).dblclick(function(ao){ao.stopPropagation()})}var ah=this.view.high-this.view.low,af=(aj.low-this.view.low)*am;if(this.left_offset){af-=this.left_offset}ai.css({position:"absolute",top:0,left:af,height:""});al.append(ai);ae.max_height=Math.max(ae.max_height,ai.height());ae.content_div.css("height",ae.max_height+"px");al.children().css("height",ae.max_height+"px")},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},add_track:function(ac){ac.track_id=this.track_id+"_"+this.child_tracks.length;ac.container_div.attr("id","track_"+ac.track_id);this.child_tracks_container.append(ac.container_div);C(ac.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(ac);this.view.has_changes=true},remove_track:function(ac){ac.container_div.fadeOut("slow",function(){$(this).remove()})}});var Y=function(ac,ad){this.hidden=true;j.call(this,null,ac,ad);this.container_div.addClass("label-track")};n(Y.prototype,j.prototype,{_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var x=function(ac){this.hidden=true;j.call(this,null,ac,ac.top_labeltrack);J.call(this);ac.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:ac.dbkey};this.data_manager=new E(y,this,false);this.tile_cache=new c(r)};n(x.prototype,J.prototype,{draw_tile:function(ak,ah,ad,am){var ag=this,ae=N*ah;if(am>this.view.canvas_manager.char_width_px){if(ak===null){ag.content_div.css("height","0px");return}var af=this.view.canvas_manager.new_canvas();var al=af.getContext("2d");af.width=Math.ceil(ae*am+ag.left_offset);af.height=ag.height_px;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.round(ai*am);al.fillText(ak[ai],ac+ag.left_offset,10)}return new b(ad,ah,af,ak)}this.content_div.css("height","0px")}});var k=function(ag,ae,ah,ac,af){var ad=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ag,ae,ae.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ah;this.dataset_id=ac;this.original_dataset_id=ac;this.data_manager=new O(y,this);this.tile_cache=new c(r);this.track_config=new W({track:this,params:[{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:af,onchange:function(){ad.vertical_range=ad.prefs.max_value-ad.prefs.min_value;$("#linetrack_"+ad.track_id+"_minval").text(ad.prefs.min_value);$("#linetrack_"+ad.track_id+"_maxval").text(ad.prefs.max_value);ad.tile_cache.clear();ad.request_draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,J.prototype,{add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){af=true;ad.show()},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.content_div).css("height",ag);ac.height_px=ag;ac.request_draw(true)}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.track_config.values.height=ac.height_px}).appendTo(ac.container_div)},predraw_init:function(){var ac=this,ad=ac.view.tracks.indexOf(ac);ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ae){ac.container_div.addClass("line-track");var ag=ae.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){ac.prefs.min_value=ag.min;ac.prefs.max_value=ag.max;$("#track_"+ad+"_minval").val(ac.prefs.min_value);$("#track_"+ad+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ad+"_minval").text(u(ac.prefs.min_value));var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ad+"_maxval").text(u(ac.prefs.max_value));af.css({position:"absolute",top:"24px",left:"10px"});af.prependTo(ac.container_div);ah.css({position:"absolute",bottom:"2px",left:"10px"});ah.prependTo(ac.container_div)})},draw_tile:function(am,ag,ad,al){if(this.vertical_range===undefined){return}var ah=ad*N*ag,af=N*ag,ac=Math.ceil(af*al),aj=this.height_px;var ae=this.view.canvas_manager.new_canvas();ae.width=ac,ae.height=aj;var ak=ae.getContext("2d");var ai=new I.LinePainter(am.data,ah,ah+af,this.prefs,this.mode);ai.draw(ak,ac,aj);return new b(ad,ag,ae,am.data)}});var e=function(ac,ah,ag,ak,aj,ae,af,ai){var ad=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new W({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){ad.tile_cache.clear();ad.request_draw()}});this.prefs=this.track_config.values;j.call(this,ac,ah,ah.viewport_container);J.call(this,ae,af,ai);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ag;this.dataset_id=ak;this.original_dataset_id=ak;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new O(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{postdraw_actions:function(ar,ac,at,aq){J.prototype.postdraw_actions.call(this,ar,aq);var af=this;if(aq){var ah=af.content_div.children();var ai=false;for(var ag=ah.length-1,am=0;ag>=am;ag--){var ae=$(ah[ag]);if(ai){ae.remove()}else{if(ae.children().length!==0){ai=true}}}}if(af.mode=="Histogram"){var al=-1;for(var ag=0;ag<ar.length;ag++){var ap=ar[ag].max_val;if(ap>al){al=ap}}for(var ag=0;ag<ar.length;ag++){var ao=ar[ag];if(ao.max_val!==al){ao.canvas.remove();af.draw_helper(true,ac,ao.index,ao.resolution,ao.canvas.parent(),at,[],{max:al})}}}if(af.filters_manager){var ad=af.filters_manager.filters;for(var ak=0;ak<ad.length;ak++){ad[ak].update_ui_elt()}var aj=false,an;for(var ag=0;ag<ar.length;ag++){if(ar[ag].data.length){an=ar[ag].data[0];for(var ak=0;ak<ad.length;ak++){if(ad[ak].applies_to(an)){aj=true;break}}}}if(af.filters_available!==aj){af.filters_available=aj;if(!af.filters_available){af.filters_div.hide()}af.make_name_popup_menu()}}},update_auto_mode:function(ac){if(this.mode=="Auto"){if(ac=="no_detail"){ac="feature spans"}else{if(ac=="summary_tree"){ac="coverage histogram"}}this.mode_div.text("Auto ("+ac+")")}},incremental_slots:function(ag,ad,af){var ae=this.view.canvas_manager.dummy_context,ac=this.inc_slots[ag];if(!ac||(ac.mode!==af)){ac=new (p.FeatureSlotter)(ag,af==="Pack",w,function(ah){return ae.measureText(ah)});ac.mode=af;this.inc_slots[ag]=ac}return ac.slot_features(ad)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},draw_tile:function(ap,ay,aC,al,af){var av=this,aE=aC*N*ay,ad=(aC+1)*N*ay,ar=ad-aE,aw=Math.ceil(ar*al),at=this.mode,aI=25,ag=this.left_offset,aq,ah;if(at==="Auto"){if(ap.dataset_type==="summary_tree"){at=ap.dataset_type}else{if(ap.extra_info==="no_detail"){at="no_detail"}else{var aH=ap.data;if(this.view.high-this.view.low>F){at="Squish"}else{at="Pack"}}}this.update_auto_mode(at)}if(at==="summary_tree"||at==="Histogram"){ah=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ac=$("<div />").addClass("yaxislabel");ac.text(ap.max);ac.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ac.prependTo(this.container_div);var ae=this.view.canvas_manager.new_canvas();ae.width=aw+ag;ae.height=ah+P;if(ap.dataset_type!="summary_tree"){var am=this.get_summary_tree_data(ap.data,aE,ad,200);if(ap.max){am.max=ap.max}ap=am}var aF=new I.SummaryTreePainter(ap,aE,ad,this.prefs);var ax=ae.getContext("2d");ax.translate(ag,P);aF.draw(ax,aw,ah);return new l(aC,ay,ae,ap.data,ap.max)}var aq,aj=1;if(at==="no_detail"||at==="Squish"||at==="Pack"){aj=this.incremental_slots(al,ap.data,at);aq=this.inc_slots[al].slots}var ak=[];if(ap.data){var an=this.filters_manager.filters;for(var az=0,aB=ap.data.length;az<aB;az++){var ai=ap.data[az];var aA=false;var ao;for(var aD=0,aG=an.length;aD<aG;aD++){ao=an[aD];ao.update_attrs(ai);if(!ao.keep(ai)){aA=true;break}}if(!aA){ak.push(ai)}}}var au=(this.filters_manager.alpha_filter?new L(this.filters_manager.alpha_filter):null);var aF=new (this.painter)(ak,aE,ad,this.prefs,at,au,af);var ah=Math.max(aa,aF.get_required_height(aj));var ae=this.view.canvas_manager.new_canvas();ae.width=aw+ag;ae.height=ah;var ax=ae.getContext("2d");ax.fillStyle=this.prefs.block_color;ax.font=ax.canvas.manager.default_font;ax.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ap.data){ax.translate(ag,0);aF.draw(ax,aw,ah,aq)}return new M(aC,ay,ae,ap.data,ap.message)}});var Q=function(af,ad,ah,ac,ae,ag){e.call(this,af,ad,ah,ac,ae,ag);this.painter=I.VariantPainter};n(Q.prototype,J.prototype,e.prototype);var T=function(af,ad,ah,ac,ae,ag){e.call(this,af,ad,ah,ac,ae,ag);this.track_config=new W({track:this,params:[{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:ae,onchange:function(){this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.track_config.values;this.painter=I.ReadPainter;this.make_name_popup_menu()};n(T.prototype,J.prototype,e.prototype);var R=function(ag,ae,ai,ac,af,ah,ad){e.call(this,ag,ae,ai,ac,af,ah,{},ad);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(R.prototype,J.prototype,e.prototype,{predraw_init:function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=H;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}});U.View=Z;U.LineTrack=k;U.FeatureTrack=e;U.ReadTrack=T};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,x){var u=k("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=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(y){this.default_alpha=(y?y:1)};g.prototype.gen_alpha=function(y){return this.default_alpha};var n=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};n.prototype.default_prefs={};var v=function(A,C,y,z,B){n.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.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(y,C,E,F,A){n.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};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(B,D,y,A,C,z){n.call(this,B,D,y,A,C);this.alpha_generator=(z?z:new g())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(z){var y=y_scale=this.get_row_height(),A=this.mode;if(A==="no_detail"||A==="Squish"||A==="Pack"){y=z*y_scale}return y+Math.max(Math.round(y_scale/2),5)},draw:function(K,B,J,G){var E=this.data,H=this.view_start,L=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var O=this.view_end-this.view_start,N=B/O,A=this.get_row_height();for(var D=0,F=E.length;D<F;D++){var M=E[D],C=M[0],y=M[1],z=M[2],I=(G&&G[C]!==undefined?G[C]:null);if((y<L&&z>H)&&(this.mode=="Dense"||I!==null)){this.draw_element(K,this.mode,M,I,H,L,N,A,B)}}K.restore()},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.")}});var d=10,j=3,m=5,w=10,f=1,s=3,e=3,a=9,l=2,h="#ccc";var r=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=d}else{if(z==="no_detail"){y=j}else{if(z==="Squish"){y=m}else{y=w}}}return y},draw_element:function(K,D,S,F,M,ac,ag,ah,y){var P=S[0],ae=S[1],W=S[2],N=S[3],X=Math.floor(Math.max(0,(ae-M)*ag)),L=Math.ceil(Math.min(y,Math.max(0,(W-M)*ag))),V=(D==="Dense"?0:(0+F))*ah,J,aa,O=null,ai=null,B=this.prefs.block_color,Z=this.prefs.label_color;K.globalAlpha=this.alpha_generator.gen_alpha(S);if(D=="Dense"){F=1}if(D==="no_detail"){K.fillStyle=B;K.fillRect(X,V+5,L-X,f)}else{var I=S[4],U=S[5],Y=S[6],C=S[7];if(U&&Y){O=Math.floor(Math.max(0,(U-M)*ag));ai=Math.ceil(Math.min(y,Math.max(0,(Y-M)*ag)))}var af,Q;if(D==="Squish"||D==="Dense"){af=1;Q=e}else{af=5;Q=a}if(!C){if(S.strand){if(S.strand==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(S.strand==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}}else{K.fillStyle=B}K.fillRect(X,V,L-X,Q)}else{var H,R;if(D==="Squish"||D==="Dense"){K.fillStyle=h;H=V+Math.floor(e/2)+1;R=1}else{if(I){var H=V;var R=Q;if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand")}}}else{K.fillStyle=h;H+=(e/2)+1;R=1}}K.fillRect(X,H,L-X,R);for(var ad=0,A=C.length;ad<A;ad++){var E=C[ad],z=Math.floor(Math.max(0,(E[0]-M)*ag)),T=Math.ceil(Math.min(y,Math.max((E[1]-M)*ag)));if(z>T){continue}K.fillStyle=B;K.fillRect(z,V+(Q-af)/2+1,T-z,af);if(O!==undefined&&Y>U&&!(z>ai||T<O)){var 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Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",q="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",d=10,r=5,y=5;function u(ac){return Math.round(ac*1000)/1000}var c=function(ac){this.num_elements=ac;this.clear()};n(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var 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Z=function(ac,af,ae,ad,ag){this.container=ac;this.chrom=null;this.vis_id=ae;this.dbkey=ad;this.title=af;this.tracks=[];this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ag);this.canvas_manager=new ab(ac.get(0).ownerDocument);this.reset()};n(Z.prototype,{init:function(ag){var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<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 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ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){var ak=Math.round(-ai/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ac.content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX),width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ac.container.offset().left,ah=Math.max(al.pageX,am.startX)-ac.container.offset().left,ak=(ac.high-ac.low),aj=ac.viewport_container.width();ac.update_location(Math.round(ai/aj*ak)+ac.low,Math.round(ah/aj*ak)+ac.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ac.high-ac.low),aj=ac.viewport_container.width(),al=ac.low;ac.low=Math.round(ai/aj*ak)+al;ac.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,this.top_labeltrack));this.add_label_track(new Y(this,this.nav_labeltrack));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ad,ae){ad.num=t;$.extend(ad,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ac=this;$.ajax({url:chrom_url,data:ad,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ad.chrom);return}if(ag.reference){ac.add_label_track(new x(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+t+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+t+"</option>"}ac.chrom_select.html(aj);if(ae){ae()}ac.chrom_start_index=ag.start_index},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}})},change_chrom:function(ag,ad,ai){if(!ag||ag==="None"){return}var af=this;if(ag==="previous"){af.load_chroms({low:this.chrom_start_index-t});return}if(ag==="next"){af.load_chroms({low:this.chrom_start_index+t});return}var ah=$.grep(af.chrom_data,function(ak,al){return ak.chrom===ag})[0];if(ah===undefined){af.load_chroms({chrom:ag},function(){af.change_chrom(ag,ad,ai)});return}else{if(ag!==af.chrom){af.chrom=ag;af.chrom_select.val(af.chrom);af.max_high=ah.len-1;af.reset();af.request_redraw(true);for(var aj=0,ac=af.tracks.length;aj<ac;aj++){var ae=af.tracks[aj];if(ae.init){ae.init()}}}if(ad!==undefined&&ai!==undefined){af.low=Math.max(ad,0);af.high=Math.min(ai,af.max_high)}af.reset_overview();af.request_redraw()}},go_to:function(ag){var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0].replace(/,/g,""),10);af=parseInt(ah[1].replace(/,/g,""),10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_track:function(ac){ac.view=this;ac.track_id=this.track_id_counter;this.tracks.push(ac);if(ac.init){ac.init()}ac.container_div.attr("id","track_"+ac.track_id);C(ac.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1;this.has_changes=true;this.update_intro_div()},add_label_track:function(ac){ac.view=this;this.label_tracks.push(ac)},remove_track:function(ad){this.has_changes=true;delete this.tracks[this.tracks.indexOf(ad)];this.num_tracks-=1;var ac=this;ad.container_div.fadeOut("slow",function(){$(this).remove();ac.update_intro_div()})},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.tracks),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}requestAnimationFrame(function(){ai._redraw(ak)})},_redraw:function(am){var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution=Math.pow(z,Math.ceil(Math.log((this.high-this.low)/N)/Math.log(z)));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae&&ae.enabled){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.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(ac){$.when(ac.get_overview_tile()).then(function(ad){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ad.canvas);view.overview_highlight.show().height(ad.canvas.height());view.overview_viewport.height(ad.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ac;ac.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 o=function(ae,ai){this.track=ae;this.name=ai.name;this.params=[];var ap=ai.params;for(var af=0;af<ap.length;af++){var ak=ap[af],ad=ak.name,ao=ak.label,ag=unescape(ak.html),aq=ak.value,am=ak.type;if(am==="number"){this.params[this.params.length]=new g(ad,ao,ag,aq,ak.min,ak.max)}else{if(am=="select"){this.params[this.params.length]=new K(ad,ao,ag,aq)}else{console.log("WARNING: unrecognized tool parameter type:",ad,am)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(at){at.stopPropagation()}).click(function(at){at.stopPropagation()}).bind("dblclick",function(at){at.stopPropagation()});var an=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var al=this.params;var aj=this;$.each(this.params,function(au,ax){var aw=$("<div>").addClass("param-row").appendTo(aj.parent_div);var at=$("<div>").addClass("param-label").text(ax.label).appendTo(aw);var av=$("<div/>").addClass("slider").html(ax.html).appendTo(aw);av.find(":input").val(ax.value);$("<div style='clear: both;'/>").appendTo(aw)});this.parent_div.find("input").click(function(){$(this).select()});var ar=$("<div>").addClass("param-row").appendTo(this.parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ar);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ar);var aj=this;ac.click(function(){aj.run_on_region()});ah.click(function(){aj.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ac={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ae=this.track,ad=ac.tool_id+ae.tool_region_and_parameters_str(ac.chrom,ac.low,ac.high),af;if(ae instanceof e){af=new R(ad,view,ae.hda_ldda,undefined,{},{},ae);af.change_mode(ae.mode)}this.track.add_track(af);af.content_div.text("Starting job.");this.run(ac,af,function(ag){af.dataset_id=ag.dataset_id;af.content_div.text("Running job.");af.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(G)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var K=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=ae;this.value=af};var g=function(ae,ad,ag,ah,af,ac){K.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};var h=function(ad,ac,ae,af){this.name=ad;this.index=ac;this.tool_id=ae;this.tool_exp_name=af};var S=function(ad,ac,ae,af){h.call(this,ad,ac,ae,af);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};n(S.prototype,{applies_to:function(ac){if(ac.length>this.index){return true}return false},keep:function(ac){if(!this.applies_to(ac)){return true}var ad=parseFloat(ac[this.index]);return(isNaN(ad)||(ad>=this.low&&ad<=this.high))},update_attrs:function(ad){var ac=false;if(!this.applies_to(ad)){return ac}if(ad[this.index]<this.min){this.min=Math.floor(ad[this.index]);ac=true}if(ad[this.index]>this.max){this.max=Math.ceil(ad[this.index]);ac=true}return ac},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ae=function(ah,af){var ag=af-ah;return(ag<=2?0.01:1)};var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ae(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(am,at){this.track=am;this.filters=[];for(var an=0;an<at.length;an++){var ao=at[an],au=ao.name,ac=ao.type,af=ao.index,ar=ao.tool_id,aq=ao.tool_exp_name;if(ac==="int"||ac==="float"){this.filters[an]=new S(au,af,ar,aq)}else{console.log("ERROR: unsupported filter: ",au,ac)}}var ag=function(av,aw,ax){av.click(function(){var ay=aw.text();max=parseFloat(ax.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ax.slider("option","values")){input_size=2*input_size+1;multi_value=true}aw.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ay).appendTo(aw).focus().select().click(function(az){az.stopPropagation()}).blur(function(){$(this).remove();aw.text(ay)}).keyup(function(aD){if(aD.keyCode===27){$(this).trigger("blur")}else{if(aD.keyCode===13){var aB=ax.slider("option","min"),az=ax.slider("option","max"),aC=function(aE){return(isNaN(aE)||aE>az||aE<aB)},aA=$(this).val();if(!multi_value){aA=parseFloat(aA);if(aC(aA)){alert("Parameter value must be in the range ["+aB+"-"+az+"]");return $(this)}}else{aA=aA.split("-");aA=[parseFloat(aA[0]),parseFloat(aA[1])];if(aC(aA[0])||aC(aA[1])){alert("Parameter value must be in the range ["+aB+"-"+az+"]");return $(this)}}ax.slider((multi_value?"values":"value"),aA)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(av){av.stopPropagation()}).click(function(av){av.stopPropagation()}).bind("dblclick",function(av){av.stopPropagation()}).bind("keydown",function(av){av.stopPropagation()});var ap=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ak=this;$.each(this.filters,function(ay,aA){aA.container=$("<div/>").addClass("slider-row").appendTo(ap);var az=$("<div/>").addClass("elt-label").appendTo(aA.container);var ax=$("<span/>").addClass("slider-name").text(aA.name+" ").appendTo(az);var aw=$("<span/>");var aC=$("<span/>").addClass("slider-value").appendTo(az).append("[").append(aw).append("]");var av=$("<div/>").addClass("slider").appendTo(aA.container);aA.control_element=$("<div/>").attr("id",aA.name+"-filter-control").appendTo(av);var aB=[0,0];aA.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aE,aF){var aD=aF.values;aw.text(aD[0]+"-"+aD[1]);aA.low=aD[0];aA.high=aD[1];ak.track.request_draw(true,true)},change:function(aD,aE){aA.control_element.slider("option","slide").call(aA.control_element,aD,aE)}});aA.slider=aA.control_element;aA.slider_label=aw;ag(aC,aw,aA.control_element);$("<div style='clear: both;'/>").appendTo(aA.container)});if(this.filters.length!==0){var ah=$("<div/>").addClass("param-row").appendTo(ap);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ah);var ae=this;aj.click(function(){ae.run_on_dataset()})}var al=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ai=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(al),ad=$("<select/>").attr("name","alpha_dropdown").appendTo(al);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ad);for(var an=0;an<this.filters.length;an++){$("<option/>").attr("value",an).text(this.filters[an].name).appendTo(ad)}ad.change(function(){$(this).children("option:selected").each(function(){var av=parseInt($(this).val());ak.alpha_filter=(av>=0?ak.filters[av]:null);ak.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};n(X.prototype,{reset_filters:function(){for(var ac=0;ac<this.filters.length;ac++){filter=this.filters[ac];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!=ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!=ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var L=function(ad,ac){I.AlphaGenerator.call(this,ac);this.filter=ad};L.prototype.gen_alpha=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var W=function(ac){this.track=ac.track;this.params=ac.params;this.values={};if(ac.saved_values){this.restore_values(ac.saved_values)}this.onchange=ac.onchange};n(W.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var ad=this;var ac=$("<div />");$.each(this.params,function(ah,af){if(!af.hidden){var ae="param_"+ah;var am=$("<div class='form-row' />").appendTo(ac);am.append($("<label />").attr("for",ae).text(af.label+":"));if(af.type==="bool"){am.append($('<input type="checkbox" />').attr("id",ae).attr("name",ae).attr("checked",ad.values[af.key]))}else{if(af.type==="color"){var aj=ad.values[af.key];var ai=$("<input />").attr("id",ae).attr("name",ae).val(aj);var ak=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ag=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ak);var al=$("<div/>").appendTo(ag).farbtastic({width:100,height:100,callback:ai,color:aj});$("<div />").append(ai).append(ak).appendTo(am).bind("click",function(an){ak.css({left:$(this).position().left+($(ai).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ak.hide();$(document).unbind("click.color-picker")});an.stopPropagation()})}else{am.append($("<input />").attr("id",ae).attr("name",ae).val(ad.values[af.key]))}}}});return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange()}}});var b=function(ae,ad,ac,af){this.index=ae;this.low=ae*N*ad;this.high=(ae+1)*N*ad;this.resolution=ad;this.canvas=$("<div class='track-tile'/>").append(ac);this.data=af;this.stale=false};var l=function(ae,ad,ac,af,ag){b.call(this,ae,ad,ac,af);this.max_val=ag};var M=function(ae,ad,ac,ag,af){b.call(this,ae,ad,ac,ag);this.message=af};var j=function(ad,ac,ag,ae,af){this.name=ad;this.view=ac;this.parent_element=ag;this.data_url=(ae?ae:default_data_url);this.data_url_extra_params={};this.data_query_wait=(af?af:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").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 class='draghandle' />").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.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"ToolDataFeatureTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.initial_canvas=undefined;ac.content_div.css("height","auto");ac.container_div.removeClass("nodata error pending");if(!ac.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id,chrom:ac.view.chrom},function(ad){if(!ad||ad==="error"||ad.kind==="error"){ac.container_div.addClass("error");ac.content_div.text(m);if(ad.message){var af=ac.view.tracks.indexOf(ac);var ae=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ad.message+"</pre>",{Close:hide_modal})});ac.content_div.append(ae)}}else{if(ad==="no converter"){ac.container_div.addClass("error");ac.content_div.text(G)}else{if(ad==="no data"||(ad.data!==undefined&&(ad.data===null||ad.data.length===0))){ac.container_div.addClass("nodata");ac.content_div.text(B)}else{if(ad==="pending"){ac.container_div.addClass("pending");ac.content_div.text(q);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(ad.status==="data"){if(ad.valid_chroms){ac.valid_chroms=ad.valid_chroms;ac.make_name_popup_menu()}ac.content_div.text(V);if(ac.view.chrom){ac.content_div.text("");ac.content_div.css("height",ac.height_px+"px");ac.enabled=true;$.when(ac.predraw_init()).done(function(){ac.container_div.removeClass("nodata error pending");ac.request_draw()})}}}}}}})},predraw_init:function(){},update_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(aj,ah,ak){var ad=this,al=ad.view;this.filters_manager=(aj!==undefined?new X(this,aj):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ah!==undefined&&obj_length(ah)>0?new o(this,ah):undefined);this.is_overview=false;this.parent_track=ak;this.child_tracks=[];if(ad.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ad.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();ad.container_div.append(ad.child_tracks_container);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(ad.display_modes!==undefined){if(ad.mode_div===undefined){ad.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ad.header_div);var ae=(ad.track_config&&ad.track_config.values.mode?ad.track_config.values.mode:ad.display_modes[0]);ad.mode=ae;ad.mode_div.text(ae);var ac={};for(var af=0,ai=ad.display_modes.length;af<ai;af++){var ag=ad.display_modes[af];ac[ag]=function(am){return function(){ad.change_mode(am)}}(ag)}make_popupmenu(ad.mode_div,ac)}else{ad.mode_div.hide()}}this.make_name_popup_menu()};n(J.prototype,j.prototype,{change_mode:function(ad){var ac=this;ac.mode_div.text(ad);ac.mode=ad;ac.track_config.values.mode=ad;ac.tile_cache.clear();ac.request_draw()},make_name_popup_menu:function(){var ad=this;var ac={};ac[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ad.is_overview){ad.view.reset_overview()}else{ad.view.set_overview(ad)}};ac["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ad.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Track",ad.track_config.build_form(),{Cancel:aj,OK:ah})};if(ad.filters_available>0){var ag=(ad.filters_div.is(":visible")?"Hide filters":"Show filters");ac[ag]=function(){ad.filters_visible=(ad.filters_div.is(":visible"));if(ad.filters_visible){ad.filters_manager.reset_filters()}ad.filters_div.toggle();ad.make_name_popup_menu()}}if(ad.tool){var ag=(ad.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ac[ag]=function(){if(!ad.dynamic_tool_div.is(":visible")){ad.update_name(ad.name+ad.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ad.revert_name()}ad.dynamic_tool_div.toggle();ad.make_name_popup_menu()}}if(ad.valid_chroms){ac["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ad.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ae=view;var af=function(){$("#no-tracks").show()};if(this.parent_track){ae=this.parent_track;af=function(){}}ac.Remove=function(){ae.remove_track(ad);if(ae.num_tracks===0){af()}};make_popupmenu(ad.name_div,ac)},set_is_overview:function(ac){this.is_overview=ac;this.make_name_popup_menu()},get_overview_tile:function(){var ac=this;view=ac.view,resolution=Math.pow(z,Math.ceil(Math.log((view.max_high-view.max_low)/N)/Math.log(z))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ac.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ac.data_url_extra_params)).then(function(ad){var af=ac._gen_tile_cache_key(view_width,w_scale,0),ah=ac.tile_cache.get(af);if(!ah){ah=ac.draw_tile(ad,resolution,0,w_scale);ac.tile_cache.set(af,ah)}var ak=$(ah.canvas.find("canvas")),ag=ak.clone(),aj=ak.get(0).getContext("2d"),ae=ag.get(0).getContext("2d"),ai=aj.getImageData(0,0,aj.canvas.width,aj.canvas.height);ae.putImageData(ai,-ac.left_offset,(ah.data.dataset_type==="summary_tree"?P:0));new_tile=new b(-1,resolution,ag);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},_draw:function(ae,an){if(!this.dataset_id){return}var am=this.view.low,ai=this.view.high,ak=ai-am,af=this.view.container.width(),aq=af/ak,ah=this.view.resolution,ap=$("<div style='position: relative;'></div>");if(!an){this.content_div.children().remove()}this.content_div.append(ap);this.max_height=0;var ad=Math.floor(am/ah/N);var al=true;var ao=[];var ac=0;while((ad*N*ah)<ai){tile=this.draw_helper(ae,af,ad,ah,ap,aq);if(tile){ao.push(tile)}else{al=false}ad+=1;ac++}var ag=this;if(al){ag.postdraw_actions(ao,af,aq,an)}for(var aj=0;aj<this.child_tracks.length;aj++){this.child_tracks[aj].request_draw(ae,an)}},postdraw_actions:function(ag,ah,ai,ac){var ae=this;var af=false;for(var ad=0;ad<ag.length;ad++){if(ag[ad].message){af=true;break}}if(af){for(var ad=0;ad<ag.length;ad++){tile=ag[ad];if(!tile.message){tile.canvas.css("padding-top",A)}}}},draw_helper:function(ad,ae,af,ai,ao,at,ap,aj){var ag=this,an=this._gen_tile_cache_key(ae,at,af),ak=af*N*ai,ar=ak+N*ai;var al=(ad?undefined:ag.tile_cache.get(an));if(al){ag.show_tile(al,ao,at);return al}var am=function(au){return("isResolved" in au)};var ah=true;var ac=ag.data_manager.get_data(ak,ar,ag.mode,ai,ag.data_url_extra_params);if(am(ac)){ah=false}var aq;if(view.reference_track&&at>view.canvas_manager.char_width_px){aq=view.reference_track.data_manager.get_data(ak,ar,ag.mode,ai,view.reference_track.data_url_extra_params);if(am(aq)){ah=false}}if(ah){n(ac,aj);var al=ag.draw_tile(ac,ai,af,at,aq);ag.tile_cache.set(an,al);if(al!==undefined){ag.show_tile(al,ao,at)}return al}$.when(ac,aq).then(function(){view.request_redraw()});return null},show_tile:function(aj,al,am){var ae=this,ad=aj.canvas,ai=ad;if(aj.message){var an=$("<div/>"),ak=$("<div/>").addClass("tile-message").text(aj.message).css({height:A-1,width:aj.canvas.width}).appendTo(an),ag=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ak),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ak);an.append(ad);ai=an;ag.click(function(){aj.stale=true;ae.data_manager.get_more_data(aj.low,aj.high,ae.mode,aj.resolution,{},ae.data_manager.DEEP_DATA_REQ);ae.request_draw()}).dblclick(function(ao){ao.stopPropagation()});ac.click(function(){aj.stale=true;ae.data_manager.get_more_data(aj.low,aj.high,ae.mode,aj.resolution,{},ae.data_manager.BROAD_DATA_REQ);ae.request_draw()}).dblclick(function(ao){ao.stopPropagation()})}var ah=this.view.high-this.view.low,af=(aj.low-this.view.low)*am;if(this.left_offset){af-=this.left_offset}ai.css({position:"absolute",top:0,left:af,height:""});al.append(ai);ae.max_height=Math.max(ae.max_height,ai.height());ae.content_div.css("height",ae.max_height+"px");al.children().css("height",ae.max_height+"px")},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},add_track:function(ac){ac.track_id=this.track_id+"_"+this.child_tracks.length;ac.container_div.attr("id","track_"+ac.track_id);this.child_tracks_container.append(ac.container_div);C(ac.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(ac);this.view.has_changes=true},remove_track:function(ac){ac.container_div.fadeOut("slow",function(){$(this).remove()})}});var Y=function(ac,ad){this.hidden=true;j.call(this,null,ac,ad);this.container_div.addClass("label-track")};n(Y.prototype,j.prototype,{_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var x=function(ac){this.hidden=true;j.call(this,null,ac,ac.top_labeltrack);J.call(this);ac.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:ac.dbkey};this.data_manager=new E(y,this,false);this.tile_cache=new c(r)};n(x.prototype,J.prototype,{draw_tile:function(ak,ah,ad,am){var ag=this,ae=N*ah;if(am>this.view.canvas_manager.char_width_px){if(ak===null){ag.content_div.css("height","0px");return}var af=this.view.canvas_manager.new_canvas();var al=af.getContext("2d");af.width=Math.ceil(ae*am+ag.left_offset);af.height=ag.height_px;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.round(ai*am);al.fillText(ak[ai],ac+ag.left_offset,10)}return new b(ad,ah,af,ak)}this.content_div.css("height","0px")}});var k=function(ag,ae,ah,ac,af){var ad=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ag,ae,ae.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ah;this.dataset_id=ac;this.original_dataset_id=ac;this.data_manager=new O(y,this);this.tile_cache=new c(r);this.track_config=new W({track:this,params:[{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:af,onchange:function(){ad.vertical_range=ad.prefs.max_value-ad.prefs.min_value;$("#linetrack_"+ad.track_id+"_minval").text(ad.prefs.min_value);$("#linetrack_"+ad.track_id+"_maxval").text(ad.prefs.max_value);ad.tile_cache.clear();ad.request_draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,J.prototype,{add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){af=true;ad.show()},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.content_div).css("height",ag);ac.height_px=ag;ac.request_draw(true)}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.track_config.values.height=ac.height_px}).appendTo(ac.container_div)},predraw_init:function(){var ac=this,ad=ac.view.tracks.indexOf(ac);ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ae){ac.container_div.addClass("line-track");var ag=ae.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){ac.prefs.min_value=ag.min;ac.prefs.max_value=ag.max;$("#track_"+ad+"_minval").val(ac.prefs.min_value);$("#track_"+ad+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ad+"_minval").text(u(ac.prefs.min_value));var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ad+"_maxval").text(u(ac.prefs.max_value));af.css({position:"absolute",top:"24px",left:"10px"});af.prependTo(ac.container_div);ah.css({position:"absolute",bottom:"2px",left:"10px"});ah.prependTo(ac.container_div)})},draw_tile:function(am,ag,ad,al){if(this.vertical_range===undefined){return}var ah=ad*N*ag,af=N*ag,ac=Math.ceil(af*al),aj=this.height_px;var ae=this.view.canvas_manager.new_canvas();ae.width=ac,ae.height=aj;var ak=ae.getContext("2d");var ai=new I.LinePainter(am.data,ah,ah+af,this.prefs,this.mode);ai.draw(ak,ac,aj);return new b(ad,ag,ae,am.data)}});var e=function(ac,ah,ag,ak,aj,ae,af,ai){var ad=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new W({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){ad.tile_cache.clear();ad.request_draw()}});this.prefs=this.track_config.values;j.call(this,ac,ah,ah.viewport_container);J.call(this,ae,af,ai);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ag;this.dataset_id=ak;this.original_dataset_id=ak;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new O(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{postdraw_actions:function(ar,ac,at,aq){J.prototype.postdraw_actions.call(this,ar,aq);var af=this;if(aq){var ah=af.content_div.children();var ai=false;for(var ag=ah.length-1,am=0;ag>=am;ag--){var ae=$(ah[ag]);if(ai){ae.remove()}else{if(ae.children().length!==0){ai=true}}}}if(af.mode=="Histogram"){var al=-1;for(var ag=0;ag<ar.length;ag++){var ap=ar[ag].max_val;if(ap>al){al=ap}}for(var ag=0;ag<ar.length;ag++){var ao=ar[ag];if(ao.max_val!==al){ao.canvas.remove();af.draw_helper(true,ac,ao.index,ao.resolution,ao.canvas.parent(),at,[],{max:al})}}}if(af.filters_manager){var ad=af.filters_manager.filters;for(var ak=0;ak<ad.length;ak++){ad[ak].update_ui_elt()}var aj=false,an;for(var ag=0;ag<ar.length;ag++){if(ar[ag].data.length){an=ar[ag].data[0];for(var ak=0;ak<ad.length;ak++){if(ad[ak].applies_to(an)){aj=true;break}}}}if(af.filters_available!==aj){af.filters_available=aj;if(!af.filters_available){af.filters_div.hide()}af.make_name_popup_menu()}}},update_auto_mode:function(ac){if(this.mode=="Auto"){if(ac=="no_detail"){ac="feature spans"}else{if(ac=="summary_tree"){ac="coverage histogram"}}this.mode_div.text("Auto ("+ac+")")}},incremental_slots:function(ag,ad,af){var ae=this.view.canvas_manager.dummy_context,ac=this.inc_slots[ag];if(!ac||(ac.mode!==af)){ac=new (p.FeatureSlotter)(ag,af==="Pack",w,function(ah){return ae.measureText(ah)});ac.mode=af;this.inc_slots[ag]=ac}return ac.slot_features(ad)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},draw_tile:function(ap,ay,aC,al,af){var av=this,aE=aC*N*ay,ad=(aC+1)*N*ay,ar=ad-aE,aw=Math.ceil(ar*al),at=this.mode,aI=25,ag=this.left_offset,aq,ah;if(at==="Auto"){if(ap.dataset_type==="summary_tree"){at=ap.dataset_type}else{if(ap.extra_info==="no_detail"){at="no_detail"}else{var aH=ap.data;if(this.view.high-this.view.low>F){at="Squish"}else{at="Pack"}}}this.update_auto_mode(at)}if(at==="summary_tree"||at==="Histogram"){ah=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ac=$("<div />").addClass("yaxislabel");ac.text(ap.max);ac.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ac.prependTo(this.container_div);var ae=this.view.canvas_manager.new_canvas();ae.width=aw+ag;ae.height=ah+P;if(ap.dataset_type!="summary_tree"){var am=this.get_summary_tree_data(ap.data,aE,ad,200);if(ap.max){am.max=ap.max}ap=am}var aF=new I.SummaryTreePainter(ap,aE,ad,this.prefs);var ax=ae.getContext("2d");ax.translate(ag,P);aF.draw(ax,aw,ah);return new l(aC,ay,ae,ap.data,ap.max)}var aq,aj=1;if(at==="no_detail"||at==="Squish"||at==="Pack"){aj=this.incremental_slots(al,ap.data,at);aq=this.inc_slots[al].slots}var ak=[];if(ap.data){var an=this.filters_manager.filters;for(var az=0,aB=ap.data.length;az<aB;az++){var ai=ap.data[az];var aA=false;var ao;for(var aD=0,aG=an.length;aD<aG;aD++){ao=an[aD];ao.update_attrs(ai);if(!ao.keep(ai)){aA=true;break}}if(!aA){ak.push(ai)}}}var au=(this.filters_manager.alpha_filter?new L(this.filters_manager.alpha_filter):null);var aF=new (this.painter)(ak,aE,ad,this.prefs,at,au,af);var ah=Math.max(aa,aF.get_required_height(aj));var ae=this.view.canvas_manager.new_canvas();ae.width=aw+ag;ae.height=ah;var ax=ae.getContext("2d");ax.fillStyle=this.prefs.block_color;ax.font=ax.canvas.manager.default_font;ax.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ap.data){ax.translate(ag,0);aF.draw(ax,aw,ah,aq)}return new M(aC,ay,ae,ap.data,ap.message)}});var Q=function(af,ad,ah,ac,ae,ag){e.call(this,af,ad,ah,ac,ae,ag);this.painter=I.VariantPainter};n(Q.prototype,J.prototype,e.prototype);var T=function(af,ad,ah,ac,ae,ag){e.call(this,af,ad,ah,ac,ae,ag);this.track_config=new W({track:this,params:[{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:ae,onchange:function(){this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.track_config.values;this.painter=I.ReadPainter;this.make_name_popup_menu()};n(T.prototype,J.prototype,e.prototype);var R=function(ag,ae,ai,ac,af,ah,ad){e.call(this,ag,ae,ai,ac,af,ah,{},ad);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(R.prototype,J.prototype,e.prototype,{predraw_init:function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=H;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}});U.View=Z;U.LineTrack=k;U.FeatureTrack=e;U.ReadTrack=T};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,x){var u=k("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=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(y){this.default_alpha=(y?y:1)};g.prototype.gen_alpha=function(y){return this.default_alpha};var n=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};n.prototype.default_prefs={};var v=function(A,C,y,z,B){n.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.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(y,C,E,F,A){n.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};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 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ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=h;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&ref_seq){var K=ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=h;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var 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T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+l-O,C+8)}else{R.textAlign="right";R.fillText(J,D-l-O,C+8)}R.fillStyle=V}}});x.AlphaGenerator=g;x.SummaryTreePainter=v;x.LinePainter=c;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.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 Thu Aug 25 11:28:01 2011 -0400 +++ b/static/scripts/trackster.js Thu Aug 25 11:37:07 2011 -0400 @@ -1280,7 +1280,7 @@ // No element to filter on. return true; } - var val = parseInt(element[this.index]); + var val = parseFloat(element[this.index]); return (isNaN(val) || (val >= this.low && val <= this.high)); }, /** Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: create a set of shared functions for managing the user interface and use functions in both visualization editor and display.
by Bitbucket 25 Aug '11

25 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/cf761c5af7b3/ changeset: cf761c5af7b3 user: jgoecks date: 2011-08-25 17:28:01 summary: Trackster: create a set of shared functions for managing the user interface and use functions in both visualization editor and display. affected #: 4 files (6.2 KB) --- a/static/scripts/trackster.js Thu Aug 25 10:37:18 2011 -0400 +++ b/static/scripts/trackster.js Thu Aug 25 11:28:01 2011 -0400 @@ -464,7 +464,7 @@ /** * View object manages complete viz view, including tracks and user interactions. */ -var View = function( container, title, vis_id, dbkey, callback ) { +var View = function(container, title, vis_id, dbkey, callback) { this.container = container; this.chrom = null; this.vis_id = vis_id; @@ -826,6 +826,7 @@ sortable( track.container_div, '.draghandle' ); this.track_id_counter += 1; this.num_tracks += 1; + this.has_changes = true; this.update_intro_div(); }, add_label_track: function (label_track) { @@ -993,9 +994,9 @@ view.overview_track.set_is_overview(false); } view.overview_track = track; - view.has_changes = true; track.set_is_overview(true); }); + view.has_changes = true; }, /** Close and reset overview. */ reset_overview: function() { --- a/templates/tracks/browser.mako Thu Aug 25 10:37:18 2011 -0400 +++ b/templates/tracks/browser.mako Thu Aug 25 11:28:01 2011 -0400 @@ -42,7 +42,7 @@ <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", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic" )} +${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic" )} <script type="text/javascript"> @@ -57,51 +57,8 @@ chrom_url = "${h.url_for( action='chroms' )}", dataset_state_url = "${h.url_for( action='dataset_state' )}", converted_datasets_state_url = "${h.url_for( action='converted_datasets_state' )}", - addable_track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack }, view; - - /** - * Add bookmark. - */ - var add_bookmark = function(position, annotation) { - var - bookmarks_container = $("#bookmarks-container"), - new_bookmark = $("<div/>").addClass("bookmark").appendTo(bookmarks_container), - delete_icon_container = $("<div/>").addClass("delete-icon-container").appendTo(new_bookmark).click(function (){ - // Remove bookmark. - new_bookmark.slideUp("fast"); - new_bookmark.remove(); - view.has_changes = true; - return false; - }), - delete_icon = $("<a href=''/>").addClass("icon-button delete").appendTo(delete_icon_container), - position_div = $("<div/>").addClass("position").appendTo(new_bookmark), - position_link = $("<a href=''/>").text(position).appendTo(position_div).click(function() { - view.go_to(position); - return false; - }); - annotation_div = get_editable_text_elt(annotation, true).addClass("annotation").appendTo(new_bookmark); - view.has_changes = true; - return new_bookmark; - }; - - /** - * Use track data to add a track to a view. - * TODO: rename function? - */ - var add_async_success = function(track_data) { - var td = track_data, - new_track = new addable_track_types[track_data.track_type]( - track_data.name, view, track_data.hda_ldda, track_data.dataset_id, - track_data.prefs, track_data.filters, track_data.tool ); - view.add_track(new_track); - // Should replace with live event but can't get working - sortable(new_track.container_div, ".draghandle"); - view.has_changes = true; - $("#no-tracks").hide(); - }; - /** * Use a popup grid to add more tracks. */ @@ -144,7 +101,7 @@ [ arguments[0] ] ); for (var i= 0; i < track_defs.length; i++) { - add_async_success(track_defs[i]); + view.add_track( track_from_dict(track_defs[i]) ); } }); hide_modal(); @@ -165,6 +122,7 @@ %if config: var callback; %if 'viewport' in config: + // TODO: find better way to handle this code. var callback = function() { view.change_chrom( '${config['viewport']['chrom']}', ${config['viewport']['start']}, ${config['viewport']['end']} ); // Set overview. @@ -180,51 +138,20 @@ } } %endif - } + view.has_changes = false; + }; %endif - view = new View( $("#browser-container"), "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}", callback ); - view.editor = true; - ## A little ugly and redundant, but it gets the job done moving the config from python to JS: - var tracks_config = JSON.parse('${ h.to_json_string( config.get('tracks') ) }'); - var track_config, track, parent_track, parent_obj; - for (var i = 0; i < tracks_config.length; i++) { - track_config = tracks_config[i]; - track = new addable_track_types[track_config["track_type"]]( - track_config['name'], - view, - track_config['hda_ldda'], - track_config['dataset_id'], - track_config['prefs'], - track_config['filters'], - track_config['tool'], - (track_config.is_child ? parent_track : undefined)); - parent_obj = view; - if (track_config.is_child) { - parent_obj = parent_track; - } - else { - // New parent track is this track. - parent_track = track; - } - parent_obj.add_track(track); - } - init(); - - // Load bookmarks. - var bookmarks = JSON.parse('${ h.to_json_string( config.get('bookmarks') ) }'), - bookmark; - for (var i = 0; i < bookmarks.length; i++) { - bookmark = bookmarks[i]; - add_bookmark(bookmark['position'], bookmark['annotation']); - } - - // View has no changes as of yet. - view.has_changes = false; + view = create_visualization( $("#browser-container"), "${config.get('title') | h}", + "${config.get('vis_id')}", "${config.get('dbkey')}", callback, + JSON.parse('${ h.to_json_string( config.get('tracks') ) }'), + JSON.parse('${ h.to_json_string( config.get('bookmarks') ) }') + ); + init_editor(); %else: var continue_fn = function() { - view = new View( $("#browser-container"), $("#new-title").val(), undefined, $("#new-dbkey").val() ); + view = create_visualization( $("#browser-container"), $("#new-title").val(), undefined, $("#new-dbkey").val() ); view.editor = true; - init(); + init_editor(); hide_modal(); }; $.ajax({ @@ -242,11 +169,10 @@ }); %endif - // Execute initializer for EDITOR specific javascript - function init() { - if (view.num_tracks === 0) { - $("#no-tracks").show(); - } + /** + * Initialization for editor-specific functions. + */ + function init_editor() { $("#title").text(view.title + " (" + view.dbkey + ")"); window.onbeforeunload = function() { @@ -260,13 +186,16 @@ url: "${h.url_for( action='add_track_async' )}", data: { hda_id: "${add_dataset}" }, dataType: "json", - success: add_async_success + success: function(track_data) { view.add_track( track_from_dict(track_data) ) } }); %endif - $("#viz-options-button").css( "position", "relative" ); - make_popupmenu( $("#viz-options-button"), { + // + // Make actions menu. + // + $("#viz-actions-button").css( "position", "relative" ); + make_popupmenu( $("#viz-actions-button"), { "Add Tracks": add_tracks, "Save": function() { // Show saving dialog box @@ -344,34 +273,8 @@ annotation = "Bookmark description"; return add_bookmark(position, annotation); }); - - // - // Keyboard navigation. Scroll ~7% of height when scrolling up/down. - // - $(document).keydown(function(e) { - // Do not navigate if arrow keys used in input element. - if ($(e.srcElement).is(':input')) { - return; - } - - // Key codes: left == 37, up == 38, right == 39, down == 40 - switch(e.which) { - case 37: - view.move_fraction(0.25); - break - case 38: - var change = Math.round(view.viewport_container.height()/15.0); - view.viewport_container.scrollTo('-=' + change + 'px'); - break; - case 39: - view.move_fraction(-0.25); - break; - case 40: - var change = Math.round(view.viewport_container.height()/15.0); - view.viewport_container.scrollTo('+=' + change + 'px'); - break; - } - }); + + init_keyboard_nav(view); }; }); @@ -384,7 +287,7 @@ <div class="unified-panel-header-inner"><div style="float:left;" id="title"></div><div style="float: right"> - <a id="viz-options-button" class='panel-header-button popup' href="javascript:void(0)" target="galaxy_main">${_('Options')}</a> + <a id="viz-actions-button" class='panel-header-button popup' href="javascript:void(0)" target="galaxy_main">${_('Actions')}</a></div></div></div> --- a/templates/visualization/display.mako Thu Aug 25 10:37:18 2011 -0400 +++ b/templates/visualization/display.mako Thu Aug 25 11:28:01 2011 -0400 @@ -8,7 +8,7 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]--> - ${h.js( "jquery.event.drag", "jquery.autocomplete", "jquery.mousewheel", "jquery.autocomplete", "trackster", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic" )} + ${h.js( "jquery.event.drag", "jquery.autocomplete", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic" )} </%def><%def name="stylesheets()"> @@ -86,64 +86,19 @@ $("#right-border").click(function() { view.resize_window(); }); } - // Create view and add tracks. + // Create visualization. var callback; %if 'viewport' in config: var callback = function() { view.change_chrom( '${config['viewport']['chrom']}', ${config['viewport']['start']}, ${config['viewport']['end']} ); } %endif - view = new View(container_element, "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}", callback); - ## A little ugly and redundant, but it gets the job done moving the config from python to JS: - var tracks_config = JSON.parse('${ h.to_json_string( config.get('tracks') ) }'); - var track_config, track, parent_track, parent_obj; - for (var i = 0; i < tracks_config.length; i++) { - track_config = tracks_config[i]; - track = new addable_track_types[track_config["track_type"]]( - track_config['name'], - view, - track_config['hda_ldda'], - track_config['dataset_id'], - track_config['prefs'], - track_config['filters'], - track_config['tool'], - (track_config.is_child ? parent_track : undefined)); - parent_obj = view; - if (track_config.is_child) { - parent_obj = parent_track; - } - else { - // New parent track is this track. - parent_track = track; - } - parent_obj.add_track(track); - } + view = create_visualization( container_element, "${config.get('title') | h}", + "${config.get('vis_id')}", "${config.get('dbkey')}", callback, + JSON.parse('${ h.to_json_string( config.get('tracks') ) }'), + JSON.parse('${ h.to_json_string( config.get('bookmarks') ) }') + ); - // - // Keyboard navigation. Scroll ~7% of height when scrolling up/down. - // - $(document).keydown(function(e) { - // Do not navigate if arrow keys used in input element. - if ($(e.srcElement).is(':input')) { - return; - } - - // Key codes: left == 37, up == 38, right == 39, down == 40 - switch(e.which) { - case 37: - view.move_fraction(0.25); - break - case 38: - var change = Math.round(view.viewport_container.height()/15.0); - view.viewport_container.scrollTo('-=' + change + 'px'); - break; - case 39: - view.move_fraction(-0.25); - break; - case 40: - var change = Math.round(view.viewport_container.height()/15.0); - view.viewport_container.scrollTo('+=' + change + 'px'); - break; - } - }); + // Set up keyboard navigation. + init_keyboard_nav(view); }); </script> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: John Duddy: APIs to add histories, add items to histories, and list the status
by Bitbucket 25 Aug '11

25 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/317d2d4b1f7d/ changeset: 317d2d4b1f7d user: John Duddy date: 2011-08-22 21:29:49 summary: APIs to add histories, add items to histories, and list the status of datasets within a history affected #: 2 files (4.1 KB) --- a/lib/galaxy/web/api/histories.py Mon Aug 22 10:45:22 2011 -0400 +++ b/lib/galaxy/web/api/histories.py Mon Aug 22 12:29:49 2011 -0700 @@ -7,6 +7,9 @@ from galaxy.web.base.controller import * from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * +from galaxy.model import Dataset +import galaxy.datatypes +from galaxy.util.bunch import Bunch log = logging.getLogger( __name__ ) @@ -17,20 +20,19 @@ """ GET /api/histories Displays a collection (list) of histories. - """ - try: - query = trans.sa_session.query( trans.app.model.History ).filter( trans.app.model.History.table.c.deleted == False ) - current_user_role_ids = [ role.id for role in trans.get_current_user_roles() ] - user = trans.get_user() - query = query.filter_by( user=user, deleted=False ) + """ + try: + query = trans.sa_session.query( trans.app.model.History ).filter_by( user=trans.user, deleted=False ).order_by( + desc(trans.app.model.History.table.c.update_time)).all() except Exception, e: log.debug("Error in history API: %s" % str(e)) + rval = [] try: for history in query: - item = history.get_api_value() + item = history.get_api_value(value_mapper={'id':trans.security.encode_id}) item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) - item['id'] = trans.security.encode_id( item['id'] ) + # item['id'] = trans.security.encode_id( item['id'] ) rval.append( item ) except Exception, e: log.debug("Error in history API at constructing return list: %s" % str(e)) @@ -39,26 +41,63 @@ @web.expose_api def show( self, trans, id, **kwd ): """ - GET /api/histories/{encoded_library_id} + GET /api/histories/{encoded_history_id} Displays information about a history. """ history_id = id params = util.Params( kwd ) + + def traverse( datasets ): + rval = {} + states = Dataset.states + for key, state in states.items(): + rval[state] = 0 + #log.debug("History API: Init rval %s" % rval) + for dataset in datasets: + item = dataset.get_api_value( view='element' ) + #log.debug("History API: Set rval %s" % item['state']) + if not item['deleted']: + rval[item['state']] = rval[item['state']] + 1 + return rval + try: decoded_history_id = trans.security.decode_id( history_id ) except TypeError: trans.response.status = 400 - return "Malformed history id ( %s ) specified, unable to decode." % str( library_id ) + return "Malformed history id ( %s ) specified, unable to decode." % str( history_id ) try: - history = trans.sa_session.query( trans.app.model.History ).get( decoded_history_id ) + history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id) + if history.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0: + trans.response.status = 400 + return("History is not owned by or shared with current user") except: - history = None + trans.response.status = 400 + return "That history does not exist." + try: - if not history or not ( trans.user_is_admin() or trans.app.security_agent.can_access_history( trans.get_current_user_roles(), history ) ): - trans.response.status = 400 - return "Invalid history id ( %s ) specified." % str( history_id ) - item = history.get_api_value( view='element' ) + item = history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) + num_sets = len( [hda.id for hda in history.datasets if not hda.deleted] ) + states = Dataset.states + state = states.ERROR + if num_sets == 0: + state = states.NEW + else: + summary = traverse(history.datasets) + #log.debug("History API: Status summary %s" % summary) + if summary[states.ERROR] > 0 or summary[states.FAILED_METADATA] > 0: + state = states.ERROR + elif summary[states.RUNNING] > 0 or summary[states.SETTING_METADATA] > 0: + state = states.RUNNING + elif summary[states.QUEUED] > 0: + state = states.QUEUED + elif summary[states.OK] == num_sets: + state = states.OK + #item['user'] = item['user'].username item['contents_url'] = url_for( 'history_contents', history_id=history_id ) + #item['datasets'] = len( item['datasets'] ) + item['state'] = state + #log.debug("History API: State %s for %d datasets" % (state, num_sets)) except Exception, e: log.debug("Error in history API at showing history detail: %s" % str(e)) return item @@ -69,5 +108,48 @@ POST /api/histories Creates a new history. """ - trans.response.status = 403 - return "Not implemented." + params = util.Params( payload ) + hist_name = util.restore_text( params.get( 'name', None ) ) + new_history = trans.app.model.History( user=trans.user, name=hist_name ) + + trans.sa_session.add( new_history ) + trans.sa_session.flush() + item = new_history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) + return item + @web.expose_api + def delete( self, trans, id, **kwd ): + """ + DELETE /api/histories/{encoded_history_id} + Deletes a history + """ + history_id = id + params = util.Params( kwd ) + + try: + decoded_history_id = trans.security.decode_id( history_id ) + except TypeError: + trans.response.status = 400 + return "Malformed history id ( %s ) specified, unable to decode." % str( history_id ) + try: + history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id) + if history.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0: + trans.response.status = 400 + return("History is not owned by or shared with current user") + except: + trans.response.status = 400 + return "That history does not exist." + history.deleted = True + # If deleting the current history, make a new current. + if history == trans.get_history(): + trans.new_history() + if trans.app.config.allow_user_dataset_purge: + for hda in history.datasets: + hda.purged = True + trans.sa_session.add( hda ) + if hda.dataset.user_can_purge: + try: + hda.dataset.full_delete() + trans.sa_session.add( hda.dataset ) + except: + trans.sa_session.flush() --- a/lib/galaxy/web/api/history_contents.py Mon Aug 22 10:45:22 2011 -0400 +++ b/lib/galaxy/web/api/history_contents.py Mon Aug 22 12:29:49 2011 -0700 @@ -21,42 +21,23 @@ """ GET /api/histories/{encoded_history_id}/contents Displays a collection (list) of history contents - """ - rval = [] - current_user_roles = trans.get_current_user_roles() - def traverse( folder ): - admin = trans.user_is_admin() - rval = [] - for subfolder in folder.active_folders: - if not admin: - can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) - if (admin or can_access) and not subfolder.deleted: - subfolder.api_path = folder.api_path + '/' + subfolder.name - subfolder.api_type = 'folder' - rval.append( subfolder ) - rval.extend( traverse( subfolder ) ) - for ld in folder.datasets: - if not admin: - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) - if (admin or can_access) and not ld.deleted: - ld.api_path = folder.api_path + '/' + ld.name - ld.api_type = 'file' - rval.append( ld ) - return rval - #log.debug("Entering Content API for history with %s" % str(history_id)) + """ try: decoded_history_id = trans.security.decode_id( history_id ) except TypeError: trans.response.status = 400 return "Malformed history id ( %s ) specified, unable to decode." % str( history_id ) try: - history = trans.sa_session.query( trans.app.model.History ).get( decoded_history_id ) + history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id) + if history.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0: + trans.response.status = 400 + return("History is not owned by or shared with current user") except: - history = None - if not history or not ( trans.user_is_admin() or trans.app.security_agent.can_access_history( current_user_roles, history ) ): trans.response.status = 400 - return "Invalid history id ( %s ) specified." % str( history_id ) - #log.debug("History item %s" % str(history)) + return "That history does not exist." + + rval = [] try: for dataset in history.datasets: api_type = "file" @@ -93,10 +74,12 @@ try: content = trans.sa_session.query( model_class ).get( decoded_content_id ) except: - content = None - if not content or ( not trans.user_is_admin() and not trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), content, trans.user ) ): trans.response.status = 400 return "Invalid %s id ( %s ) specified." % ( content_type, str( content_id ) ) + if content.history.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0: + trans.response.status = 400 + return("History is not owned by or shared with current user") item = content.get_api_value( view='element' ) if not item['deleted']: # Problem: Method url_for cannot use the dataset controller @@ -106,14 +89,21 @@ # url_for is being phased out, so new applications should use url item['download_url'] = url(controller='dataset', action='display', dataset_id=trans.security.encode_id(decoded_content_id), to_ext=content.ext) except Exception, e: - log.debug("Error in history API at listing dataset: %s" % str(e)) + log.debug("Error in history API at listing dataset: %s" % str(e)) return item @web.expose_api def create( self, trans, history_id, payload, **kwd ): """ - POST /api/libraries/{encoded_library_id}/contents - Creates a new history content item (file or folder). - """ - trans.response.status = 403 - return "Not implemented." + POST /api/libraries/{encoded_history_id}/contents + Creates a new history content item. """ + params = util.Params( payload ) + history_id = util.restore_text( params.get( 'history_id', None ) ) + ldda_id = util.restore_text( params.get( 'ldda_id', None ) ) + add_to_history = True + decoded_history_id = trans.security.decode_id( history_id ) + ld_t, ld_id = trans.security.decode_string_id(ldda_id).split('.') + history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id) + ldda = trans.sa_session.query(self.app.model.LibraryDatasetDatasetAssociation).get(ld_id) + hda = ldda.to_history_dataset_association(history, add_to_history=add_to_history) + history.add_dataset(hda) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Minor tool help updates.
by Bitbucket 25 Aug '11

25 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d57affe81874/ changeset: d57affe81874 user: dan date: 2011-08-25 16:00:09 summary: Minor tool help updates. affected #: 28 files (7.7 KB) --- a/tools/fastq/fastq_combiner.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_combiner.xml Thu Aug 25 10:00:09 2011 -0400 @@ -66,5 +66,12 @@ Specifying a set of quality scores is optional; when not provided, the output will be fastqsanger or fastqcssanger (when a csfasta is provided) with each quality score being the maximal allowed value (93). Use this tool, for example, to convert 454-type output to FASTQ. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + </help></tool> --- a/tools/fastq/fastq_filter.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_filter.xml Thu Aug 25 10:00:09 2011 -0400 @@ -307,5 +307,12 @@ Adapter bases in color space reads are excluded from filtering. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_groomer.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_groomer.xml Thu Aug 25 10:00:09 2011 -0400 @@ -358,6 +358,12 @@ Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + .. _Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.: http://www.ncbi.nlm.nih.gov/pubmed/20015970 --- a/tools/fastq/fastq_manipulation.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_manipulation.xml Thu Aug 25 10:00:09 2011 -0400 @@ -417,5 +417,13 @@ 2. Click **Add new Manipulate Reads**, change **Manipulate Reads on** to "Sequence Content", set **Sequence Manipulation Type** to "Change Adapter Base" and set **New Adapter** to "" (an empty text field). 3. Click **Add new Manipulate Reads**, change **Manipulate Reads on** to "Sequence Content", set **Sequence Manipulation Type** to "String Translate" and set **From** to "0123." and **To** to "ACGTN". 4. Click Execute. The new history item will contained double-encoded psuedo-nucleotide space reads. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_masker_by_quality.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_masker_by_quality.xml Thu Aug 25 10:00:09 2011 -0400 @@ -49,5 +49,12 @@ This tool is not available for use on color space (csSanger) formats. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_paired_end_joiner.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_paired_end_joiner.xml Thu Aug 25 10:00:09 2011 -0400 @@ -51,5 +51,12 @@ +HWI-EAS91_1_30788AAXX:7:21:1542:1758 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_paired_end_splitter.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_paired_end_splitter.xml Thu Aug 25 10:00:09 2011 -0400 @@ -52,5 +52,12 @@ +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_stats.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_stats.xml Thu Aug 25 10:00:09 2011 -0400 @@ -60,5 +60,12 @@ Adapter bases in color space reads are excluded from statistics. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_to_fasta.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_to_fasta.xml Thu Aug 25 10:00:09 2011 -0400 @@ -29,5 +29,12 @@ This tool converts FASTQ sequencing reads to FASTA sequences. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_to_tabular.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_to_tabular.xml Thu Aug 25 10:00:09 2011 -0400 @@ -90,5 +90,12 @@ Note the sequences and quality strings have been truncated for display purposes in the above tables. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_trimmer.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_trimmer.xml Thu Aug 25 10:00:09 2011 -0400 @@ -109,5 +109,12 @@ Trimming a color space read will cause any adapter base to be lost. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_trimmer_by_quality.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_trimmer_by_quality.xml Thu Aug 25 10:00:09 2011 -0400 @@ -134,5 +134,12 @@ Trimming a color space read will cause any adapter base to be lost. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/tabular_to_fastq.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/tabular_to_fastq.xml Thu Aug 25 10:00:09 2011 -0400 @@ -33,5 +33,12 @@ This tool attempts to convert a tabular file containing sequencing read data to a FASTQ formatted file. The FASTQ Groomer tool should always be used on the output of this tool. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/maf/genebed_maf_to_fasta.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/genebed_maf_to_fasta.xml Thu Aug 25 10:00:09 2011 -0400 @@ -87,6 +87,12 @@ * stitches blocks together and resolves overlaps based on alignment score; * outputs alignments in FASTA format. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + </help></tool> --- a/tools/maf/interval2maf.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/interval2maf.xml Thu Aug 25 10:00:09 2011 -0400 @@ -283,5 +283,12 @@ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/interval2maf_pairwise.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/interval2maf_pairwise.xml Thu Aug 25 10:00:09 2011 -0400 @@ -39,5 +39,12 @@ .. image:: ./static/images/maf_icons/interval2maf.png +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/interval_maf_to_merged_fasta.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/interval_maf_to_merged_fasta.xml Thu Aug 25 10:00:09 2011 -0400 @@ -103,5 +103,12 @@ .. image:: ./static/images/maf_icons/stitchMaf.png +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_by_block_number.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_by_block_number.xml Thu Aug 25 10:00:09 2011 -0400 @@ -28,5 +28,13 @@ **What it does** This tool takes a list of block numbers, one per line, and extracts the corresponding MAF blocks from the provided file. Block numbers start at 0. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_filter.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_filter.xml Thu Aug 25 10:00:09 2011 -0400 @@ -191,5 +191,12 @@ You can also provide a size range and limit your output to the MAF blocks which fall within the specified range. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_limit_size.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_limit_size.xml Thu Aug 25 10:00:09 2011 -0400 @@ -24,5 +24,13 @@ **What it does** This tool takes a MAF file and a size range and extracts the MAF blocks which fall within the specified range. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_limit_to_species.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_limit_to_species.xml Thu Aug 25 10:00:09 2011 -0400 @@ -39,6 +39,13 @@ * **Exclude blocks with have only one species** - if this option is set to **YES** all single sequence alignment blocks WILL NOT be returned. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_reverse_complement.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_reverse_complement.xml Thu Aug 25 10:00:09 2011 -0400 @@ -41,5 +41,13 @@ s hg17.chr7 31156555 58 - 158628139 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAATGAATAAACCACAAATT s panTro1.chr6 31691510 58 - 161576975 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAACGAATAAACCACAAATT s mm5.chr6 120816549 54 - 149721531 CCTCTTCCACTGAGGAATTTCTTTTTTTAAATGATGAGCAATCAATGAAACG----TT + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_split_by_species.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_split_by_species.xml Thu Aug 25 10:00:09 2011 -0400 @@ -211,6 +211,13 @@ - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; - An "e" line containing information about the size of the gap between the alignments that span the current block. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_stats.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_stats.xml Thu Aug 25 10:00:09 2011 -0400 @@ -108,5 +108,13 @@ ======== =========== ======== where **coverage** is the number of nucleotides divided by the total length of the provided intervals. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_thread_for_species.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_thread_for_species.xml Thu Aug 25 10:00:09 2011 -0400 @@ -48,6 +48,11 @@ s hg17.chr7 127471195 389 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG s panTro1.chr6 129885076 389 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ </help> --- a/tools/maf/maf_to_bed.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_to_bed.xml Thu Aug 25 10:00:09 2011 -0400 @@ -123,6 +123,12 @@ 5. score - A score between 0 and 1000. 6. strand - Defines the strand - either '+' or '-'. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + </help><code file="maf_to_bed_code.py"/> --- a/tools/maf/maf_to_fasta.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_to_fasta.xml Thu Aug 25 10:00:09 2011 -0400 @@ -188,6 +188,12 @@ - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; - An "e" line containing information about the size of the gap between the alignments that span the current block. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + </help></tool> --- a/tools/maf/maf_to_interval.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_to_interval.xml Thu Aug 25 10:00:09 2011 -0400 @@ -121,6 +121,12 @@ - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; - An "e" line containing information about the size of the gap between the alignments that span the current block. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + </help></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Cleanup display of shared visualizations.
by Bitbucket 24 Aug '11

24 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9986212ed733/ changeset: 9986212ed733 user: jgoecks date: 2011-08-24 23:15:34 summary: Cleanup display of shared visualizations. affected #: 1 file (7 bytes) --- a/templates/visualization/display.mako Wed Aug 24 16:43:02 2011 -0400 +++ b/templates/visualization/display.mako Wed Aug 24 17:15:34 2011 -0400 @@ -58,7 +58,7 @@ </%def><%def name="render_item( visualization, config )"> - <div id="${visualization.id}" class="unified-panel-body" style="overflow:none;top:0px;"></div> + <div id="${trans.security.encode_id( visualization.id )}" class="unified-panel-body" style="overflow:none;top:0px;"></div><script type="text/javascript"> // TODO: much of this code is copied from browser.mako -- create shared base and use in both places. @@ -76,15 +76,14 @@ converted_datasets_state_url = "${h.url_for( controller='/tracks', action='converted_datasets_state' )}", addable_track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack }, view, - container_element = $("#${visualization.id}"); + container_element = $("#${trans.security.encode_id( visualization.id )}"); $(function() { if (container_element.parents(".item-content").length > 0) { // Embedded viz container_element.parents(".item-content").css( { "max-height": "none", "overflow": "visible" } ); } else { // Viewing just one shared viz - // TODO: need live or just bind click? - $("#right-border").live("click", function() { view.resize_window(); }); + $("#right-border").click(function() { view.resize_window(); }); } // Create view and add tracks. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: sam2interval: Add read_name column
by Bitbucket 24 Aug '11

24 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/606085ebe5f5/ changeset: 606085ebe5f5 user: kanwei date: 2011-08-24 22:43:02 summary: sam2interval: Add read_name column affected #: 4 files (18.4 KB) --- a/test-data/sam2interval_noprintAll.dat Wed Aug 24 15:33:07 2011 -0400 +++ b/test-data/sam2interval_noprintAll.dat Wed Aug 24 16:43:02 2011 -0400 @@ -1,7 +1,7 @@ -#chrom start end strand -ref 6 22 + -ref 8 19 + -ref 8 14 + -ref 15 40 + -ref 28 33 - -ref 36 45 - +#chrom start end strand read_name +ref 6 22 + r001 +ref 8 19 + r002 +ref 8 14 + r003 +ref 15 40 + r004 +ref 28 33 - r003 +ref 36 45 - r001 --- a/test-data/sam2interval_printAll.dat Wed Aug 24 15:33:07 2011 -0400 +++ b/test-data/sam2interval_printAll.dat Wed Aug 24 16:43:02 2011 -0400 @@ -1,4 +1,4 @@ -#chrom start end strand +#chrom start end strand read_name ref 6 22 + r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA * ref 8 19 + r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * ref 8 14 + r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 --- a/test-data/sam2interval_with_unmapped_reads_noprintAll.dat Wed Aug 24 15:33:07 2011 -0400 +++ b/test-data/sam2interval_with_unmapped_reads_noprintAll.dat Wed Aug 24 16:43:02 2011 -0400 @@ -1,927 +1,927 @@ -#chrom start end strand -chrM 6565 6641 - -chrM 4096 4172 - -chrM 14759 14835 - -chrM 1244 1320 - -chrM 5317 5393 + -chrM 10934 11010 - -chr1 567534 567610 - -chrM 16407 16483 - -chrM 8684 8760 + -chrM 4952 5028 - -chr1 567927 568003 - -chrM 6830 6906 - -chrM 7432 7508 + -chrM 5342 5418 - -chrM 3199 3275 - -chrM 1392 1468 + -chrM 7909 7985 + -chr2 49456941 49457017 - -chrM 16239 16315 + -chrM 11515 11591 - -chrM 7343 7419 - -chrM 5628 5704 + -chrM 9238 9314 + -chrM 202 278 - -chrM 10065 10141 + -chrM 9875 9951 + -chrM 9031 9107 - -chr1 564778 564854 - -chrM 5333 5409 - -chrM 435 511 + -chrM 4066 4142 + -chrM 6214 6290 + -chrM 7217 7293 - -chrM 11261 11337 - -chrM 14521 14597 - -chrM 3593 3669 - -chr17 22023720 22023796 - -chrM 12846 12922 - -chrM 7047 7123 - -chrM 2693 2769 + -chrM 8062 8138 - -chrM 6159 6235 + -chr1 566417 566493 - -chrM 3031 3107 - -chrM 6276 6352 + -chrM 14786 14862 - -chrM 10589 10665 + -chrM 16248 16324 - -chrM 7319 7395 + -chrM 3527 3603 + -chrM 13998 14074 + -chrM 13229 13305 + -chrM 7456 7532 - -chrM 5109 5185 - 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-chrM 2462 2538 - -chrM 8469 8545 + -chrM 11092 11168 - -chrM 6473 6549 + -chrM 16220 16296 - -chrM 4832 4908 + -chr17 22023725 22023801 - -chr1 567374 567450 - -chrM 11821 11897 + -chrM 8061 8137 - -chr5 134260199 134260275 - -chrM 9877 9953 - -chrM 11833 11909 + -chrM 3658 3734 - -chrM 861 937 - -chrM 5607 5683 + -chrM 8622 8698 - -chrM 9468 9544 + -chrM 10362 10438 - -chrM 3138 3214 + -chrM 4320 4396 - -chr1 567521 567597 - -chrM 8468 8544 + -chrM 3891 3967 - -chrM 13657 13733 - -chrM 9922 9998 - -chrM 15865 15941 + -chrM 5353 5429 - -chrM 8744 8820 + -chrM 5339 5415 + -chrM 3734 3810 + -chrM 4252 4328 + -chrM 13502 13578 + -chrM 16346 16422 + +#chrom start end strand read_name +chrM 6565 6641 - GA5:3:1:24:1745#0/1 +chrM 4096 4172 - GA5:3:1:23:263#0/1 +chrM 14759 14835 - GA5:3:1:24:1658#0/1 +chrM 1244 1320 - GA5:3:1:24:1108#0/1 +chrM 5317 5393 + GA5:3:1:24:1272#0/1 +chrM 10934 11010 - GA5:3:1:25:1989#0/1 +chr1 567534 567610 - GA5:3:1:25:1877#0/1 +chrM 16407 16483 - GA5:3:1:25:1203#0/1 +chrM 8684 8760 + GA5:3:1:24:1720#0/1 +chrM 4952 5028 - GA5:3:1:25:74#0/1 +chr1 567927 568003 - GA5:3:1:26:129#0/1 +chrM 6830 6906 - GA5:3:1:27:1860#0/1 +chrM 7432 7508 + GA5:3:1:26:303#0/1 +chrM 5342 5418 - GA5:3:1:27:509#0/1 +chrM 3199 3275 - GA5:3:1:27:1876#0/1 +chrM 1392 1468 + GA5:3:1:27:462#0/1 +chrM 7909 7985 + GA5:3:1:27:1826#0/1 +chr2 49456941 49457017 - GA5:3:1:28:1961#0/1 +chrM 16239 16315 + GA5:3:1:25:1902#0/1 +chrM 11515 11591 - GA5:3:1:28:704#0/1 +chrM 7343 7419 - GA5:3:1:29:78#0/1 +chrM 5628 5704 + GA5:3:1:29:65#0/1 +chrM 9238 9314 + GA5:3:1:30:571#0/1 +chrM 202 278 - GA5:3:1:30:1418#0/1 +chrM 10065 10141 + GA5:3:1:31:1998#0/1 +chrM 9875 9951 + GA5:3:1:32:1159#0/1 +chrM 9031 9107 - GA5:3:1:32:1723#0/1 +chr1 564778 564854 - GA5:3:1:32:1365#0/1 +chrM 5333 5409 - GA5:3:1:33:300#0/1 +chrM 435 511 + GA5:3:1:33:625#0/1 +chrM 4066 4142 + GA5:3:1:33:1597#0/1 +chrM 6214 6290 + GA5:3:1:32:1051#0/1 +chrM 7217 7293 - GA5:3:1:33:1476#0/1 +chrM 11261 11337 - GA5:3:1:34:1493#0/1 +chrM 14521 14597 - GA5:3:1:35:718#0/1 +chrM 3593 3669 - GA5:3:1:35:1074#0/1 +chr17 22023720 22023796 - GA5:3:1:35:1946#0/1 +chrM 12846 12922 - GA5:3:1:36:143#0/1 +chrM 7047 7123 - GA5:3:1:38:1282#0/1 +chrM 2693 2769 + GA5:3:1:36:258#0/1 +chrM 8062 8138 - GA5:3:1:38:1622#0/1 +chrM 6159 6235 + GA5:3:1:39:651#0/1 +chr1 566417 566493 - GA5:3:1:40:1756#0/1 +chrM 3031 3107 - GA5:3:1:41:277#0/1 +chrM 6276 6352 + GA5:3:1:41:24#0/1 +chrM 14786 14862 - GA5:3:1:42:1739#0/1 +chrM 10589 10665 + GA5:3:1:44:1997#0/1 +chrM 16248 16324 - GA5:3:1:42:449#0/1 +chrM 7319 7395 + GA5:3:1:44:1202#0/1 +chrM 3527 3603 + GA5:3:1:44:1689#0/1 +chrM 13998 14074 + GA5:3:1:45:1004#0/1 +chrM 13229 13305 + GA5:3:1:46:1996#0/1 +chrM 7456 7532 - GA5:3:1:46:1624#0/1 +chrM 5109 5185 - GA5:3:1:47:148#0/1 +chrM 2909 2985 + GA5:3:1:46:1928#0/1 +chr13 110076579 110076655 + GA5:3:1:48:345#0/1 +chr1 566432 566508 - GA5:3:1:49:208#0/1 +chr1 565743 565819 - GA5:3:1:48:1620#0/1 +chrM 3155 3231 - GA5:3:1:48:1536#0/1 +chrM 4657 4733 + GA5:3:1:49:1377#0/1 +chrM 7368 7444 + GA5:3:1:51:1072#0/1 +chrM 5329 5405 - GA5:3:1:51:78#0/1 +chrM 2171 2247 - GA5:3:1:51:851#0/1 +chr1 568282 568358 + GA5:3:1:52:518#0/1 +chrM 4376 4452 + GA5:3:1:52:796#0/1 +chrM 14645 14721 - GA5:3:1:52:192#0/1 +chrM 4694 4770 - GA5:3:1:55:1412#0/1 +chrM 2412 2488 + GA5:3:1:53:1458#0/1 +chrM 9057 9133 - GA5:3:1:55:1305#0/1 +chrM 10527 10603 + GA5:3:1:55:855#0/1 +chr1 564493 564569 - GA5:3:1:55:451#0/1 +chrM 7102 7178 + GA5:3:1:55:299#0/1 +chrM 10896 10972 - GA5:3:1:55:1194#0/1 +chrM 13626 13702 + GA5:3:1:56:1499#0/1 +chrM 5609 5685 + GA5:3:1:57:959#0/1 +chrM 7666 7742 - GA5:3:1:56:473#0/1 +chrM 14730 14806 + GA5:3:1:56:636#0/1 +chrM 10682 10758 + GA5:3:1:57:1408#0/1 +chrM 5069 5145 + GA5:3:1:58:763#0/1 +chr1 566474 566550 - GA5:3:1:59:688#0/1 +chrM 9140 9216 + GA5:3:1:59:791#0/1 +chrM 16340 16416 - GA5:3:1:59:503#0/1 +chr1 565718 565794 - GA5:3:1:61:1190#0/1 +chrM 6732 6808 + GA5:3:1:58:1920#0/1 +chrM 16239 16315 + GA5:3:1:57:1111#0/1 +chrM 3180 3256 - GA5:3:1:61:1838#0/1 +chrM 13789 13865 + GA5:3:1:61:722#0/1 +chrM 10350 10426 + GA5:3:1:62:1796#0/1 +chrM 10519 10595 - GA5:3:1:62:1469#0/1 +chrM 5391 5467 + GA5:3:1:63:1214#0/1 +chrM 6420 6496 - GA5:3:1:61:594#0/1 +chrM 745 821 - GA5:3:1:62:1922#0/1 +chrM 1023 1099 + GA5:3:1:63:762#0/1 +chr1 569720 569796 + GA5:3:1:61:900#0/1 +chr1 569272 569348 + GA5:3:1:63:462#0/1 +chrM 10091 10167 + GA5:3:1:63:709#0/1 +chrM 10937 11013 - GA5:3:1:63:1686#0/1 +chrM 6460 6536 - GA5:3:1:64:1185#0/1 +chrM 12342 12418 + GA5:3:1:64:1804#0/1 +chrM 8694 8770 - GA5:3:1:67:480#0/1 +chrM 2104 2180 + GA5:3:1:65:500#0/1 +chrM 16386 16462 - GA5:3:1:68:398#0/1 +chrM 3224 3300 + GA5:3:1:67:298#0/1 +chr1 564901 564977 - GA5:3:1:67:612#0/1 +chr1 564729 564805 - GA5:3:1:68:336#0/1 +chrM 6453 6529 - GA5:3:1:68:1266#0/1 +chrM 9602 9678 - GA5:3:1:68:1282#0/1 +chrM 5756 5832 + GA5:3:1:72:332#0/1 +chrM 10562 10638 + GA5:3:1:72:1394#0/1 +chrM 2816 2892 + GA5:3:1:69:117#0/1 +chrM 9681 9757 - GA5:3:1:72:1576#0/1 +chrM 11237 11313 - GA5:3:1:72:1817#0/1 +chrM 3920 3996 - GA5:3:1:72:1884#0/1 +chrM 8192 8268 + GA5:3:1:73:1128#0/1 +chrM 1720 1796 - GA5:3:1:73:1334#0/1 +chrM 14707 14783 - GA5:3:1:73:870#0/1 +chrM 11125 11201 - GA5:3:1:73:743#0/1 +chr1 569107 569183 + GA5:3:1:73:124#0/1 +chrM 9111 9187 + GA5:3:1:73:1774#0/1 +chrM 3908 3984 + GA5:3:1:74:276#0/1 +chrM 14018 14094 - GA5:3:1:74:1707#0/1 +chrM 11284 11360 - GA5:3:1:75:739#0/1 +chrM 3592 3668 - GA5:3:1:75:1808#0/1 +chrM 14471 14547 + GA5:3:1:75:1740#0/1 +chrM 2865 2941 - GA5:3:1:76:1071#0/1 +chrM 9703 9779 + GA5:3:1:78:1517#0/1 +chrM 16034 16110 - GA5:3:1:77:509#0/1 +chr5 134262582 134262658 - GA5:3:1:77:84#0/1 +chrM 2197 2273 - GA5:3:1:77:137#0/1 +chrM 15072 15148 - GA5:3:1:79:1703#0/1 +chrM 13030 13106 - GA5:3:1:78:1438#0/1 +chrM 12457 12533 - GA5:3:1:80:1988#0/1 +chrM 1868 1944 - GA5:3:1:79:708#0/1 +chrM 10249 10325 + GA5:3:1:81:1195#0/1 +chrM 12210 12286 + GA5:3:1:82:274#0/1 +chrM 4022 4098 - GA5:3:1:82:806#0/1 +chrM 16199 16275 + GA5:3:1:83:1274#0/1 +chrM 13120 13196 - GA5:3:1:83:13#0/1 +chrM 13023 13099 - GA5:3:1:83:466#0/1 +chrM 8719 8795 - GA5:3:1:82:161#0/1 +chrM 8674 8750 - GA5:3:1:84:1918#0/1 +chr1 569410 569486 - GA5:3:1:86:1188#0/1 +chrM 16066 16142 - GA5:3:1:85:383#0/1 +chr11 10529687 10529763 - GA5:3:1:85:419#0/1 +chrM 7208 7284 - GA5:3:1:86:1840#0/1 +chrM 10193 10269 + GA5:3:1:86:1396#0/1 +chrM 1280 1356 - GA5:3:1:86:1670#0/1 +chrM 14135 14211 - GA5:3:1:87:1553#0/1 +chrM 131 207 - GA5:3:1:87:968#0/1 +chrM 847 923 - GA5:3:1:88:944#0/1 +chrM 8651 8727 - GA5:3:1:88:722#0/1 +chrM 14879 14955 + GA5:3:1:88:1905#0/1 +chrM 15558 15634 - GA5:3:1:90:183#0/1 +chrM 2986 3062 - GA5:3:1:91:1288#0/1 +chrM 2502 2578 + GA5:3:1:91:1865#0/1 +chrM 9781 9857 - GA5:3:1:93:1339#0/1 +chrM 13380 13456 - GA5:3:1:93:289#0/1 +chr3 96335987 96336063 - GA5:3:1:91:1901#0/1 +chrM 7094 7170 - GA5:3:1:93:31#0/1 +chrM 15731 15807 - GA5:3:1:93:607#0/1 +chrM 12004 12080 + GA5:3:1:90:1958#0/1 +chrM 12835 12911 + GA5:3:1:93:1806#0/1 +chrM 3314 3390 - GA5:3:1:94:1167#0/1 +chrM 4030 4106 + GA5:3:1:94:636#0/1 +chr1 569884 569960 - GA5:3:1:93:1176#0/1 +chrM 6647 6723 + GA5:3:1:94:131#0/1 +chr1 566600 566676 - GA5:3:1:95:952#0/1 +chrM 2430 2506 + GA5:3:1:94:989#0/1 +chrM 12833 12909 + GA5:3:1:94:703#0/1 +chr1 568256 568332 + GA5:3:1:95:1072#0/1 +chrM 13222 13298 - GA5:3:1:95:866#0/1 +chrM 10321 10397 - GA5:3:1:96:1665#0/1 +chrM 8614 8690 - GA5:3:1:96:1702#0/1 +chrM 6581 6657 + GA5:3:1:97:734#0/1 +chrM 3526 3602 + GA5:3:1:97:239#0/1 +chrM 11413 11489 + GA5:3:1:98:1829#0/1 +chrM 9826 9902 - GA5:3:1:98:1819#0/1 +chr5 134259175 134259251 - GA5:3:1:98:222#0/1 +chrM 3314 3390 - GA5:3:1:99:476#0/1 +chrM 11146 11222 - GA5:3:1:98:271#0/1 +chrM 2735 2811 + GA5:3:1:98:770#0/1 +chrM 1695 1771 + GA5:3:1:100:1425#0/1 +chrM 3333 3409 - GA5:3:1:99:1469#0/1 +chr1 567391 567467 - GA5:3:1:100:1178#0/1 +chrM 3110 3186 - GA5:3:1:101:849#0/1 +chr1 567574 567650 - GA5:3:1:102:707#0/1 +chrM 15552 15628 + GA5:3:1:103:1995#0/1 +chrX 125606487 125606563 - GA5:3:1:99:740#0/1 +chrM 9205 9281 + GA5:3:1:103:300#0/1 +chr5 134260176 134260252 - GA5:3:1:103:505#0/1 +chrM 3023 3099 - GA5:3:1:103:1266#0/1 +chr1 566110 566186 + GA5:3:1:103:637#0/1 +chr1 569285 569361 - GA5:3:1:104:856#0/1 +chrM 12692 12768 + GA5:3:1:100:1609#0/1 +chrM 10442 10518 + GA5:3:1:104:645#0/1 +chrM 8008 8084 + GA5:3:1:104:948#0/1 +chr1 567269 567345 + GA5:3:1:105:775#0/1 +chrM 10796 10872 + GA5:3:1:104:1070#0/1 +chrM 2903 2979 - GA5:3:1:104:1800#0/1 +chrM 10349 10425 + GA5:3:1:106:1608#0/1 +chr13 110076645 110076721 - GA5:3:1:108:1351#0/1 +chrM 9283 9359 - GA5:3:1:107:1114#0/1 +chrM 2816 2892 + GA5:3:1:108:1305#0/1 +chrM 2816 2892 + GA5:3:1:108:615#0/1 +chrM 6529 6605 + GA5:3:1:110:954#0/1 +chrM 16312 16388 - GA5:3:1:111:941#0/1 +chrM 5295 5371 + GA5:3:1:111:207#0/1 +chrM 4061 4137 - GA5:3:1:112:1363#0/1 +chrM 5949 6025 + GA5:3:1:112:974#0/1 +chrM 2680 2756 - GA5:3:1:113:519#0/1 +chrM 4032 4108 + GA5:3:1:112:1748#0/1 +chrM 13081 13157 + GA5:3:1:113:728#0/1 +chrM 2979 3055 - GA5:3:1:113:1888#0/1 +chrM 2335 2411 + GA5:3:1:113:1937#0/1 +chr1 567560 567636 + GA5:3:1:114:1152#0/1 +chrM 14790 14866 + GA5:3:1:114:1895#0/1 +chrM 1316 1392 - GA5:3:1:114:910#0/1 +chr1 568495 568571 - GA5:3:1:114:1273#0/1 +chrM 15907 15983 + GA5:3:1:115:1736#0/1 +chrM 3937 4013 + GA5:3:1:116:1034#0/1 +chrM 2357 2433 + GA5:3:1:116:1207#0/1 +chr1 567258 567334 + GA5:3:1:115:454#0/1 +chrM 10600 10676 - GA5:3:1:116:898#0/1 +chrM 8474 8550 - GA5:3:1:116:1215#0/1 +chrM 11515 11591 - GA5:3:1:117:1182#0/1 +chr1 567287 567363 + GA5:3:1:117:422#0/1 +chrM 11167 11243 + GA5:3:1:118:1611#0/1 +chrM 15521 15597 - GA5:3:1:117:643#0/1 +chrM 10943 11019 - GA5:3:1:118:598#0/1 +chrM 6201 6277 + GA5:3:1:118:1255#0/1 +chrM 12696 12772 - GA5:3:1:120:134#0/1 +chrM 10796 10872 + GA5:3:1:119:783#0/1 +chrM 2960 3036 - GA5:3:1:120:1597#0/1 +chrM 14774 14850 + GA5:3:1:120:122#0/1 +chrM 9545 9621 + GA5:3:1:121:1197#0/1 +chrM 1007 1083 - GA5:3:1:121:1070#0/1 +chrM 14806 14882 - GA5:3:1:121:277#0/1 +chrM 14909 14985 - GA5:3:1:122:604#0/1 +chrM 9123 9199 + GA5:3:1:123:334#0/1 +chrM 7198 7274 - GA5:3:1:123:1597#0/1 +chr1 568855 568931 - GA5:3:1:122:153#0/1 +chrM 11186 11262 - GA5:3:1:123:1737#0/1 +chrM 1094 1170 + GA5:3:1:125:126#0/1 +chrM 1754 1830 + GA5:3:1:125:1359#0/1 +chrM 6393 6469 + GA5:3:1:126:1749#0/1 +chrM 8906 8982 - GA5:3:1:126:102#0/1 +chrM 3919 3995 - GA5:3:1:127:288#0/1 +chrM 10951 11027 + GA5:3:1:126:1454#0/1 +chrM 6624 6700 - GA5:3:1:127:711#0/1 +chrM 7883 7959 + GA5:3:1:130:1391#0/1 +chr1 567275 567351 + GA5:3:1:129:1716#0/1 +chrM 6483 6559 + GA5:3:1:131:1895#0/1 +chrM 9937 10013 - GA5:3:1:132:1632#0/1 +chrM 6529 6605 - GA5:3:1:132:1866#0/1 +chrM 3650 3726 - GA5:3:1:131:1555#0/1 +chrM 10905 10981 - GA5:3:1:133:152#0/1 +chrM 8023 8099 + GA5:3:1:133:261#0/1 +chrM 10902 10978 + GA5:3:1:133:884#0/1 +chrM 6461 6537 + GA5:3:1:133:793#0/1 +chrM 13049 13125 - GA5:3:1:134:409#0/1 +chrM 11515 11591 - GA5:3:1:134:937#0/1 +chrM 5360 5436 - GA5:3:1:135:4#0/1 +chrM 11605 11681 + GA5:3:1:136:764#0/1 +chrM 2357 2433 - GA5:3:1:136:1126#0/1 +chrM 6309 6385 + GA5:3:1:137:774#0/1 +chr1 567281 567357 + GA5:3:1:136:1459#0/1 +chr7 45291595 45291671 - GA5:3:1:137:385#0/1 +chrM 14614 14690 - GA5:3:1:138:1810#0/1 +chrM 2978 3054 - GA5:3:1:138:422#0/1 +chrM 7048 7124 - GA5:3:1:138:1360#0/1 +chrM 11084 11160 - GA5:3:1:139:124#0/1 +chrM 2259 2335 - GA5:3:1:139:1525#0/1 +chrM 5416 5492 - GA5:3:1:140:1536#0/1 +chr5 134263614 134263690 - GA5:3:1:140:1015#0/1 +chrM 14179 14255 - GA5:3:1:140:1072#0/1 +chr1 566599 566675 + GA5:3:1:141:9#0/1 +chrM 14895 14971 - GA5:3:1:141:734#0/1 +chr13 110076472 110076548 + GA5:3:1:141:473#0/1 +chrM 7849 7925 - GA5:3:1:141:1890#0/1 +chrM 14822 14898 + GA5:3:1:143:1226#0/1 +chr1 569878 569954 + GA5:3:1:142:635#0/1 +chrM 3272 3348 - GA5:3:1:141:548#0/1 +chrM 12276 12352 - GA5:3:1:143:1775#0/1 +chrM 5839 5915 + GA5:3:1:144:603#0/1 +chrM 9009 9085 + GA5:3:1:143:1215#0/1 +chr1 569321 569397 - GA5:3:1:145:350#0/1 +chrM 11416 11492 - GA5:3:1:145:644#0/1 +chrM 3866 3942 - GA5:3:1:146:75#0/1 +chrM 11415 11491 - GA5:3:1:145:1743#0/1 +chrM 9583 9659 - GA5:3:1:146:229#0/1 +chrM 10422 10498 - GA5:3:1:146:1848#0/1 +chrM 9066 9142 + GA5:3:1:147:11#0/1 +chrM 11515 11591 - GA5:3:1:147:148#0/1 +chrM 15452 15528 + GA5:3:1:148:1088#0/1 +chrM 239 315 + GA5:3:1:147:1796#0/1 +chrM 16322 16398 + GA5:3:1:148:200#0/1 +chrM 1012 1088 - GA5:3:1:149:607#0/1 +chrM 6176 6252 - GA5:3:1:150:1681#0/1 +chrM 10809 10885 + GA5:3:1:145:528#0/1 +chr1 568094 568170 - GA5:3:1:151:1905#0/1 +chrM 13321 13397 - GA5:3:1:152:1759#0/1 +chrM 5752 5828 - GA5:3:1:151:117#0/1 +chrM 4132 4208 + GA5:3:1:152:348#0/1 +chrM 16250 16326 - GA5:3:1:150:1406#0/1 +chrM 10796 10872 + GA5:3:1:153:1969#0/1 +chrM 11898 11974 - GA5:3:1:155:1916#0/1 +chr1 564877 564953 + GA5:3:1:154:190#0/1 +chrM 8256 8332 + GA5:3:1:155:1870#0/1 +chrM 15488 15564 + GA5:3:1:156:1707#0/1 +chrM 2804 2880 + GA5:3:1:157:280#0/1 +chrM 4878 4954 + GA5:3:1:156:977#0/1 +chrM 11258 11334 - GA5:3:1:157:1848#0/1 +chrM 4153 4229 + GA5:3:1:158:172#0/1 +chrM 11225 11301 - GA5:3:1:158:451#0/1 +chrM 892 968 - GA5:3:1:159:1719#0/1 +chrM 4399 4475 - GA5:3:1:158:1248#0/1 +chr18 45379660 45379736 - GA5:3:1:158:147#0/1 +chrM 9171 9247 - GA5:3:1:160:1547#0/1 +chrM 3176 3252 + GA5:3:1:160:687#0/1 +chrM 1013 1089 - GA5:3:1:161:170#0/1 +chrM 6704 6780 + GA5:3:1:161:1744#0/1 +chrM 8749 8825 - GA5:3:1:161:1370#0/1 +chrM 7066 7142 + GA5:3:1:161:786#0/1 +chrM 11180 11256 + GA5:3:1:163:213#0/1 +chrM 8322 8398 + GA5:3:1:163:300#0/1 +chr1 567957 568033 + GA5:3:1:163:493#0/1 +chrM 12819 12895 - GA5:3:1:163:1069#0/1 +chr5 134260214 134260290 + GA5:3:1:165:1929#0/1 +chrM 420 496 + GA5:3:1:164:263#0/1 +chrM 3397 3473 - GA5:3:1:164:1037#0/1 +chrM 9718 9794 - GA5:3:1:166:14#0/1 +chr5 134263411 134263487 - GA5:3:1:167:897#0/1 +chrM 14912 14988 - GA5:3:1:166:1121#0/1 +chr1 568792 568868 - GA5:3:1:168:466#0/1 +chrM 14376 14452 - GA5:3:1:169:469#0/1 +chrM 15473 15549 - GA5:3:1:170:1990#0/1 +chrM 4212 4288 + GA5:3:1:168:531#0/1 +chrM 235 311 + GA5:3:1:169:257#0/1 +chrM 5094 5170 + GA5:3:1:170:206#0/1 +chrM 4701 4777 - GA5:3:1:174:968#0/1 +chr1 567602 567678 - GA5:3:1:174:359#0/1 +chrM 10938 11014 + GA5:3:1:174:1235#0/1 +chrM 420 496 + GA5:3:1:174:1870#0/1 +chrM 5114 5190 + GA5:3:1:175:842#0/1 +chrM 11791 11867 - GA5:3:1:176:1895#0/1 +chrM 11390 11466 + GA5:3:1:179:872#0/1 +chrM 1225 1301 - GA5:3:1:178:724#0/1 +chrM 3047 3123 - GA5:3:1:180:469#0/1 +chrM 4385 4461 - GA5:3:1:179:0#0/1 +chrM 11200 11276 - GA5:3:1:183:1380#0/1 +chrM 3851 3927 - GA5:3:1:181:113#0/1 +chrM 4926 5002 + GA5:3:1:183:1147#0/1 +chrM 2816 2892 + GA5:3:1:178:594#0/1 +chrM 7291 7367 + GA5:3:1:184:1316#0/1 +chrM 11092 11168 - GA5:3:1:184:595#0/1 +chrM 26 102 + GA5:3:1:184:321#0/1 +chrM 10355 10431 + GA5:3:1:185:1665#0/1 +chrM 1568 1644 + GA5:3:1:185:1489#0/1 +chrM 11392 11468 + GA5:3:1:186:48#0/1 +chrM 5798 5874 - GA5:3:1:186:1149#0/1 +chrM 14694 14770 + GA5:3:1:185:695#0/1 +chrM 13875 13951 - GA5:3:1:186:79#0/1 +chr1 567902 567978 - GA5:3:1:188:1579#0/1 +chr1 568804 568880 - GA5:3:1:188:143#0/1 +chrM 4812 4888 - GA5:3:1:189:54#0/1 +chr1 568073 568149 + GA5:3:1:190:47#0/1 +chrM 4558 4634 - GA5:3:1:190:942#0/1 +chrM 6420 6496 + GA5:3:1:190:1501#0/1 +chrM 12281 12357 + GA5:3:1:190:10#0/1 +chr1 567571 567647 - GA5:3:1:190:115#0/1 +chrM 4033 4109 - GA5:3:1:191:1028#0/1 +chrM 15496 15572 + GA5:3:1:191:679#0/1 +chrM 3602 3678 + GA5:3:1:191:1675#0/1 +chrM 9106 9182 - GA5:3:1:191:1941#0/1 +chr5 134263406 134263482 - GA5:3:1:192:946#0/1 +chrM 16051 16127 - GA5:3:1:192:307#0/1 +chrM 10840 10916 + GA5:3:1:192:907#0/1 +chrM 6801 6877 + GA5:3:1:192:632#0/1 +chrM 2799 2875 - GA5:3:1:193:1404#0/1 +chrM 12419 12495 + GA5:3:1:193:1223#0/1 +chrM 1101 1177 + GA5:3:1:194:286#0/1 +chrM 10421 10497 + GA5:3:1:194:290#0/1 +chrM 11275 11351 - GA5:3:1:194:1585#0/1 +chrM 11075 11151 + GA5:3:1:195:193#0/1 +chrM 7886 7962 - GA5:3:1:194:1786#0/1 +chrM 16033 16109 + GA5:3:1:196:162#0/1 +chrM 4255 4331 - GA5:3:1:195:1872#0/1 +chrM 13766 13842 - GA5:3:1:196:137#0/1 +chrM 15943 16019 - GA5:3:1:196:1042#0/1 +chrM 6064 6140 - GA5:3:1:196:1036#0/1 +chr1 567894 567970 + GA5:3:1:196:367#0/1 +chrM 10668 10744 - GA5:3:1:197:1705#0/1 +chrM 8496 8572 + GA5:3:1:198:1613#0/1 +chrM 16271 16347 - GA5:3:1:196:1626#0/1 +chr1 569382 569458 - GA5:3:1:199:1635#0/1 +chrM 7950 8026 - GA5:3:1:200:1321#0/1 +chrM 7717 7793 + GA5:3:1:201:872#0/1 +chrM 9241 9317 - GA5:3:1:202:100#0/1 +chrM 13783 13859 - GA5:3:1:202:706#0/1 +chrM 4885 4961 - GA5:3:1:202:865#0/1 +chrM 3929 4005 - GA5:3:1:203:1231#0/1 +chrM 3741 3817 + GA5:3:1:204:528#0/1 +chr9 33658974 33659050 - GA5:3:1:204:1789#0/1 +chrM 11889 11965 + GA5:3:1:205:1026#0/1 +chrM 13119 13195 - GA5:3:1:204:1298#0/1 +chrM 3874 3950 + GA5:3:1:206:68#0/1 +chrM 3422 3498 + GA5:3:1:201:1544#0/1 +chr5 134259813 134259889 - GA5:3:1:206:918#0/1 +chrM 15043 15119 + GA5:3:1:206:600#0/1 +chrM 6634 6710 - GA5:3:1:206:155#0/1 +chrM 11221 11297 + GA5:3:1:206:1358#0/1 +chrM 13462 13538 + GA5:3:1:206:749#0/1 +chrM 10796 10872 + GA5:3:1:207:1409#0/1 +chrM 5955 6031 + GA5:3:1:208:683#0/1 +chr11 10529688 10529764 - GA5:3:1:207:1021#0/1 +chrM 2862 2938 - GA5:3:1:207:1762#0/1 +chrM 8157 8233 + GA5:3:1:209:281#0/1 +chrM 6781 6857 + GA5:3:1:208:655#0/1 +chr1 567555 567631 + GA5:3:1:210:1081#0/1 +chrM 2089 2165 - GA5:3:1:208:1256#0/1 +chrM 10663 10739 - GA5:3:1:210:680#0/1 +chrM 13240 13316 - GA5:3:1:211:142#0/1 +chrM 15437 15513 + GA5:3:1:212:1819#0/1 +chr1 566620 566696 + GA5:3:1:212:226#0/1 +chrM 5680 5756 - GA5:3:1:212:276#0/1 +chrM 77 153 - GA5:3:1:210:1710#0/1 +chrM 9139 9215 + GA5:3:1:213:1377#0/1 +chr1 564695 564771 + GA5:3:1:214:617#0/1 +chrM 3155 3231 + GA5:3:1:214:175#0/1 +chrM 2816 2892 + GA5:3:1:214:1567#0/1 +chrM 7477 7553 + GA5:3:1:214:262#0/1 +chrM 8879 8955 + GA5:3:1:214:933#0/1 +chrM 8860 8936 + GA5:3:1:214:217#0/1 +chrM 4706 4782 + GA5:3:1:216:1701#0/1 +chrM 6466 6542 - GA5:3:1:217:891#0/1 +chrM 13439 13515 + GA5:3:1:215:1144#0/1 +chrM 4166 4242 + GA5:3:1:217:568#0/1 +chrM 9147 9223 - GA5:3:1:217:1664#0/1 +chr3 96336311 96336387 - GA5:3:1:217:1833#0/1 +chrM 9272 9348 - GA5:3:1:218:216#0/1 +chrM 10928 11004 - GA5:3:1:218:1358#0/1 +chrM 5040 5116 + GA5:3:1:218:1630#0/1 +chrM 10030 10106 + GA5:3:1:219:1693#0/1 +chrM 14452 14528 - GA5:3:1:219:677#0/1 +chrM 13808 13884 - GA5:3:1:219:1089#0/1 +chrM 310 386 - GA5:3:1:220:1479#0/1 +chrM 6445 6521 - GA5:3:1:220:184#0/1 +chrM 9707 9783 - GA5:3:1:221:910#0/1 +chrM 6447 6523 - GA5:3:1:221:216#0/1 +chrM 7578 7654 + GA5:3:1:221:1614#0/1 +chrM 4896 4972 + GA5:3:1:221:147#0/1 +chrM 11515 11591 - GA5:3:1:223:1221#0/1 +chrM 10946 11022 - GA5:3:1:222:1733#0/1 +chrM 6842 6918 + GA5:3:1:225:1169#0/1 +chrM 495 571 + GA5:3:1:220:485#0/1 +chrM 5505 5581 - GA5:3:1:224:1266#0/1 +chrM 11721 11797 + GA5:3:1:219:833#0/1 +chrM 15651 15727 - GA5:3:1:225:1130#0/1 +chrM 2110 2186 + GA5:3:1:226:398#0/1 +chr1 568855 568931 - GA5:3:1:227:1794#0/1 +chrM 8051 8127 - GA5:3:1:227:995#0/1 +chrM 14308 14384 - GA5:3:1:225:1174#0/1 +chr1 567878 567954 + GA5:3:1:227:1815#0/1 +chrM 6304 6380 - GA5:3:1:229:1982#0/1 +chrM 7969 8045 - GA5:3:1:228:1113#0/1 +chrM 6293 6369 - GA5:3:1:230:1016#0/1 +chrM 818 894 + GA5:3:1:231:1353#0/1 +chrM 14261 14337 - GA5:3:1:232:1298#0/1 +chrM 11374 11450 + GA5:3:1:232:514#0/1 +chrM 8045 8121 - GA5:3:1:233:1217#0/1 +chrM 8681 8757 + GA5:3:1:232:1971#0/1 +chrM 3486 3562 - GA5:3:1:233:1277#0/1 +chr1 566494 566570 + GA5:3:1:233:903#0/1 +chrM 9878 9954 - GA5:3:1:233:970#0/1 +chr1 564505 564581 + GA5:3:1:234:1415#0/1 +chrM 11417 11493 + GA5:3:1:234:1143#0/1 +chrM 15652 15728 + GA5:3:1:235:1863#0/1 +chrM 5104 5180 + GA5:3:1:235:1036#0/1 +chrM 3164 3240 + GA5:3:1:235:1129#0/1 +chrM 11719 11795 - GA5:3:1:235:4#0/1 +chrM 395 471 + GA5:3:1:235:1636#0/1 +chrM 3166 3242 + GA5:3:1:236:962#0/1 +chrM 9042 9118 + GA5:3:1:233:1838#0/1 +chrM 10915 10991 + GA5:3:1:235:1166#0/1 +chrM 8037 8113 - GA5:3:1:237:525#0/1 +chrM 10604 10680 - GA5:3:1:237:37#0/1 +chrM 15976 16052 + GA5:3:1:237:967#0/1 +chrM 7775 7851 - GA5:3:1:237:1496#0/1 +chrM 11581 11657 - GA5:3:1:237:1125#0/1 +chrM 773 849 - GA5:3:1:239:1057#0/1 +chrM 16288 16364 - GA5:3:1:238:1759#0/1 +chrM 1281 1357 + GA5:3:1:239:855#0/1 +chrM 1657 1733 + GA5:3:1:240:348#0/1 +chrM 10176 10252 - GA5:3:1:240:94#0/1 +chrM 3185 3261 - GA5:3:1:241:1734#0/1 +chrM 6377 6453 - GA5:3:1:241:968#0/1 +chrM 11399 11475 + GA5:3:1:244:198#0/1 +chrM 10678 10754 - GA5:3:1:244:1599#0/1 +chrM 1452 1528 - GA5:3:1:244:1912#0/1 +chrM 11618 11694 - GA5:3:1:245:362#0/1 +chrM 13579 13655 - GA5:3:1:244:1135#0/1 +chrM 15858 15934 + GA5:3:1:244:1621#0/1 +chrM 9293 9369 - GA5:3:1:245:1065#0/1 +chrM 1083 1159 + GA5:3:1:246:764#0/1 +chrM 2816 2892 + GA5:3:1:246:701#0/1 +chrM 2730 2806 + GA5:3:1:247:437#0/1 +chrM 8902 8978 + GA5:3:1:247:26#0/1 +chrM 4252 4328 + GA5:3:1:247:820#0/1 +chrM 11609 11685 - GA5:3:1:248:1725#0/1 +chrM 10880 10956 + GA5:3:1:247:565#0/1 +chrM 13288 13364 - GA5:3:1:250:163#0/1 +chrM 676 752 + GA5:3:1:250:1216#0/1 +chrM 793 869 - GA5:3:1:250:872#0/1 +chrM 8931 9007 + GA5:3:1:252:1164#0/1 +chrM 3544 3620 + GA5:3:1:251:243#0/1 +chrM 3696 3772 + GA5:3:1:253:1759#0/1 +chrM 9368 9444 - GA5:3:1:253:92#0/1 +chrM 2816 2892 + GA5:3:1:255:789#0/1 +chrM 9102 9178 + GA5:3:1:252:1110#0/1 +chrM 2980 3056 - GA5:3:1:254:530#0/1 +chr1 567271 567347 + GA5:3:1:256:840#0/1 +chrM 9582 9658 - GA5:3:1:255:732#0/1 +chrM 13325 13401 - GA5:3:1:256:794#0/1 +chrM 7896 7972 + GA5:3:1:258:1864#0/1 +chrM 3345 3421 - GA5:3:1:257:1754#0/1 +chrM 16365 16441 + GA5:3:1:258:566#0/1 +chrM 10811 10887 - GA5:3:1:257:1992#0/1 +chr1 569902 569978 - GA5:3:1:259:193#0/1 +chrM 3314 3390 - GA5:3:1:259:466#0/1 +chrM 15883 15959 - GA5:3:1:259:841#0/1 +chr1 564724 564800 - GA5:3:1:259:1579#0/1 +chrM 4714 4790 - GA5:3:1:261:1344#0/1 +chrM 16468 16544 - GA5:3:1:261:260#0/1 +chrM 6558 6634 - GA5:3:1:262:807#0/1 +chrM 8279 8355 + GA5:3:1:262:1989#0/1 +chrM 1881 1957 + GA5:3:1:263:989#0/1 +chrM 10313 10389 - GA5:3:1:263:1859#0/1 +chrM 12145 12221 + GA5:3:1:265:357#0/1 +chrM 12198 12274 + GA5:3:1:265:1168#0/1 +chrM 13527 13603 - GA5:3:1:266:1591#0/1 +chrM 11054 11130 - GA5:3:1:267:532#0/1 +chrM 2819 2895 + GA5:3:1:267:178#0/1 +chrM 15764 15840 + GA5:3:1:268:587#0/1 +chrM 13208 13284 + GA5:3:1:261:133#0/1 +chrM 516 592 + GA5:3:1:268:1979#0/1 +chrM 14986 15062 + GA5:3:1:265:1679#0/1 +chrM 6236 6312 + GA5:3:1:269:0#0/1 +chrM 9719 9795 + GA5:3:1:271:508#0/1 +chrM 10293 10369 - GA5:3:1:273:745#0/1 +chrM 11050 11126 + GA5:3:1:273:1161#0/1 +chrM 1352 1428 - GA5:3:1:273:1629#0/1 +chrM 843 919 + GA5:3:1:273:1611#0/1 +chr5 79947252 79947328 - GA5:3:1:273:1624#0/1 +chrM 4199 4275 - GA5:3:1:273:1799#0/1 +chrM 14674 14750 - GA5:3:1:274:687#0/1 +chrM 15289 15365 - GA5:3:1:275:50#0/1 +chrM 13553 13629 - GA5:3:1:275:1970#0/1 +chrM 2816 2892 + GA5:3:1:277:718#0/1 +chrM 10274 10350 - GA5:3:1:276:84#0/1 +chrM 691 767 - GA5:3:1:276:1892#0/1 +chrM 3523 3599 + GA5:3:1:277:1982#0/1 +chr1 567903 567979 + GA5:3:1:276:1692#0/1 +chrM 11291 11367 + GA5:3:1:277:1664#0/1 +chrM 9494 9570 - GA5:3:1:277:675#0/1 +chrM 9917 9993 - GA5:3:1:279:1440#0/1 +chrM 2184 2260 + GA5:3:1:280:910#0/1 +chrM 2202 2278 - GA5:3:1:281:1665#0/1 +chrM 14827 14903 + GA5:3:1:281:1721#0/1 +chrM 9116 9192 - GA5:3:1:281:1007#0/1 +chrM 12049 12125 - GA5:3:1:281:410#0/1 +chr6 62284081 62284157 + GA5:3:1:281:1663#0/1 +chrM 8153 8229 + GA5:3:1:282:874#0/1 +chrM 6592 6668 - GA5:3:1:281:517#0/1 +chrM 7578 7654 + GA5:3:1:283:920#0/1 +chrM 3314 3390 - GA5:3:1:284:512#0/1 +chrM 12063 12139 - GA5:3:1:285:1895#0/1 +chrM 7082 7158 - GA5:3:1:283:1465#0/1 +chrM 13050 13126 - GA5:3:1:285:854#0/1 +chrM 3747 3823 - GA5:3:1:285:1775#0/1 +chrM 10833 10909 - GA5:3:1:286:905#0/1 +chrM 10742 10818 - GA5:3:1:289:717#0/1 +chrM 11066 11142 - GA5:3:1:290:290#0/1 +chrM 2816 2892 + GA5:3:1:290:211#0/1 +chrM 3553 3629 - GA5:3:1:291:533#0/1 +chr1 569068 569144 - GA5:3:1:291:102#0/1 +chrM 9590 9666 + GA5:3:1:292:1628#0/1 +chrM 2048 2124 - GA5:3:1:291:832#0/1 +chrM 9815 9891 + GA5:3:1:292:992#0/1 +chrM 3314 3390 - GA5:3:1:292:1448#0/1 +chrM 13055 13131 + GA5:3:1:293:912#0/1 +chrM 2760 2836 - GA5:3:1:294:548#0/1 +chrM 3779 3855 - GA5:3:1:294:1438#0/1 +chrM 10951 11027 - GA5:3:1:294:431#0/1 +chrM 1532 1608 - GA5:3:1:295:1615#0/1 +chrM 11772 11848 + GA5:3:1:296:711#0/1 +chrM 1359 1435 + GA5:3:1:295:1527#0/1 +chrM 15988 16064 - GA5:3:1:298:1240#0/1 +chrM 4956 5032 + GA5:3:1:299:1039#0/1 +chrM 2963 3039 - GA5:3:1:297:1448#0/1 +chr1 567336 567412 - GA5:3:1:300:1225#0/1 +chrM 2110 2186 - GA5:3:1:301:1093#0/1 +chrM 3258 3334 + GA5:3:1:301:1802#0/1 +chr5 134263454 134263530 - GA5:3:1:301:1236#0/1 +chrM 8869 8945 + GA5:3:1:301:363#0/1 +chrM 9229 9305 + GA5:3:1:301:751#0/1 +chrM 6579 6655 - GA5:3:1:302:403#0/1 +chrM 5779 5855 - GA5:3:1:302:560#0/1 +chrM 12474 12550 + GA5:3:1:302:1689#0/1 +chrM 2034 2110 - GA5:3:1:302:958#0/1 +chrM 3141 3217 - GA5:3:1:303:1216#0/1 +chrM 12218 12294 - GA5:3:1:304:1597#0/1 +chrM 9137 9213 + GA5:3:1:304:715#0/1 +chrM 942 1018 - GA5:3:1:304:207#0/1 +chrM 2929 3005 + GA5:3:1:306:340#0/1 +chrM 1414 1490 - GA5:3:1:307:1969#0/1 +chrM 5327 5403 - GA5:3:1:307:1941#0/1 +chr17 22023721 22023797 - GA5:3:1:309:428#0/1 +chrM 11067 11143 + GA5:3:1:310:278#0/1 +chrM 12329 12405 + GA5:3:1:312:1973#0/1 +chrM 12612 12688 + GA5:3:1:310:1459#0/1 +chr1 567541 567617 + GA5:3:1:313:706#0/1 +chrM 2818 2894 + GA5:3:1:314:1246#0/1 +chrM 12488 12564 - GA5:3:1:313:1472#0/1 +chrM 5293 5369 + GA5:3:1:315:338#0/1 +chrM 8194 8270 + GA5:3:1:314:132#0/1 +chrM 11313 11389 - GA5:3:1:316:472#0/1 +chrM 15065 15141 - GA5:3:1:316:1193#0/1 +chrM 14965 15041 - GA5:3:1:315:772#0/1 +chrM 10333 10409 - GA5:3:1:314:418#0/1 +chrM 8351 8427 + GA5:3:1:316:938#0/1 +chrM 3535 3611 - GA5:3:1:316:1359#0/1 +chrM 6366 6442 - GA5:3:1:317:1923#0/1 +chrM 2738 2814 - GA5:3:1:317:60#0/1 +chr17 22023745 22023821 + GA5:3:1:316:537#0/1 +chrM 16084 16160 - GA5:3:1:317:897#0/1 +chr1 569903 569979 + GA5:3:1:318:574#0/1 +chrM 832 908 - GA5:3:1:318:1958#0/1 +chrM 5348 5424 - GA5:3:1:318:305#0/1 +chrM 15288 15364 - GA5:3:1:319:671#0/1 +chrM 12508 12584 - GA5:3:1:319:15#0/1 +chrM 5346 5422 + GA5:3:1:320:1170#0/1 +chrM 5850 5926 - GA5:3:1:320:1921#0/1 +chrM 7255 7331 - GA5:3:1:318:1966#0/1 +chrM 13798 13874 + GA5:3:1:320:1346#0/1 +chr1 564464 564540 - GA5:3:1:320:380#0/1 +chrM 8421 8497 + GA5:3:1:322:241#0/1 +chrM 6910 6986 - GA5:3:1:322:946#0/1 +chrM 15124 15200 - GA5:3:1:322:1386#0/1 +chrM 7287 7363 + GA5:3:1:323:711#0/1 +chrM 4946 5022 + GA5:3:1:324:1685#0/1 +chrM 14314 14390 + GA5:3:1:324:375#0/1 +chrM 15363 15439 - GA5:3:1:324:1120#0/1 +chrM 2346 2422 + GA5:3:1:319:1499#0/1 +chrM 11124 11200 + GA5:3:1:324:466#0/1 +chr1 567514 567590 + GA5:3:1:324:1231#0/1 +chrM 4665 4741 - GA5:3:1:325:1750#0/1 +chrM 3366 3442 - GA5:3:1:325:41#0/1 +chr1 569857 569933 - GA5:3:1:325:13#0/1 +chrM 4786 4862 - GA5:3:1:325:1334#0/1 +chrM 3536 3612 - GA5:3:1:326:1009#0/1 +chrM 8273 8349 - GA5:3:1:326:785#0/1 +chrM 10604 10680 + GA5:3:1:326:827#0/1 +chrM 8343 8419 + GA5:3:1:325:1773#0/1 +chrM 7121 7197 - GA5:3:1:326:1761#0/1 +chrM 2816 2892 + GA5:3:1:327:1725#0/1 +chrM 1589 1665 - GA5:3:1:327:1413#0/1 +chrM 5372 5448 - GA5:3:1:327:426#0/1 +chr1 568483 568559 - GA5:3:1:329:486#0/1 +chrM 15853 15929 - GA5:3:1:328:806#0/1 +chrM 2861 2937 + GA5:3:1:329:1087#0/1 +chrM 7209 7285 + GA5:3:1:329:842#0/1 +chrM 9836 9912 - GA5:3:1:329:478#0/1 +chrM 12185 12261 - GA5:3:1:330:1136#0/1 +chrM 13832 13908 - GA5:3:1:330:166#0/1 +chrM 7789 7865 + GA5:3:1:331:1027#0/1 +chrM 4318 4394 - GA5:3:1:331:810#0/1 +chrM 9787 9863 + GA5:3:1:331:278#0/1 +chrM 14017 14093 - GA5:3:1:331:1947#0/1 +chrM 13058 13134 - GA5:3:1:332:325#0/1 +chrM 6046 6122 - GA5:3:1:333:155#0/1 +chrM 2350 2426 + GA5:3:1:327:364#0/1 +chrM 7201 7277 - GA5:3:1:333:1601#0/1 +chrM 11145 11221 + GA5:3:1:334:1026#0/1 +chrM 6757 6833 - GA5:3:1:333:1545#0/1 +chrM 9485 9561 + GA5:3:1:335:1755#0/1 +chrM 12688 12764 - GA5:3:1:335:1597#0/1 +chrM 5083 5159 + GA5:3:1:335:941#0/1 +chrM 11354 11430 - GA5:3:1:336:1945#0/1 +chrM 16485 16561 - GA5:3:1:336:87#0/1 +chrM 12347 12423 + GA5:3:1:336:221#0/1 +chrM 7204 7280 + GA5:3:1:336:1091#0/1 +chrM 8040 8116 - GA5:3:1:336:1916#0/1 +chrM 3701 3777 - GA5:3:1:336:531#0/1 +chrM 400 476 - GA5:3:1:337:420#0/1 +chrM 10483 10559 + GA5:3:1:338:1754#0/1 +chr1 569286 569362 - GA5:3:1:338:1991#0/1 +chrM 7122 7198 - GA5:3:1:339:1836#0/1 +chrM 7081 7157 - GA5:3:1:339:1286#0/1 +chr5 134259841 134259917 - GA5:3:1:340:1081#0/1 +chrM 10965 11041 + GA5:3:1:340:385#0/1 +chrM 708 784 + GA5:3:1:341:78#0/1 +chrM 4655 4731 - GA5:3:1:341:366#0/1 +chrM 1182 1258 - GA5:3:1:342:1207#0/1 +chrM 2748 2824 + GA5:3:1:342:1904#0/1 +chr1 565770 565846 + GA5:3:1:342:1812#0/1 +chrM 5147 5223 + GA5:3:1:344:169#0/1 +chrM 5507 5583 + GA5:3:1:343:17#0/1 +chrM 1750 1826 - GA5:3:1:343:800#0/1 +chrM 11017 11093 - GA5:3:1:344:692#0/1 +chrM 11224 11300 - GA5:3:1:345:1886#0/1 +chrM 3825 3901 - GA5:3:1:346:432#0/1 +chrM 15613 15689 - GA5:3:1:349:1448#0/1 +chrM 7536 7612 - GA5:3:1:347:786#0/1 +chrM 13045 13121 - GA5:3:1:349:804#0/1 +chrM 14403 14479 - GA5:3:1:349:1239#0/1 +chrM 12541 12617 - GA5:3:1:350:754#0/1 +chrM 13561 13637 - GA5:3:1:350:38#0/1 +chrM 110 186 + GA5:3:1:350:918#0/1 +chrM 7145 7221 - GA5:3:1:351:999#0/1 +chr17 22023719 22023795 - GA5:3:1:351:950#0/1 +chrM 3397 3473 - GA5:3:1:352:1006#0/1 +chrM 3390 3466 + GA5:3:1:351:312#0/1 +chrM 2344 2420 - GA5:3:1:352:1832#0/1 +chrM 7891 7967 - GA5:3:1:352:1360#0/1 +chrM 10934 11010 - GA5:3:1:353:352#0/1 +chrM 15433 15509 - GA5:3:1:352:63#0/1 +chrM 3337 3413 + GA5:3:1:353:844#0/1 +chrM 6474 6550 - GA5:3:1:354:1491#0/1 +chrM 11837 11913 + GA5:3:1:353:1239#0/1 +chrM 13862 13938 + GA5:3:1:354:768#0/1 +chrM 5411 5487 - GA5:3:1:354:27#0/1 +chrM 10514 10590 + GA5:3:1:354:1355#0/1 +chrM 8413 8489 + GA5:3:1:356:1541#0/1 +chrM 15375 15451 - GA5:3:1:356:1351#0/1 +chr1 569717 569793 + GA5:3:1:356:611#0/1 +chrM 11380 11456 + GA5:3:1:357:1820#0/1 +chr1 566164 566240 - GA5:3:1:357:1690#0/1 +chr1 566667 566743 + GA5:3:1:357:1552#0/1 +chrM 3173 3249 + GA5:3:1:358:1526#0/1 +chrM 10233 10309 - GA5:3:1:358:1454#0/1 +chrM 3992 4068 - GA5:3:1:358:1695#0/1 +chrM 16338 16414 + GA5:3:1:359:766#0/1 +chrM 9010 9086 - GA5:3:1:358:230#0/1 +chrM 12729 12805 + GA5:3:1:356:1079#0/1 +chrM 6394 6470 - GA5:3:1:359:1358#0/1 +chrM 6142 6218 + GA5:3:1:360:524#0/1 +chrM 4363 4439 - GA5:3:1:361:850#0/1 +chrM 2944 3020 - GA5:3:1:361:1260#0/1 +chr5 134263378 134263454 - GA5:3:1:359:470#0/1 +chrM 13831 13907 - GA5:3:1:362:271#0/1 +chrM 13023 13099 - GA5:3:1:362:103#0/1 +chrM 10640 10716 + GA5:3:1:362:514#0/1 +chrM 2145 2221 - GA5:3:1:362:795#0/1 +chrM 12006 12082 - GA5:3:1:362:1043#0/1 +chrM 5093 5169 - GA5:3:1:363:1544#0/1 +chrM 9773 9849 + GA5:3:1:363:1013#0/1 +chrM 1591 1667 + GA5:3:1:363:1219#0/1 +chrM 443 519 + GA5:3:1:363:1680#0/1 +chrM 10852 10928 - GA5:3:1:362:1409#0/1 +chrM 16255 16331 - GA5:3:1:363:1573#0/1 +chrM 15014 15090 + GA5:3:1:363:392#0/1 +chrM 11515 11591 - GA5:3:1:364:678#0/1 +chrM 2816 2892 + GA5:3:1:364:591#0/1 +chrM 12031 12107 + GA5:3:1:364:940#0/1 +chrM 3700 3776 + GA5:3:1:364:738#0/1 +chrM 7218 7294 - GA5:3:1:364:1037#0/1 +chrM 3314 3390 - GA5:3:1:365:1803#0/1 +chrM 3935 4011 - GA5:3:1:365:1779#0/1 +chrM 9536 9612 - GA5:3:1:365:997#0/1 +chrM 3994 4070 - GA5:3:1:365:284#0/1 +chrM 9513 9589 + GA5:3:1:365:1695#0/1 +chrM 4616 4692 - GA5:3:1:365:754#0/1 +chr11 10530763 10530839 + GA5:3:1:367:1331#0/1 +chrM 13156 13232 + GA5:3:1:367:431#0/1 +chrM 12212 12288 + GA5:3:1:369:624#0/1 +chrM 1964 2040 - GA5:3:1:369:1920#0/1 +chr1 567269 567345 - GA5:3:1:369:424#0/1 +chrM 5448 5524 + GA5:3:1:370:1782#0/1 +chrM 978 1054 - GA5:3:1:370:600#0/1 +chrM 4651 4727 - GA5:3:1:370:288#0/1 +chr3 96336206 96336282 - GA5:3:1:370:1039#0/1 +chrM 10537 10613 + GA5:3:1:370:1508#0/1 +chrM 10640 10716 + GA5:3:1:370:534#0/1 +chrM 12895 12971 - GA5:3:1:370:355#0/1 +chr1 566580 566656 + GA5:3:1:371:462#0/1 +chrM 2816 2892 + GA5:3:1:373:1838#0/1 +chrM 7637 7713 - GA5:3:1:372:98#0/1 +chrM 3874 3950 + GA5:3:1:374:721#0/1 +chr5 134263381 134263457 - GA5:3:1:372:440#0/1 +chr5 79947212 79947288 - GA5:3:1:374:1080#0/1 +chrM 3041 3117 + GA5:3:1:375:1437#0/1 +chr1 564478 564554 - GA5:3:1:375:612#0/1 +chrM 8018 8094 - GA5:3:1:376:1174#0/1 +chrM 11377 11453 + GA5:3:1:376:67#0/1 +chrM 2600 2676 - GA5:3:1:376:558#0/1 +chrM 6442 6518 + GA5:3:1:377:685#0/1 +chrM 465 541 + GA5:3:1:376:1630#0/1 +chrM 10317 10393 - GA5:3:1:377:444#0/1 +chrM 13465 13541 - GA5:3:1:377:1241#0/1 +chrM 2687 2763 - GA5:3:1:378:252#0/1 +chrM 1579 1655 + GA5:3:1:379:967#0/1 +chrM 5460 5536 + GA5:3:1:383:215#0/1 +chrM 54 130 + GA5:3:1:381:1161#0/1 +chrM 8424 8500 - GA5:3:1:383:837#0/1 +chrM 6234 6310 - GA5:3:1:384:782#0/1 +chrM 11515 11591 - GA5:3:1:384:317#0/1 +chrM 3784 3860 - GA5:3:1:385:117#0/1 +chrM 2816 2892 + GA5:3:1:385:153#0/1 +chrM 8859 8935 + GA5:3:1:385:1135#0/1 +chrM 5082 5158 + GA5:3:1:386:1152#0/1 +chrM 6666 6742 + GA5:3:1:387:1466#0/1 +chrM 14287 14363 + GA5:3:1:387:1263#0/1 +chrM 4369 4445 + GA5:3:1:386:884#0/1 +chrM 12361 12437 + GA5:3:1:389:597#0/1 +chrM 3314 3390 - GA5:3:1:389:1104#0/1 +chrM 2148 2224 + GA5:3:1:390:1824#0/1 +chr5 134259835 134259911 + GA5:3:1:390:1946#0/1 +chrM 12519 12595 - GA5:3:1:391:1187#0/1 +chrM 3582 3658 + GA5:3:1:390:1884#0/1 +chrM 11384 11460 + GA5:3:1:391:272#0/1 +chrM 11431 11507 + GA5:3:1:392:1874#0/1 +chrM 11288 11364 - GA5:3:1:393:162#0/1 +chrM 1805 1881 - GA5:3:1:392:1394#0/1 +chrM 10179 10255 + GA5:3:1:393:1056#0/1 +chrM 3314 3390 - GA5:3:1:393:860#0/1 +chrM 8780 8856 - GA5:3:1:394:1561#0/1 +chrM 3734 3810 + GA5:3:1:395:207#0/1 +chr11 10530095 10530171 + GA5:3:1:390:112#0/1 +chrM 1385 1461 + GA5:3:1:397:1357#0/1 +chrM 9675 9751 + GA5:3:1:398:1207#0/1 +chrM 11084 11160 + GA5:3:1:398:12#0/1 +chrM 8583 8659 + GA5:3:1:399:941#0/1 +chrM 3305 3381 + GA5:3:1:399:1072#0/1 +chrM 8512 8588 - GA5:3:1:399:1299#0/1 +chrM 11287 11363 - GA5:3:1:400:488#0/1 +chrM 4790 4866 + GA5:3:1:399:542#0/1 +chrM 1435 1511 - GA5:3:1:400:748#0/1 +chr1 567255 567331 - GA5:3:1:401:673#0/1 +chrM 566 642 - GA5:3:1:402:1934#0/1 +chrM 13143 13219 - GA5:3:1:402:1807#0/1 +chrM 12171 12247 - GA5:3:1:402:283#0/1 +chrM 11264 11340 + GA5:3:1:399:1484#0/1 +chrM 9209 9285 - GA5:3:1:402:1896#0/1 +chrM 10940 11016 - GA5:3:1:403:1595#0/1 +chrM 11515 11591 - GA5:3:1:404:1551#0/1 +chrM 6685 6761 - GA5:3:1:405:1600#0/1 +chrM 184 260 - GA5:3:1:403:1870#0/1 +chrM 31 107 + GA5:3:1:404:716#0/1 +chrM 11170 11246 + GA5:3:1:405:1184#0/1 +chrM 15089 15165 - GA5:3:1:406:336#0/1 +chrM 8123 8199 - GA5:3:1:405:1223#0/1 +chrM 12144 12220 - GA5:3:1:406:283#0/1 +chrM 5813 5889 - GA5:3:1:406:97#0/1 +chrM 15487 15563 + GA5:3:1:407:686#0/1 +chrM 7975 8051 - GA5:3:1:406:381#0/1 +chrM 14369 14445 + GA5:3:1:407:315#0/1 +chrM 4772 4848 + GA5:3:1:407:846#0/1 +chrM 16483 16559 - GA5:3:1:407:692#0/1 +chrM 8096 8172 - GA5:3:1:408:761#0/1 +chrM 34 110 - GA5:3:1:408:87#0/1 +chrM 10347 10423 + GA5:3:1:408:1553#0/1 +chrM 14112 14188 + GA5:3:1:409:1433#0/1 +chrM 6575 6651 + GA5:3:1:409:571#0/1 +chrM 696 772 + GA5:3:1:412:395#0/1 +chrM 11790 11866 - GA5:3:1:410:1990#0/1 +chrM 16268 16344 - GA5:3:1:411:1317#0/1 +chr13 110076567 110076643 + GA5:3:1:412:346#0/1 +chrM 1687 1763 + GA5:3:1:412:1157#0/1 +chrM 10936 11012 - GA5:3:1:414:1810#0/1 +chrM 3994 4070 + GA5:3:1:414:1062#0/1 +chr1 566609 566685 + GA5:3:1:414:1864#0/1 +chrM 3842 3918 + GA5:3:1:414:976#0/1 +chrM 9306 9382 - GA5:3:1:413:1773#0/1 +chrM 16224 16300 - GA5:3:1:415:897#0/1 +chrM 3903 3979 - GA5:3:1:416:214#0/1 +chrM 2943 3019 - GA5:3:1:415:549#0/1 +chrM 14533 14609 - GA5:3:1:417:1892#0/1 +chrM 11515 11591 - GA5:3:1:417:1023#0/1 +chrM 8482 8558 - GA5:3:1:418:1783#0/1 +chrM 11515 11591 - GA5:3:1:419:1023#0/1 +chr1 565758 565834 + GA5:3:1:419:1785#0/1 +chrM 8485 8561 - GA5:3:1:419:892#0/1 +chrM 3314 3390 - GA5:3:1:420:168#0/1 +chrM 11316 11392 - GA5:3:1:420:617#0/1 +chrM 2370 2446 - GA5:3:1:421:271#0/1 +chrM 14762 14838 + GA5:3:1:417:1426#0/1 +chr1 568483 568559 - GA5:3:1:423:731#0/1 +chrM 3019 3095 + GA5:3:1:424:54#0/1 +chr1 564926 565002 - GA5:3:1:424:1669#0/1 +chrM 12573 12649 - GA5:3:1:424:594#0/1 +chrM 2816 2892 + GA5:3:1:425:382#0/1 +chrM 14111 14187 - GA5:3:1:425:932#0/1 +chrM 2462 2538 - GA5:3:1:425:1589#0/1 +chrM 8469 8545 + GA5:3:1:421:1967#0/1 +chrM 11092 11168 - GA5:3:1:425:162#0/1 +chrM 6473 6549 + GA5:3:1:426:1489#0/1 +chrM 16220 16296 - GA5:3:1:427:1426#0/1 +chrM 4832 4908 + GA5:3:1:427:1780#0/1 +chr17 22023725 22023801 - GA5:3:1:427:1140#0/1 +chr1 567374 567450 - GA5:3:1:427:420#0/1 +chrM 11821 11897 + GA5:3:1:429:1694#0/1 +chrM 8061 8137 - GA5:3:1:430:378#0/1 +chr5 134260199 134260275 - GA5:3:1:429:1507#0/1 +chrM 9877 9953 - GA5:3:1:431:248#0/1 +chrM 11833 11909 + GA5:3:1:428:1466#0/1 +chrM 3658 3734 - GA5:3:1:432:1011#0/1 +chrM 861 937 - GA5:3:1:432:381#0/1 +chrM 5607 5683 + GA5:3:1:432:886#0/1 +chrM 8622 8698 - GA5:3:1:433:1453#0/1 +chrM 9468 9544 + GA5:3:1:433:1188#0/1 +chrM 10362 10438 - GA5:3:1:434:1170#0/1 +chrM 3138 3214 + GA5:3:1:436:428#0/1 +chrM 4320 4396 - GA5:3:1:435:1711#0/1 +chr1 567521 567597 - GA5:3:1:436:1244#0/1 +chrM 8468 8544 + GA5:3:1:437:1704#0/1 +chrM 3891 3967 - GA5:3:1:437:1581#0/1 +chrM 13657 13733 - GA5:3:1:438:1005#0/1 +chrM 9922 9998 - GA5:3:1:439:1607#0/1 +chrM 15865 15941 + GA5:3:1:438:1116#0/1 +chrM 5353 5429 - GA5:3:1:437:120#0/1 +chrM 8744 8820 + GA5:3:1:440:1464#0/1 +chrM 5339 5415 + GA5:3:1:440:140#0/1 +chrM 3734 3810 + GA5:3:1:440:823#0/1 +chrM 4252 4328 + GA5:3:1:441:633#0/1 +chrM 13502 13578 + GA5:3:1:442:1663#0/1 +chrM 16346 16422 + GA5:3:1:443:1999#0/1 --- a/tools/samtools/sam2interval.py Wed Aug 24 15:33:07 2011 -0400 +++ b/tools/samtools/sam2interval.py Wed Aug 24 16:43:02 2011 -0400 @@ -68,7 +68,7 @@ cigar = re.compile( '\d+M|\d+N|\d+D|\d+P' ) - print '#chrom\tstart\tend\tstrand' # provide a (partial) header so that strand is automatically set in metadata + print '#chrom\tstart\tend\tstrand\tread_name' # provide a (partial) header so that strand is automatically set in metadata for line in infile: line = line.rstrip( '\r\n' ) @@ -90,7 +90,7 @@ if options.prt_all: print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, line) else: - print '%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand) + print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, read_name) if __name__ == "__main__": main() 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: Fix sending mail when the receipient is a list (as in sample tracking mail routines).
by Bitbucket 24 Aug '11

24 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d0c9c238ddbf/ changeset: d0c9c238ddbf user: natefoo date: 2011-08-24 21:33:07 summary: Fix sending mail when the receipient is a list (as in sample tracking mail routines). affected #: 1 file (93 bytes) --- a/lib/galaxy/util/__init__.py Wed Aug 24 14:42:56 2011 -0400 +++ b/lib/galaxy/util/__init__.py Wed Aug 24 15:33:07 2011 -0400 @@ -572,8 +572,11 @@ """ Sends an email. """ + header_to = to + if isinstance( to, list ): + header_to = ', '.join( to ) msg = MIMEText( body ) - msg[ 'To' ] = to + msg[ 'To' ] = header_to msg[ 'From' ] = frm msg[ 'Subject' ] = subject if config.smtp_server is None: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Pack scripts.
by Bitbucket 24 Aug '11

24 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dc5884c1be86/ changeset: dc5884c1be86 user: jgoecks date: 2011-08-24 20:42:56 summary: Pack scripts. affected #: 1 file (521 bytes) --- a/static/scripts/packed/trackster.js Wed Aug 24 14:38:29 2011 -0400 +++ b/static/scripts/packed/trackster.js Wed Aug 24 14:42:56 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,U){var n=f("class").extend,p=f("slotting"),I=f("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"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")};n(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var C=function(ac,ad){ac.bind("drag",{handle:ad,relative:true},function(ah,ai){var ag=$(this).parent();var af=ag.children();var ae;for(ae=0;ae<af.length;ae++){if(ai.offsetY<$(af.get(ae)).position().top){break}}if(ae===af.length){if(this!==af.get(ae-1)){ag.append(this)}}else{if(this!==af.get(ae)){$(this).insertBefore(af.get(ae))}}}).bind("dragstart",function(){$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css("border","0px")})};U.sortable=C;var aa=16,D=9,A=20,P=D+2,w=100,F=12000,N=200,z=5,s=10,H=5000,t=100,m="There was an error in indexing this dataset. 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"+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ad,ae){ad.num=t;$.extend(ad,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ac=this;$.ajax({url:chrom_url,data:ad,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ad.chrom);return}if(ag.reference){ac.add_label_track(new x(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+t+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+t+"</option>"}ac.chrom_select.html(aj);if(ae){ae()}ac.chrom_start_index=ag.start_index},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}})},change_chrom:function(ag,ad,ai){if(!ag||ag==="None"){return}var af=this;if(ag==="previous"){af.load_chroms({low:this.chrom_start_index-t});return}if(ag==="next"){af.load_chroms({low:this.chrom_start_index+t});return}var ah=$.grep(af.chrom_data,function(ak,al){return ak.chrom===ag})[0];if(ah===undefined){af.load_chroms({chrom:ag},function(){af.change_chrom(ag,ad,ai)});return}else{if(ag!==af.chrom){af.chrom=ag;af.chrom_select.val(af.chrom);af.max_high=ah.len-1;af.reset();af.request_redraw(true);for(var aj=0,ac=af.tracks.length;aj<ac;aj++){var ae=af.tracks[aj];if(ae.init){ae.init()}}}if(ad!==undefined&&ai!==undefined){af.low=Math.max(ad,0);af.high=Math.min(ai,af.max_high)}af.reset_overview();af.request_redraw()}},go_to:function(ag){var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0].replace(/,/g,""),10);af=parseInt(ah[1].replace(/,/g,""),10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_track:function(ac){ac.view=this;ac.track_id=this.track_id_counter;this.tracks.push(ac);if(ac.init){ac.init()}ac.container_div.attr("id","track_"+ac.track_id);C(ac.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1;this.update_intro_div()},add_label_track:function(ac){ac.view=this;this.label_tracks.push(ac)},remove_track:function(ad){this.has_changes=true;delete this.tracks[this.tracks.indexOf(ad)];this.num_tracks-=1;var ac=this;ad.container_div.fadeOut("slow",function(){$(this).remove();ac.update_intro_div()})},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad){var ac=this;requestAnimationFrame(function(){ac.redraw(ad)})},redraw:function(aj){var ah=this.low,ad=this.high;if(ah<this.max_low){ah=this.max_low}if(ad>this.max_high){ad=this.max_high}var ai=this.high-this.low;if(this.high!==0&&ai<this.min_separation){ad=ah+this.min_separation}this.low=Math.floor(ah);this.high=Math.ceil(ad);this.resolution=Math.pow(z,Math.ceil(Math.log((this.high-this.low)/N)/Math.log(z)));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=13;this.overview_box.css({left:ac,width:Math.max(ak,ag)}).show();if(ag<ak){this.overview_box.css("left",ac-(ak-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ag})}this.update_location(this.low,this.high);if(!aj){for(var ae=0,af=this.tracks.length;ae<af;ae++){if(this.tracks[ae]&&this.tracks[ae].enabled){this.tracks[ae].draw()}}for(ae=0,af=this.label_tracks.length;ae<af;ae++){this.label_tracks[ae].draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.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(ac){$.when(ac.get_overview_tile()).then(function(ad){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ad.canvas);view.overview_highlight.show().height(ad.canvas.height());view.overview_viewport.height(ad.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ac;view.has_changes=true;ac.set_is_overview(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 o=function(ae,ai){this.track=ae;this.name=ai.name;this.params=[];var ap=ai.params;for(var af=0;af<ap.length;af++){var ak=ap[af],ad=ak.name,ao=ak.label,ag=unescape(ak.html),aq=ak.value,am=ak.type;if(am==="number"){this.params[this.params.length]=new g(ad,ao,ag,aq,ak.min,ak.max)}else{if(am=="select"){this.params[this.params.length]=new K(ad,ao,ag,aq)}else{console.log("WARNING: unrecognized tool parameter type:",ad,am)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(at){at.stopPropagation()}).click(function(at){at.stopPropagation()}).bind("dblclick",function(at){at.stopPropagation()});var an=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var al=this.params;var aj=this;$.each(this.params,function(au,ax){var aw=$("<div>").addClass("param-row").appendTo(aj.parent_div);var at=$("<div>").addClass("param-label").text(ax.label).appendTo(aw);var av=$("<div/>").addClass("slider").html(ax.html).appendTo(aw);av.find(":input").val(ax.value);$("<div style='clear: both;'/>").appendTo(aw)});this.parent_div.find("input").click(function(){$(this).select()});var ar=$("<div>").addClass("param-row").appendTo(this.parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ar);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ar);var aj=this;ac.click(function(){aj.run_on_region()});ah.click(function(){aj.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ac={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ae=this.track,ad=ac.tool_id+ae.tool_region_and_parameters_str(ac.chrom,ac.low,ac.high),af;if(ae instanceof e){af=new R(ad,view,ae.hda_ldda,undefined,{},{},ae);af.change_mode(ae.mode)}this.track.add_track(af);af.content_div.text("Starting job.");this.run(ac,af,function(ag){af.dataset_id=ag.dataset_id;af.content_div.text("Running job.");af.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(G)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var K=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=ae;this.value=af};var g=function(ae,ad,ag,ah,af,ac){K.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};var h=function(ad,ac,ae,af){this.name=ad;this.index=ac;this.tool_id=ae;this.tool_exp_name=af};var S=function(ad,ac,ae,af){h.call(this,ad,ac,ae,af);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};n(S.prototype,{applies_to:function(ac){if(ac.length>this.index){return true}return false},keep:function(ac){if(!this.applies_to(ac)){return true}var ad=parseInt(ac[this.index]);return(isNaN(ad)||(ad>=this.low&&ad<=this.high))},update_attrs:function(ad){var ac=false;if(!this.applies_to(ad)){return ac}if(ad[this.index]<this.min){this.min=Math.floor(ad[this.index]);ac=true}if(ad[this.index]>this.max){this.max=Math.ceil(ad[this.index]);ac=true}return ac},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ae=function(ah,af){var ag=af-ah;return(ag<=2?0.01:1)};var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ae(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(am,at){this.track=am;this.filters=[];for(var an=0;an<at.length;an++){var ao=at[an],au=ao.name,ac=ao.type,af=ao.index,ar=ao.tool_id,aq=ao.tool_exp_name;if(ac==="int"||ac==="float"){this.filters[an]=new S(au,af,ar,aq)}else{console.log("ERROR: unsupported filter: ",au,ac)}}var ag=function(av,aw,ax){av.click(function(){var ay=aw.text();max=parseFloat(ax.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ax.slider("option","values")){input_size=2*input_size+1;multi_value=true}aw.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ay).appendTo(aw).focus().select().click(function(az){az.stopPropagation()}).blur(function(){$(this).remove();aw.text(ay)}).keyup(function(aD){if(aD.keyCode===27){$(this).trigger("blur")}else{if(aD.keyCode===13){var aB=ax.slider("option","min"),az=ax.slider("option","max"),aC=function(aE){return(isNaN(aE)||aE>az||aE<aB)},aA=$(this).val();if(!multi_value){aA=parseFloat(aA);if(aC(aA)){alert("Parameter value must be in the range ["+aB+"-"+az+"]");return $(this)}}else{aA=aA.split("-");aA=[parseFloat(aA[0]),parseFloat(aA[1])];if(aC(aA[0])||aC(aA[1])){alert("Parameter value must be in the range ["+aB+"-"+az+"]");return $(this)}}ax.slider((multi_value?"values":"value"),aA)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(av){av.stopPropagation()}).click(function(av){av.stopPropagation()}).bind("dblclick",function(av){av.stopPropagation()}).bind("keydown",function(av){av.stopPropagation()});var ap=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ak=this;$.each(this.filters,function(ay,aA){aA.container=$("<div/>").addClass("slider-row").appendTo(ap);var az=$("<div/>").addClass("elt-label").appendTo(aA.container);var ax=$("<span/>").addClass("slider-name").text(aA.name+" ").appendTo(az);var aw=$("<span/>");var aC=$("<span/>").addClass("slider-value").appendTo(az).append("[").append(aw).append("]");var av=$("<div/>").addClass("slider").appendTo(aA.container);aA.control_element=$("<div/>").attr("id",aA.name+"-filter-control").appendTo(av);var aB=[0,0];aA.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aD,aE){aB=aE.values;aw.text(aE.values[0]+"-"+aE.values[1]);setTimeout(function(){if(aE.values[0]==aB[0]&&aE.values[1]==aB[1]){var aF=aE.values;aw.text(aF[0]+"-"+aF[1]);aA.low=aF[0];aA.high=aF[1];ak.track.draw(true,true)}},50)},change:function(aD,aE){aA.control_element.slider("option","slide").call(aA.control_element,aD,aE)}});aA.slider=aA.control_element;aA.slider_label=aw;ag(aC,aw,aA.control_element);$("<div style='clear: both;'/>").appendTo(aA.container)});if(this.filters.length!==0){var ah=$("<div/>").addClass("param-row").appendTo(ap);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ah);var ae=this;aj.click(function(){ae.run_on_dataset()})}var al=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ai=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(al),ad=$("<select/>").attr("name","alpha_dropdown").appendTo(al);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ad);for(var an=0;an<this.filters.length;an++){$("<option/>").attr("value",an).text(this.filters[an].name).appendTo(ad)}ad.change(function(){$(this).children("option:selected").each(function(){var av=parseInt($(this).val());ak.alpha_filter=(av>=0?ak.filters[av]:null);ak.track.draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};n(X.prototype,{reset_filters:function(){for(var ac=0;ac<this.filters.length;ac++){filter=this.filters[ac];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!=ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!=ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var L=function(ad,ac){I.AlphaGenerator.call(this,ac);this.filter=ad};L.prototype.gen_alpha=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var W=function(ac){this.track=ac.track;this.params=ac.params;this.values={};if(ac.saved_values){this.restore_values(ac.saved_values)}this.onchange=ac.onchange};n(W.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var ad=this;var ac=$("<div />");$.each(this.params,function(ah,af){if(!af.hidden){var ae="param_"+ah;var am=$("<div class='form-row' />").appendTo(ac);am.append($("<label />").attr("for",ae).text(af.label+":"));if(af.type==="bool"){am.append($('<input type="checkbox" />').attr("id",ae).attr("name",ae).attr("checked",ad.values[af.key]))}else{if(af.type==="color"){var aj=ad.values[af.key];var ai=$("<input />").attr("id",ae).attr("name",ae).val(aj);var ak=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ag=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ak);var al=$("<div/>").appendTo(ag).farbtastic({width:100,height:100,callback:ai,color:aj});$("<div />").append(ai).append(ak).appendTo(am).bind("click",function(an){ak.css({left:$(this).position().left+($(ai).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ak.hide();$(document).unbind("click.color-picker")});an.stopPropagation()})}else{am.append($("<input />").attr("id",ae).attr("name",ae).val(ad.values[af.key]))}}}});return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange()}}});var b=function(ae,ad,ac,af){this.index=ae;this.low=ae*N*ad;this.high=(ae+1)*N*ad;this.resolution=ad;this.canvas=$("<div class='track-tile'/>").append(ac);this.data=af;this.stale=false};var l=function(ae,ad,ac,af,ag){b.call(this,ae,ad,ac,af);this.max_val=ag};var M=function(ae,ad,ac,ag,af){b.call(this,ae,ad,ac,ag);this.message=af};var j=function(ad,ac,ag,ae,af){this.name=ad;this.view=ac;this.parent_element=ag;this.data_url=(ae?ae:default_data_url);this.data_url_extra_params={};this.data_query_wait=(af?af:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").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 class='draghandle' />").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.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"ToolDataFeatureTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.initial_canvas=undefined;ac.content_div.css("height","auto");ac.container_div.removeClass("nodata error pending");if(!ac.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id,chrom:ac.view.chrom},function(ad){if(!ad||ad==="error"||ad.kind==="error"){ac.container_div.addClass("error");ac.content_div.text(m);if(ad.message){var af=ac.view.tracks.indexOf(ac);var ae=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ad.message+"</pre>",{Close:hide_modal})});ac.content_div.append(ae)}}else{if(ad==="no converter"){ac.container_div.addClass("error");ac.content_div.text(G)}else{if(ad==="no data"||(ad.data!==undefined&&(ad.data===null||ad.data.length===0))){ac.container_div.addClass("nodata");ac.content_div.text(B)}else{if(ad==="pending"){ac.container_div.addClass("pending");ac.content_div.text(q);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(ad.status==="data"){if(ad.valid_chroms){ac.valid_chroms=ad.valid_chroms;ac.make_name_popup_menu()}ac.content_div.text(V);if(ac.view.chrom){ac.content_div.text("");ac.content_div.css("height",ac.height_px+"px");ac.enabled=true;$.when(ac.predraw_init()).done(function(){ac.container_div.removeClass("nodata error pending");ac.draw()})}}}}}}})},predraw_init:function(){},update_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(aj,ah,ak){var ad=this,al=ad.view;this.filters_manager=(aj!==undefined?new X(this,aj):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ah!==undefined&&obj_length(ah)>0?new o(this,ah):undefined);this.is_overview=false;this.parent_track=ak;this.child_tracks=[];if(ad.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ad.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();ad.container_div.append(ad.child_tracks_container);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(ad.display_modes!==undefined){if(ad.mode_div===undefined){ad.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ad.header_div);var ae=(ad.track_config&&ad.track_config.values.mode?ad.track_config.values.mode:ad.display_modes[0]);ad.mode=ae;ad.mode_div.text(ae);var ac={};for(var af=0,ai=ad.display_modes.length;af<ai;af++){var ag=ad.display_modes[af];ac[ag]=function(am){return function(){ad.change_mode(am)}}(ag)}make_popupmenu(ad.mode_div,ac)}else{ad.mode_div.hide()}}this.make_name_popup_menu()};n(J.prototype,j.prototype,{change_mode:function(ad){var ac=this;ac.mode_div.text(ad);ac.mode=ad;ac.track_config.values.mode=ad;ac.tile_cache.clear();ac.draw()},make_name_popup_menu:function(){var ad=this;var ac={};ac[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ad.is_overview){ad.view.reset_overview()}else{ad.view.set_overview(ad)}};ac["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ad.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Track",ad.track_config.build_form(),{Cancel:aj,OK:ah})};if(ad.filters_available>0){var ag=(ad.filters_div.is(":visible")?"Hide filters":"Show filters");ac[ag]=function(){ad.filters_visible=(ad.filters_div.is(":visible"));if(ad.filters_visible){ad.filters_manager.reset_filters()}ad.filters_div.toggle();ad.make_name_popup_menu()}}if(ad.tool){var ag=(ad.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ac[ag]=function(){if(!ad.dynamic_tool_div.is(":visible")){ad.update_name(ad.name+ad.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ad.revert_name()}ad.dynamic_tool_div.toggle();ad.make_name_popup_menu()}}if(ad.valid_chroms){ac["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ad.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ae=view;var af=function(){$("#no-tracks").show()};if(this.parent_track){ae=this.parent_track;af=function(){}}ac.Remove=function(){ae.remove_track(ad);if(ae.num_tracks===0){af()}};make_popupmenu(ad.name_div,ac)},set_is_overview:function(ac){this.is_overview=ac;this.make_name_popup_menu()},get_overview_tile:function(){var ac=this;view=ac.view,resolution=Math.pow(z,Math.ceil(Math.log((view.max_high-view.max_low)/N)/Math.log(z))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ac.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ac.data_url_extra_params)).then(function(ad){var af=ac._gen_tile_cache_key(view_width,w_scale,0),ah=ac.tile_cache.get(af);if(!ah){ah=ac.draw_tile(ad,resolution,0,w_scale);ac.tile_cache.set(af,ah)}var ak=$(ah.canvas.find("canvas")),ag=ak.clone(),aj=ak.get(0).getContext("2d"),ae=ag.get(0).getContext("2d"),ai=aj.getImageData(0,0,aj.canvas.width,aj.canvas.height);ae.putImageData(ai,-ac.left_offset,(ah.data.dataset_type==="summary_tree"?P:0));new_tile=new b(-1,resolution,ag);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},draw:function(ae,an){if(!this.dataset_id){return}var am=this.view.low,ai=this.view.high,ak=ai-am,af=this.view.container.width(),aq=af/ak,ah=this.view.resolution,ap=$("<div style='position: relative;'></div>");if(!an){this.content_div.children().remove()}this.content_div.append(ap);this.max_height=0;var ad=Math.floor(am/ah/N);var al=true;var ao=[];var ac=0;while((ad*N*ah)<ai){tile=this.draw_helper(ae,af,ad,ah,ap,aq);if(tile){ao.push(tile)}else{al=false}ad+=1;ac++}var ag=this;if(al){ag.postdraw_actions(ao,af,aq,an)}for(var aj=0;aj<this.child_tracks.length;aj++){this.child_tracks[aj].draw(ae,an)}},postdraw_actions:function(ag,ah,ai,ac){var ae=this;var af=false;for(var ad=0;ad<ag.length;ad++){if(ag[ad].message){af=true;break}}if(af){for(var ad=0;ad<ag.length;ad++){tile=ag[ad];if(!tile.message){tile.canvas.css("padding-top",A)}}}},draw_helper:function(ad,ae,af,ai,ao,at,ap,aj){var ag=this,an=this._gen_tile_cache_key(ae,at,af),ak=af*N*ai,ar=ak+N*ai;var al=(ad?undefined:ag.tile_cache.get(an));if(al){ag.show_tile(al,ao,at);return al}var am=function(au){return("isResolved" in au)};var ah=true;var ac=ag.data_manager.get_data(ak,ar,ag.mode,ai,ag.data_url_extra_params);if(am(ac)){ah=false}var aq;if(view.reference_track&&at>view.canvas_manager.char_width_px){aq=view.reference_track.data_manager.get_data(ak,ar,ag.mode,ai,view.reference_track.data_url_extra_params);if(am(aq)){ah=false}}if(ah){n(ac,aj);var al=ag.draw_tile(ac,ai,af,at,aq);ag.tile_cache.set(an,al);if(al!==undefined){ag.show_tile(al,ao,at)}return al}$.when(ac,aq).then(function(){view.request_redraw()});return null},show_tile:function(aj,al,am){var ae=this,ad=aj.canvas,ai=ad;if(aj.message){var an=$("<div/>"),ak=$("<div/>").addClass("tile-message").text(aj.message).css({height:A-1,width:aj.canvas.width}).appendTo(an),ag=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ak),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ak);an.append(ad);ai=an;ag.click(function(){aj.stale=true;ae.data_manager.get_more_data(aj.low,aj.high,ae.mode,aj.resolution,{},ae.data_manager.DEEP_DATA_REQ);ae.draw()}).dblclick(function(ao){ao.stopPropagation()});ac.click(function(){aj.stale=true;ae.data_manager.get_more_data(aj.low,aj.high,ae.mode,aj.resolution,{},ae.data_manager.BROAD_DATA_REQ);ae.draw()}).dblclick(function(ao){ao.stopPropagation()})}var ah=this.view.high-this.view.low,af=(aj.low-this.view.low)*am;if(this.left_offset){af-=this.left_offset}ai.css({position:"absolute",top:0,left:af,height:""});al.append(ai);ae.max_height=Math.max(ae.max_height,ai.height());ae.content_div.css("height",ae.max_height+"px");al.children().css("height",ae.max_height+"px")},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},add_track:function(ac){ac.track_id=this.track_id+"_"+this.child_tracks.length;ac.container_div.attr("id","track_"+ac.track_id);this.child_tracks_container.append(ac.container_div);C(ac.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(ac);this.view.has_changes=true},remove_track:function(ac){ac.container_div.fadeOut("slow",function(){$(this).remove()})}});var Y=function(ac,ad){this.hidden=true;j.call(this,null,ac,ad);this.container_div.addClass("label-track")};n(Y.prototype,j.prototype,{draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var x=function(ac){this.hidden=true;j.call(this,null,ac,ac.top_labeltrack);J.call(this);ac.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:ac.dbkey};this.data_manager=new E(y,this,false);this.tile_cache=new c(r)};n(x.prototype,J.prototype,{draw_tile:function(ak,ah,ad,am){var ag=this,ae=N*ah;if(am>this.view.canvas_manager.char_width_px){if(ak===null){ag.content_div.css("height","0px");return}var af=this.view.canvas_manager.new_canvas();var al=af.getContext("2d");af.width=Math.ceil(ae*am+ag.left_offset);af.height=ag.height_px;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.round(ai*am);al.fillText(ak[ai],ac+ag.left_offset,10)}return new b(ad,ah,af,ak)}this.content_div.css("height","0px")}});var k=function(ag,ae,ah,ac,af){var ad=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ag,ae,ae.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ah;this.dataset_id=ac;this.original_dataset_id=ac;this.data_manager=new O(y,this);this.tile_cache=new c(r);this.track_config=new W({track:this,params:[{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:af,onchange:function(){ad.vertical_range=ad.prefs.max_value-ad.prefs.min_value;$("#linetrack_"+ad.track_id+"_minval").text(ad.prefs.min_value);$("#linetrack_"+ad.track_id+"_maxval").text(ad.prefs.max_value);ad.tile_cache.clear();ad.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,J.prototype,{add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){af=true;ad.show()},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.content_div).css("height",ag);ac.height_px=ag;ac.draw(true)}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.track_config.values.height=ac.height_px}).appendTo(ac.container_div)},predraw_init:function(){var ac=this,ad=ac.view.tracks.indexOf(ac);ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ae){ac.container_div.addClass("line-track");var ag=ae.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){ac.prefs.min_value=ag.min;ac.prefs.max_value=ag.max;$("#track_"+ad+"_minval").val(ac.prefs.min_value);$("#track_"+ad+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ad+"_minval").text(u(ac.prefs.min_value));var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ad+"_maxval").text(u(ac.prefs.max_value));af.css({position:"absolute",top:"24px",left:"10px"});af.prependTo(ac.container_div);ah.css({position:"absolute",bottom:"2px",left:"10px"});ah.prependTo(ac.container_div)})},draw_tile:function(am,ag,ad,al){if(this.vertical_range===undefined){return}var ah=ad*N*ag,af=N*ag,ac=Math.ceil(af*al),aj=this.height_px;var ae=this.view.canvas_manager.new_canvas();ae.width=ac,ae.height=aj;var ak=ae.getContext("2d");var ai=new I.LinePainter(am.data,ah,ah+af,this.prefs,this.mode);ai.draw(ak,ac,aj);return new b(ad,ag,ae,am.data)}});var e=function(ac,ah,ag,ak,aj,ae,af,ai){var ad=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new W({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){ad.tile_cache.clear();ad.draw()}});this.prefs=this.track_config.values;j.call(this,ac,ah,ah.viewport_container);J.call(this,ae,af,ai);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ag;this.dataset_id=ak;this.original_dataset_id=ak;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new O(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{postdraw_actions:function(ar,ac,at,aq){J.prototype.postdraw_actions.call(this,ar,aq);var af=this;if(aq){var ah=af.content_div.children();var ai=false;for(var ag=ah.length-1,am=0;ag>=am;ag--){var ae=$(ah[ag]);if(ai){ae.remove()}else{if(ae.children().length!==0){ai=true}}}}if(af.mode=="Histogram"){var al=-1;for(var ag=0;ag<ar.length;ag++){var ap=ar[ag].max_val;if(ap>al){al=ap}}for(var ag=0;ag<ar.length;ag++){var ao=ar[ag];if(ao.max_val!==al){ao.canvas.remove();af.draw_helper(true,ac,ao.index,ao.resolution,ao.canvas.parent(),at,[],{max:al})}}}if(af.filters_manager){var ad=af.filters_manager.filters;for(var ak=0;ak<ad.length;ak++){ad[ak].update_ui_elt()}var aj=false,an;for(var ag=0;ag<ar.length;ag++){if(ar[ag].data.length){an=ar[ag].data[0];for(var ak=0;ak<ad.length;ak++){if(ad[ak].applies_to(an)){aj=true;break}}}}if(af.filters_available!==aj){af.filters_available=aj;if(!af.filters_available){af.filters_div.hide()}af.make_name_popup_menu()}}},update_auto_mode:function(ac){if(this.mode=="Auto"){if(ac=="no_detail"){ac="feature spans"}else{if(ac=="summary_tree"){ac="coverage histogram"}}this.mode_div.text("Auto ("+ac+")")}},incremental_slots:function(ag,ad,af){var ae=this.view.canvas_manager.dummy_context,ac=this.inc_slots[ag];if(!ac||(ac.mode!==af)){ac=new (p.FeatureSlotter)(ag,af==="Pack",w,function(ah){return ae.measureText(ah)});ac.mode=af;this.inc_slots[ag]=ac}return ac.slot_features(ad)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},draw_tile:function(ap,ay,aC,al,af){var av=this,aE=aC*N*ay,ad=(aC+1)*N*ay,ar=ad-aE,aw=Math.ceil(ar*al),at=this.mode,aI=25,ag=this.left_offset,aq,ah;if(at==="Auto"){if(ap.dataset_type==="summary_tree"){at=ap.dataset_type}else{if(ap.extra_info==="no_detail"){at="no_detail"}else{var aH=ap.data;if(this.view.high-this.view.low>F){at="Squish"}else{at="Pack"}}}this.update_auto_mode(at)}if(at==="summary_tree"||at==="Histogram"){ah=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ac=$("<div />").addClass("yaxislabel");ac.text(ap.max);ac.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ac.prependTo(this.container_div);var ae=this.view.canvas_manager.new_canvas();ae.width=aw+ag;ae.height=ah+P;if(ap.dataset_type!="summary_tree"){var am=this.get_summary_tree_data(ap.data,aE,ad,200);if(ap.max){am.max=ap.max}ap=am}var aF=new I.SummaryTreePainter(ap,aE,ad,this.prefs);var ax=ae.getContext("2d");ax.translate(ag,P);aF.draw(ax,aw,ah);return new l(aC,ay,ae,ap.data,ap.max)}var aq,aj=1;if(at==="no_detail"||at==="Squish"||at==="Pack"){aj=this.incremental_slots(al,ap.data,at);aq=this.inc_slots[al].slots}var ak=[];if(ap.data){var an=this.filters_manager.filters;for(var az=0,aB=ap.data.length;az<aB;az++){var ai=ap.data[az];var aA=false;var ao;for(var aD=0,aG=an.length;aD<aG;aD++){ao=an[aD];ao.update_attrs(ai);if(!ao.keep(ai)){aA=true;break}}if(!aA){ak.push(ai)}}}var au=(this.filters_manager.alpha_filter?new L(this.filters_manager.alpha_filter):null);var aF=new (this.painter)(ak,aE,ad,this.prefs,at,au,af);var ah=Math.max(aa,aF.get_required_height(aj));var ae=this.view.canvas_manager.new_canvas();ae.width=aw+ag;ae.height=ah;var ax=ae.getContext("2d");ax.fillStyle=this.prefs.block_color;ax.font=ax.canvas.manager.default_font;ax.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ap.data){ax.translate(ag,0);aF.draw(ax,aw,ah,aq)}return new M(aC,ay,ae,ap.data,ap.message)}});var Q=function(af,ad,ah,ac,ae,ag){e.call(this,af,ad,ah,ac,ae,ag);this.painter=I.VariantPainter};n(Q.prototype,J.prototype,e.prototype);var T=function(af,ad,ah,ac,ae,ag){e.call(this,af,ad,ah,ac,ae,ag);this.track_config=new W({track:this,params:[{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:ae,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.painter=I.ReadPainter;this.make_name_popup_menu()};n(T.prototype,J.prototype,e.prototype);var R=function(ag,ae,ai,ac,af,ah,ad){e.call(this,ag,ae,ai,ac,af,ah,{},ad);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(R.prototype,J.prototype,e.prototype,{predraw_init:function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=H;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}});U.View=Z;U.LineTrack=k;U.FeatureTrack=e;U.ReadTrack=T};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 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T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+l-O,C+8)}else{R.textAlign="right";R.fillText(J,D-l-O,C+8)}R.fillStyle=V}}});x.AlphaGenerator=g;x.SummaryTreePainter=v;x.LinePainter=c;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.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 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",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",q="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",d=10,r=5,y=5;function u(ac){return Math.round(ac*1000)/1000}var c=function(ac){this.num_elements=ac;this.clear()};n(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var O=function(ad,ac,ae){c.call(this,ad);this.track=ac;this.subset=(ae!==undefined?ae:true)};n(O.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am[am.length]=ac[ah].name}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,aj,an)})},get_data:function(ac,ag,ah,ad,af){var ae=this.get_data_from_cache(ac,ag,ah);if(ae){return ae}ae=this.load_data(ac,ag,ah,ad,af);this.set_data(ac,ag,ah,ae);return ae},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get_data_from_cache(ak,af,aj);if(!al){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=al.data[al.data.length-1][2]+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,aj,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,aj,am);new_data_available.resolve(am)});return new_data_available},get_data_from_cache:function(ac,ad,ae){return this.get(this.gen_key(ac,ad,ae))},set_data:function(ad,ae,af,ac){return this.set(this.gen_key(ad,ae,af),ac)},gen_key:function(ac,ae,af){var ad=ac+"_"+ae+"_"+af;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){O.call(this,ad,ac,ae)};n(E.prototype,O.prototype,c.prototype,{load_data:function(ae,ac,ag,ah,ad,af){if(ad>1){return}return O.prototype.load_data.call(this,ae,ac,ag,ah,ad,af)}});var Z=function(ac,af,ae,ad,ag){this.container=ac;this.chrom=null;this.vis_id=ae;this.dbkey=ad;this.title=af;this.tracks=[];this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ag);this.canvas_manager=new ab(ac.get(0).ownerDocument);this.reset()};n(Z.prototype,{init:function(ag){var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<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 ad=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ag);this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.content_div.click(function(ah){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ah){ac.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ai)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ac.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){var ak=Math.round(-ai/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ac.content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX),width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ac.container.offset().left,ah=Math.max(al.pageX,am.startX)-ac.container.offset().left,ak=(ac.high-ac.low),aj=ac.viewport_container.width();ac.update_location(Math.round(ai/aj*ak)+ac.low,Math.round(ah/aj*ak)+ac.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ac.high-ac.low),aj=ac.viewport_container.width(),al=ac.low;ac.low=Math.round(ai/aj*ak)+al;ac.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,this.top_labeltrack));this.add_label_track(new Y(this,this.nav_labeltrack));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ad,ae){ad.num=t;$.extend(ad,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ac=this;$.ajax({url:chrom_url,data:ad,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ad.chrom);return}if(ag.reference){ac.add_label_track(new x(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+t+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+t+"</option>"}ac.chrom_select.html(aj);if(ae){ae()}ac.chrom_start_index=ag.start_index},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}})},change_chrom:function(ag,ad,ai){if(!ag||ag==="None"){return}var af=this;if(ag==="previous"){af.load_chroms({low:this.chrom_start_index-t});return}if(ag==="next"){af.load_chroms({low:this.chrom_start_index+t});return}var ah=$.grep(af.chrom_data,function(ak,al){return ak.chrom===ag})[0];if(ah===undefined){af.load_chroms({chrom:ag},function(){af.change_chrom(ag,ad,ai)});return}else{if(ag!==af.chrom){af.chrom=ag;af.chrom_select.val(af.chrom);af.max_high=ah.len-1;af.reset();af.request_redraw(true);for(var aj=0,ac=af.tracks.length;aj<ac;aj++){var ae=af.tracks[aj];if(ae.init){ae.init()}}}if(ad!==undefined&&ai!==undefined){af.low=Math.max(ad,0);af.high=Math.min(ai,af.max_high)}af.reset_overview();af.request_redraw()}},go_to:function(ag){var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0].replace(/,/g,""),10);af=parseInt(ah[1].replace(/,/g,""),10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_track:function(ac){ac.view=this;ac.track_id=this.track_id_counter;this.tracks.push(ac);if(ac.init){ac.init()}ac.container_div.attr("id","track_"+ac.track_id);C(ac.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1;this.update_intro_div()},add_label_track:function(ac){ac.view=this;this.label_tracks.push(ac)},remove_track:function(ad){this.has_changes=true;delete this.tracks[this.tracks.indexOf(ad)];this.num_tracks-=1;var ac=this;ad.container_div.fadeOut("slow",function(){$(this).remove();ac.update_intro_div()})},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.tracks),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}requestAnimationFrame(function(){ai._redraw(ak)})},_redraw:function(am){var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution=Math.pow(z,Math.ceil(Math.log((this.high-this.low)/N)/Math.log(z)));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae&&ae.enabled){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.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(ac){$.when(ac.get_overview_tile()).then(function(ad){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ad.canvas);view.overview_highlight.show().height(ad.canvas.height());view.overview_viewport.height(ad.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ac;view.has_changes=true;ac.set_is_overview(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 o=function(ae,ai){this.track=ae;this.name=ai.name;this.params=[];var ap=ai.params;for(var af=0;af<ap.length;af++){var ak=ap[af],ad=ak.name,ao=ak.label,ag=unescape(ak.html),aq=ak.value,am=ak.type;if(am==="number"){this.params[this.params.length]=new g(ad,ao,ag,aq,ak.min,ak.max)}else{if(am=="select"){this.params[this.params.length]=new K(ad,ao,ag,aq)}else{console.log("WARNING: unrecognized tool parameter type:",ad,am)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(at){at.stopPropagation()}).click(function(at){at.stopPropagation()}).bind("dblclick",function(at){at.stopPropagation()});var an=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var al=this.params;var aj=this;$.each(this.params,function(au,ax){var aw=$("<div>").addClass("param-row").appendTo(aj.parent_div);var at=$("<div>").addClass("param-label").text(ax.label).appendTo(aw);var av=$("<div/>").addClass("slider").html(ax.html).appendTo(aw);av.find(":input").val(ax.value);$("<div style='clear: both;'/>").appendTo(aw)});this.parent_div.find("input").click(function(){$(this).select()});var ar=$("<div>").addClass("param-row").appendTo(this.parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ar);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ar);var aj=this;ac.click(function(){aj.run_on_region()});ah.click(function(){aj.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ac={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ae=this.track,ad=ac.tool_id+ae.tool_region_and_parameters_str(ac.chrom,ac.low,ac.high),af;if(ae instanceof e){af=new R(ad,view,ae.hda_ldda,undefined,{},{},ae);af.change_mode(ae.mode)}this.track.add_track(af);af.content_div.text("Starting job.");this.run(ac,af,function(ag){af.dataset_id=ag.dataset_id;af.content_div.text("Running job.");af.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(G)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var K=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=ae;this.value=af};var g=function(ae,ad,ag,ah,af,ac){K.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};var h=function(ad,ac,ae,af){this.name=ad;this.index=ac;this.tool_id=ae;this.tool_exp_name=af};var S=function(ad,ac,ae,af){h.call(this,ad,ac,ae,af);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};n(S.prototype,{applies_to:function(ac){if(ac.length>this.index){return true}return false},keep:function(ac){if(!this.applies_to(ac)){return true}var ad=parseInt(ac[this.index]);return(isNaN(ad)||(ad>=this.low&&ad<=this.high))},update_attrs:function(ad){var ac=false;if(!this.applies_to(ad)){return ac}if(ad[this.index]<this.min){this.min=Math.floor(ad[this.index]);ac=true}if(ad[this.index]>this.max){this.max=Math.ceil(ad[this.index]);ac=true}return ac},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ae=function(ah,af){var ag=af-ah;return(ag<=2?0.01:1)};var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ae(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(am,at){this.track=am;this.filters=[];for(var an=0;an<at.length;an++){var ao=at[an],au=ao.name,ac=ao.type,af=ao.index,ar=ao.tool_id,aq=ao.tool_exp_name;if(ac==="int"||ac==="float"){this.filters[an]=new S(au,af,ar,aq)}else{console.log("ERROR: unsupported filter: ",au,ac)}}var ag=function(av,aw,ax){av.click(function(){var ay=aw.text();max=parseFloat(ax.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ax.slider("option","values")){input_size=2*input_size+1;multi_value=true}aw.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ay).appendTo(aw).focus().select().click(function(az){az.stopPropagation()}).blur(function(){$(this).remove();aw.text(ay)}).keyup(function(aD){if(aD.keyCode===27){$(this).trigger("blur")}else{if(aD.keyCode===13){var aB=ax.slider("option","min"),az=ax.slider("option","max"),aC=function(aE){return(isNaN(aE)||aE>az||aE<aB)},aA=$(this).val();if(!multi_value){aA=parseFloat(aA);if(aC(aA)){alert("Parameter value must be in the range ["+aB+"-"+az+"]");return $(this)}}else{aA=aA.split("-");aA=[parseFloat(aA[0]),parseFloat(aA[1])];if(aC(aA[0])||aC(aA[1])){alert("Parameter value must be in the range ["+aB+"-"+az+"]");return $(this)}}ax.slider((multi_value?"values":"value"),aA)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(av){av.stopPropagation()}).click(function(av){av.stopPropagation()}).bind("dblclick",function(av){av.stopPropagation()}).bind("keydown",function(av){av.stopPropagation()});var ap=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ak=this;$.each(this.filters,function(ay,aA){aA.container=$("<div/>").addClass("slider-row").appendTo(ap);var az=$("<div/>").addClass("elt-label").appendTo(aA.container);var ax=$("<span/>").addClass("slider-name").text(aA.name+" ").appendTo(az);var aw=$("<span/>");var aC=$("<span/>").addClass("slider-value").appendTo(az).append("[").append(aw).append("]");var av=$("<div/>").addClass("slider").appendTo(aA.container);aA.control_element=$("<div/>").attr("id",aA.name+"-filter-control").appendTo(av);var aB=[0,0];aA.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aE,aF){var aD=aF.values;aw.text(aD[0]+"-"+aD[1]);aA.low=aD[0];aA.high=aD[1];ak.track.request_draw(true,true)},change:function(aD,aE){aA.control_element.slider("option","slide").call(aA.control_element,aD,aE)}});aA.slider=aA.control_element;aA.slider_label=aw;ag(aC,aw,aA.control_element);$("<div style='clear: both;'/>").appendTo(aA.container)});if(this.filters.length!==0){var ah=$("<div/>").addClass("param-row").appendTo(ap);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ah);var ae=this;aj.click(function(){ae.run_on_dataset()})}var al=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ai=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(al),ad=$("<select/>").attr("name","alpha_dropdown").appendTo(al);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ad);for(var an=0;an<this.filters.length;an++){$("<option/>").attr("value",an).text(this.filters[an].name).appendTo(ad)}ad.change(function(){$(this).children("option:selected").each(function(){var av=parseInt($(this).val());ak.alpha_filter=(av>=0?ak.filters[av]:null);ak.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};n(X.prototype,{reset_filters:function(){for(var ac=0;ac<this.filters.length;ac++){filter=this.filters[ac];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!=ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!=ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var L=function(ad,ac){I.AlphaGenerator.call(this,ac);this.filter=ad};L.prototype.gen_alpha=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var W=function(ac){this.track=ac.track;this.params=ac.params;this.values={};if(ac.saved_values){this.restore_values(ac.saved_values)}this.onchange=ac.onchange};n(W.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var ad=this;var ac=$("<div />");$.each(this.params,function(ah,af){if(!af.hidden){var ae="param_"+ah;var am=$("<div class='form-row' />").appendTo(ac);am.append($("<label />").attr("for",ae).text(af.label+":"));if(af.type==="bool"){am.append($('<input type="checkbox" />').attr("id",ae).attr("name",ae).attr("checked",ad.values[af.key]))}else{if(af.type==="color"){var aj=ad.values[af.key];var ai=$("<input />").attr("id",ae).attr("name",ae).val(aj);var ak=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ag=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ak);var al=$("<div/>").appendTo(ag).farbtastic({width:100,height:100,callback:ai,color:aj});$("<div />").append(ai).append(ak).appendTo(am).bind("click",function(an){ak.css({left:$(this).position().left+($(ai).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ak.hide();$(document).unbind("click.color-picker")});an.stopPropagation()})}else{am.append($("<input />").attr("id",ae).attr("name",ae).val(ad.values[af.key]))}}}});return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange()}}});var b=function(ae,ad,ac,af){this.index=ae;this.low=ae*N*ad;this.high=(ae+1)*N*ad;this.resolution=ad;this.canvas=$("<div class='track-tile'/>").append(ac);this.data=af;this.stale=false};var l=function(ae,ad,ac,af,ag){b.call(this,ae,ad,ac,af);this.max_val=ag};var M=function(ae,ad,ac,ag,af){b.call(this,ae,ad,ac,ag);this.message=af};var j=function(ad,ac,ag,ae,af){this.name=ad;this.view=ac;this.parent_element=ag;this.data_url=(ae?ae:default_data_url);this.data_url_extra_params={};this.data_query_wait=(af?af:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").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 class='draghandle' />").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.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"ToolDataFeatureTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.initial_canvas=undefined;ac.content_div.css("height","auto");ac.container_div.removeClass("nodata error pending");if(!ac.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id,chrom:ac.view.chrom},function(ad){if(!ad||ad==="error"||ad.kind==="error"){ac.container_div.addClass("error");ac.content_div.text(m);if(ad.message){var af=ac.view.tracks.indexOf(ac);var ae=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ad.message+"</pre>",{Close:hide_modal})});ac.content_div.append(ae)}}else{if(ad==="no converter"){ac.container_div.addClass("error");ac.content_div.text(G)}else{if(ad==="no data"||(ad.data!==undefined&&(ad.data===null||ad.data.length===0))){ac.container_div.addClass("nodata");ac.content_div.text(B)}else{if(ad==="pending"){ac.container_div.addClass("pending");ac.content_div.text(q);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(ad.status==="data"){if(ad.valid_chroms){ac.valid_chroms=ad.valid_chroms;ac.make_name_popup_menu()}ac.content_div.text(V);if(ac.view.chrom){ac.content_div.text("");ac.content_div.css("height",ac.height_px+"px");ac.enabled=true;$.when(ac.predraw_init()).done(function(){ac.container_div.removeClass("nodata error pending");ac.request_draw()})}}}}}}})},predraw_init:function(){},update_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(aj,ah,ak){var ad=this,al=ad.view;this.filters_manager=(aj!==undefined?new X(this,aj):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ah!==undefined&&obj_length(ah)>0?new o(this,ah):undefined);this.is_overview=false;this.parent_track=ak;this.child_tracks=[];if(ad.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ad.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();ad.container_div.append(ad.child_tracks_container);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(ad.display_modes!==undefined){if(ad.mode_div===undefined){ad.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ad.header_div);var ae=(ad.track_config&&ad.track_config.values.mode?ad.track_config.values.mode:ad.display_modes[0]);ad.mode=ae;ad.mode_div.text(ae);var ac={};for(var af=0,ai=ad.display_modes.length;af<ai;af++){var ag=ad.display_modes[af];ac[ag]=function(am){return function(){ad.change_mode(am)}}(ag)}make_popupmenu(ad.mode_div,ac)}else{ad.mode_div.hide()}}this.make_name_popup_menu()};n(J.prototype,j.prototype,{change_mode:function(ad){var ac=this;ac.mode_div.text(ad);ac.mode=ad;ac.track_config.values.mode=ad;ac.tile_cache.clear();ac.request_draw()},make_name_popup_menu:function(){var ad=this;var ac={};ac[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ad.is_overview){ad.view.reset_overview()}else{ad.view.set_overview(ad)}};ac["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ad.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Track",ad.track_config.build_form(),{Cancel:aj,OK:ah})};if(ad.filters_available>0){var ag=(ad.filters_div.is(":visible")?"Hide filters":"Show filters");ac[ag]=function(){ad.filters_visible=(ad.filters_div.is(":visible"));if(ad.filters_visible){ad.filters_manager.reset_filters()}ad.filters_div.toggle();ad.make_name_popup_menu()}}if(ad.tool){var ag=(ad.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ac[ag]=function(){if(!ad.dynamic_tool_div.is(":visible")){ad.update_name(ad.name+ad.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ad.revert_name()}ad.dynamic_tool_div.toggle();ad.make_name_popup_menu()}}if(ad.valid_chroms){ac["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ad.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ae=view;var af=function(){$("#no-tracks").show()};if(this.parent_track){ae=this.parent_track;af=function(){}}ac.Remove=function(){ae.remove_track(ad);if(ae.num_tracks===0){af()}};make_popupmenu(ad.name_div,ac)},set_is_overview:function(ac){this.is_overview=ac;this.make_name_popup_menu()},get_overview_tile:function(){var ac=this;view=ac.view,resolution=Math.pow(z,Math.ceil(Math.log((view.max_high-view.max_low)/N)/Math.log(z))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ac.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ac.data_url_extra_params)).then(function(ad){var af=ac._gen_tile_cache_key(view_width,w_scale,0),ah=ac.tile_cache.get(af);if(!ah){ah=ac.draw_tile(ad,resolution,0,w_scale);ac.tile_cache.set(af,ah)}var ak=$(ah.canvas.find("canvas")),ag=ak.clone(),aj=ak.get(0).getContext("2d"),ae=ag.get(0).getContext("2d"),ai=aj.getImageData(0,0,aj.canvas.width,aj.canvas.height);ae.putImageData(ai,-ac.left_offset,(ah.data.dataset_type==="summary_tree"?P:0));new_tile=new b(-1,resolution,ag);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},_draw:function(ae,an){if(!this.dataset_id){return}var am=this.view.low,ai=this.view.high,ak=ai-am,af=this.view.container.width(),aq=af/ak,ah=this.view.resolution,ap=$("<div style='position: relative;'></div>");if(!an){this.content_div.children().remove()}this.content_div.append(ap);this.max_height=0;var ad=Math.floor(am/ah/N);var al=true;var ao=[];var ac=0;while((ad*N*ah)<ai){tile=this.draw_helper(ae,af,ad,ah,ap,aq);if(tile){ao.push(tile)}else{al=false}ad+=1;ac++}var ag=this;if(al){ag.postdraw_actions(ao,af,aq,an)}for(var aj=0;aj<this.child_tracks.length;aj++){this.child_tracks[aj].request_draw(ae,an)}},postdraw_actions:function(ag,ah,ai,ac){var ae=this;var af=false;for(var ad=0;ad<ag.length;ad++){if(ag[ad].message){af=true;break}}if(af){for(var ad=0;ad<ag.length;ad++){tile=ag[ad];if(!tile.message){tile.canvas.css("padding-top",A)}}}},draw_helper:function(ad,ae,af,ai,ao,at,ap,aj){var ag=this,an=this._gen_tile_cache_key(ae,at,af),ak=af*N*ai,ar=ak+N*ai;var al=(ad?undefined:ag.tile_cache.get(an));if(al){ag.show_tile(al,ao,at);return al}var am=function(au){return("isResolved" in au)};var ah=true;var ac=ag.data_manager.get_data(ak,ar,ag.mode,ai,ag.data_url_extra_params);if(am(ac)){ah=false}var aq;if(view.reference_track&&at>view.canvas_manager.char_width_px){aq=view.reference_track.data_manager.get_data(ak,ar,ag.mode,ai,view.reference_track.data_url_extra_params);if(am(aq)){ah=false}}if(ah){n(ac,aj);var al=ag.draw_tile(ac,ai,af,at,aq);ag.tile_cache.set(an,al);if(al!==undefined){ag.show_tile(al,ao,at)}return al}$.when(ac,aq).then(function(){view.request_redraw()});return null},show_tile:function(aj,al,am){var ae=this,ad=aj.canvas,ai=ad;if(aj.message){var an=$("<div/>"),ak=$("<div/>").addClass("tile-message").text(aj.message).css({height:A-1,width:aj.canvas.width}).appendTo(an),ag=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ak),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ak);an.append(ad);ai=an;ag.click(function(){aj.stale=true;ae.data_manager.get_more_data(aj.low,aj.high,ae.mode,aj.resolution,{},ae.data_manager.DEEP_DATA_REQ);ae.request_draw()}).dblclick(function(ao){ao.stopPropagation()});ac.click(function(){aj.stale=true;ae.data_manager.get_more_data(aj.low,aj.high,ae.mode,aj.resolution,{},ae.data_manager.BROAD_DATA_REQ);ae.request_draw()}).dblclick(function(ao){ao.stopPropagation()})}var ah=this.view.high-this.view.low,af=(aj.low-this.view.low)*am;if(this.left_offset){af-=this.left_offset}ai.css({position:"absolute",top:0,left:af,height:""});al.append(ai);ae.max_height=Math.max(ae.max_height,ai.height());ae.content_div.css("height",ae.max_height+"px");al.children().css("height",ae.max_height+"px")},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},add_track:function(ac){ac.track_id=this.track_id+"_"+this.child_tracks.length;ac.container_div.attr("id","track_"+ac.track_id);this.child_tracks_container.append(ac.container_div);C(ac.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(ac);this.view.has_changes=true},remove_track:function(ac){ac.container_div.fadeOut("slow",function(){$(this).remove()})}});var Y=function(ac,ad){this.hidden=true;j.call(this,null,ac,ad);this.container_div.addClass("label-track")};n(Y.prototype,j.prototype,{_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var x=function(ac){this.hidden=true;j.call(this,null,ac,ac.top_labeltrack);J.call(this);ac.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:ac.dbkey};this.data_manager=new E(y,this,false);this.tile_cache=new c(r)};n(x.prototype,J.prototype,{draw_tile:function(ak,ah,ad,am){var ag=this,ae=N*ah;if(am>this.view.canvas_manager.char_width_px){if(ak===null){ag.content_div.css("height","0px");return}var af=this.view.canvas_manager.new_canvas();var al=af.getContext("2d");af.width=Math.ceil(ae*am+ag.left_offset);af.height=ag.height_px;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.round(ai*am);al.fillText(ak[ai],ac+ag.left_offset,10)}return new b(ad,ah,af,ak)}this.content_div.css("height","0px")}});var k=function(ag,ae,ah,ac,af){var ad=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ag,ae,ae.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ah;this.dataset_id=ac;this.original_dataset_id=ac;this.data_manager=new O(y,this);this.tile_cache=new c(r);this.track_config=new W({track:this,params:[{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:af,onchange:function(){ad.vertical_range=ad.prefs.max_value-ad.prefs.min_value;$("#linetrack_"+ad.track_id+"_minval").text(ad.prefs.min_value);$("#linetrack_"+ad.track_id+"_maxval").text(ad.prefs.max_value);ad.tile_cache.clear();ad.request_draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,J.prototype,{add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){af=true;ad.show()},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.content_div).css("height",ag);ac.height_px=ag;ac.request_draw(true)}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.track_config.values.height=ac.height_px}).appendTo(ac.container_div)},predraw_init:function(){var ac=this,ad=ac.view.tracks.indexOf(ac);ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ae){ac.container_div.addClass("line-track");var ag=ae.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){ac.prefs.min_value=ag.min;ac.prefs.max_value=ag.max;$("#track_"+ad+"_minval").val(ac.prefs.min_value);$("#track_"+ad+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ad+"_minval").text(u(ac.prefs.min_value));var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ad+"_maxval").text(u(ac.prefs.max_value));af.css({position:"absolute",top:"24px",left:"10px"});af.prependTo(ac.container_div);ah.css({position:"absolute",bottom:"2px",left:"10px"});ah.prependTo(ac.container_div)})},draw_tile:function(am,ag,ad,al){if(this.vertical_range===undefined){return}var ah=ad*N*ag,af=N*ag,ac=Math.ceil(af*al),aj=this.height_px;var ae=this.view.canvas_manager.new_canvas();ae.width=ac,ae.height=aj;var ak=ae.getContext("2d");var ai=new I.LinePainter(am.data,ah,ah+af,this.prefs,this.mode);ai.draw(ak,ac,aj);return new b(ad,ag,ae,am.data)}});var e=function(ac,ah,ag,ak,aj,ae,af,ai){var ad=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new W({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){ad.tile_cache.clear();ad.request_draw()}});this.prefs=this.track_config.values;j.call(this,ac,ah,ah.viewport_container);J.call(this,ae,af,ai);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ag;this.dataset_id=ak;this.original_dataset_id=ak;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new O(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{postdraw_actions:function(ar,ac,at,aq){J.prototype.postdraw_actions.call(this,ar,aq);var af=this;if(aq){var ah=af.content_div.children();var ai=false;for(var ag=ah.length-1,am=0;ag>=am;ag--){var ae=$(ah[ag]);if(ai){ae.remove()}else{if(ae.children().length!==0){ai=true}}}}if(af.mode=="Histogram"){var al=-1;for(var ag=0;ag<ar.length;ag++){var ap=ar[ag].max_val;if(ap>al){al=ap}}for(var ag=0;ag<ar.length;ag++){var ao=ar[ag];if(ao.max_val!==al){ao.canvas.remove();af.draw_helper(true,ac,ao.index,ao.resolution,ao.canvas.parent(),at,[],{max:al})}}}if(af.filters_manager){var ad=af.filters_manager.filters;for(var ak=0;ak<ad.length;ak++){ad[ak].update_ui_elt()}var aj=false,an;for(var ag=0;ag<ar.length;ag++){if(ar[ag].data.length){an=ar[ag].data[0];for(var ak=0;ak<ad.length;ak++){if(ad[ak].applies_to(an)){aj=true;break}}}}if(af.filters_available!==aj){af.filters_available=aj;if(!af.filters_available){af.filters_div.hide()}af.make_name_popup_menu()}}},update_auto_mode:function(ac){if(this.mode=="Auto"){if(ac=="no_detail"){ac="feature spans"}else{if(ac=="summary_tree"){ac="coverage histogram"}}this.mode_div.text("Auto ("+ac+")")}},incremental_slots:function(ag,ad,af){var ae=this.view.canvas_manager.dummy_context,ac=this.inc_slots[ag];if(!ac||(ac.mode!==af)){ac=new (p.FeatureSlotter)(ag,af==="Pack",w,function(ah){return ae.measureText(ah)});ac.mode=af;this.inc_slots[ag]=ac}return ac.slot_features(ad)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},draw_tile:function(ap,ay,aC,al,af){var av=this,aE=aC*N*ay,ad=(aC+1)*N*ay,ar=ad-aE,aw=Math.ceil(ar*al),at=this.mode,aI=25,ag=this.left_offset,aq,ah;if(at==="Auto"){if(ap.dataset_type==="summary_tree"){at=ap.dataset_type}else{if(ap.extra_info==="no_detail"){at="no_detail"}else{var aH=ap.data;if(this.view.high-this.view.low>F){at="Squish"}else{at="Pack"}}}this.update_auto_mode(at)}if(at==="summary_tree"||at==="Histogram"){ah=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ac=$("<div />").addClass("yaxislabel");ac.text(ap.max);ac.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ac.prependTo(this.container_div);var ae=this.view.canvas_manager.new_canvas();ae.width=aw+ag;ae.height=ah+P;if(ap.dataset_type!="summary_tree"){var am=this.get_summary_tree_data(ap.data,aE,ad,200);if(ap.max){am.max=ap.max}ap=am}var aF=new I.SummaryTreePainter(ap,aE,ad,this.prefs);var ax=ae.getContext("2d");ax.translate(ag,P);aF.draw(ax,aw,ah);return new l(aC,ay,ae,ap.data,ap.max)}var aq,aj=1;if(at==="no_detail"||at==="Squish"||at==="Pack"){aj=this.incremental_slots(al,ap.data,at);aq=this.inc_slots[al].slots}var ak=[];if(ap.data){var an=this.filters_manager.filters;for(var az=0,aB=ap.data.length;az<aB;az++){var ai=ap.data[az];var aA=false;var ao;for(var aD=0,aG=an.length;aD<aG;aD++){ao=an[aD];ao.update_attrs(ai);if(!ao.keep(ai)){aA=true;break}}if(!aA){ak.push(ai)}}}var au=(this.filters_manager.alpha_filter?new L(this.filters_manager.alpha_filter):null);var aF=new (this.painter)(ak,aE,ad,this.prefs,at,au,af);var ah=Math.max(aa,aF.get_required_height(aj));var ae=this.view.canvas_manager.new_canvas();ae.width=aw+ag;ae.height=ah;var ax=ae.getContext("2d");ax.fillStyle=this.prefs.block_color;ax.font=ax.canvas.manager.default_font;ax.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ap.data){ax.translate(ag,0);aF.draw(ax,aw,ah,aq)}return new M(aC,ay,ae,ap.data,ap.message)}});var Q=function(af,ad,ah,ac,ae,ag){e.call(this,af,ad,ah,ac,ae,ag);this.painter=I.VariantPainter};n(Q.prototype,J.prototype,e.prototype);var T=function(af,ad,ah,ac,ae,ag){e.call(this,af,ad,ah,ac,ae,ag);this.track_config=new W({track:this,params:[{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:ae,onchange:function(){this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.track_config.values;this.painter=I.ReadPainter;this.make_name_popup_menu()};n(T.prototype,J.prototype,e.prototype);var R=function(ag,ae,ai,ac,af,ah,ad){e.call(this,ag,ae,ai,ac,af,ah,{},ad);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(R.prototype,J.prototype,e.prototype,{predraw_init:function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=H;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}});U.View=Z;U.LineTrack=k;U.FeatureTrack=e;U.ReadTrack=T};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,x){var u=k("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=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(y){this.default_alpha=(y?y:1)};g.prototype.gen_alpha=function(y){return this.default_alpha};var n=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};n.prototype.default_prefs={};var v=function(A,C,y,z,B){n.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.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(y,C,E,F,A){n.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};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(B,D,y,A,C,z){n.call(this,B,D,y,A,C);this.alpha_generator=(z?z:new g())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(z){var y=y_scale=this.get_row_height(),A=this.mode;if(A==="no_detail"||A==="Squish"||A==="Pack"){y=z*y_scale}return y+Math.max(Math.round(y_scale/2),5)},draw:function(K,B,J,G){var E=this.data,H=this.view_start,L=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var O=this.view_end-this.view_start,N=B/O,A=this.get_row_height();for(var D=0,F=E.length;D<F;D++){var M=E[D],C=M[0],y=M[1],z=M[2],I=(G&&G[C]!==undefined?G[C]:null);if((y<L&&z>H)&&(this.mode=="Dense"||I!==null)){this.draw_element(K,this.mode,M,I,H,L,N,A,B)}}K.restore()},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.")}});var d=10,j=3,m=5,w=10,f=1,s=3,e=3,a=9,l=2,h="#ccc";var r=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=d}else{if(z==="no_detail"){y=j}else{if(z==="Squish"){y=m}else{y=w}}}return y},draw_element:function(K,D,S,F,M,ac,ag,ah,y){var P=S[0],ae=S[1],W=S[2],N=S[3],X=Math.floor(Math.max(0,(ae-M)*ag)),L=Math.ceil(Math.min(y,Math.max(0,(W-M)*ag))),V=(D==="Dense"?0:(0+F))*ah,J,aa,O=null,ai=null,B=this.prefs.block_color,Z=this.prefs.label_color;K.globalAlpha=this.alpha_generator.gen_alpha(S);if(D=="Dense"){F=1}if(D==="no_detail"){K.fillStyle=B;K.fillRect(X,V+5,L-X,f)}else{var I=S[4],U=S[5],Y=S[6],C=S[7];if(U&&Y){O=Math.floor(Math.max(0,(U-M)*ag));ai=Math.ceil(Math.min(y,Math.max(0,(Y-M)*ag)))}var af,Q;if(D==="Squish"||D==="Dense"){af=1;Q=e}else{af=5;Q=a}if(!C){if(S.strand){if(S.strand==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(S.strand==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}}else{K.fillStyle=B}K.fillRect(X,V,L-X,Q)}else{var H,R;if(D==="Squish"||D==="Dense"){K.fillStyle=h;H=V+Math.floor(e/2)+1;R=1}else{if(I){var H=V;var R=Q;if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand")}}}else{K.fillStyle=h;H+=(e/2)+1;R=1}}K.fillRect(X,H,L-X,R);for(var ad=0,A=C.length;ad<A;ad++){var E=C[ad],z=Math.floor(Math.max(0,(E[0]-M)*ag)),T=Math.ceil(Math.min(y,Math.max((E[1]-M)*ag)));if(z>T){continue}K.fillStyle=B;K.fillRect(z,V+(Q-af)/2+1,T-z,af);if(O!==undefined&&Y>U&&!(z>ai||T<O)){var ab=Math.max(z,O),G=Math.min(T,ai);K.fillRect(ab,V+1,G-ab,Q);if(C.length==1&&D=="Pack"){if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}if(ab+14<G){ab+=2;G-=2}K.fillRect(ab,V+1,G-ab,Q)}}}}if(D==="Pack"&&ae>M){K.fillStyle=Z;if(M===0&&X-K.measureText(N).width<0){K.textAlign="left";K.fillText(N,L+l,V+8)}else{K.textAlign="right";K.fillText(N,X-l,V+8)}}}K.globalAlpha=1}});var b=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(b.prototype,o.prototype,{draw_element:function(R,M,G,C,U,A,J,S,P){var G=data[i],I=G[0],Q=G[1],B=G[2],L=G[3],E=Math.floor(Math.max(0,(Q-U)*J)),H=Math.ceil(Math.min(P,Math.max(0,(B-U)*J))),D=(M==="Dense"?0:(0+C))*S,y,V,z=null,K=null;if(no_label){R.fillStyle=block_color;R.fillRect(E+left_offset,D+5,H-E,1)}else{var 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ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=h;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&ref_seq){var K=ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=h;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:s))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){ae[ae.length]={type:"text",data:[Q.length,Y,E+9]}}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){q(U,af[0],af[1],af[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,V=this.prefs.block_color,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}R.fillStyle=V;if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,U,z,E[4][0],E[4][2],E[4][3],C)}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,U,z,E[5][0],E[5][2],E[5][3],C)}if(K>L){R.fillStyle=h;p(R,L-O,C+5,K-O,C+5)}}else{R.fillStyle=V;this.draw_read(R,M,I,U,z,Q,E[4],E[5],C)}if(M==="Pack"&&Q>U){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+l-O,C+8)}else{R.textAlign="right";R.fillText(J,D-l-O,C+8)}R.fillStyle=V}}});x.AlphaGenerator=g;x.SummaryTreePainter=v;x.LinePainter=c;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.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 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Remove unspecified build validator from aggregate_scores_in_intervals2 tool because it can work with a custom fasta.
by Bitbucket 24 Aug '11

24 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/08859d106924/ changeset: 08859d106924 user: natefoo date: 2011-08-24 20:38:29 summary: Remove unspecified build validator from aggregate_scores_in_intervals2 tool because it can work with a custom fasta. affected #: 1 file (415 bytes) --- a/tools/stats/aggregate_binned_scores_in_intervals.xml Wed Aug 24 13:58:48 2011 -0400 +++ b/tools/stats/aggregate_binned_scores_in_intervals.xml Wed Aug 24 14:38:29 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="aggregate_scores_in_intervals2" description="such as phastCons, GERP, binCons, and others for a set of genomic intervals" name="Aggregate datapoints" version="1.1.2"> +<tool id="aggregate_scores_in_intervals2" description="such as phastCons, GERP, binCons, and others for a set of genomic intervals" name="Aggregate datapoints" version="1.1.3"><description>Appends the average, min, max of datapoints per interval</description><command interpreter="python"> #if $score_source_type.score_source == "user" #aggregate_scores_in_intervals.py $score_source_type.input2 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $out_file1 --chrom_buffer=3 @@ -6,11 +6,7 @@ #end if# </command><inputs> - <param format="interval" name="input1" type="data" label="Interval file"> - <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg16, hg17 or hg18. Click the pencil icon in your history item to set the genome build."/> - <validator type="dataset_metadata_in_file" filename="binned_scores.loc" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build." /> - - </param> + <param format="interval" name="input1" type="data" label="Interval file"/><conditional name="score_source_type"><param name="score_source" type="select" label="Score Source"><option value="cached" selected="true">Locally Cached Scores</option> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Grouping tool: use system numpy if provided, otherwise use bundled numpy egg
by Bitbucket 24 Aug '11

24 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a609a7af3fb6/ changeset: a609a7af3fb6 user: kanwei date: 2011-08-24 19:58:48 summary: Grouping tool: use system numpy if provided, otherwise use bundled numpy egg affected #: 1 file (35 bytes) --- a/tools/stats/grouping.py Wed Aug 24 13:14:49 2011 -0400 +++ b/tools/stats/grouping.py Wed Aug 24 13:58:48 2011 -0400 @@ -6,9 +6,12 @@ This tool provides the SQL "group by" functionality. """ import sys, commands, tempfile, random -import pkg_resources -pkg_resources.require( "numpy" ) -import numpy +try: + import numpy +except: + from galaxy import eggs + eggs.require( "numpy" ) + import numpy from itertools import groupby Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Fix sam2interval.py bug due to tab spacing
by Bitbucket 24 Aug '11

24 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/298b3077412d/ changeset: 298b3077412d user: kanwei date: 2011-08-24 19:14:49 summary: Fix sam2interval.py bug due to tab spacing affected #: 1 file (83 bytes) --- a/tools/samtools/sam2interval.py Wed Aug 24 10:19:38 2011 -0400 +++ b/tools/samtools/sam2interval.py Wed Aug 24 13:14:49 2011 -0400 @@ -44,7 +44,7 @@ '-r','--ref_column', dest='ref_col', default = '3', - help='Column containing name of the refernce sequence coordinate. 1-based') + help='Column containing name of the reference sequence coordinate. 1-based') parser.add_option( '-e','--read_column', @@ -53,26 +53,18 @@ help='Column containing read name. 1-based') parser.add_option( - '-d','--debug', - dest='debug', - action='store_true', - default = False, - help='Print debugging info') - - parser.add_option( '-p','--print_all', dest='prt_all', action='store_true', default = False, help='Print coordinates and original SAM?') - - + options, args = parser.parse_args() if options.input_sam: - infile = open ( options.input_sam, 'r') + infile = open ( options.input_sam, 'r') else: - infile = sys.stdin + infile = sys.stdin cigar = re.compile( '\d+M|\d+N|\d+D|\d+P' ) @@ -93,12 +85,12 @@ read_name = fields[ int( options.read_col ) - 1 ] ref_name = fields[ int( options.ref_col ) - 1 ] - if not ref_name == '*': - # Do not print lines with unmapped reads that contain '*' instead of chromosome name - if options.prt_all: - print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, line) - else: - print '%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand) + if ref_name != '*': + # Do not print lines with unmapped reads that contain '*' instead of chromosome name + if options.prt_all: + print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, line) + else: + print '%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand) if __name__ == "__main__": main() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: route track drawing through requestAnimationFrame framework.
by Bitbucket 24 Aug '11

24 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/708bcc6dd9ef/ changeset: 708bcc6dd9ef user: jgoecks date: 2011-08-24 16:19:38 summary: Trackster: route track drawing through requestAnimationFrame framework. affected #: 1 file (2.2 KB) --- a/static/scripts/trackster.js Wed Aug 24 01:11:54 2011 -0400 +++ b/static/scripts/trackster.js Wed Aug 24 10:19:38 2011 -0400 @@ -472,6 +472,7 @@ this.title = title; this.tracks = []; this.label_tracks = []; + this.tracks_to_be_redrawn = []; this.max_low = 0; this.max_high = 0; this.num_tracks = 0; @@ -479,7 +480,7 @@ this.zoom_factor = 3; this.min_separation = 30; this.has_changes = false; - this.init( callback ); + this.init(callback); this.canvas_manager = new CanvasManager( container.get(0).ownerDocument ); this.reset(); }; @@ -849,11 +850,51 @@ this.high = this.max_high; this.viewport_container.find(".yaxislabel").remove(); }, - request_redraw: function( nodraw ) { - var view = this; - requestAnimationFrame( function() { view.redraw( nodraw ) } ); + /** + * Request that view redraw some or all tracks. If a track is not specificied, redraw all tracks. + */ + request_redraw: function(nodraw, force, clear_after, track) { + var + view = this, + // Either redrawing a single track or all view's tracks. + track_list = (track ? [track] : view.tracks), + track_index; + + // Add/update tracks in track list to redraw list. + var track; + for (var i = 0; i < track_list.length; i++) { + track = track_list[i]; + + // Because list elements are arrays, need to look for track index manually. + track_index = -1; + for (var j = 0; j < view.tracks_to_be_redrawn.length; j++) { + if (view.tracks_to_be_redrawn[j][0] === track) { + track_index = j; + break; + } + } + + // Add track to list or update draw parameters. + if (track_index < 0) { + // Track not in list yet. + view.tracks_to_be_redrawn.push([track, force, clear_after]); + } + else { + // Track already in list; update force and clear_after. + view.tracks_to_be_redrawn[i][1] = force; + view.tracks_to_be_redrawn[i][2] = clear_after; + } + } + + // Set up redraw. + requestAnimationFrame(function() { view._redraw(nodraw) }); }, - redraw: function(nodraw) { + /** + * Redraws view and tracks. + * NOTE: this method should never be called directly; request_redraw() should be used so + * that requestAnimationFrame can manage redrawing. + */ + _redraw: function(nodraw) { var low = this.low, high = this.high; @@ -890,13 +931,18 @@ this.update_location(this.low, this.high); if (!nodraw) { - for (var i = 0, len = this.tracks.length; i < len; i++) { - if (this.tracks[i] && this.tracks[i].enabled) { - this.tracks[i].draw(); + var track, force, clear_after; + for (var i = 0, len = this.tracks_to_be_redrawn.length; i < len; i++) { + track = this.tracks_to_be_redrawn[i][0]; + force = this.tracks_to_be_redrawn[i][1]; + clear_after = this.tracks_to_be_redrawn[i][2]; + if (track && track.enabled) { + track._draw(force, clear_after); } } + this.tracks_to_be_redrawn = []; for (i = 0, len = this.label_tracks.length; i < len; i++) { - this.label_tracks[i].draw(); + this.label_tracks[i]._draw(); } } }, @@ -1426,7 +1472,7 @@ filter.low = values[0]; filter.high = values[1]; // Redraw track. - manager.track.draw(true, true); + manager.track.request_draw(true, true); }, change: function(event, ui) { filter.control_element.slider("option", "slide").call(filter.control_element, event, ui); @@ -1470,7 +1516,7 @@ $(this).children("option:selected").each(function() { var filterIndex = parseInt($(this).val()); manager.alpha_filter = (filterIndex >= 0 ? manager.filters[filterIndex] : null); - manager.track.draw(true, true); + manager.track.request_draw(true, true); }) }); @@ -1840,7 +1886,7 @@ // predraw_init may be asynchronous, wait for it and then draw $.when(track.predraw_init()).done(function() { track.container_div.removeClass("nodata error pending"); - track.draw() + track.request_draw() }); } } @@ -1956,7 +2002,7 @@ track.mode = name; track.track_config.values['mode'] = name; track.tile_cache.clear(); - track.draw(); + track.request_draw(); }, /** * Make popup menu for track name. @@ -2124,10 +2170,18 @@ return width + '_' + w_scale + '_' + tile_index; }, /** + * Request that track be drawn. + */ + request_draw: function(force, clear_after) { + this.view.request_redraw(false, force, clear_after, this); + }, + /** * Draw track. It is possible to force a redraw rather than use cached tiles and/or clear old * tiles after drawing new tiles. + * NOTE: this function should never be called directly; use request_draw() so that requestAnimationFrame + * can manage drawing. */ - draw: function(force, clear_after) { + _draw: function(force, clear_after) { // Cannot draw without dataset_id; dataset_id may not be set if track dynamically created // and is waiting for dataset. if (!this.dataset_id) { return; } @@ -2164,12 +2218,12 @@ // Use interval to check if tiles have been drawn. When all tiles are drawn, call post-draw actions. var track = this; - if ( all_tiles_drawn ) { + if (all_tiles_drawn) { track.postdraw_actions(drawn_tiles, width, w_scale, clear_after); } // Draw child tracks. for (var i = 0; i < this.child_tracks.length; i++) { - this.child_tracks[i].draw(force, clear_after); + this.child_tracks[i].request_draw(force, clear_after); } }, /** @@ -2291,7 +2345,7 @@ // Mark tile as stale, request more data, and redraw track. tile.stale = true; track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.DEEP_DATA_REQ); - track.draw(); + track.request_draw(); }).dblclick(function(e) { // Do not propogate as this would normally zoom in. e.stopPropagation(); @@ -2301,7 +2355,7 @@ // Mark tile as stale, request more data, and redraw track. tile.stale = true; track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.BROAD_DATA_REQ); - track.draw(); + track.request_draw(); }).dblclick(function(e) { // Do not propogate as this would normally zoom in. e.stopPropagation(); @@ -2364,8 +2418,8 @@ Track.call( this, null, view, parent_element ); this.container_div.addClass( "label-track" ); }; -extend( LabelTrack.prototype, Track.prototype, { - draw: function() { +extend(LabelTrack.prototype, Track.prototype, { + _draw: function() { var view = this.view, range = view.high - view.low, tickDistance = Math.floor( Math.pow( 10, Math.floor( Math.log( range ) / Math.log( 10 ) ) ) ), @@ -2465,7 +2519,7 @@ $('#linetrack_' + track.track_id + '_minval').text(track.prefs.min_value); $('#linetrack_' + track.track_id + '_maxval').text(track.prefs.max_value); track.tile_cache.clear(); - track.draw(); + track.request_draw(); } }); @@ -2501,13 +2555,13 @@ var new_height = Math.min( Math.max( d.original_height + d.deltaY, track.min_height_px ), track.max_height_px ); $(track.content_div).css( 'height', new_height ); track.height_px = new_height; - track.draw( true ); + track.request_draw(true); }).bind( "dragend", function( e, d ) { track.tile_cache.clear(); in_drag = false; - if ( ! in_handle ) { drag_control.hide(); } + if (!in_handle) { drag_control.hide(); } track.track_config.values.height = track.height_px; - }).appendTo( track.container_div ); + }).appendTo(track.container_div); }, predraw_init: function() { var track = this, @@ -2587,7 +2641,7 @@ saved_values: prefs, onchange: function() { track.tile_cache.clear(); - track.draw(); + track.request_draw(); } }); this.prefs = this.track_config.values; @@ -2976,7 +3030,7 @@ saved_values: prefs, onchange: function() { this.track.tile_cache.clear(); - this.track.draw(); + this.track.request_draw(); } }); this.prefs = this.track_config.values; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: Simplified Custom Builds page... show less by default
by Bitbucket 24 Aug '11

24 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e85b513b66be/ changeset: e85b513b66be user: kanwei date: 2011-08-24 07:11:54 summary: Simplified Custom Builds page... show less by default affected #: 1 file (261 bytes) --- a/templates/user/dbkeys.mako Wed Aug 24 00:45:31 2011 -0400 +++ b/templates/user/dbkeys.mako Wed Aug 24 01:11:54 2011 -0400 @@ -56,6 +56,10 @@ pre.toggle(); }); }); + $("#installed_builds").hide(); + $("#show_installed_builds").click(function() { + $("#installed_builds").show(); + }); }); </script> @@ -72,10 +76,8 @@ % elif lines_skipped > 0: <div class="warningmessagelarge">Skipped ${lines_skipped} lines that could not be parsed. (Line was either blank or not 2-column, with 2nd column being an integer)</div> % endif - - <h2>Custom Database/Builds</h2> - <p>Current custom builds:</p> + <h3>Current Custom Builds:</h3> % if dbkeys: <table id="custom_dbkeys" class="colored" cellspacing="0" cellpadding="0"> @@ -110,12 +112,17 @@ % else: <p>You currently have no custom builds.</p> % endif - <p>Builds with system-installed len files: <em>${installed_len_files}</em></p> - <br /> + <p> + <a id="show_installed_builds" href="javascript:void(0);">Show loaded, system-installed builds</a> + <blockquote id="installed_builds">${installed_len_files}</blockquote> + </p> + + <hr /> + <h3>Add a Custom Build</h3><form action="dbkeys" method="post" enctype="multipart/form-data"><div class="toolForm" style="float: left;"> - <div class="toolFormTitle">Add a Custom Build</div> + <div class="toolFormTitle">New Build</div><div class="toolFormBody"><div class="form-row"><label for="name">Build Name (eg: Mouse):</label> @@ -128,8 +135,8 @@ <div class="form-row"><label for="len_file">Upload .len file:</label><input type="file" id="len_file" name="len_file" /><br /> - <label for="len_text">Or paste length info below:</label> - <textarea id="len_text" name="len_text" cols="30" rows="10"></textarea> + <label for="len_text">Or enter/paste length info below:</label> + <textarea id="len_text" name="len_text" cols="30" rows="8"></textarea></div><div class="form-row"><input type="submit" name="add" value="Submit"/></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.

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commit/galaxy-central: kanwei: Tool versioning: now store version information in hda/ldda tables. Information is kept when copied between hda/ldda, and now displayed in the "Show Info" pages for hdas and lddas.
by Bitbucket 24 Aug '11

24 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f3a18916bfd4/ changeset: f3a18916bfd4 user: kanwei date: 2011-08-24 06:45:31 summary: Tool versioning: now store version information in hda/ldda tables. Information is kept when copied between hda/ldda, and now displayed in the "Show Info" pages for hdas and lddas. affected #: 6 files (761 bytes) --- a/lib/galaxy/jobs/__init__.py Tue Aug 23 17:27:58 2011 -0400 +++ b/lib/galaxy/jobs/__init__.py Wed Aug 24 00:45:31 2011 -0400 @@ -534,7 +534,7 @@ if self.version_string_cmd: version_filename = self.get_version_string_path() if os.path.exists(version_filename): - self.version_string = "Tool version: %s" % open(version_filename).read() + self.version_string = open(version_filename).read() os.unlink(version_filename) if self.app.config.outputs_to_working_directory: @@ -587,7 +587,8 @@ dataset.blurb = 'done' dataset.peek = 'no peek' - dataset.info = context['stdout'] + context['stderr'] + self.version_string + dataset.info = context['stdout'] + context['stderr'] + dataset.tool_version = self.version_string dataset.set_size() if context['stderr']: dataset.blurb = "error" --- a/lib/galaxy/model/__init__.py Tue Aug 23 17:27:58 2011 -0400 +++ b/lib/galaxy/model/__init__.py Wed Aug 24 00:45:31 2011 -0400 @@ -753,7 +753,7 @@ """A base class for all 'dataset instances', HDAs, LDAs, etc""" states = Dataset.states permitted_actions = Dataset.permitted_actions - def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None, + def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, tool_version=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, parent_id=None, validation_errors=None, visible=True, create_dataset=False, sa_session=None ): self.name = name or "Unnamed dataset" @@ -761,6 +761,7 @@ self.info = info self.blurb = blurb self.peek = peek + self.tool_version = tool_version self.extension = extension self.designation = designation self.metadata = metadata or dict() @@ -1020,6 +1021,7 @@ info=self.info, blurb=self.blurb, peek=self.peek, + tool_version=self.tool_version, extension=self.extension, dbkey=self.dbkey, dataset = self.dataset, @@ -1057,6 +1059,7 @@ info=self.info, blurb=self.blurb, peek=self.peek, + tool_version=self.tool_version, extension=self.extension, dbkey=self.dbkey, dataset=self.dataset, @@ -1410,6 +1413,7 @@ info=self.info, blurb=self.blurb, peek=self.peek, + tool_version=self.tool_version, extension=self.extension, dbkey=self.dbkey, dataset=self.dataset, @@ -1434,6 +1438,7 @@ info=self.info, blurb=self.blurb, peek=self.peek, + tool_version=self.tool_version, extension=self.extension, dbkey=self.dbkey, dataset=self.dataset, --- a/lib/galaxy/model/mapping.py Tue Aug 23 17:27:58 2011 -0400 +++ b/lib/galaxy/model/mapping.py Wed Aug 24 00:45:31 2011 -0400 @@ -113,6 +113,7 @@ Column( "info", TrimmedString( 255 ) ), Column( "blurb", TrimmedString( 255 ) ), Column( "peek" , TEXT ), + Column( "tool_version" , TEXT ), Column( "extension", TrimmedString( 64 ) ), Column( "metadata", MetadataType(), key="_metadata" ), Column( "parent_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ), @@ -305,6 +306,7 @@ Column( "info", TrimmedString( 255 ) ), Column( "blurb", TrimmedString( 255 ) ), Column( "peek" , TEXT ), + Column( "tool_version" , TEXT ), Column( "extension", TrimmedString( 64 ) ), Column( "metadata", MetadataType(), key="_metadata" ), Column( "parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), --- a/templates/library/common/ldda_info.mako Tue Aug 23 17:27:58 2011 -0400 +++ b/templates/library/common/ldda_info.mako Wed Aug 24 00:45:31 2011 -0400 @@ -100,6 +100,13 @@ ${ldda.get_size( nice_size=True )} <div style="clear: both"></div></div> + %if ldda.tool_version: + <div class="form-row"> + <label>Tool version:</label> + ${ldda.tool_version} + <div style="clear: both"></div> + </div> + %endif <div class="form-row"><label>Data type:</label> ${ldda.ext} @@ -154,7 +161,7 @@ %endfor %if ldda.peek != "no peek": <div class="form-row"> - <div id="info${ldda.id}" class="historyItemBody"> + <div id="info${ldda.id}" class="historyItemBody"><label>Peek:</label><div><pre id="peek${ldda.id}" class="peek">${ldda.display_peek()}</pre></div></div> --- a/templates/show_params.mako Tue Aug 23 17:27:58 2011 -0400 +++ b/templates/show_params.mako Wed Aug 24 00:45:31 2011 -0400 @@ -49,6 +49,7 @@ <tr><td>Filesize:</td><td>${nice_size(hda.dataset.file_size)}</td></tr><tr><td>Dbkey:</td><td>${hda.dbkey}</td></tr><tr><td>Format:</td><td>${hda.ext}</td></tr> + <tr><td>Tool Version:</td><td>${hda.tool_version}</td></tr></table><br /><table class="tabletip"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: remove throttling during dynamic filtering because it's not needed with requestAnimationFrame.
by Bitbucket 23 Aug '11

23 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1447e4ebe7c8/ changeset: 1447e4ebe7c8 user: jgoecks date: 2011-08-23 23:27:58 summary: Trackster: remove throttling during dynamic filtering because it's not needed with requestAnimationFrame. affected #: 1 file (645 bytes) --- a/static/scripts/trackster.js Tue Aug 23 17:21:37 2011 -0400 +++ b/static/scripts/trackster.js Tue Aug 23 17:27:58 2011 -0400 @@ -1419,25 +1419,14 @@ max: -Number.MIN_VALUE, values: [0, 0], slide: function(event, ui) { - // - // Always update UI values, but set timeout for doing more--especially drawing-- - // so that viz is more responsive. - // TODO: remove this because it's no longer necessary as we have requestAnimationFrame(). - // - prev_values = ui.values; - values_span.text(ui.values[0] + "-" + ui.values[1]); - setTimeout(function() { - if (ui.values[0] == prev_values[0] && ui.values[1] == prev_values[1]) { - var values = ui.values; - // Set new values in UI. - values_span.text(values[0] + "-" + values[1]); - // Set new values in filter. - filter.low = values[0]; - filter.high = values[1]; - // Redraw track. - manager.track.draw(true, true); - } - }, 50); + var values = ui.values; + // Set new values in UI. + values_span.text(values[0] + "-" + values[1]); + // Set new values in filter. + filter.low = values[0]; + filter.high = values[1]; + // Redraw track. + manager.track.draw(true, true); }, change: function(event, ui) { filter.control_element.slider("option", "slide").call(filter.control_element, event, ui); 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: make it possible to set features' transparency based on attribute values.
by Bitbucket 23 Aug '11

23 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dbc0cf838411/ changeset: dbc0cf838411 user: jgoecks date: 2011-08-23 23:21:37 summary: Trackster: make it possible to set features' transparency based on attribute values. affected #: 4 files (4.8 KB) --- a/static/june_2007_style/blue/trackster.css Mon Aug 22 16:31:50 2011 -0400 +++ b/static/june_2007_style/blue/trackster.css Tue Aug 23 17:21:37 2011 -0400 @@ -39,9 +39,12 @@ .top-labeltrack{position:relative;border-bottom:solid #999 1px;} .nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #333 1px;} input{font:10px verdana;} -.dynamic-tool,.filters{width:410px;margin-left:0.25em;padding-bottom:0.5em;} +.dynamic-tool,.filters{margin-left:0.25em;padding-bottom:0.5em;} +.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;} -.slider-label{float:left;font-weight:bold;} +.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;} .param-row{margin-top:0.2em;margin-left:1em;} --- a/static/june_2007_style/trackster.css.tmpl Mon Aug 22 16:31:50 2011 -0400 +++ b/static/june_2007_style/trackster.css.tmpl Tue Aug 23 17:21:37 2011 -0400 @@ -231,17 +231,28 @@ font: 10px verdana; } .dynamic-tool, .filters { - width: 410px; margin-left: 0.25em; padding-bottom:0.5em; } +.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; } -.slider-label { +.elt-label { float: left; font-weight: bold; + margin-right: 1em; } .slider { float: right; --- a/static/scripts/packed/trackster.js Mon Aug 22 16:31:50 2011 -0400 +++ b/static/scripts/packed/trackster.js Tue Aug 23 17:21:37 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 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,T){var n=f("class").extend,p=f("slotting"),I=f("painters");var Z=function(aa,ab){this.document=aa;this.default_font=ab!==undefined?ab:"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")};n(Z.prototype,{load_pattern:function(aa,ae){var ab=this.patterns,ac=this.dummy_context,ad=new Image();ad.src=image_path+ae;ad.onload=function(){ab[aa]=ac.createPattern(ad,"repeat")}},get_pattern:function(aa){return this.patterns[aa]},new_canvas:function(){var aa=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(aa)}aa.manager=this;return aa}});var C=function(aa,ab){aa.bind("drag",{handle:ab,relative:true},function(af,ag){var ae=$(this).parent();var ad=ae.children();var ac;for(ac=0;ac<ad.length;ac++){if(ag.offsetY<$(ad.get(ac)).position().top){break}}if(ac===ad.length){if(this!==ad.get(ac-1)){ae.append(this)}}else{if(this!==ad.get(ac)){$(this).insertBefore(ad.get(ac))}}}).bind("dragstart",function(){$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css("border","0px")})};T.sortable=C;var D=9,A=20,O=D+2,w=100,F=12000,M=200,z=5,s=10,H=5000,t=100,m="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",q="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",d=10,r=5,y=5;function u(aa){return Math.round(aa*1000)/1000}var c=function(aa){this.num_elements=aa;this.clear()};n(c.prototype,{get:function(ab){var aa=this.key_ary.indexOf(ab);if(aa!==-1){if(this.obj_cache[ab].stale){this.key_ary.splice(aa,1);delete this.obj_cache[ab]}else{this.move_key_to_end(ab,aa)}}return this.obj_cache[ab]},set:function(ab,ac){if(!this.obj_cache[ab]){if(this.key_ary.length>=this.num_elements){var aa=this.key_ary.shift();delete this.obj_cache[aa]}this.key_ary.push(ab)}this.obj_cache[ab]=ac;return ac},move_key_to_end:function(ab,aa){this.key_ary.splice(aa,1);this.key_ary.push(ab)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var N=function(ab,aa,ac){c.call(this,ab);this.track=aa;this.subset=(ac!==undefined?ac:true)};n(N.prototype,c.prototype,{load_data:function(aj,ae,ah,ab,ag){var ai=this.track.view.chrom,ad={chrom:ai,low:aj,high:ae,mode:ah,resolution:ab,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ad,ag);if(this.track.filters_manager){var ak=[];var aa=this.track.filters_manager.filters;for(var af=0;af<aa.length;af++){ak[ak.length]=aa[af].name}ad.filter_cols=JSON.stringify(ak)}var ac=this;return $.getJSON(this.track.data_url,ad,function(al){ac.set_data(aj,ae,ah,al)})},get_data:function(aa,ae,af,ab,ad){var ac=this.get_data_from_cache(aa,ae,af);if(ac){return ac}ac=this.load_data(aa,ae,af,ab,ad);this.set_data(aa,ae,af,ac);return ac},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ai,ad,ah,ac,ag,ae){var aj=this.get_data_from_cache(ai,ad,ah);if(!aj){console.log("ERROR: no current data for: ",this.track,ai,ad,ah,ac,ag);return}aj.stale=true;var 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ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){var ai=Math.round(-ag/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div />").css({height:aa.content_div.height()+aa.top_labeltrack.height()+aa.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX),width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-aa.container.offset().left,af=Math.max(aj.pageX,ak.startX)-aa.container.offset().left,ai=(aa.high-aa.low),ah=aa.viewport_container.width();aa.update_location(Math.round(ag/ah*ai)+aa.low,Math.round(af/ah*ai)+aa.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(aa.high-aa.low),ah=aa.viewport_container.width(),aj=aa.low;aa.low=Math.round(ag/ah*ai)+aj;aa.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();aa.redraw()});this.add_label_track(new X(this,this.top_labeltrack));this.add_label_track(new X(this,this.nav_labeltrack));$(window).bind("resize",function(){aa.resize_window()});$(document).bind("redraw",function(){aa.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(aa,ab){this.location_span.text(commatize(aa)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(aa)+"-"+commatize(ab))},load_chroms:function(ab,ac){ab.num=t;$.extend(ab,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var aa=this;$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ae){if(ae.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ae.reference){aa.add_label_track(new x(aa))}aa.chrom_data=ae.chrom_info;var ah='<option value="">Select Chrom/Contig</option>';for(var ag=0,ad=aa.chrom_data.length;ag<ad;ag++){var af=aa.chrom_data[ag].chrom;ah+='<option value="'+af+'">'+af+"</option>"}if(ae.prev_chroms){ah+='<option value="previous">Previous '+t+"</option>"}if(ae.next_chroms){ah+='<option value="next">Next '+t+"</option>"}aa.chrom_select.html(ah);if(ac){ac()}aa.chrom_start_index=ae.start_index},error:function(){alert("Could not load chroms for this dbkey:",aa.dbkey)}})},change_chrom:function(ae,ab,ag){if(!ae||ae==="None"){return}var ad=this;if(ae==="previous"){ad.load_chroms({low:this.chrom_start_index-t});return}if(ae==="next"){ad.load_chroms({low:this.chrom_start_index+t});return}var af=$.grep(ad.chrom_data,function(ai,aj){return ai.chrom===ae})[0];if(af===undefined){ad.load_chroms({chrom:ae},function(){ad.change_chrom(ae,ab,ag)});return}else{if(ae!==ad.chrom){ad.chrom=ae;ad.chrom_select.val(ad.chrom);ad.max_high=af.len-1;ad.reset();ad.redraw(true);for(var ah=0,aa=ad.tracks.length;ah<aa;ah++){var ac=ad.tracks[ah];if(ac.init){ac.init()}}}if(ab!==undefined&&ag!==undefined){ad.low=Math.max(ab,0);ad.high=Math.min(ag,ad.max_high)}ad.reset_overview();ad.redraw()}},go_to:function(ae){var ai=this,aa,ad,ab=ae.split(":"),ag=ab[0],ah=ab[1];if(ah!==undefined){try{var af=ah.split("-");aa=parseInt(af[0].replace(/,/g,""),10);ad=parseInt(af[1].replace(/,/g,""),10)}catch(ac){return false}}ai.change_chrom(ag,aa,ad)},move_fraction:function(ac){var aa=this;var ab=aa.high-aa.low;this.move_delta(ac*ab)},move_delta:function(ac){var aa=this;var ab=aa.high-aa.low;if(aa.low-ac<aa.max_low){aa.low=aa.max_low;aa.high=aa.max_low+ab}else{if(aa.high-ac>aa.max_high){aa.high=aa.max_high;aa.low=aa.max_high-ab}else{aa.high-=ac;aa.low-=ac}}aa.redraw()},add_track:function(aa){aa.view=this;aa.track_id=this.track_id_counter;this.tracks.push(aa);if(aa.init){aa.init()}aa.container_div.attr("id","track_"+aa.track_id);C(aa.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1;this.update_intro_div()},add_label_track:function(aa){aa.view=this;this.label_tracks.push(aa)},remove_track:function(ab){this.has_changes=true;delete this.tracks[this.tracks.indexOf(ab)];this.num_tracks-=1;var aa=this;ab.container_div.fadeOut("slow",function(){$(this).remove();aa.update_intro_div()})},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ah){var ag=this.high-this.low,af=this.low,ab=this.high;if(af<this.max_low){af=this.max_low}if(ab>this.max_high){ab=this.max_high}if(this.high!==0&&ag<this.min_separation){ab=af+this.min_separation}this.low=Math.floor(af);this.high=Math.ceil(ab);this.resolution=Math.pow(z,Math.ceil(Math.log((this.high-this.low)/M)/Math.log(z)));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var aa=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=13;this.overview_box.css({left:aa,width:Math.max(ai,ae)}).show();if(ae<ai){this.overview_box.css("left",aa-(ai-ae)/2)}if(this.overview_highlight){this.overview_highlight.css({left:aa,width:ae})}this.update_location(this.low,this.high);if(!ah){for(var ac=0,ad=this.tracks.length;ac<ad;ac++){if(this.tracks[ac]&&this.tracks[ac].enabled){this.tracks[ac].draw()}}for(ac=0,ad=this.label_tracks.length;ac<ad;ac++){this.label_tracks[ac].draw()}}},zoom_in:function(ab,ac){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ad=this.high-this.low,ae=ad/2+this.low,aa=(ad/this.zoom_factor)/2;if(ab){ae=ab/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ae-aa);this.high=Math.round(ae+aa);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var ab=this.high-this.low,ac=ab/2+this.low,aa=(ab*this.zoom_factor)/2;this.low=Math.round(ac-aa);this.high=Math.round(ac+aa);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},set_overview:function(aa){$.when(aa.get_overview_tile()).then(function(ab){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ab.canvas);view.overview_highlight.show().height(ab.canvas.height());view.overview_viewport.height(ab.canvas.height()+view.overview_box.height());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=aa;view.has_changes=true;aa.set_is_overview(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 o=function(ac,ag){this.track=ac;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],ab=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params[this.params.length]=new g(ab,am,ae,ao,ai.min,ai.max)}else{if(ak=="select"){this.params[this.params.length]=new K(ab,am,ae,ao)}else{console.log("WARNING: unrecognized tool parameter type:",ab,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).click(function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("slider").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: both;'/>").appendTo(au)});this.parent_div.find("input").click(function(){$(this).select()});var ap=$("<div>").addClass("param-row").appendTo(this.parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ap);var aa=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ap);var ah=this;aa.click(function(){ah.run_on_region()});af.click(function(){ah.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var aa={};this.parent_div.find(":input").each(function(){var ab=$(this).attr("name"),ac=$(this).val();aa[ab]=JSON.stringify(ac)});return aa},get_param_values:function(){var ab=[];var aa={};this.parent_div.find(":input").each(function(){var ac=$(this).attr("name"),ad=$(this).val();if(ac){ab[ab.length]=ad}});return ab},run_on_dataset:function(){var aa=this;aa.run({dataset_id:this.track.original_dataset_id,tool_id:aa.name},null,function(ab){show_modal(aa.name+" is Running",aa.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ac=this.track,ab=aa.tool_id+ac.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),ad;if(ac instanceof e){ad=new Q(ab,view,ac.hda_ldda,undefined,{},{},ac);ad.change_mode(ac.mode)}this.track.add_track(ad);ad.content_div.text("Starting job.");this.run(aa,ad,function(ae){ad.dataset_id=ae.dataset_id;ad.content_div.text("Running job.");ad.init()})},run:function(ab,ac,ad){$.extend(ab,this.get_param_values_dict());var aa=function(){$.getJSON(rerun_tool_url,ab,function(ae){if(ae==="no converter"){ac.container_div.addClass("error");ac.content_div.text(G)}else{if(ae.error){ac.container_div.addClass("error");ac.content_div.text(v+ae.message)}else{if(ae==="pending"){ac.container_div.addClass("pending");ac.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(aa,2000)}else{ad(ae)}}}})};aa()}});var K=function(ab,aa,ac,ad){this.name=ab;this.label=aa;this.html=ac;this.value=ad};var g=function(ac,ab,ae,af,ad,aa){K.call(this,ac,ab,ae,af);this.min=ad;this.max=aa};var h=function(ab,aa,ac,ad){this.name=ab;this.index=aa;this.tool_id=ac;this.tool_exp_name=ad};var R=function(ab,aa,ac,ad){h.call(this,ab,aa,ac,ad);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};n(R.prototype,{applies_to:function(aa){if(aa.length>this.index){return true}return false},keep:function(aa){if(!this.applies_to(aa)){return true}var ab=parseInt(aa[this.index]);return(isNaN(ab)||(ab>=this.low&&ab<=this.high))},update_attrs:function(ab){var aa=false;if(!this.applies_to(ab)){return aa}if(ab[this.index]<this.min){this.min=Math.floor(ab[this.index]);aa=true}if(ab[this.index]>this.max){this.max=Math.ceil(ab[this.index]);aa=true}return aa},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ac=function(af,ad){var ae=ad-af;return(ae<=2?0.01:1)};var ab=this.slider.slider("option","min"),aa=this.slider.slider("option","max");if(this.min<ab||this.max>aa){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ac(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var W=function(ac,al){this.track=ac;this.filters=[];for(var ag=0;ag<al.length;ag++){var aa=al[ag],ab=aa.name,ak=aa.type,ai=aa.index,an=aa.tool_id,ad=aa.tool_exp_name;if(ak==="int"||ak==="float"){this.filters[ag]=new R(ab,ai,an,ad)}else{console.log("ERROR: unsupported filter: ",ab,ak)}}var aj=function(ao,ap,aq){ao.click(function(){var ar=ap.text();max=parseFloat(aq.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aq.slider("option","values")){input_size=2*input_size+1;multi_value=true}ap.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ar).appendTo(ap).focus().select().click(function(at){at.stopPropagation()}).blur(function(){$(this).remove();ap.text(ar)}).keyup(function(ax){if(ax.keyCode===27){$(this).trigger("blur")}else{if(ax.keyCode===13){var av=aq.slider("option","min"),at=aq.slider("option","max"),aw=function(ay){return(isNaN(ay)||ay>at||ay<av)},au=$(this).val();if(!multi_value){au=parseFloat(au);if(aw(au)){alert("Parameter value must be in the range ["+av+"-"+at+"]");return $(this)}}else{au=au.split("-");au=[parseFloat(au[0]),parseFloat(au[1])];if(aw(au[0])||aw(au[1])){alert("Parameter value must be in the range ["+av+"-"+at+"]");return $(this)}}aq.slider((multi_value?"values":"value"),au)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(ao){ao.stopPropagation()}).click(function(ao){ao.stopPropagation()}).bind("dblclick",function(ao){ao.stopPropagation()}).bind("keydown",function(ao){ao.stopPropagation()});var ae=this;$.each(this.filters,function(ar,au){au.container=$("<div/>").addClass("slider-row").appendTo(ae.parent_div);var at=$("<div/>").addClass("slider-label").appendTo(au.container);var aq=$("<span/>").addClass("slider-name").text(au.name+" ").appendTo(at);var ap=$("<span/>");var aw=$("<span/>").addClass("slider-value").appendTo(at).append("[").append(ap).append("]");var ao=$("<div/>").addClass("slider").appendTo(au.container);au.control_element=$("<div/>").attr("id",au.name+"-filter-control").appendTo(ao);var av=[0,0];au.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ax,ay){av=ay.values;ap.text(ay.values[0]+"-"+ay.values[1]);setTimeout(function(){if(ay.values[0]==av[0]&&ay.values[1]==av[1]){var az=ay.values;ap.text(az[0]+"-"+az[1]);au.low=az[0];au.high=az[1];ae.track.draw(true,true)}},50)},change:function(ax,ay){au.control_element.slider("option","slide").call(au.control_element,ax,ay)}});au.slider=au.control_element;au.slider_label=ap;aj(aw,ap,au.control_element);$("<div style='clear: both;'/>").appendTo(au.container)});if(this.filters.length!=0){var am=$("<div>").addClass("param-row").appendTo(this.parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(am);var af=this;ah.click(function(){af.run_on_dataset()})}};n(W.prototype,{reset_filters:function(){for(var aa=0;aa<this.filters.length;aa++){filter=this.filters[aa];filter.slider.slider("option","values",[filter.min,filter.max])}},run_on_dataset:function(){var ai=function(am,ak,al){if(!(ak in am)){am[ak]=al}return am[ak]};var ac={},aa,ab,ad;for(var ae=0;ae<this.filters.length;ae++){aa=this.filters[ae];if(aa.tool_id){if(aa.min!=aa.low){ab=ai(ac,aa.tool_id,[]);ab[ab.length]=aa.tool_exp_name+" >= "+aa.low}if(aa.max!=aa.high){ab=ai(ac,aa.tool_id,[]);ab[ab.length]=aa.tool_exp_name+" <= "+aa.high}}}var ag=[];for(var aj in ac){ag[ag.length]=[aj,ac[aj]]}var ah=ag.length;(function af(aq,an){var al=an[0],am=al[0],ap=al[1],ao="("+ap.join(") and (")+")",ak={cond:ao,input:aq,target_dataset_id:aq,tool_id:am},an=an.slice(1);$.getJSON(run_tool_url,ak,function(ar){if(ar.error){show_modal("Filter Dataset","Error running tool "+am,{Close:hide_modal})}else{if(an.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{af(ar.dataset_id,an)}}})})(this.track.dataset_id,ag)}});var V=function(aa){this.track=aa.track;this.params=aa.params;this.values={};if(aa.saved_values){this.restore_values(aa.saved_values)}this.onchange=aa.onchange};n(V.prototype,{restore_values:function(aa){var ab=this;$.each(this.params,function(ac,ad){if(aa[ad.key]!==undefined){ab.values[ad.key]=aa[ad.key]}else{ab.values[ad.key]=ad.default_value}})},build_form:function(){var ab=this;var aa=$("<div />");$.each(this.params,function(af,ad){if(!ad.hidden){var ac="param_"+af;var ak=$("<div class='form-row' />").appendTo(aa);ak.append($("<label />").attr("for",ac).text(ad.label+":"));if(ad.type==="bool"){ak.append($('<input type="checkbox" />').attr("id",ac).attr("name",ac).attr("checked",ab.values[ad.key]))}else{if(ad.type==="color"){var ah=ab.values[ad.key];var ag=$("<input />").attr("id",ac).attr("name",ac).val(ah);var ai=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ae=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ai);var aj=$("<div/>").appendTo(ae).farbtastic({width:100,height:100,callback:ag,color:ah});$("<div />").append(ag).append(ai).appendTo(ak).bind("click",function(al){ai.css({left:$(this).position().left+($(ag).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ai.hide();$(document).unbind("click.color-picker")});al.stopPropagation()})}else{ak.append($("<input />").attr("id",ac).attr("name",ac).val(ab.values[ad.key]))}}}});return aa},update_from_form:function(aa){var ac=this;var ab=false;$.each(this.params,function(ad,af){if(!af.hidden){var ag="param_"+ad;var ae=aa.find("#"+ag).val();if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae)}else{if(af.type==="bool"){ae=aa.find("#"+ag).is(":checked")}}}if(ae!==ac.values[af.key]){ac.values[af.key]=ae;ab=true}}});if(ab){this.onchange()}}});var b=function(ac,ab,aa,ad){this.index=ac;this.low=ac*M*ab;this.high=(ac+1)*M*ab;this.resolution=ab;this.canvas=$("<div class='track-tile'/>").append(aa);this.data=ad;this.stale=false};var l=function(ac,ab,aa,ad,ae){b.call(this,ac,ab,aa,ad);this.max_val=ae};var L=function(ac,ab,aa,ae,ad){b.call(this,ac,ab,aa,ae);this.message=ad};var j=function(ab,aa,ae,ac,ad){this.name=ab;this.view=aa;this.parent_element=ae;this.data_url=(ac?ac:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ad?ad:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<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=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Q){return"ToolDataFeatureTrack"}else{if(this instanceof P){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.initial_canvas=undefined;aa.content_div.css("height","auto");aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.content_div.text(m);if(ab.message){var ad=aa.view.tracks.indexOf(aa);var ac=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.content_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.content_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text(q);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.make_name_popup_menu()}aa.content_div.text(U);if(aa.view.chrom){aa.content_div.text("");aa.content_div.css("height",aa.height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){aa.container_div.removeClass("nodata error pending");aa.draw()})}}}}}}})},predraw_init:function(){},update_name:function(aa){this.old_name=this.name;this.name=aa;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(ah,af,ai){var ab=this,aj=ab.view;this.filters_manager=(ah!==undefined?new W(this,ah):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(af!==undefined&&obj_length(af)>0?new o(this,af):undefined);this.is_overview=false;this.parent_track=ai;this.child_tracks=[];if(ab.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ab.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();ab.container_div.append(ab.child_tracks_container);if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ab.display_modes!==undefined){if(ab.mode_div===undefined){ab.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ab.header_div);var ac=(ab.track_config&&ab.track_config.values.mode?ab.track_config.values.mode:ab.display_modes[0]);ab.mode=ac;ab.mode_div.text(ac);var aa={};for(var ad=0,ag=ab.display_modes.length;ad<ag;ad++){var ae=ab.display_modes[ad];aa[ae]=function(ak){return function(){ab.change_mode(ak)}}(ae)}make_popupmenu(ab.mode_div,aa)}else{ab.mode_div.hide()}}this.make_name_popup_menu()};n(J.prototype,j.prototype,{change_mode:function(ab){var aa=this;aa.mode_div.text(ab);aa.mode=ab;aa.track_config.values.mode=ab;aa.tile_cache.clear();aa.draw()},make_name_popup_menu:function(){var ab=this;var aa={};aa[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ab.is_overview){ab.view.reset_overview()}else{ab.view.set_overview(ab)}};aa["Edit configuration"]=function(){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ab.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure Track",ab.track_config.build_form(),{Cancel:ah,OK:af})};if(ab.filters_available>0){var ae=(ab.filters_div.is(":visible")?"Hide filters":"Show filters");aa[ae]=function(){ab.filters_visible=(ab.filters_div.is(":visible"));if(ab.filters_visible){ab.filters_manager.reset_filters()}ab.filters_div.toggle();ab.make_name_popup_menu()}}if(ab.tool){var ae=(ab.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");aa[ae]=function(){if(!ab.dynamic_tool_div.is(":visible")){ab.update_name(ab.name+ab.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ab.revert_name()}ab.dynamic_tool_div.toggle();ab.make_name_popup_menu()}}if(ab.valid_chroms){aa["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ab.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ac=view;var ad=function(){$("#no-tracks").show()};if(this.parent_track){ac=this.parent_track;ad=function(){}}aa.Remove=function(){ac.remove_track(ab);if(ac.num_tracks===0){ad()}};make_popupmenu(ab.name_div,aa)},set_is_overview:function(aa){this.is_overview=aa;this.make_name_popup_menu()},get_overview_tile:function(){var aa=this;view=aa.view,resolution=Math.pow(z,Math.ceil(Math.log((view.max_high-view.max_low)/M)/Math.log(z))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(aa.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,aa.data_url_extra_params)).then(function(ab){var ad=aa._gen_tile_cache_key(view_width,w_scale,0),af=aa.tile_cache.get(ad);if(af){var ai=$(af.canvas.find("canvas")),ae=ai.clone(),ah=ai.get(0).getContext("2d"),ac=ae.get(0).getContext("2d"),ag=ah.getImageData(0,0,ah.canvas.width,ah.canvas.height);ac.putImageData(ag,-aa.left_offset,(af.data.dataset_type==="summary_tree"?O:0));af=new b(-1,resolution,ae)}else{af=aa.draw_tile(ab,resolution,null,w_scale,null,true);aa.tile_cache.set(ad,af)}overview_tile.resolve(af)});return overview_tile},_gen_tile_cache_key:function(ab,ac,aa){return ab+"_"+ac+"_"+aa},draw:function(aa,ac){if(!this.dataset_id){return}var at=this.view.low,ag=this.view.high,ai=ag-at,ak=this.view.container.width(),ae=ak/ai,al=this.view.resolution,ad=$("<div style='position: relative;'></div>");if(!ac){this.content_div.children().remove()}this.content_div.append(ad);this.max_height=0;var an=Math.floor(at/al/M);var af=[];var ao=0;while((an*M*al)<ag){var ar=this._gen_tile_cache_key(ak,ae,an);var ah=this.tile_cache.get(ar);var ap=an*M*this.view.resolution;var ab=ap+M*this.view.resolution;if(!aa&&ah){af.push(ah);this.show_tile(ah,ad,ae)}else{this.delayed_draw(aa,ar,an,al,ad,ae,af)}an+=1;ao++}var aj=this;var aq=setInterval(function(){if(af.length===ao){clearInterval(aq);aj.postdraw_actions(af,ac)}},50);for(var am=0;am<this.child_tracks.length;am++){this.child_tracks[am].draw(aa,ac)}},postdraw_actions:function(ae,aa){var ac=this;var ad=false;for(var ab=0;ab<ae.length;ab++){if(ae[ab].message){ad=true;break}}if(ad){for(var ab=0;ab<ae.length;ab++){tile=ae[ab];if(!tile.message){tile.canvas.css("padding-top",A)}}}},delayed_draw:function(ab,ai,ac,ae,aj,am,ak,af){var ad=this,ag=ac*M*ae,al=ag+M*ae;var ah=function(av,an,ap,ao,at,au,aq){var ar=ad.draw_tile(an,ap,ao,au,aq);ad.tile_cache.set(ai,ar);if(ar===undefined){return}ad.show_tile(ar,at,au);ak.push(ar)};var aa=setTimeout(function(){if(ag<=ad.view.high&&al>=ad.view.low){var an=(ab?undefined:ad.tile_cache.get(ai));if(an){ad.show_tile(an,aj,am);ak.push(an)}else{$.when(ad.data_manager.get_data(ag,al,ad.mode,ae,ad.data_url_extra_params)).then(function(ao){n(ao,af);if(view.reference_track&&am>view.canvas_manager.char_width_px){$.when(view.reference_track.data_manager.get_data(ag,al,ad.mode,ae,view.reference_track.data_url_extra_params)).then(function(ap){ah(aa,ao,ae,ac,aj,am,ap)})}else{ah(aa,ao,ae,ac,aj,am)}})}}},50)},show_tile:function(ah,aj,ak){var ac=this,ab=ah.canvas,ag=ab;if(ah.message){var al=$("<div/>"),ai=$("<div/>").addClass("tile-message").text(ah.message).css({height:A-1,width:ah.canvas.width}).appendTo(al),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ai),aa=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ai);al.append(ab);ag=al;ae.click(function(){ah.stale=true;ac.data_manager.get_more_data(ah.low,ah.high,ac.mode,ah.resolution,{},ac.data_manager.DEEP_DATA_REQ);ac.draw()}).dblclick(function(am){am.stopPropagation()});aa.click(function(){ah.stale=true;ac.data_manager.get_more_data(ah.low,ah.high,ac.mode,ah.resolution,{},ac.data_manager.BROAD_DATA_REQ);ac.draw()}).dblclick(function(am){am.stopPropagation()})}var af=this.view.high-this.view.low,ad=(ah.low-this.view.low)*ak;if(this.left_offset){ad-=this.left_offset}ag.css({position:"absolute",top:0,left:ad,height:""});aj.append(ag);ac.max_height=Math.max(ac.max_height,ag.height());ac.content_div.css("height",ac.max_height+"px");aj.children().css("height",ac.max_height+"px")},tool_region_and_parameters_str:function(ac,aa,ad){var ab=this,ae=(ac!==undefined&&aa!==undefined&&ad!==undefined?ac+":"+aa+"-"+ad:"all");return" - region=["+ae+"], parameters=["+ab.tool.get_param_values().join(", ")+"]"},add_track:function(aa){aa.track_id=this.track_id+"_"+this.child_tracks.length;aa.container_div.attr("id","track_"+aa.track_id);this.child_tracks_container.append(aa.container_div);C(aa.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(aa);this.view.has_changes=true},remove_track:function(aa){aa.container_div.fadeOut("slow",function(){$(this).remove()})}});var X=function(aa,ab){this.hidden=true;j.call(this,null,aa,ab);this.container_div.addClass("label-track")};n(X.prototype,j.prototype,{draw:function(){var ac=this.view,ad=ac.high-ac.low,ag=Math.floor(Math.pow(10,Math.floor(Math.log(ad)/Math.log(10)))),aa=Math.floor(ac.low/ag)*ag,ae=this.view.container.width(),ab=$("<div style='position: relative; height: 1.3em;'></div>");while(aa<ac.high){var af=(aa-ac.low)/ad*ae;ab.append($("<div class='label'>"+commatize(aa)+"</div>").css({position:"absolute",left:af-1}));aa+=ag}this.content_div.children(":first").remove();this.content_div.append(ab)}});var x=function(aa){this.hidden=true;j.call(this,null,aa,aa.top_labeltrack);J.call(this);aa.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:aa.dbkey};this.data_manager=new E(y,this,false);this.tile_cache=new c(r)};n(x.prototype,J.prototype,{draw_tile:function(ai,af,ab,ak){var ae=this,ac=M*af;if(ak>this.view.canvas_manager.char_width_px){if(ai===null){ae.content_div.css("height","0px");return}var ad=this.view.canvas_manager.new_canvas();var aj=ad.getContext("2d");ad.width=Math.ceil(ac*ak+ae.left_offset);ad.height=ae.height_px;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var ag=0,ah=ai.length;ag<ah;ag++){var aa=Math.round(ag*ak);aj.fillText(ai[ag],aa+ae.left_offset,10)}return new b(ab,af,ad,ai)}this.content_div.css("height","0px")}});var k=function(ae,ac,af,aa,ad){var ab=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ae,ac,ac.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=af;this.dataset_id=aa;this.original_dataset_id=aa;this.data_manager=new N(y,this);this.tile_cache=new c(r);this.track_config=new V({track:this,params:[{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:ad,onchange:function(){ab.vertical_range=ab.prefs.max_value-ab.prefs.min_value;$("#linetrack_"+ab.track_id+"_minval").text(ab.prefs.min_value);$("#linetrack_"+ab.track_id+"_maxval").text(ab.prefs.max_value);ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,J.prototype,{add_resize_handle:function(){var aa=this;var ad=false;var ac=false;var ab=$("<div class='track-resize'>");$(aa.container_div).hover(function(){ad=true;ab.show()},function(){ad=false;if(!ac){ab.hide()}});ab.hide().bind("dragstart",function(ae,af){ac=true;af.original_height=$(aa.content_div).height()}).bind("drag",function(af,ag){var ae=Math.min(Math.max(ag.original_height+ag.deltaY,aa.min_height_px),aa.max_height_px);$(aa.content_div).css("height",ae);aa.height_px=ae;aa.draw(true)}).bind("dragend",function(ae,af){aa.tile_cache.clear();ac=false;if(!ad){ab.hide()}aa.track_config.values.height=aa.height_px}).appendTo(aa.container_div)},predraw_init:function(){var aa=this,ab=aa.view.tracks.indexOf(aa);aa.vertical_range=undefined;return $.getJSON(aa.data_url,{stats:true,chrom:aa.view.chrom,low:null,high:null,hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id},function(ac){aa.container_div.addClass("line-track");var ae=ac.data;if(isNaN(parseFloat(aa.prefs.min_value))||isNaN(parseFloat(aa.prefs.max_value))){aa.prefs.min_value=ae.min;aa.prefs.max_value=ae.max;$("#track_"+ab+"_minval").val(aa.prefs.min_value);$("#track_"+ab+"_maxval").val(aa.prefs.max_value)}aa.vertical_range=aa.prefs.max_value-aa.prefs.min_value;aa.total_frequency=ae.total_frequency;aa.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_minval").text(u(aa.prefs.min_value));var ad=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_maxval").text(u(aa.prefs.max_value));ad.css({position:"absolute",top:"24px",left:"10px"});ad.prependTo(aa.container_div);af.css({position:"absolute",bottom:"2px",left:"10px"});af.prependTo(aa.container_div)})},draw_tile:function(ak,ae,ab,aj){if(this.vertical_range===undefined){return}var af=ab*M*ae,ad=M*ae,aa=Math.ceil(ad*aj),ah=this.height_px;var ac=this.view.canvas_manager.new_canvas();ac.width=aa,ac.height=ah;var ai=ac.getContext("2d");var ag=new I.LinePainter(ak.data,af,af+ad,this.prefs,this.mode);ag.draw(ai,aa,ah);return new b(ab,ae,ac,ak.data)}});var e=function(aa,af,ae,ai,ah,ac,ad,ag){var ab=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ah,onchange:function(){ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;j.call(this,aa,af,af.viewport_container);J.call(this,ac,ad,ag);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ae;this.dataset_id=ai;this.original_dataset_id=ai;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new N(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{postdraw_actions:function(ao,an){J.prototype.postdraw_actions.call(this,ao,an);var ac=this;if(an){var ae=ac.content_div.children();var af=false;for(var ad=ae.length-1,aj=0;ad>=aj;ad--){var ab=$(ae[ad]);if(af){ab.remove()}else{if(ab.children().length!==0){af=true}}}}if(ac.mode=="Histogram"){var ai=-1;for(var ad=0;ad<ao.length;ad++){var am=ao[ad].max_val;if(am>ai){ai=am}}for(var ad=0;ad<ao.length;ad++){if(ao[ad].max_val!==ai){var al=ao[ad];al.canvas.remove();ac.delayed_draw(true,ac._gen_tile_cache_key(width,w_scale,al.index),al.index,al.resolution,parent_element,w_scale,[],{max:ai})}}}if(ac.filters_manager){var aa=ac.filters_manager.filters;for(var ah=0;ah<aa.length;ah++){aa[ah].update_ui_elt()}var ag=false,ak;for(var ad=0;ad<ao.length;ad++){if(ao[ad].data.length){ak=ao[ad].data[0];for(var ah=0;ah<aa.length;ah++){if(aa[ah].applies_to(ak)){ag=true;break}}}}if(ac.filters_available!==ag){ac.filters_available=ag;if(!ac.filters_available){ac.filters_div.hide()}ac.make_name_popup_menu()}}},update_auto_mode:function(aa){if(this.mode=="Auto"){if(aa=="no_detail"){aa="feature spans"}else{if(aa=="summary_tree"){aa="coverage histogram"}}this.mode_div.text("Auto ("+aa+")")}},incremental_slots:function(ae,ab,ad){var ac=this.view.canvas_manager.dummy_context,aa=this.inc_slots[ae];if(!aa||(aa.mode!==ad)){aa=new (p.FeatureSlotter)(ae,ad==="Pack",w,function(af){return ac.measureText(af)});aa.mode=ad;this.inc_slots[ae]=aa}return aa.slot_features(ab)},get_summary_tree_data:function(ae,ah,ac,ap){if(ap>ac-ah){ap=ac-ah}var al=Math.floor((ac-ah)/ap),ao=[],ad=0;var af=0,ag=0,ak,an=0,ai=[],am,aj;var ab=function(at,ar,au,aq){at[0]=ar+au*aq;at[1]=ar+(au+1)*aq};while(an<ap&&af!==ae.length){var aa=false;for(;an<ap&&!aa;an++){ab(ai,ah,an,al);for(ag=af;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){aa=true;break}}if(aa){break}}data_start_index=ag;ao[ao.length]=am=[ai[0],0];for(;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){am[1]++}else{break}}if(am[1]>ad){ad=am[1]}an++}return{max:ad,delta:al,data:ao}},draw_tile:function(an,aw,aA,aj,ad,ar){var at=this,aC=aA*M*aw,ab=(aA+1)*M*aw,ap=ab-aC,au=Math.ceil(ap*aj),aq=this.mode,aG=25,ae=this.left_offset,ao,af;if(aq==="Auto"){if(an.dataset_type==="summary_tree"){aq=an.dataset_type}else{if(an.extra_info==="no_detail"){aq="no_detail"}else{var aF=an.data;if(this.view.high-this.view.low>F){aq="Squish"}else{aq="Pack"}}}this.update_auto_mode(aq)}if(aq==="summary_tree"||aq==="Histogram"){af=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var aa=$("<div />").addClass("yaxislabel");aa.text(an.max);aa.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});aa.prependTo(this.container_div);var ac=this.view.canvas_manager.new_canvas();ac.width=au+ae;ac.height=af+(!ar?O:0);if(an.dataset_type!="summary_tree"){var ak=this.get_summary_tree_data(an.data,aC,ab,200);if(an.max){ak.max=an.max}an=ak}var aD=new I.SummaryTreePainter(an,aC,ab,this.prefs);var av=ac.getContext("2d");if(!ar){av.translate(ae,O)}aD.draw(av,au,af);return new l(aA,aw,ac,an.data,an.max)}var ao,ah=1;if(aq==="no_detail"||aq==="Squish"||aq==="Pack"){ah=this.incremental_slots(aj,an.data,aq);ao=this.inc_slots[aj].slots}var ai=[];if(an.data){var al=this.filters_manager.filters;for(var ax=0,az=an.data.length;ax<az;ax++){var ag=an.data[ax];var ay=false;var am;for(var aB=0,aE=al.length;aB<aE;aB++){am=al[aB];am.update_attrs(ag);if(!am.keep(ag)){ay=true;break}}if(!ay){ai.push(ag)}}}var aD=new (this.painter)(ai,aC,ab,this.prefs,aq,ad);var af=aD.get_required_height(ah);var ac=this.view.canvas_manager.new_canvas();ac.width=au+ae;ac.height=af;var av=ac.getContext("2d");av.fillStyle=this.prefs.block_color;av.font=av.canvas.manager.default_font;av.textAlign="right";this.container_div.find(".yaxislabel").remove();if(an.data){if(!ar){av.translate(ae,0)}aD.draw(av,au,af,ao)}return new L(aA,aw,ac,an.data,an.message)}});var P=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.painter=I.VariantPainter};n(P.prototype,J.prototype,e.prototype);var S=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.track_config=new V({track:this,params:[{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:ac,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.painter=I.ReadPainter;this.make_name_popup_menu()};n(S.prototype,J.prototype,e.prototype);var 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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(j,w){var t=j("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var 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b=function(z,B,x,y,A){n.call(this,z,B,x,y,A)};t(b.prototype,n.prototype,{draw_element:function(Q,L,F,B,T,z,I,R,O){var F=data[i],H=F[0],P=F[1],A=F[2],K=F[3],D=Math.floor(Math.max(0,(P-T)*I)),G=Math.ceil(Math.min(O,Math.max(0,(A-T)*I))),C=(L==="Dense"?0:(0+B))*R,x,U,y=null,J=null;if(no_label){Q.fillStyle=block_color;Q.fillRect(D+left_offset,C+5,G-D,1)}else{var S=F[4],N=F[5],E=F[6];x=9;U=1;Q.fillRect(D+left_offset,C,G-D,x);if(L!=="Dense"&&K!==undefined&&P>T){Q.fillStyle=label_color;if(T===0&&D-Q.measureText(K).width<0){Q.textAlign="left";Q.fillText(K,G+2+left_offset,C+8)}else{Q.textAlign="right";Q.fillText(K,D-2+left_offset,C+8)}Q.fillStyle=block_color}var M=S+" / "+N;if(P>T&&Q.measureText(M).width<(G-D)){Q.fillStyle="white";Q.textAlign="center";Q.fillText(M,left_offset+D+(G-D)/2,C+8);Q.fillStyle=block_color}}}});var s=function(A,C,x,z,B,y){n.call(this,A,C,x,z,B);this.ref_seq=y};s.prototype.default_prefs=t({},n.prototype.default_prefs,{show_insertions:false});t(s.prototype,n.prototype,{get_row_height:function(){var x,y=this.mode;if(y==="Dense"){x=d}else{if(y==="Squish"){x=l}else{x=v;if(this.prefs.show_insertions){x*=2}}}return x},draw_read:function(T,O,K,Y,z,S,H,E,D){T.textAlign="center";var R=this,y=[Y,z],N=0,U=0,Q=0;ref_seq=this.ref_seq,char_width_px=T.canvas.manager.char_width_px;var ad=[];if((O==="Pack"||this.mode==="Auto")&&E!==undefined&&K>char_width_px){Q=Math.round(K/2)}if(!H){H=[[0,E.length]]}for(var L=0,W=H.length;L<W;L++){var I=H[L],A="MIDNSHP=X"[I[0]],M=I[1];if(A==="H"||A==="S"){N-=M}var F=S+N,ac=Math.floor(Math.max(0,(F-Y)*K)),G=Math.floor(Math.max(0,(F+M-Y)*K));if(ac===G){G+=1}switch(A){case"H":break;case"S":case"M":case"=":if(is_overlap([F,F+M],y)){var P=E.slice(U,U+M);if(Q>0){T.fillStyle=this.prefs.block_color;T.fillRect(ac-Q,D+1,G-ac,9);T.fillStyle=g;for(var 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ab=Math.floor(Math.max(0,(F+aa-Y)*K));T.fillText(P[aa],ab-(G-ac)/2,D)}}else{T.fillStyle="yellow";T.fillRect(C,D+(this.mode!=="Dense"?2:5),G-ac,(O!=="Dense"?e:r))}}else{if((O==="Pack"||this.mode==="Auto")&&E!==undefined&&K>char_width_px){ad[ad.length]={type:"text",data:[P.length,X,D+9]}}else{}}}U+=M;break;case"X":U+=M;break}}T.fillStyle="yellow";var Z,B,ae;for(var V=0;V<ad.length;V++){Z=ad[V];B=Z.type;ae=Z.data;if(B==="text"){T.save();T.font="bold "+T.font;T.fillText(ae[0],ae[1],ae[2]);T.restore()}else{if(B=="triangle"){p(T,ae[0],ae[1],ae[2])}}}},draw_element:function(Q,L,D,A,T,y,H,R,O){var G=D[0],P=D[1],z=D[2],I=D[3],C=Math.floor(Math.max(0,(P-T)*H)),E=Math.ceil(Math.min(O,Math.max(0,(z-T)*H))),B=(L==="Dense"?0:(0+A))*R,U=this.prefs.block_color,F=this.prefs.label_color,N=0;if((L==="Pack"||this.mode==="Auto")&&H>Q.canvas.manager.char_width_px){var N=Math.round(H/2)}Q.fillStyle=U;if(D[5] instanceof Array){var M=Math.floor(Math.max(0,(D[4][0]-T)*H)),K=Math.ceil(Math.min(O,Math.max(0,(D[4][1]-T)*H))),J=Math.floor(Math.max(0,(D[5][0]-T)*H)),x=Math.ceil(Math.min(O,Math.max(0,(D[5][1]-T)*H)));if(D[4][1]>=T&&D[4][0]<=y&&D[4][2]){this.draw_read(Q,L,H,T,y,D[4][0],D[4][2],D[4][3],B)}if(D[5][1]>=T&&D[5][0]<=y&&D[5][2]){this.draw_read(Q,L,H,T,y,D[5][0],D[5][2],D[5][3],B)}if(J>K){Q.fillStyle=g;o(Q,K-N,B+5,J-N,B+5)}}else{Q.fillStyle=U;this.draw_read(Q,L,H,T,y,P,D[4],D[5],B)}if(L==="Pack"&&P>T){Q.fillStyle=this.prefs.label_color;var S=1;if(S===0&&C-Q.measureText(I).width<0){Q.textAlign="left";Q.fillText(I,E+k-N,B+8)}else{Q.textAlign="right";Q.fillText(I,C-k-N,B+8)}Q.fillStyle=U}}});w.SummaryTreePainter=u;w.LinePainter=c;w.LinkedFeaturePainter=q;w.ReadPainter=s;w.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,U){var n=f("class").extend,p=f("slotting"),I=f("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"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")};n(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var C=function(ac,ad){ac.bind("drag",{handle:ad,relative:true},function(ah,ai){var ag=$(this).parent();var af=ag.children();var ae;for(ae=0;ae<af.length;ae++){if(ai.offsetY<$(af.get(ae)).position().top){break}}if(ae===af.length){if(this!==af.get(ae-1)){ag.append(this)}}else{if(this!==af.get(ae)){$(this).insertBefore(af.get(ae))}}}).bind("dragstart",function(){$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css("border","0px")})};U.sortable=C;var aa=16,D=9,A=20,P=D+2,w=100,F=12000,N=200,z=5,s=10,H=5000,t=100,m="There was an error in indexing this dataset. 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Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",q="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",d=10,r=5,y=5;function u(ac){return Math.round(ac*1000)/1000}var c=function(ac){this.num_elements=ac;this.clear()};n(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var O=function(ad,ac,ae){c.call(this,ad);this.track=ac;this.subset=(ae!==undefined?ae:true)};n(O.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am[am.length]=ac[ah].name}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,aj,an)})},get_data:function(ac,ag,ah,ad,af){var ae=this.get_data_from_cache(ac,ag,ah);if(ae){return ae}ae=this.load_data(ac,ag,ah,ad,af);this.set_data(ac,ag,ah,ae);return ae},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get_data_from_cache(ak,af,aj);if(!al){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=al.data[al.data.length-1][2]+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,aj,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,aj,am);new_data_available.resolve(am)});return new_data_available},get_data_from_cache:function(ac,ad,ae){return this.get(this.gen_key(ac,ad,ae))},set_data:function(ad,ae,af,ac){return this.set(this.gen_key(ad,ae,af),ac)},gen_key:function(ac,ae,af){var ad=ac+"_"+ae+"_"+af;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){O.call(this,ad,ac,ae)};n(E.prototype,O.prototype,c.prototype,{load_data:function(ae,ac,ag,ah,ad,af){if(ad>1){return}return O.prototype.load_data.call(this,ae,ac,ag,ah,ad,af)}});var Z=function(ac,af,ae,ad,ag){this.container=ac;this.chrom=null;this.vis_id=ae;this.dbkey=ad;this.title=af;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ag);this.canvas_manager=new ab(ac.get(0).ownerDocument);this.reset()};n(Z.prototype,{init:function(ag){var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to 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Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ad=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ag);this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.content_div.click(function(ah){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ah){ac.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ai)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ac.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){var ak=Math.round(-ai/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ac.content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX),width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ac.container.offset().left,ah=Math.max(al.pageX,am.startX)-ac.container.offset().left,ak=(ac.high-ac.low),aj=ac.viewport_container.width();ac.update_location(Math.round(ai/aj*ak)+ac.low,Math.round(ah/aj*ak)+ac.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ac.high-ac.low),aj=ac.viewport_container.width(),al=ac.low;ac.low=Math.round(ai/aj*ak)+al;ac.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,this.top_labeltrack));this.add_label_track(new Y(this,this.nav_labeltrack));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ad,ae){ad.num=t;$.extend(ad,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ac=this;$.ajax({url:chrom_url,data:ad,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ad.chrom);return}if(ag.reference){ac.add_label_track(new x(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+t+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+t+"</option>"}ac.chrom_select.html(aj);if(ae){ae()}ac.chrom_start_index=ag.start_index},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}})},change_chrom:function(ag,ad,ai){if(!ag||ag==="None"){return}var af=this;if(ag==="previous"){af.load_chroms({low:this.chrom_start_index-t});return}if(ag==="next"){af.load_chroms({low:this.chrom_start_index+t});return}var ah=$.grep(af.chrom_data,function(ak,al){return ak.chrom===ag})[0];if(ah===undefined){af.load_chroms({chrom:ag},function(){af.change_chrom(ag,ad,ai)});return}else{if(ag!==af.chrom){af.chrom=ag;af.chrom_select.val(af.chrom);af.max_high=ah.len-1;af.reset();af.request_redraw(true);for(var aj=0,ac=af.tracks.length;aj<ac;aj++){var ae=af.tracks[aj];if(ae.init){ae.init()}}}if(ad!==undefined&&ai!==undefined){af.low=Math.max(ad,0);af.high=Math.min(ai,af.max_high)}af.reset_overview();af.request_redraw()}},go_to:function(ag){var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0].replace(/,/g,""),10);af=parseInt(ah[1].replace(/,/g,""),10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_track:function(ac){ac.view=this;ac.track_id=this.track_id_counter;this.tracks.push(ac);if(ac.init){ac.init()}ac.container_div.attr("id","track_"+ac.track_id);C(ac.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1;this.update_intro_div()},add_label_track:function(ac){ac.view=this;this.label_tracks.push(ac)},remove_track:function(ad){this.has_changes=true;delete this.tracks[this.tracks.indexOf(ad)];this.num_tracks-=1;var ac=this;ad.container_div.fadeOut("slow",function(){$(this).remove();ac.update_intro_div()})},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad){var ac=this;requestAnimationFrame(function(){ac.redraw(ad)})},redraw:function(aj){var ah=this.low,ad=this.high;if(ah<this.max_low){ah=this.max_low}if(ad>this.max_high){ad=this.max_high}var ai=this.high-this.low;if(this.high!==0&&ai<this.min_separation){ad=ah+this.min_separation}this.low=Math.floor(ah);this.high=Math.ceil(ad);this.resolution=Math.pow(z,Math.ceil(Math.log((this.high-this.low)/N)/Math.log(z)));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=13;this.overview_box.css({left:ac,width:Math.max(ak,ag)}).show();if(ag<ak){this.overview_box.css("left",ac-(ak-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ag})}this.update_location(this.low,this.high);if(!aj){for(var ae=0,af=this.tracks.length;ae<af;ae++){if(this.tracks[ae]&&this.tracks[ae].enabled){this.tracks[ae].draw()}}for(ae=0,af=this.label_tracks.length;ae<af;ae++){this.label_tracks[ae].draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.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(ac){$.when(ac.get_overview_tile()).then(function(ad){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ad.canvas);view.overview_highlight.show().height(ad.canvas.height());view.overview_viewport.height(ad.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ac;view.has_changes=true;ac.set_is_overview(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 o=function(ae,ai){this.track=ae;this.name=ai.name;this.params=[];var ap=ai.params;for(var af=0;af<ap.length;af++){var ak=ap[af],ad=ak.name,ao=ak.label,ag=unescape(ak.html),aq=ak.value,am=ak.type;if(am==="number"){this.params[this.params.length]=new g(ad,ao,ag,aq,ak.min,ak.max)}else{if(am=="select"){this.params[this.params.length]=new K(ad,ao,ag,aq)}else{console.log("WARNING: unrecognized tool parameter type:",ad,am)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(at){at.stopPropagation()}).click(function(at){at.stopPropagation()}).bind("dblclick",function(at){at.stopPropagation()});var an=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var al=this.params;var aj=this;$.each(this.params,function(au,ax){var aw=$("<div>").addClass("param-row").appendTo(aj.parent_div);var at=$("<div>").addClass("param-label").text(ax.label).appendTo(aw);var av=$("<div/>").addClass("slider").html(ax.html).appendTo(aw);av.find(":input").val(ax.value);$("<div style='clear: both;'/>").appendTo(aw)});this.parent_div.find("input").click(function(){$(this).select()});var ar=$("<div>").addClass("param-row").appendTo(this.parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ar);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ar);var aj=this;ac.click(function(){aj.run_on_region()});ah.click(function(){aj.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ac={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ae=this.track,ad=ac.tool_id+ae.tool_region_and_parameters_str(ac.chrom,ac.low,ac.high),af;if(ae instanceof e){af=new R(ad,view,ae.hda_ldda,undefined,{},{},ae);af.change_mode(ae.mode)}this.track.add_track(af);af.content_div.text("Starting job.");this.run(ac,af,function(ag){af.dataset_id=ag.dataset_id;af.content_div.text("Running job.");af.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(G)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be 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ac}if(ad[this.index]<this.min){this.min=Math.floor(ad[this.index]);ac=true}if(ad[this.index]>this.max){this.max=Math.ceil(ad[this.index]);ac=true}return ac},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ae=function(ah,af){var ag=af-ah;return(ag<=2?0.01:1)};var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ae(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(am,at){this.track=am;this.filters=[];for(var an=0;an<at.length;an++){var ao=at[an],au=ao.name,ac=ao.type,af=ao.index,ar=ao.tool_id,aq=ao.tool_exp_name;if(ac==="int"||ac==="float"){this.filters[an]=new S(au,af,ar,aq)}else{console.log("ERROR: unsupported filter: ",au,ac)}}var ag=function(av,aw,ax){av.click(function(){var ay=aw.text();max=parseFloat(ax.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ax.slider("option","values")){input_size=2*input_size+1;multi_value=true}aw.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ay).appendTo(aw).focus().select().click(function(az){az.stopPropagation()}).blur(function(){$(this).remove();aw.text(ay)}).keyup(function(aD){if(aD.keyCode===27){$(this).trigger("blur")}else{if(aD.keyCode===13){var aB=ax.slider("option","min"),az=ax.slider("option","max"),aC=function(aE){return(isNaN(aE)||aE>az||aE<aB)},aA=$(this).val();if(!multi_value){aA=parseFloat(aA);if(aC(aA)){alert("Parameter value must be in the range ["+aB+"-"+az+"]");return $(this)}}else{aA=aA.split("-");aA=[parseFloat(aA[0]),parseFloat(aA[1])];if(aC(aA[0])||aC(aA[1])){alert("Parameter value must be in the range ["+aB+"-"+az+"]");return $(this)}}ax.slider((multi_value?"values":"value"),aA)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(av){av.stopPropagation()}).click(function(av){av.stopPropagation()}).bind("dblclick",function(av){av.stopPropagation()}).bind("keydown",function(av){av.stopPropagation()});var ap=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ak=this;$.each(this.filters,function(ay,aA){aA.container=$("<div/>").addClass("slider-row").appendTo(ap);var az=$("<div/>").addClass("elt-label").appendTo(aA.container);var ax=$("<span/>").addClass("slider-name").text(aA.name+" ").appendTo(az);var aw=$("<span/>");var aC=$("<span/>").addClass("slider-value").appendTo(az).append("[").append(aw).append("]");var av=$("<div/>").addClass("slider").appendTo(aA.container);aA.control_element=$("<div/>").attr("id",aA.name+"-filter-control").appendTo(av);var aB=[0,0];aA.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aD,aE){aB=aE.values;aw.text(aE.values[0]+"-"+aE.values[1]);setTimeout(function(){if(aE.values[0]==aB[0]&&aE.values[1]==aB[1]){var aF=aE.values;aw.text(aF[0]+"-"+aF[1]);aA.low=aF[0];aA.high=aF[1];ak.track.draw(true,true)}},50)},change:function(aD,aE){aA.control_element.slider("option","slide").call(aA.control_element,aD,aE)}});aA.slider=aA.control_element;aA.slider_label=aw;ag(aC,aw,aA.control_element);$("<div style='clear: both;'/>").appendTo(aA.container)});if(this.filters.length!==0){var ah=$("<div/>").addClass("param-row").appendTo(ap);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ah);var ae=this;aj.click(function(){ae.run_on_dataset()})}var al=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ai=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(al),ad=$("<select/>").attr("name","alpha_dropdown").appendTo(al);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ad);for(var an=0;an<this.filters.length;an++){$("<option/>").attr("value",an).text(this.filters[an].name).appendTo(ad)}ad.change(function(){$(this).children("option:selected").each(function(){var av=parseInt($(this).val());ak.alpha_filter=(av>=0?ak.filters[av]:null);ak.track.draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};n(X.prototype,{reset_filters:function(){for(var ac=0;ac<this.filters.length;ac++){filter=this.filters[ac];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!=ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!=ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var L=function(ad,ac){I.AlphaGenerator.call(this,ac);this.filter=ad};L.prototype.gen_alpha=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var W=function(ac){this.track=ac.track;this.params=ac.params;this.values={};if(ac.saved_values){this.restore_values(ac.saved_values)}this.onchange=ac.onchange};n(W.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var ad=this;var ac=$("<div />");$.each(this.params,function(ah,af){if(!af.hidden){var ae="param_"+ah;var am=$("<div class='form-row' />").appendTo(ac);am.append($("<label />").attr("for",ae).text(af.label+":"));if(af.type==="bool"){am.append($('<input type="checkbox" />').attr("id",ae).attr("name",ae).attr("checked",ad.values[af.key]))}else{if(af.type==="color"){var aj=ad.values[af.key];var ai=$("<input />").attr("id",ae).attr("name",ae).val(aj);var ak=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ag=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ak);var al=$("<div/>").appendTo(ag).farbtastic({width:100,height:100,callback:ai,color:aj});$("<div />").append(ai).append(ak).appendTo(am).bind("click",function(an){ak.css({left:$(this).position().left+($(ai).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ak.hide();$(document).unbind("click.color-picker")});an.stopPropagation()})}else{am.append($("<input />").attr("id",ae).attr("name",ae).val(ad.values[af.key]))}}}});return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange()}}});var b=function(ae,ad,ac,af){this.index=ae;this.low=ae*N*ad;this.high=(ae+1)*N*ad;this.resolution=ad;this.canvas=$("<div class='track-tile'/>").append(ac);this.data=af;this.stale=false};var l=function(ae,ad,ac,af,ag){b.call(this,ae,ad,ac,af);this.max_val=ag};var M=function(ae,ad,ac,ag,af){b.call(this,ae,ad,ac,ag);this.message=af};var j=function(ad,ac,ag,ae,af){this.name=ad;this.view=ac;this.parent_element=ag;this.data_url=(ae?ae:default_data_url);this.data_url_extra_params={};this.data_query_wait=(af?af:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").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 class='draghandle' />").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.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"ToolDataFeatureTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.initial_canvas=undefined;ac.content_div.css("height","auto");ac.container_div.removeClass("nodata error pending");if(!ac.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id,chrom:ac.view.chrom},function(ad){if(!ad||ad==="error"||ad.kind==="error"){ac.container_div.addClass("error");ac.content_div.text(m);if(ad.message){var af=ac.view.tracks.indexOf(ac);var ae=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ad.message+"</pre>",{Close:hide_modal})});ac.content_div.append(ae)}}else{if(ad==="no converter"){ac.container_div.addClass("error");ac.content_div.text(G)}else{if(ad==="no data"||(ad.data!==undefined&&(ad.data===null||ad.data.length===0))){ac.container_div.addClass("nodata");ac.content_div.text(B)}else{if(ad==="pending"){ac.container_div.addClass("pending");ac.content_div.text(q);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(ad.status==="data"){if(ad.valid_chroms){ac.valid_chroms=ad.valid_chroms;ac.make_name_popup_menu()}ac.content_div.text(V);if(ac.view.chrom){ac.content_div.text("");ac.content_div.css("height",ac.height_px+"px");ac.enabled=true;$.when(ac.predraw_init()).done(function(){ac.container_div.removeClass("nodata error pending");ac.draw()})}}}}}}})},predraw_init:function(){},update_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(aj,ah,ak){var ad=this,al=ad.view;this.filters_manager=(aj!==undefined?new X(this,aj):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ah!==undefined&&obj_length(ah)>0?new o(this,ah):undefined);this.is_overview=false;this.parent_track=ak;this.child_tracks=[];if(ad.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ad.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();ad.container_div.append(ad.child_tracks_container);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(ad.display_modes!==undefined){if(ad.mode_div===undefined){ad.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ad.header_div);var ae=(ad.track_config&&ad.track_config.values.mode?ad.track_config.values.mode:ad.display_modes[0]);ad.mode=ae;ad.mode_div.text(ae);var ac={};for(var af=0,ai=ad.display_modes.length;af<ai;af++){var ag=ad.display_modes[af];ac[ag]=function(am){return function(){ad.change_mode(am)}}(ag)}make_popupmenu(ad.mode_div,ac)}else{ad.mode_div.hide()}}this.make_name_popup_menu()};n(J.prototype,j.prototype,{change_mode:function(ad){var ac=this;ac.mode_div.text(ad);ac.mode=ad;ac.track_config.values.mode=ad;ac.tile_cache.clear();ac.draw()},make_name_popup_menu:function(){var ad=this;var ac={};ac[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ad.is_overview){ad.view.reset_overview()}else{ad.view.set_overview(ad)}};ac["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ad.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Track",ad.track_config.build_form(),{Cancel:aj,OK:ah})};if(ad.filters_available>0){var ag=(ad.filters_div.is(":visible")?"Hide filters":"Show filters");ac[ag]=function(){ad.filters_visible=(ad.filters_div.is(":visible"));if(ad.filters_visible){ad.filters_manager.reset_filters()}ad.filters_div.toggle();ad.make_name_popup_menu()}}if(ad.tool){var ag=(ad.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ac[ag]=function(){if(!ad.dynamic_tool_div.is(":visible")){ad.update_name(ad.name+ad.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ad.revert_name()}ad.dynamic_tool_div.toggle();ad.make_name_popup_menu()}}if(ad.valid_chroms){ac["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ad.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ae=view;var af=function(){$("#no-tracks").show()};if(this.parent_track){ae=this.parent_track;af=function(){}}ac.Remove=function(){ae.remove_track(ad);if(ae.num_tracks===0){af()}};make_popupmenu(ad.name_div,ac)},set_is_overview:function(ac){this.is_overview=ac;this.make_name_popup_menu()},get_overview_tile:function(){var ac=this;view=ac.view,resolution=Math.pow(z,Math.ceil(Math.log((view.max_high-view.max_low)/N)/Math.log(z))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ac.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ac.data_url_extra_params)).then(function(ad){var af=ac._gen_tile_cache_key(view_width,w_scale,0),ah=ac.tile_cache.get(af);if(!ah){ah=ac.draw_tile(ad,resolution,0,w_scale);ac.tile_cache.set(af,ah)}var ak=$(ah.canvas.find("canvas")),ag=ak.clone(),aj=ak.get(0).getContext("2d"),ae=ag.get(0).getContext("2d"),ai=aj.getImageData(0,0,aj.canvas.width,aj.canvas.height);ae.putImageData(ai,-ac.left_offset,(ah.data.dataset_type==="summary_tree"?P:0));new_tile=new b(-1,resolution,ag);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},draw:function(ae,an){if(!this.dataset_id){return}var am=this.view.low,ai=this.view.high,ak=ai-am,af=this.view.container.width(),aq=af/ak,ah=this.view.resolution,ap=$("<div style='position: relative;'></div>");if(!an){this.content_div.children().remove()}this.content_div.append(ap);this.max_height=0;var ad=Math.floor(am/ah/N);var al=true;var ao=[];var ac=0;while((ad*N*ah)<ai){tile=this.draw_helper(ae,af,ad,ah,ap,aq);if(tile){ao.push(tile)}else{al=false}ad+=1;ac++}var ag=this;if(al){ag.postdraw_actions(ao,af,aq,an)}for(var aj=0;aj<this.child_tracks.length;aj++){this.child_tracks[aj].draw(ae,an)}},postdraw_actions:function(ag,ah,ai,ac){var ae=this;var af=false;for(var ad=0;ad<ag.length;ad++){if(ag[ad].message){af=true;break}}if(af){for(var ad=0;ad<ag.length;ad++){tile=ag[ad];if(!tile.message){tile.canvas.css("padding-top",A)}}}},draw_helper:function(ad,ae,af,ai,ao,at,ap,aj){var ag=this,an=this._gen_tile_cache_key(ae,at,af),ak=af*N*ai,ar=ak+N*ai;var al=(ad?undefined:ag.tile_cache.get(an));if(al){ag.show_tile(al,ao,at);return al}var am=function(au){return("isResolved" in au)};var ah=true;var ac=ag.data_manager.get_data(ak,ar,ag.mode,ai,ag.data_url_extra_params);if(am(ac)){ah=false}var aq;if(view.reference_track&&at>view.canvas_manager.char_width_px){aq=view.reference_track.data_manager.get_data(ak,ar,ag.mode,ai,view.reference_track.data_url_extra_params);if(am(aq)){ah=false}}if(ah){n(ac,aj);var al=ag.draw_tile(ac,ai,af,at,aq);ag.tile_cache.set(an,al);if(al!==undefined){ag.show_tile(al,ao,at)}return al}$.when(ac,aq).then(function(){view.request_redraw()});return null},show_tile:function(aj,al,am){var ae=this,ad=aj.canvas,ai=ad;if(aj.message){var an=$("<div/>"),ak=$("<div/>").addClass("tile-message").text(aj.message).css({height:A-1,width:aj.canvas.width}).appendTo(an),ag=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ak),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ak);an.append(ad);ai=an;ag.click(function(){aj.stale=true;ae.data_manager.get_more_data(aj.low,aj.high,ae.mode,aj.resolution,{},ae.data_manager.DEEP_DATA_REQ);ae.draw()}).dblclick(function(ao){ao.stopPropagation()});ac.click(function(){aj.stale=true;ae.data_manager.get_more_data(aj.low,aj.high,ae.mode,aj.resolution,{},ae.data_manager.BROAD_DATA_REQ);ae.draw()}).dblclick(function(ao){ao.stopPropagation()})}var ah=this.view.high-this.view.low,af=(aj.low-this.view.low)*am;if(this.left_offset){af-=this.left_offset}ai.css({position:"absolute",top:0,left:af,height:""});al.append(ai);ae.max_height=Math.max(ae.max_height,ai.height());ae.content_div.css("height",ae.max_height+"px");al.children().css("height",ae.max_height+"px")},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},add_track:function(ac){ac.track_id=this.track_id+"_"+this.child_tracks.length;ac.container_div.attr("id","track_"+ac.track_id);this.child_tracks_container.append(ac.container_div);C(ac.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(ac);this.view.has_changes=true},remove_track:function(ac){ac.container_div.fadeOut("slow",function(){$(this).remove()})}});var Y=function(ac,ad){this.hidden=true;j.call(this,null,ac,ad);this.container_div.addClass("label-track")};n(Y.prototype,j.prototype,{draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var x=function(ac){this.hidden=true;j.call(this,null,ac,ac.top_labeltrack);J.call(this);ac.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:ac.dbkey};this.data_manager=new E(y,this,false);this.tile_cache=new c(r)};n(x.prototype,J.prototype,{draw_tile:function(ak,ah,ad,am){var ag=this,ae=N*ah;if(am>this.view.canvas_manager.char_width_px){if(ak===null){ag.content_div.css("height","0px");return}var af=this.view.canvas_manager.new_canvas();var al=af.getContext("2d");af.width=Math.ceil(ae*am+ag.left_offset);af.height=ag.height_px;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.round(ai*am);al.fillText(ak[ai],ac+ag.left_offset,10)}return new b(ad,ah,af,ak)}this.content_div.css("height","0px")}});var k=function(ag,ae,ah,ac,af){var ad=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ag,ae,ae.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ah;this.dataset_id=ac;this.original_dataset_id=ac;this.data_manager=new O(y,this);this.tile_cache=new c(r);this.track_config=new W({track:this,params:[{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:af,onchange:function(){ad.vertical_range=ad.prefs.max_value-ad.prefs.min_value;$("#linetrack_"+ad.track_id+"_minval").text(ad.prefs.min_value);$("#linetrack_"+ad.track_id+"_maxval").text(ad.prefs.max_value);ad.tile_cache.clear();ad.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,J.prototype,{add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){af=true;ad.show()},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.content_div).css("height",ag);ac.height_px=ag;ac.draw(true)}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.track_config.values.height=ac.height_px}).appendTo(ac.container_div)},predraw_init:function(){var ac=this,ad=ac.view.tracks.indexOf(ac);ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ae){ac.container_div.addClass("line-track");var ag=ae.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){ac.prefs.min_value=ag.min;ac.prefs.max_value=ag.max;$("#track_"+ad+"_minval").val(ac.prefs.min_value);$("#track_"+ad+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ad+"_minval").text(u(ac.prefs.min_value));var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ad+"_maxval").text(u(ac.prefs.max_value));af.css({position:"absolute",top:"24px",left:"10px"});af.prependTo(ac.container_div);ah.css({position:"absolute",bottom:"2px",left:"10px"});ah.prependTo(ac.container_div)})},draw_tile:function(am,ag,ad,al){if(this.vertical_range===undefined){return}var ah=ad*N*ag,af=N*ag,ac=Math.ceil(af*al),aj=this.height_px;var ae=this.view.canvas_manager.new_canvas();ae.width=ac,ae.height=aj;var ak=ae.getContext("2d");var ai=new I.LinePainter(am.data,ah,ah+af,this.prefs,this.mode);ai.draw(ak,ac,aj);return new b(ad,ag,ae,am.data)}});var e=function(ac,ah,ag,ak,aj,ae,af,ai){var ad=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new W({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){ad.tile_cache.clear();ad.draw()}});this.prefs=this.track_config.values;j.call(this,ac,ah,ah.viewport_container);J.call(this,ae,af,ai);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ag;this.dataset_id=ak;this.original_dataset_id=ak;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new O(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{postdraw_actions:function(ar,ac,at,aq){J.prototype.postdraw_actions.call(this,ar,aq);var af=this;if(aq){var ah=af.content_div.children();var ai=false;for(var ag=ah.length-1,am=0;ag>=am;ag--){var ae=$(ah[ag]);if(ai){ae.remove()}else{if(ae.children().length!==0){ai=true}}}}if(af.mode=="Histogram"){var al=-1;for(var ag=0;ag<ar.length;ag++){var ap=ar[ag].max_val;if(ap>al){al=ap}}for(var ag=0;ag<ar.length;ag++){var ao=ar[ag];if(ao.max_val!==al){ao.canvas.remove();af.draw_helper(true,ac,ao.index,ao.resolution,ao.canvas.parent(),at,[],{max:al})}}}if(af.filters_manager){var ad=af.filters_manager.filters;for(var ak=0;ak<ad.length;ak++){ad[ak].update_ui_elt()}var aj=false,an;for(var ag=0;ag<ar.length;ag++){if(ar[ag].data.length){an=ar[ag].data[0];for(var ak=0;ak<ad.length;ak++){if(ad[ak].applies_to(an)){aj=true;break}}}}if(af.filters_available!==aj){af.filters_available=aj;if(!af.filters_available){af.filters_div.hide()}af.make_name_popup_menu()}}},update_auto_mode:function(ac){if(this.mode=="Auto"){if(ac=="no_detail"){ac="feature spans"}else{if(ac=="summary_tree"){ac="coverage histogram"}}this.mode_div.text("Auto ("+ac+")")}},incremental_slots:function(ag,ad,af){var ae=this.view.canvas_manager.dummy_context,ac=this.inc_slots[ag];if(!ac||(ac.mode!==af)){ac=new (p.FeatureSlotter)(ag,af==="Pack",w,function(ah){return ae.measureText(ah)});ac.mode=af;this.inc_slots[ag]=ac}return ac.slot_features(ad)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},draw_tile:function(ap,ay,aC,al,af){var av=this,aE=aC*N*ay,ad=(aC+1)*N*ay,ar=ad-aE,aw=Math.ceil(ar*al),at=this.mode,aI=25,ag=this.left_offset,aq,ah;if(at==="Auto"){if(ap.dataset_type==="summary_tree"){at=ap.dataset_type}else{if(ap.extra_info==="no_detail"){at="no_detail"}else{var aH=ap.data;if(this.view.high-this.view.low>F){at="Squish"}else{at="Pack"}}}this.update_auto_mode(at)}if(at==="summary_tree"||at==="Histogram"){ah=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ac=$("<div />").addClass("yaxislabel");ac.text(ap.max);ac.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ac.prependTo(this.container_div);var ae=this.view.canvas_manager.new_canvas();ae.width=aw+ag;ae.height=ah+P;if(ap.dataset_type!="summary_tree"){var am=this.get_summary_tree_data(ap.data,aE,ad,200);if(ap.max){am.max=ap.max}ap=am}var aF=new I.SummaryTreePainter(ap,aE,ad,this.prefs);var ax=ae.getContext("2d");ax.translate(ag,P);aF.draw(ax,aw,ah);return new l(aC,ay,ae,ap.data,ap.max)}var aq,aj=1;if(at==="no_detail"||at==="Squish"||at==="Pack"){aj=this.incremental_slots(al,ap.data,at);aq=this.inc_slots[al].slots}var ak=[];if(ap.data){var an=this.filters_manager.filters;for(var az=0,aB=ap.data.length;az<aB;az++){var ai=ap.data[az];var aA=false;var ao;for(var aD=0,aG=an.length;aD<aG;aD++){ao=an[aD];ao.update_attrs(ai);if(!ao.keep(ai)){aA=true;break}}if(!aA){ak.push(ai)}}}var au=(this.filters_manager.alpha_filter?new L(this.filters_manager.alpha_filter):null);var aF=new (this.painter)(ak,aE,ad,this.prefs,at,au,af);var ah=Math.max(aa,aF.get_required_height(aj));var ae=this.view.canvas_manager.new_canvas();ae.width=aw+ag;ae.height=ah;var ax=ae.getContext("2d");ax.fillStyle=this.prefs.block_color;ax.font=ax.canvas.manager.default_font;ax.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ap.data){ax.translate(ag,0);aF.draw(ax,aw,ah,aq)}return new M(aC,ay,ae,ap.data,ap.message)}});var Q=function(af,ad,ah,ac,ae,ag){e.call(this,af,ad,ah,ac,ae,ag);this.painter=I.VariantPainter};n(Q.prototype,J.prototype,e.prototype);var T=function(af,ad,ah,ac,ae,ag){e.call(this,af,ad,ah,ac,ae,ag);this.track_config=new W({track:this,params:[{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:ae,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.painter=I.ReadPainter;this.make_name_popup_menu()};n(T.prototype,J.prototype,e.prototype);var R=function(ag,ae,ai,ac,af,ah,ad){e.call(this,ag,ae,ai,ac,af,ah,{},ad);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(R.prototype,J.prototype,e.prototype,{predraw_init:function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=H;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}});U.View=Z;U.LineTrack=k;U.FeatureTrack=e;U.ReadTrack=T};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,x){var u=k("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=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(y){this.default_alpha=(y?y:1)};g.prototype.gen_alpha=function(y){return this.default_alpha};var n=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};n.prototype.default_prefs={};var v=function(A,C,y,z,B){n.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.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(y,C,E,F,A){n.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};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(B,D,y,A,C,z){n.call(this,B,D,y,A,C);this.alpha_generator=(z?z:new g())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(z){var y=y_scale=this.get_row_height(),A=this.mode;if(A==="no_detail"||A==="Squish"||A==="Pack"){y=z*y_scale}return y+Math.max(Math.round(y_scale/2),5)},draw:function(K,B,J,G){var E=this.data,H=this.view_start,L=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var O=this.view_end-this.view_start,N=B/O,A=this.get_row_height();for(var D=0,F=E.length;D<F;D++){var M=E[D],C=M[0],y=M[1],z=M[2],I=(G&&G[C]!==undefined?G[C]:null);if((y<L&&z>H)&&(this.mode=="Dense"||I!==null)){this.draw_element(K,this.mode,M,I,H,L,N,A,B)}}K.restore()},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.")}});var d=10,j=3,m=5,w=10,f=1,s=3,e=3,a=9,l=2,h="#ccc";var r=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=d}else{if(z==="no_detail"){y=j}else{if(z==="Squish"){y=m}else{y=w}}}return y},draw_element:function(K,D,S,F,M,ac,ag,ah,y){var P=S[0],ae=S[1],W=S[2],N=S[3],X=Math.floor(Math.max(0,(ae-M)*ag)),L=Math.ceil(Math.min(y,Math.max(0,(W-M)*ag))),V=(D==="Dense"?0:(0+F))*ah,J,aa,O=null,ai=null,B=this.prefs.block_color,Z=this.prefs.label_color;K.globalAlpha=this.alpha_generator.gen_alpha(S);if(D=="Dense"){F=1}if(D==="no_detail"){K.fillStyle=B;K.fillRect(X,V+5,L-X,f)}else{var I=S[4],U=S[5],Y=S[6],C=S[7];if(U&&Y){O=Math.floor(Math.max(0,(U-M)*ag));ai=Math.ceil(Math.min(y,Math.max(0,(Y-M)*ag)))}var af,Q;if(D==="Squish"||D==="Dense"){af=1;Q=e}else{af=5;Q=a}if(!C){if(S.strand){if(S.strand==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(S.strand==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}}else{K.fillStyle=B}K.fillRect(X,V,L-X,Q)}else{var H,R;if(D==="Squish"||D==="Dense"){K.fillStyle=h;H=V+Math.floor(e/2)+1;R=1}else{if(I){var H=V;var R=Q;if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand")}}}else{K.fillStyle=h;H+=(e/2)+1;R=1}}K.fillRect(X,H,L-X,R);for(var ad=0,A=C.length;ad<A;ad++){var E=C[ad],z=Math.floor(Math.max(0,(E[0]-M)*ag)),T=Math.ceil(Math.min(y,Math.max((E[1]-M)*ag)));if(z>T){continue}K.fillStyle=B;K.fillRect(z,V+(Q-af)/2+1,T-z,af);if(O!==undefined&&Y>U&&!(z>ai||T<O)){var ab=Math.max(z,O),G=Math.min(T,ai);K.fillRect(ab,V+1,G-ab,Q);if(C.length==1&&D=="Pack"){if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}if(ab+14<G){ab+=2;G-=2}K.fillRect(ab,V+1,G-ab,Q)}}}}if(D==="Pack"&&ae>M){K.fillStyle=Z;if(M===0&&X-K.measureText(N).width<0){K.textAlign="left";K.fillText(N,L+l,V+8)}else{K.textAlign="right";K.fillText(N,X-l,V+8)}}}K.globalAlpha=1}});var b=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(b.prototype,o.prototype,{draw_element:function(R,M,G,C,U,A,J,S,P){var G=data[i],I=G[0],Q=G[1],B=G[2],L=G[3],E=Math.floor(Math.max(0,(Q-U)*J)),H=Math.ceil(Math.min(P,Math.max(0,(B-U)*J))),D=(M==="Dense"?0:(0+C))*S,y,V,z=null,K=null;if(no_label){R.fillStyle=block_color;R.fillRect(E+left_offset,D+5,H-E,1)}else{var T=G[4],O=G[5],F=G[6];y=9;V=1;R.fillRect(E+left_offset,D,H-E,y);if(M!=="Dense"&&L!==undefined&&Q>U){R.fillStyle=label_color;if(U===0&&E-R.measureText(L).width<0){R.textAlign="left";R.fillText(L,H+2+left_offset,D+8)}else{R.textAlign="right";R.fillText(L,E-2+left_offset,D+8)}R.fillStyle=block_color}var N=T+" / "+O;if(Q>U&&R.measureText(N).width<(H-E)){R.fillStyle="white";R.textAlign="center";R.fillText(N,left_offset+E+(H-E)/2,D+8);R.fillStyle=block_color}}}});var t=function(C,E,y,B,D,z,A){o.call(this,C,E,y,B,D,z);this.ref_seq=A};t.prototype.default_prefs=u({},o.prototype.default_prefs,{show_insertions:false});u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=d}else{if(z==="Squish"){y=m}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0;ref_seq=this.ref_seq,char_width_px=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=h;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&ref_seq){var K=ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=h;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:s))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){ae[ae.length]={type:"text",data:[Q.length,Y,E+9]}}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){q(U,af[0],af[1],af[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,V=this.prefs.block_color,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}R.fillStyle=V;if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,U,z,E[4][0],E[4][2],E[4][3],C)}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,U,z,E[5][0],E[5][2],E[5][3],C)}if(K>L){R.fillStyle=h;p(R,L-O,C+5,K-O,C+5)}}else{R.fillStyle=V;this.draw_read(R,M,I,U,z,Q,E[4],E[5],C)}if(M==="Pack"&&Q>U){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+l-O,C+8)}else{R.textAlign="right";R.fillText(J,D-l-O,C+8)}R.fillStyle=V}}});x.AlphaGenerator=g;x.SummaryTreePainter=v;x.LinePainter=c;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.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 Aug 22 16:31:50 2011 -0400 +++ b/static/scripts/trackster.js Tue Aug 23 17:21:37 2011 -0400 @@ -24,7 +24,7 @@ }; /** - * Find browser's reeuestAnimationFrame method or fallback on a setTimeout + * Find browser's requestAnimationFrame method or fallback on a setTimeout */ var requestAnimationFrame = (function(){ return window.requestAnimationFrame || @@ -35,7 +35,7 @@ function( callback, element ) { window.setTimeout(callback, 1000 / 60); }; - })(); +})(); /** @@ -1197,6 +1197,7 @@ // Name to use for filter when building expression for tool. this.tool_exp_name = tool_exp_name; }; + /** * Number filters have a min, max as well as a low, high; low and high are used */ @@ -1379,7 +1380,9 @@ }); }; - // Create filtering div. + // + // Create parent div. + // this.parent_div = $("<div/>").addClass("filters").hide(); // Disable dragging, double clicking, keys on div so that actions on slider do not impact viz. this.parent_div.bind("drag", function(e) { @@ -1391,12 +1394,17 @@ }).bind("keydown", function(e) { e.stopPropagation(); }); + + // + // Create sliders div. + // + 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(manager.parent_div); + filter.container = $("<div/>").addClass("slider-row").appendTo(sliders_div); // Set up filter label (name, values). - var filter_label = $("<div/>").addClass("slider-label").appendTo(filter.container) + var filter_label = $("<div/>").addClass("elt-label").appendTo(filter.container) var name_span = $("<span/>").addClass("slider-name").text(filter.name + " ").appendTo(filter_label); var values_span = $("<span/>"); var values_span_container = $("<span/>").addClass("slider-value").appendTo(filter_label).append("[").append(values_span).append("]"); @@ -1414,6 +1422,7 @@ // // Always update UI values, but set timeout for doing more--especially drawing-- // so that viz is more responsive. + // TODO: remove this because it's no longer necessary as we have requestAnimationFrame(). // prev_values = ui.values; values_span.text(ui.values[0] + "-" + ui.values[1]); @@ -1445,25 +1454,52 @@ }); // Add button to filter complete dataset. - if (this.filters.length != 0) { - var run_buttons_row = $("<div>").addClass("param-row").appendTo(this.parent_div); - var run_on_dataset_button = $("<input type='submit'>").attr("value", "Run on complete dataset").appendTo(run_buttons_row); + if (this.filters.length !== 0) { + var run_buttons_row = $("<div/>").addClass("param-row").appendTo(sliders_div); + var run_on_dataset_button = $("<input type='submit'/>").attr("value", "Run on complete dataset").appendTo(run_buttons_row); var filter_manager = this; run_on_dataset_button.click( function() { filter_manager.run_on_dataset(); }); } + + // + // Create filtering display controls. + // + 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.draw(true, true); + }) + }); + + // Clear floating. + // Add to clear floating layout. + $("<div style='clear: both;'/>").appendTo(this.parent_div); }; extend(FiltersManager.prototype, { /** - * Reset filters to min and max. + * Reset filters so that they do not impact track display. */ reset_filters: function() { for (var i = 0; i < this.filters.length; i++) { filter = this.filters[i]; filter.slider.slider("option", "values", [filter.min, filter.max]); } + this.alpha_filter = null; }, run_on_dataset: function() { // Get or create dictionary item. @@ -1551,6 +1587,24 @@ }); /** + * Generates alpha values based on filter and feature's value for filter. + */ +var FilterAlphaGenerator = function(filter, default_alpha) { + painters.AlphaGenerator.call(this, default_alpha); + this.filter = filter; +}; + +FilterAlphaGenerator.prototype.gen_alpha = function(feature_data) { + // If filter is not initalized yet, return default alpha. + if (this.filter.high === Number.MAX_VALUE || this.filter.low === -Number.MAX_VALUE || this.filter.low === this.filter.high) { + return this.default_alpha; + } + + // Alpha 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 ) ); +}; + +/** * Container for track configuration data. */ var TrackConfig = function( options ) { @@ -1562,7 +1616,7 @@ } this.onchange = options.onchange } -extend( TrackConfig.prototype, { +extend(TrackConfig.prototype, { restore_values: function( values ) { var track_config = this; $.each( this.params, function( index, param ) { @@ -2860,7 +2914,7 @@ slots = this.inc_slots[w_scale].slots; } - // Filter features + // Filter features. var filtered = []; if ( result.data ) { var filters = this.filters_manager.filters; @@ -2877,14 +2931,15 @@ } } if (!hide_feature) { - filtered.push( feature ); + filtered.push(feature); } } - } + } - // Create painter, and canvas of sufficient size to contain all features + // 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); // 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, ref_seq); + var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_generator, ref_seq); var required_height = Math.max(MIN_TRACK_HEIGHT, painter.get_required_height(slots_required)); var canvas = this.view.canvas_manager.new_canvas(); @@ -3213,11 +3268,25 @@ }; /** + * Base class for all alpha generators. + */ +var AlphaGenerator = function(default_alpha) { + this.default_alpha = (default_alpha ? default_alpha : 1); +}; + +/** + * Base method for generating an alpha channel value; returns default alpha if not implemented. + */ +AlphaGenerator.prototype.gen_alpha = function(data) { + return this.default_alpha; +}; + +/** * Base class for painters * * -- Mode and prefs are both optional */ -var Painter = function( data, view_start, view_end, prefs, mode ) { +var Painter = function(data, view_start, view_end, prefs, mode) { // Data and data properties this.data = data; // View @@ -3233,13 +3302,13 @@ /** * SummaryTreePainter, a histogram showing number of intervals in a region */ -var SummaryTreePainter = function( data, view_start, view_end, prefs, mode ) { - Painter.call( this, data, view_start, view_end, prefs, mode ); +var SummaryTreePainter = function(data, view_start, view_end, prefs, mode) { + Painter.call(this, data, view_start, view_end, prefs, mode); } SummaryTreePainter.prototype.default_prefs = { show_counts: false }; -SummaryTreePainter.prototype.draw = function( ctx, width, height ) { +SummaryTreePainter.prototype.draw = function(ctx, width, height) { var view_start = this.view_start, view_range = this.view_end - this.view_start, @@ -3276,7 +3345,7 @@ ctx.restore(); } -var LinePainter = function( data, view_start, view_end, prefs, mode ) { +var LinePainter = function(data, view_start, view_end, prefs, mode) { Painter.call( this, data, view_start, view_end, prefs, mode ); if ( this.prefs.min_value === undefined ) { var min_value = Infinity; @@ -3296,7 +3365,7 @@ LinePainter.prototype.default_prefs = { min_value: undefined, max_value: undefined, mode: "Histogram", color: "#000", overflow_color: "#F66" }; -LinePainter.prototype.draw = function( ctx, width, height ) { +LinePainter.prototype.draw = function(ctx, width, height) { var in_path = false, min_value = this.prefs.min_value, @@ -3406,14 +3475,14 @@ /** * 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) { +var FeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_generator) { Painter.call(this, data, view_start, view_end, prefs, mode); + this.alpha_generator = (alpha_generator ? alpha_generator : new AlphaGenerator()); } FeaturePainter.prototype.default_prefs = { block_color: "#FFF", connector_color: "#FFF" }; -extend(FeaturePainter.prototype, { - +extend(FeaturePainter.prototype, { get_required_height: function(rows_required) { // y_scale is the height per row var required_height = y_scale = this.get_row_height(), mode = this.mode; @@ -3479,9 +3548,9 @@ LABEL_SPACING = 2, CONNECTOR_COLOR = "#ccc"; -var LinkedFeaturePainter = function(data, view_start, view_end, prefs, mode) { - FeaturePainter.call(this, data, view_start, view_end, prefs, mode); -} +var LinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_generator) { + FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_generator); +}; extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, { @@ -3518,18 +3587,15 @@ f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, thickness, y_start, thick_start = null, thick_end = null, + // TODO: is there any reason why block, label color cannot be set at the Painter level? block_color = this.prefs.block_color, label_color = this.prefs.label_color; + + // Set global alpha. + ctx.globalAlpha = this.alpha_generator.gen_alpha(feature); - // Dense mode displays the same for all data. - /* - if (mode === "Dense") { - ctx.fillStyle = block_color; - ctx.fillRect(f_start, y_center, f_end - f_start, DENSE_FEATURE_HEIGHT); - } - */ - - if ( mode == "Dense" ) { + // In dense mode, put all data in top slot. + if (mode == "Dense") { slot = 1; } @@ -3626,8 +3692,7 @@ 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); + 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, // draw arrows over it if in pack mode @@ -3658,15 +3723,18 @@ ctx.textAlign = "right"; ctx.fillText(feature_name, f_start - LABEL_SPACING, y_center + 8); } - ctx.fillStyle = block_color; + //ctx.fillStyle = block_color; } } + + // Reset global alpha. + ctx.globalAlpha = 1; } }); -var VariantPainter = function(data, view_start, view_end, prefs, mode) { - FeaturePainter.call(this, data, view_start, view_end, prefs, mode); +var VariantPainter = function(data, view_start, view_end, prefs, mode, alpha_generator) { + FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_generator); } extend(VariantPainter.prototype, FeaturePainter.prototype, { @@ -3720,8 +3788,8 @@ } }); -var ReadPainter = function(data, view_start, view_end, prefs, mode, ref_seq) { - FeaturePainter.call(this, data, view_start, view_end, prefs, mode); +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); this.ref_seq = ref_seq; }; @@ -4007,6 +4075,7 @@ } }); +exports.AlphaGenerator = AlphaGenerator; 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.

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commit/galaxy-central: greg: Add the ability to switch between tool shed repository revsions when viewing tool metadata.
by Bitbucket 22 Aug '11

22 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b1f22f337651/ changeset: b1f22f337651 user: greg date: 2011-08-22 22:31:50 summary: Add the ability to switch between tool shed repository revsions when viewing tool metadata. affected #: 3 files (1.5 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Mon Aug 22 16:19:49 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Mon Aug 22 16:31:50 2011 -0400 @@ -1157,12 +1157,17 @@ tool = None break is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) + changeset_revision_select_field = build_changeset_revision_select_field( trans, + repository, + selected_value=changeset_revision, + add_id_to_name=False ) return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako", repository=repository, tool=tool, metadata=metadata, changeset_revision=changeset_revision, revision_label=revision_label, + changeset_revision_select_field=changeset_revision_select_field, is_malicious=is_malicious, message=message, status=status ) --- a/templates/webapps/community/repository/manage_repository.mako Mon Aug 22 16:19:49 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Mon Aug 22 16:31:50 2011 -0400 @@ -19,7 +19,7 @@ browse_label = 'Browse or delete repository files' else: browse_label = 'Browse repository files' - can_set_malicious = metadata and can_set_metadata and is_admin + can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip %><%! --- a/templates/webapps/community/repository/view_tool_metadata.mako Mon Aug 22 16:19:49 2011 -0400 +++ b/templates/webapps/community/repository/view_tool_metadata.mako Mon Aug 22 16:31:50 2011 -0400 @@ -71,14 +71,31 @@ <div class="toolForm"><div class="toolFormTitle">Repository revision</div><div class="toolFormBody"> - <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> - %else: - ${revision_label} - %endif - </div> + %if len( changeset_revision_select_field.options ) > 1: + <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=metadata[ 'id' ] )}" method="post" > + <div class="form-row"> + <% + if changeset_revision == repository.tip: + tip_str = 'repository tip' + else: + tip_str = '' + %> + ${changeset_revision_select_field.get_html()} <i>${tip_str}</i> + <div class="toolParamHelp" style="clear: both;"> + Select a revision to inspect and download versions of tools from this repository. + </div> + </div> + </form> + %else: + <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> + %else: + ${revision_label} + %endif + </div> + %endif </div></div><p/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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