galaxy-commits July 2011

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commit/galaxy-central: jgoecks: Trackster: implement start_val parameter for data providers and use parameter to provide incremental fetching of data. Only 'deep' fetching is currently supported.
by Bitbucket 06 Jul '11

06 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/75eceb82013e/ changeset: 75eceb82013e user: jgoecks date: 2011-07-06 16:20:57 summary: Trackster: implement start_val parameter for data providers and use parameter to provide incremental fetching of data. Only 'deep' fetching is currently supported. affected #: 4 files (1.4 KB) --- a/lib/galaxy/visualization/tracks/data_providers.py Wed Jul 06 09:52:28 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Wed Jul 06 10:20:57 2011 -0400 @@ -72,10 +72,11 @@ # Override. pass - def get_data( self, chrom, start, end, max_vals=None, **kwargs ): + def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): """ - Returns data in region defined by chrom, start, and end. If max_vals - is set, returns at most max_vals. + Returns data in region defined by chrom, start, and end. start_val and + max_vals are used to denote the data to return: start_val is the first value to + return and max_vals indicates the number of values to return. """ # Override. pass @@ -215,7 +216,7 @@ # Cleanup. bamfile.close() - def get_data( self, chrom, start, end, max_vals=sys.maxint, **kwargs ): + def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ): """ Fetch reads in the region. @@ -253,8 +254,10 @@ # Encode reads as list of lists. results = [] paired_pending = {} - for read in data: - if len(results) > max_vals: + for count, read in enumerate( data ): + if count < start_val: + continue + if count-start_val >= max_vals: message = ERROR_MAX_VALS % ( max_vals, "reads" ) break qname = read.qname @@ -319,7 +322,7 @@ f.close() return all_dat is not None - def get_data( self, chrom, start, end, max_vals=None, **kwargs ): + def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): # Bigwig has the possibility of it being a standalone bigwig file, in which case we use # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset f, bbi = self._get_dataset() @@ -481,11 +484,14 @@ return tabix.fetch(reference=chrom, start=start, end=end) - def get_data( self, chrom, start, end, max_vals=None, **kwargs ): + def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): iterator = self.get_iterator( chrom, start, end ) - return self.process_data( iterator, max_vals, **kwargs ) - + return self.process_data( iterator, start_val, max_vals, **kwargs ) + class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ): + """ + Interval index files used only for GFF files. + """ col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } def write_data_to_file( self, chrom, start, end, filename ): @@ -501,12 +507,11 @@ out.write(interval.raw_line + '\n') out.close() - def get_data( self, chrom, start, end, max_vals=sys.maxint, **kwargs ): + def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ): start, end = int(start), int(end) source = open( self.original_dataset.file_name ) index = Indexes( self.converted_dataset.file_name ) results = [] - count = 0 message = None # If chrom is not found in indexes, try removing the first three @@ -525,14 +530,15 @@ # filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) no_detail = ( "no_detail" in kwargs ) - for start, end, offset in index.find(chrom, start, end): - if count >= max_vals: + for count, val in enumerate( index.find(chrom, start, end) ): + start, end, offset = val[0], val[1], val[2] + if count < start_val: + continue + if count-start_val >= max_vals: message = ERROR_MAX_VALS % ( max_vals, "features" ) break - count += 1 source.seek( offset ) # TODO: can we use column metadata to fill out payload? - # TODO: use function to set payload data # GFF dataset. reader = GFFReaderWrapper( source, fix_strand=True ) @@ -549,7 +555,7 @@ Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ - def process_data( self, iterator, max_vals=sys.maxint, **kwargs ): + def process_data( self, iterator, start_val=0, max_vals=sys.maxint, **kwargs ): # # Build data to return. Payload format is: # [ <guid/offset>, <start>, <end>, <name>, <score>, <strand>, <thick_start>, @@ -559,14 +565,14 @@ # filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) no_detail = ( "no_detail" in kwargs ) - count = 0 rval = [] message = None - for line in iterator: - if count >= max_vals: + for count, line in enumerate( iterator ): + if count < start_val: + continue + if count-start_val >= max_vals: message = ERROR_MAX_VALS % ( max_vals, "features" ) break - count += 1 # TODO: can we use column metadata to fill out payload? # TODO: use function to set payload data @@ -625,16 +631,16 @@ col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } - def process_data( self, iterator, max_vals=sys.maxint, **kwargs ): + def process_data( self, iterator, start_val=0, max_vals=sys.maxint, **kwargs ): rval = [] - count = 0 message = None - for line in iterator: - if count >= max_vals: + for count, line in enumerate( iterator ): + if count < start_val: + continue + if count-start_val >= max_vals: message = ERROR_MAX_VALS % ( "max_vals", "features" ) break - count += 1 feature = line.split() payload = [ hash(line), int(feature[1])-1, int(feature[1]), @@ -657,22 +663,23 @@ NOTE: this data provider does not use indices, and hence will be very slow for large datasets. """ - def get_data( self, chrom, start, end, max_vals=sys.maxint, **kwargs ): + def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ): start, end = int( start ), int( end ) source = open( self.original_dataset.file_name ) results = [] - count = 0 message = None offset = 0 - for feature in GFFReaderWrapper( source, fix_strand=True ): + for count, feature in enumerate( GFFReaderWrapper( source, fix_strand=True ) ): + if count < start_val: + continue + if count-start_val >= max_vals: + message = ERROR_MAX_VALS % ( max_vals, "reads" ) + break + feature_start, feature_end = convert_gff_coords_to_bed( [ feature.start, feature.end ] ) if feature.chrom != chrom or feature_start < start or feature_end > end: continue - if count >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "features" ) - break - count += 1 payload = package_gff_feature( feature ) payload.insert( 0, offset ) results.append( payload ) --- a/lib/galaxy/web/controllers/tracks.py Wed Jul 06 09:52:28 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Wed Jul 06 10:20:57 2011 -0400 @@ -469,7 +469,7 @@ return { "status": messages.DATA, "valid_chroms": valid_chroms } @web.json - def data( self, trans, hda_ldda, dataset_id, chrom, low, high, max_vals=5000, **kwargs ): + def data( self, trans, hda_ldda, dataset_id, chrom, low, high, start_val=0, max_vals=5000, **kwargs ): """ Provides a block of data from a dataset. """ @@ -526,7 +526,7 @@ data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps ) # Get and return data from data_provider. - data = data_provider.get_data( chrom, low, high, max_vals, **kwargs ) + data = data_provider.get_data( chrom, low, high, int(start_val), int(max_vals), **kwargs ) message = None if isinstance(data, dict) and 'message' in data: message = data['message'] --- a/static/scripts/packed/trackster.js Wed Jul 06 09:52:28 2011 -0400 +++ b/static/scripts/packed/trackster.js Wed Jul 06 10:20:57 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(){$(this).css("border","0px")})};T.sortable=C;var D=9,A=18,O=D+2,w=100,F=12000,M=200,z=5,s=10,H=5000,t=100,m="There was an error in indexing this dataset. 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ab=this.high-this.low,ac=ab/2+this.low,aa=(ab*this.zoom_factor)/2;this.low=Math.round(ac-aa);this.high=Math.round(ac+aa);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var o=function(ac,ag){this.track=ac;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],ab=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params[this.params.length]=new g(ab,am,ae,ao,ai.min,ai.max)}else{if(ak=="select"){this.params[this.params.length]=new K(ab,am,ae,ao)}else{console.log("WARNING: unrecognized tool parameter type:",ab,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).bind("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},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,function(ae){ad.dataset_id=ae.dataset_id;ad.content_div.text("Running job.");ad.init()})},run:function(ab,ac){$.extend(ab,this.get_param_values_dict());var aa=function(){$.getJSON(rerun_tool_url,ab,function(ad){if(ad==="no converter"){new_track.container_div.addClass("error");new_track.content_div.text(G)}else{if(ad.error){new_track.container_div.addClass("error");new_track.content_div.text(v+ad.message)}else{if(ad==="pending"){new_track.container_div.addClass("pending");new_track.content_div.text("Converting input data so that it can be easily reused.");setTimeout(aa,2000)}else{ac(ad)}}}})};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.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(){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()}).bind("click",function(ao){ao.stopPropagation()}).bind("dblclick",function(ao){ao.stopPropagation()}).bind("keydown",function(ao){ao.stopPropagation()});var ae=this;$.each(this.filters,function(av,ap){var ar=$("<div/>").addClass("slider-row").appendTo(ae.parent_div);var ao=$("<div/>").addClass("slider-label").appendTo(ar);var ax=$("<span/>").addClass("slider-name").text(ap.name+" ").appendTo(ao);var aq=$("<span/>");var at=$("<span/>").addClass("slider-value").appendTo(ao).append("[").append(aq).append("]");var aw=$("<div/>").addClass("slider").appendTo(ar);ap.control_element=$("<div/>").attr("id",ap.name+"-filter-control").appendTo(aw);var au=[0,0];ap.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ay,az){au=az.values;aq.text(az.values[0]+"-"+az.values[1]);setTimeout(function(){if(az.values[0]==au[0]&&az.values[1]==au[1]){var aA=az.values;aq.text(aA[0]+"-"+aA[1]);ap.low=aA[0];ap.high=aA[1];ae.track.draw(true,true)}},50)},change:function(ay,az){ap.control_element.slider("option","slide").call(ap.control_element,ay,az)}});ap.slider=ap.control_element;ap.slider_label=aq;aj(at,aq,ap.control_element);$("<div style='clear: both;'/>").appendTo(ar)});if(this.filters.length!=0){var am=$("<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;$.each(this.params,function(ad,af){if(!af.hidden){var ag="param_"+ad;var ae=aa.find("#"+ag).val();if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae)}else{if(af.type==="bool"){ae=aa.find("#"+ag).is(":checked")}}}if(ae!==ac.values[af.key]){ac.values[af.key]=ae;ab=true}}});if(ab){this.onchange()}}});var b=function(ac,ab,aa){this.index=ac;this.resolution=ab;this.canvas=$("<div class='track-tile'/>").append(aa);this.stale=false};var l=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.max_val=ad};var L=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);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=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Q){return"ToolDataFeatureTrack"}else{if(this instanceof P){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_cache.clear();aa.initial_canvas=undefined;aa.content_div.css("height","auto");aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}$.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=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.content_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.content_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text(q);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.make_name_popup_menu()}aa.content_div.text(U);if(aa.view.chrom){aa.content_div.text("");aa.content_div.css("height",aa.height_px+"px");aa.enabled=true;$.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.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["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(){$("#no-tracks").show()};if(this.parent_track){ac=this.parent_track;ad=function(){}}aa.Remove=function(){ac.remove_track(ab);if(ac.num_tracks===0){ad()}};make_popupmenu(ab.name_div,aa)},draw:function(aa,ac){if(!this.dataset_id){return}var au=this.view.low,ag=this.view.high,ai=ag-au,ak=this.view.container.width(),ae=ak/ai,al=this.view.resolution,ad=$("<div style='position: relative;'></div>"),am=function(aw,ax,av){return aw+"_"+ax+"_"+av};if(!ac){this.content_div.children().remove()}this.content_div.append(ad);this.max_height=0;var ao=Math.floor(au/al/M);var af=[];var ap=0;while((ao*M*al)<ag){var at=am(ak,ae,ao);var ah=this.tile_cache.get(at);var aq=ao*M*this.view.resolution;var ab=aq+M*this.view.resolution;if(!aa&&ah){af[af.length]=ah;this.show_tile(ah,ad,aq,ab,ae)}else{this.delayed_draw(aa,at,ao,al,ad,ae,af)}ao+=1;ap++}var aj=this;var ar=setInterval(function(){if(af.length===ap){clearInterval(ar);if(ac){var aA=aj.content_div.children();var aB=false;for(var az=aA.length-1,aF=0;az>=aF;az--){var ay=$(aA[az]);if(aB){ay.remove()}else{if(ay.children().length!==0){aB=true}}}}if(aj instanceof e&&aj.mode=="Histogram"){var aE=-1;for(var az=0;az<af.length;az++){var aH=af[az].max_val;if(aH>aE){aE=aH}}for(var az=0;az<af.length;az++){if(af[az].max_val!==aE){var aG=af[az];aG.canvas.remove();aj.delayed_draw(true,am(ak,ae,aG.index),aG.index,aG.resolution,ad,ae,[],{max:aE})}}}if(aj.filters_manager){var ax=aj.filters_manager.filters;for(var aD=0;aD<ax.length;aD++){ax[aD].update_ui_elt()}var aC=false;if(aj.example_feature){for(var aD=0;aD<ax.length;aD++){if(ax[aD].applies_to(aj.example_feature)){aC=true;break}}}if(aj.filters_available!==aC){aj.filters_available=aC;if(!aj.filters_available){aj.filters_div.hide()}aj.make_name_popup_menu()}}var av=false;for(var aw=0;aw<af.length;aw++){if(af[aw].message){av=true;break}}if(av){for(var aw=0;aw<af.length;aw++){aG=af[aw];if(!aG.message){aG.canvas.css("padding-top",A)}}}}},50);for(var an=0;an<this.child_tracks.length;an++){this.child_tracks[an].draw(aa,ac)}},delayed_draw:function(ab,ai,ac,ae,aj,am,ak,af){var ad=this,ag=ac*M*ae,al=ag+M*ae;var ah=function(av,an,ap,ao,at,au,aq){var ar=ad.draw_tile(an,ap,ao,au,aq);ad.tile_cache.set(ai,ar);if(ar===undefined){return}ad.show_tile(ar,at,ag,al,au);ak[ak.length]=ar};var aa=setTimeout(function(){if(ag<=ad.view.high&&al>=ad.view.low){var an=(ab?undefined:ad.tile_cache.get(ai));if(an){ad.show_tile(an,aj,ag,al,am);ak[ak.length]=an}else{$.when(ad.data_cache.get_data(view.chrom,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){$.when(view.reference_track.data_cache.get_data(view.chrom,ag,al,ad.mode,ae,view.reference_track.data_url_extra_params)).then(function(ap){ah(aa,ao,ae,ac,aj,am,ap)})}else{ah(aa,ao,ae,ac,aj,am)}})}}},50)},show_tile:function(ah,aj,ae,ak,am){var ab=this,aa=ah.canvas,af=aa;if(ah.message){var al=$("<div/>"),ai=$("<div/>").addClass("tile-message").text(ah.message).css({height:A-1,width:ah.canvas.width}).appendTo(al),ag=$("<button/>").text("Show more").css("margin-left","0.5em").appendTo(ai);al.append(aa);af=al;ag.click(function(){var an=ab.data_cache.get_data(ab.view.chrom,ae,ak,ab.mode,ah.resolution);an.stale=true;ah.stale=true;ab.data_cache.get_data(ab.view.chrom,ae,ak,ab.mode,ah.resolution,{max_vals:an.data.length*2});ab.draw()}).dblclick(function(an){an.stopPropagation()})}var ad=this.view.high-this.view.low,ac=(ae-this.view.low)*am;if(this.left_offset){ac-=this.left_offset}af.css({position:"absolute",top:0,left:ac,height:""});aj.append(af);ab.max_height=Math.max(ab.max_height,af.height());ab.content_div.css("height",ab.max_height+"px");aj.children().css("height",ab.max_height+"px")},set_overview:function(){var aa=this.view;if(this.initial_canvas&&this.is_overview){aa.overview_close.show();aa.overview_viewport.append(this.initial_canvas);aa.overview_highlight.show().height(this.initial_canvas.height());aa.overview_viewport.height(this.initial_canvas.height()+aa.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(ac,aa,ad){var ab=this,ae=(ac!==undefined&&aa!==undefined&&ad!==undefined?ac+":"+aa+"-"+ad:"all");return" - region=["+ae+"], parameters=["+ab.tool.get_param_values().join(", ")+"]"},add_track:function(aa){aa.track_id=this.track_id+"_"+this.child_tracks.length;aa.container_div.attr("id","track_"+aa.track_id);this.child_tracks_container.append(aa.container_div);C(aa.container_div,".child-track-icon");if(!$(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_cache=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)}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_cache=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(ad,ae,ac)}});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_cache=new N(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{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,av,az,aj,ad){var ar=this,aB=az*M*av,ab=(az+1)*M*av,ap=ab-aB,at=Math.ceil(ap*aj),aq=this.mode,aF=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 aE=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=at+ae;ac.height=af+O;if(an.dataset_type!="summary_tree"){var ak=this.get_summary_tree_data(an.data,aB,ab,200);if(an.max){ak.max=an.max}an=ak}var aC=new I.SummaryTreePainter(an,aB,ab,this.prefs);var au=ac.getContext("2d");au.translate(ae,O);aC.draw(au,at,af);return new l(az,av,ac,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 aw=0,ay=an.data.length;aw<ay;aw++){var ag=an.data[aw];var ax=false;var am;for(var aA=0,aD=al.length;aA<aD;aA++){am=al[aA];am.update_attrs(ag);if(!am.keep(ag)){ax=true;break}}if(!ax){ai.push(ag)}}}var aC=new (this.painter)(ai,aB,ab,this.prefs,aq,ad);var af=aC.get_required_height(ah);var ac=this.view.canvas_manager.new_canvas();ac.width=at+ae;ac.height=af;var au=ac.getContext("2d");au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";this.container_div.find(".yaxislabel").remove();if(an.data){this.example_feature=(an.data.length?an.data[0]:undefined);au.translate(ae,0);aC.draw(au,at,af,ao)}return new L(az,av,ac,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 Q=function(ae,ac,ag,aa,ad,af,ab){e.call(this,ae,ac,ag,aa,ad,af,{},ab);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(Q.prototype,J.prototype,e.prototype,{predraw_init:function(){var ab=this;var aa=function(){if(ab.data_cache.size()===0){setTimeout(aa,300)}else{ab.data_url=default_data_url;ab.data_query_wait=H;ab.dataset_state_url=converted_datasets_state_url;$.getJSON(ab.dataset_state_url,{dataset_id:ab.dataset_id,hda_ldda:ab.hda_ldda},function(ac){})}};aa()}});T.View=Y;T.LineTrack=k;T.FeatureTrack=e;T.ReadTrack=S};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(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 C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var m=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};m.prototype.default_prefs={};var u=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.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(x,B,D,E,z){m.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var T=Math.round(J+G/I*J);if(H!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,T,L,1)}M.beginPath();var Q,D,B;if(S.length>1){B=Math.ceil((S[1][0]-S[0][0])*A)}else{B=10}for(var N=0,O=S.length;N<O;N++){M.fillStyle=this.prefs.color;Q=Math.round((S[N][0]-z)*A);D=S[N][1];var P=false,F=false;if(D===null){if(E&&H==="Filled"){M.lineTo(Q,x)}E=false;continue}if(D<G){F=true;D=G}else{if(D>C){P=true;D=C}}if(H==="Histogram"){D=Math.round(D/I*x);M.fillRect(Q,T,B,-D)}else{if(H==="Intensity"){D=255-Math.floor((D-G)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(Q,0,B,x)}else{D=Math.round(x-(D-G)/I*x);if(E){M.lineTo(Q,D)}else{E=true;if(H==="Filled"){M.moveTo(Q,x);M.lineTo(Q,D)}else{M.moveTo(Q,D)}}}}M.fillStyle=this.prefs.overflow_color;if(P||F){var R;if(H==="Histogram"||H==="Intensity"){R=B}else{Q-=2;R=4}if(P){M.fillRect(Q,0,R,3)}if(F){M.fillRect(Q,x-3,R,3)}}M.fillStyle=this.prefs.color}if(H==="Filled"){if(E){M.lineTo(Q,T);M.lineTo(0,T)}M.fill()}else{M.stroke()}M.restore()};var n=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};t(n.prototype,{get_required_height:function(y){var x=y_scale=this.get_row_height(),z=this.mode;if(z==="no_detail"||z==="Squish"||z==="Pack"){x=y*y_scale}return x+Math.max(Math.round(y_scale/2),5)},draw:function(J,A,I,F){var D=this.data,G=this.view_start,K=this.view_end;J.save();J.fillStyle=this.prefs.block_color;J.textAlign="right";var N=this.view_end-this.view_start,M=A/N,z=this.get_row_height();for(var C=0,E=D.length;C<E;C++){var L=D[C],B=L[0],x=L[1],y=L[2],H=(F&&F[B]!==undefined?F[B]:null);if((x<K&&y>G)&&(this.mode=="Dense"||H!==null)){this.draw_element(J,this.mode,L,H,G,K,M,z,A)}}J.restore()}});var d=10,h=3,l=5,v=10,f=1,r=3,e=3,a=9,k=2,g="#ccc";var q=function(z,B,x,y,A){n.call(this,z,B,x,y,A)};t(q.prototype,n.prototype,{get_row_height:function(){var y=this.mode,x;if(y==="Dense"){x=d}else{if(y==="no_detail"){x=h}else{if(y==="Squish"){x=l}else{x=v}}}return x},draw_element:function(J,C,R,E,L,ab,af,ag,x){var 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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 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, 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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...",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 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Y=function(aa,ad,ac,ab,ae){this.container=aa;this.chrom=null;this.vis_id=ac;this.dbkey=ab;this.title=ad;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(ae);this.canvas_manager=new Z(aa.get(0).ownerDocument);this.reset()};n(Y.prototype,{init:function(ad){var ac=this.container,aa=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ac);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ac);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ac);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=$("<div/>").addClass("intro").text("Select a chrom from the dropdown 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/>").click(function(){aa.zoom_in();aa.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ad);this.chrom_select.bind("change",function(){aa.change_chrom(aa.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(ae){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ae){aa.zoom_in(ae.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ae,af){this.current_x=af.offsetX}).bind("drag",function(ae,ag){var ah=ag.offsetX-this.current_x;this.current_x=ag.offsetX;var af=Math.round(ah/aa.viewport_container.width()*(aa.max_high-aa.max_low));aa.move_delta(-af)});this.overview_close.bind("click",function(){for(var af=0,ae=aa.tracks.length;af<ae;af++){aa.tracks[af].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",aa.overview_box.height());aa.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(ae,af){if(ae.clientX>aa.viewport_container.width()-16){return false}}).bind("dragstart",function(ae,af){af.original_low=aa.low;af.current_height=ae.clientY;af.current_x=af.offsetX}).bind("drag",function(ag,ai){var ae=$(this);var aj=ai.offsetX-ai.current_x;var af=ae.scrollTop()-(ag.clientY-ai.current_height);ae.scrollTop(af);ai.current_height=ag.clientY;ai.current_x=ai.offsetX;var ah=Math.round(aj/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}).bind("mousewheel",function(ag,ai,af,ae){if(af){var ah=Math.round(-af/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}});this.top_labeltrack.bind("dragstart",function(ae,af){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(ai,aj){$(aj.proxy).css({left:Math.min(ai.pageX,aj.startX),width:Math.abs(ai.pageX-aj.startX)});var af=Math.min(ai.pageX,aj.startX)-aa.container.offset().left,ae=Math.max(ai.pageX,aj.startX)-aa.container.offset().left,ah=(aa.high-aa.low),ag=aa.viewport_container.width();aa.update_location(Math.round(af/ag*ah)+aa.low,Math.round(ae/ag*ah)+aa.low)}).bind("dragend",function(aj,ak){var af=Math.min(aj.pageX,ak.startX),ae=Math.max(aj.pageX,ak.startX),ah=(aa.high-aa.low),ag=aa.viewport_container.width(),ai=aa.low;aa.low=Math.round(af/ag*ah)+ai;aa.high=Math.round(ae/ag*ah)+ai;$(ak.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();$(window).trigger("resize")},update_location:function(aa,ab){this.location_span.text(commatize(aa)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(aa)+"-"+commatize(ab))},load_chroms:function(ab,ac){ab.num=t;$.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;if(!ad.chrom){ad.intro_div.show()}else{ad.intro_div.hide()}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},add_label_track:function(aa){aa.view=this;this.label_tracks.push(aa)},remove_track:function(aa){this.has_changes=true;aa.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(aa)];this.num_tracks-=1},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()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});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()}).bind("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},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,function(ae){ad.dataset_id=ae.dataset_id;ad.content_div.text("Running job.");ad.init()})},run:function(ab,ac){$.extend(ab,this.get_param_values_dict());var aa=function(){$.getJSON(rerun_tool_url,ab,function(ad){if(ad==="no converter"){new_track.container_div.addClass("error");new_track.content_div.text(G)}else{if(ad.error){new_track.container_div.addClass("error");new_track.content_div.text(v+ad.message)}else{if(ad==="pending"){new_track.container_div.addClass("pending");new_track.content_div.text("Converting input data so that it can be easily reused.");setTimeout(aa,2000)}else{ac(ad)}}}})};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.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(){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()}).bind("click",function(ao){ao.stopPropagation()}).bind("dblclick",function(ao){ao.stopPropagation()}).bind("keydown",function(ao){ao.stopPropagation()});var ae=this;$.each(this.filters,function(av,ap){var ar=$("<div/>").addClass("slider-row").appendTo(ae.parent_div);var ao=$("<div/>").addClass("slider-label").appendTo(ar);var ax=$("<span/>").addClass("slider-name").text(ap.name+" ").appendTo(ao);var aq=$("<span/>");var at=$("<span/>").addClass("slider-value").appendTo(ao).append("[").append(aq).append("]");var aw=$("<div/>").addClass("slider").appendTo(ar);ap.control_element=$("<div/>").attr("id",ap.name+"-filter-control").appendTo(aw);var au=[0,0];ap.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ay,az){au=az.values;aq.text(az.values[0]+"-"+az.values[1]);setTimeout(function(){if(az.values[0]==au[0]&&az.values[1]==au[1]){var aA=az.values;aq.text(aA[0]+"-"+aA[1]);ap.low=aA[0];ap.high=aA[1];ae.track.draw(true,true)}},50)},change:function(ay,az){ap.control_element.slider("option","slide").call(ap.control_element,ay,az)}});ap.slider=ap.control_element;ap.slider_label=aq;aj(at,aq,ap.control_element);$("<div style='clear: both;'/>").appendTo(ar)});if(this.filters.length!=0){var am=$("<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;$.each(this.params,function(ad,af){if(!af.hidden){var ag="param_"+ad;var ae=aa.find("#"+ag).val();if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae)}else{if(af.type==="bool"){ae=aa.find("#"+ag).is(":checked")}}}if(ae!==ac.values[af.key]){ac.values[af.key]=ae;ab=true}}});if(ab){this.onchange()}}});var b=function(ac,ab,aa){this.index=ac;this.low=ac*M*ab;this.high=(ac+1)*M*ab;this.resolution=ab;this.canvas=$("<div class='track-tile'/>").append(aa);this.stale=false};var l=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.max_val=ad};var L=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);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=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.content_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.content_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text(q);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.make_name_popup_menu()}aa.content_div.text(U);if(aa.view.chrom){aa.content_div.text("");aa.content_div.css("height",aa.height_px+"px");aa.enabled=true;$.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.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["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(){$("#no-tracks").show()};if(this.parent_track){ac=this.parent_track;ad=function(){}}aa.Remove=function(){ac.remove_track(ab);if(ac.num_tracks===0){ad()}};make_popupmenu(ab.name_div,aa)},draw:function(aa,ac){if(!this.dataset_id){return}var au=this.view.low,ag=this.view.high,ai=ag-au,ak=this.view.container.width(),ae=ak/ai,al=this.view.resolution,ad=$("<div style='position: relative;'></div>"),am=function(aw,ax,av){return aw+"_"+ax+"_"+av};if(!ac){this.content_div.children().remove()}this.content_div.append(ad);this.max_height=0;var ao=Math.floor(au/al/M);var af=[];var ap=0;while((ao*M*al)<ag){var at=am(ak,ae,ao);var ah=this.tile_cache.get(at);var aq=ao*M*this.view.resolution;var ab=aq+M*this.view.resolution;if(!aa&&ah){af[af.length]=ah;this.show_tile(ah,ad,ae)}else{this.delayed_draw(aa,at,ao,al,ad,ae,af)}ao+=1;ap++}var aj=this;var ar=setInterval(function(){if(af.length===ap){clearInterval(ar);if(ac){var aA=aj.content_div.children();var aB=false;for(var az=aA.length-1,aF=0;az>=aF;az--){var ay=$(aA[az]);if(aB){ay.remove()}else{if(ay.children().length!==0){aB=true}}}}if(aj instanceof e&&aj.mode=="Histogram"){var aE=-1;for(var az=0;az<af.length;az++){var aH=af[az].max_val;if(aH>aE){aE=aH}}for(var az=0;az<af.length;az++){if(af[az].max_val!==aE){var aG=af[az];aG.canvas.remove();aj.delayed_draw(true,am(ak,ae,aG.index),aG.index,aG.resolution,ad,ae,[],{max:aE})}}}if(aj.filters_manager){var ax=aj.filters_manager.filters;for(var aD=0;aD<ax.length;aD++){ax[aD].update_ui_elt()}var aC=false;if(aj.example_feature){for(var aD=0;aD<ax.length;aD++){if(ax[aD].applies_to(aj.example_feature)){aC=true;break}}}if(aj.filters_available!==aC){aj.filters_available=aC;if(!aj.filters_available){aj.filters_div.hide()}aj.make_name_popup_menu()}}var av=false;for(var aw=0;aw<af.length;aw++){if(af[aw].message){av=true;break}}if(av){for(var aw=0;aw<af.length;aw++){aG=af[aw];if(!aG.message){aG.canvas.css("padding-top",A)}}}}},50);for(var an=0;an<this.child_tracks.length;an++){this.child_tracks[an].draw(aa,ac)}},delayed_draw:function(ab,ai,ac,ae,aj,am,ak,af){var ad=this,ag=ac*M*ae,al=ag+M*ae;var ah=function(av,an,ap,ao,at,au,aq){var ar=ad.draw_tile(an,ap,ao,au,aq);ad.tile_cache.set(ai,ar);if(ar===undefined){return}ad.show_tile(ar,at,au);ak[ak.length]=ar};var aa=setTimeout(function(){if(ag<=ad.view.high&&al>=ad.view.low){var an=(ab?undefined:ad.tile_cache.get(ai));if(an){ad.show_tile(an,aj,am);ak[ak.length]=an}else{$.when(ad.data_manager.get_data(ag,al,ae,ad.data_url_extra_params)).then(function(ao){n(ao,af);if(view.reference_track&&am>view.canvas_manager.char_width_px){$.when(view.reference_track.data_manager.get_data(ag,al,ae,view.reference_track.data_url_extra_params)).then(function(ap){ah(aa,ao,ae,ac,aj,am,ap)})}else{ah(aa,ao,ae,ac,aj,am)}})}}},50)},show_tile:function(ag,ai,aj){var ab=this,aa=ag.canvas,ae=aa;if(ag.message){var ak=$("<div/>"),ah=$("<div/>").addClass("tile-message").text(ag.message).css({height:A-1,width:ag.canvas.width}).appendTo(ak),af=$("<div/>").text("Show more").addClass("action-button").css({"padding-top":0,"padding-bottom":0}).appendTo(ah);ak.append(aa);ae=ak;af.click(function(){ag.stale=true;ab.data_manager.get_more_data(ag.low,ag.high,ag.resolution,{},ab.data_manager.DEEP_DATA_REQ);ab.draw()}).dblclick(function(al){al.stopPropagation()})}var ad=this.view.high-this.view.low,ac=(ag.low-this.view.low)*aj;if(this.left_offset){ac-=this.left_offset}ae.css({position:"absolute",top:0,left:ac,height:""});ai.append(ae);ab.max_height=Math.max(ab.max_height,ae.height());ab.content_div.css("height",ab.max_height+"px");ai.children().css("height",ab.max_height+"px")},set_overview:function(){var aa=this.view;if(this.initial_canvas&&this.is_overview){aa.overview_close.show();aa.overview_viewport.append(this.initial_canvas);aa.overview_highlight.show().height(this.initial_canvas.height());aa.overview_viewport.height(this.initial_canvas.height()+aa.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(ac,aa,ad){var ab=this,ae=(ac!==undefined&&aa!==undefined&&ad!==undefined?ac+":"+aa+"-"+ad:"all");return" - region=["+ae+"], parameters=["+ab.tool.get_param_values().join(", ")+"]"},add_track:function(aa){aa.track_id=this.track_id+"_"+this.child_tracks.length;aa.container_div.attr("id","track_"+aa.track_id);this.child_tracks_container.append(aa.container_div);C(aa.container_div,".child-track-icon");if(!$(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)}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)}});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,{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,av,az,aj,ad){var ar=this,aB=az*M*av,ab=(az+1)*M*av,ap=ab-aB,at=Math.ceil(ap*aj),aq=this.mode,aF=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 aE=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=at+ae;ac.height=af+O;if(an.dataset_type!="summary_tree"){var ak=this.get_summary_tree_data(an.data,aB,ab,200);if(an.max){ak.max=an.max}an=ak}var aC=new I.SummaryTreePainter(an,aB,ab,this.prefs);var au=ac.getContext("2d");au.translate(ae,O);aC.draw(au,at,af);return new l(az,av,ac,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 aw=0,ay=an.data.length;aw<ay;aw++){var ag=an.data[aw];var ax=false;var am;for(var aA=0,aD=al.length;aA<aD;aA++){am=al[aA];am.update_attrs(ag);if(!am.keep(ag)){ax=true;break}}if(!ax){ai.push(ag)}}}var aC=new (this.painter)(ai,aB,ab,this.prefs,aq,ad);var af=aC.get_required_height(ah);var ac=this.view.canvas_manager.new_canvas();ac.width=at+ae;ac.height=af;var au=ac.getContext("2d");au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";this.container_div.find(".yaxislabel").remove();if(an.data){this.example_feature=(an.data.length?an.data[0]:undefined);au.translate(ae,0);aC.draw(au,at,af,ao)}return new L(az,av,ac,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 Q=function(ae,ac,ag,aa,ad,af,ab){e.call(this,ae,ac,ag,aa,ad,af,{},ab);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(Q.prototype,J.prototype,e.prototype,{predraw_init:function(){var ab=this;var aa=function(){if(ab.data_manager.size()===0){setTimeout(aa,300)}else{ab.data_url=default_data_url;ab.data_query_wait=H;ab.dataset_state_url=converted_datasets_state_url;$.getJSON(ab.dataset_state_url,{dataset_id:ab.dataset_id,hda_ldda:ab.hda_ldda},function(ac){})}};aa()}});T.View=Y;T.LineTrack=k;T.FeatureTrack=e;T.ReadTrack=S};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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c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file --- a/static/scripts/trackster.js Wed Jul 06 09:52:28 2011 -0400 +++ b/static/scripts/trackster.js Wed Jul 06 10:20:57 2011 -0400 @@ -370,10 +370,8 @@ // Set parameters based on request type. // if (req_type === this.DEEP_DATA_REQ) { - // HACK: for now, just up the max vals and request all data; in the future, - // need server to recognize min_vals and max_vals to specify range of data to - // return. - $.extend(extra_params, {max_vals: cur_data.data.length * 2}); + // Use same interval but set start_val to skip data that's already in cur_data. + $.extend(extra_params, {start_val: cur_data.data.length + 1}); } else if (req_type === this.BROAD_DATA_REQ) { // Set low to be past the last feature returned. @@ -393,7 +391,7 @@ this.set_data(low, high, mode, new_data_available); $.when(new_data_request).then(function(result) { if (result.data) { - //result.data.append(cur_data.data); + result.data = cur_data.data.concat(result.data); } data_manager.set_data(low, high, mode, result); new_data_available.resolve(result); 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 patch from Assaf Gordon to fix the cleanup_dataset.py script, correcting the behavior of setting the info_only flag to True when running delete_datasets.sh and purge_datasets.sh.
by Bitbucket 06 Jul '11

06 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a5e0a5d3c0a1/ changeset: a5e0a5d3c0a1 user: greg date: 2011-07-06 15:52:28 summary: Add patch from Assaf Gordon to fix the cleanup_dataset.py script, correcting the behavior of setting the info_only flag to True when running delete_datasets.sh and purge_datasets.sh. affected #: 1 file (265 bytes) --- a/scripts/cleanup_datasets/cleanup_datasets.py Wed Jul 06 09:45:41 2011 +1000 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Wed Jul 06 09:52:28 2011 -0400 @@ -411,10 +411,13 @@ app.sa_session.add( metadata_file ) app.sa_session.flush() print "%s" % metadata_file.file_name - print "Deleting dataset id", dataset.id - dataset.deleted = True - app.sa_session.add( dataset ) - app.sa_session.flush() + if not info_only: + print "Deleting dataset id", dataset.id + dataset.deleted = True + app.sa_session.add( dataset ) + app.sa_session.flush() + else: + print "Dataset %i will be deleted (without 'info_only' mode)" % ( dataset.id ) def _purge_dataset( app, dataset, remove_from_disk, info_only = False ): if dataset.deleted: @@ -433,6 +436,8 @@ dataset.purged = True app.sa_session.add( dataset ) app.sa_session.flush() + else: + print "Dataset %i will be purged (without 'info_only' mode)" % (dataset.id) else: print "This dataset (%i) is not purgable, the file (%s) will not be removed.\n" % ( dataset.id, dataset.file_name ) except OSError, exc: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 06 Jul '11

06 Jul '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/94e63070cbb1/ changeset: 94e63070cbb1 user: fubar date: 2011-07-06 01:44:56 summary: Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository This is a backout of commit 5765 affected #: 250 files (5.2 KB) --- a/lib/galaxy/security/__init__.py Tue Jul 05 12:40:43 2011 +1000 +++ b/lib/galaxy/security/__init__.py Wed Jul 06 09:44:56 2011 +1000 @@ -1005,8 +1005,7 @@ ucsc_main = ( 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', 'hgw4.cse.ucsc.edu', 'hgw5.cse.ucsc.edu', 'hgw6.cse.ucsc.edu', 'hgw7.cse.ucsc.edu', 'hgw8.cse.ucsc.edu' ), ucsc_test = ( 'hgwdev.cse.ucsc.edu', ), - ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ), - ucsc_bhri = ('ucsc.omics.bhri.internal','galaxy.omics.bhri.internal'), + ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ) ) def __init__( self, model, permitted_actions=None ): self.model = model @@ -1037,7 +1036,7 @@ # We're going to search in order, but if the remote site is load # balancing their connections (as UCSC does), this is okay. try: - if socket.gethostbyname( server ) == addr or server == '127.0.0.1' or server == '172.16.0.38': + if socket.gethostbyname( server ) == addr: break # remote host is in the server list except ( socket.error, socket.gaierror ): pass # can't resolve, try next --- a/lib/galaxy/tools/__init__.py Tue Jul 05 12:40:43 2011 +1000 +++ b/lib/galaxy/tools/__init__.py Wed Jul 06 09:44:56 2011 +1000 @@ -922,8 +922,6 @@ if not self.check_values: return for input in self.inputs.itervalues(): - if input.name not in value: - value[input.name] = input.get_initial_value( None, value ) if isinstance( input, ToolParameter ): callback( "", input, value[input.name] ) else: --- a/lib/galaxy/tools/parameters/basic.py Tue Jul 05 12:40:43 2011 +1000 +++ b/lib/galaxy/tools/parameters/basic.py Wed Jul 06 09:44:56 2011 +1000 @@ -748,6 +748,9 @@ # Dependency on a value that does not yet exist if isinstance( dep_value, RuntimeValue ): return True + #dataset not ready yet + if hasattr( self, 'ref_input' ) and isinstance( dep_value, self.tool.app.model.HistoryDatasetAssociation ) and ( dep_value.is_pending or not isinstance( dep_value.datatype, self.ref_input.formats ) ): + return True # Dynamic, but all dependenceis are known and have values return False def get_initial_value( self, trans, context ): @@ -878,6 +881,7 @@ self.force_select = string_as_bool( elem.get( "force_select", True )) self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) + self.ref_input = None self.default_value = elem.get( "default_value", None ) self.is_dynamic = True def from_html( self, value, trans=None, context={} ): @@ -973,7 +977,7 @@ if not dataset.metadata.columns: # Only allow late validation if the dataset is not yet ready # (since we have reason to expect the metadata to be ready eventually) - if dataset.is_pending: + if dataset.is_pending or not isinstance( dataset.datatype, self.ref_input.formats ): return True # No late validation return False @@ -1353,7 +1357,7 @@ selected = ( value and ( hda in value ) ) field.add_option( "%s: %s" % ( hid, hda_name ), hda.id, selected ) else: - target_ext, converted_dataset = hda.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) ) + target_ext, converted_dataset = hda.find_conversion_destination( self.formats ) if target_ext: if converted_dataset: hda = converted_dataset @@ -1402,13 +1406,22 @@ pass #no valid options def dataset_collector( datasets ): def is_convertable( dataset ): - target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = self.converter_safe( context, trans ) ) + target_ext, converted_dataset = dataset.find_conversion_destination( self.formats ) if target_ext is not None: return True return False for i, data in enumerate( datasets ): - if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): - if self.options and self._options_filter_attribute( data ) != filter_value: + if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED]: + is_valid = False + if isinstance( data.datatype, self.formats ): + is_valid = True + else: + target_ext, converted_dataset = data.find_conversion_destination( self.formats ) + if target_ext: + is_valid = True + if converted_dataset: + data = converted_dataset + if not is_valid or ( self.options and self._options_filter_attribute( data ) != filter_value ): continue most_recent_dataset[0] = data # Also collect children via association object --- a/lib/galaxy/web/framework/middleware/remoteuser.py Tue Jul 05 12:40:43 2011 +1000 +++ b/lib/galaxy/web/framework/middleware/remoteuser.py Wed Jul 06 09:44:56 2011 +1000 @@ -36,7 +36,6 @@ """ UCSC_MAIN_SERVERS = ( - 'omics.bhri.internal', 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', @@ -50,7 +49,6 @@ 'lowepub.cse.ucsc.edu', ) - class RemoteUser( object ): def __init__( self, app, maildomain=None, ucsc_display_sites=[], admin_users=[] ): self.app = app @@ -58,7 +56,7 @@ self.allow_ucsc_main = False self.allow_ucsc_archaea = False self.admin_users = admin_users - if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites or 'bhri' in ucsc_display_sites: + if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites: self.allow_ucsc_main = True if 'archaea' in ucsc_display_sites: self.allow_ucsc_archaea = True --- a/scripts/cleanup_datasets/purge_libraries.sh Tue Jul 05 12:40:43 2011 +1000 +++ b/scripts/cleanup_datasets/purge_libraries.sh Wed Jul 06 09:44:56 2011 +1000 @@ -1,5 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -#python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 2 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log --- a/tool-data/shared/ucsc/ucsc_build_sites.txt Tue Jul 05 12:40:43 2011 +1000 +++ b/tool-data/shared/ucsc/ucsc_build_sites.txt Wed Jul 06 09:44:56 2011 +1000 @@ -1,6 +1,5 @@ #Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,felCat3,apiMel2,monDom4,apiMel1,ce2 -bhri http://ucsc.omics.bhri.internal/cgi-bin/hgTracks? hg18,hg19,mm8,mm9,rn4 #Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 #Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn --- a/tool_conf.xml.sample Tue Jul 05 12:40:43 2011 +1000 +++ b/tool_conf.xml.sample Wed Jul 06 09:44:56 2011 +1000 @@ -368,7 +368,6 @@ </section><section name="NGS: Simulation" id="ngs-simulation"><tool file="ngs_simulation/ngs_simulation.xml" /> - <tool file="rgenetics/EpiD.xml" /></section><section name="SNP/WGA: Data; Filters" id="rgdat"><label text="Data: Import and upload" id="rgimport" /> --- a/tools/data_source/ucsc_tablebrowser.xml Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/data_source/ucsc_tablebrowser.xml Wed Jul 06 09:44:56 2011 +1000 @@ -5,27 +5,27 @@ initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed. --><tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source"> - <description>table browser</description> - <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://ucsc.omics.bhri.internal/cgi-bin/hgTables" check_values="false" method="get"> - <display>go to UCSC Table Browser $GALAXY_URL</display> - <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> - <param name="tool_id" type="hidden" value="ucsc_table_direct1" /> - <param name="sendToGalaxy" type="hidden" value="1" /> - <param name="hgta_compressType" type="hidden" value="none" /> - <param name="hgta_outputType" type="hidden" value="bed" /> - </inputs> - <request_param_translation> + <description>table browser</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get"> + <display>go to UCSC Table Browser $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> + <param name="tool_id" type="hidden" value="ucsc_table_direct1" /> + <param name="sendToGalaxy" type="hidden" value="1" /> + <param name="hgta_compressType" type="hidden" value="none" /> + <param name="hgta_outputType" type="hidden" value="bed" /> + </inputs> + <request_param_translation><request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /><request_param galaxy_name="URL" remote_name="URL" missing="" /><request_param galaxy_name="dbkey" remote_name="db" missing="?" /><request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> - <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> - <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" > + <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> + <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="auto" ><value_translation> - <value galaxy_value="tabular" remote_value="primaryTable" /> - <value galaxy_value="tabular" remote_value="selectedFields" /> + <value galaxy_value="auto" remote_value="primaryTable" /> + <value galaxy_value="auto" remote_value="selectedFields" /><value galaxy_value="wig" remote_value="wigData" /><value galaxy_value="interval" remote_value="tab" /><value galaxy_value="html" remote_value="hyperlinks" /> @@ -33,10 +33,10 @@ <value galaxy_value="gtf" remote_value="gff" /></value_translation></request_param> - </request_param_translation> - <uihints minwidth="800"/> - <outputs> - <data name="output" format="tabular" /> - </outputs> - <options sanitize="False" refresh="True"/> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/> + </outputs> + <options sanitize="False" refresh="True"/></tool> --- a/tools/meme/meme.xml Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/meme/meme.xml Wed Jul 06 09:44:56 2011 +1000 @@ -304,7 +304,7 @@ </when></conditional> - <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="True"> + <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"><validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator></param> --- a/tools/peak_calling/macs_wrapper.py Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/peak_calling/macs_wrapper.py Wed Jul 06 09:44:56 2011 +1000 @@ -51,8 +51,7 @@ cmdline = "macs -t %s" % ",".join( options['input_chipseq'] ) if options['input_control']: cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) ) - cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s %s" %\ - ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['futurefdr'] ) + cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s --lambdaset='%s' %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['lambdaset'], options['futurefdr'] ) if 'wig' in options: wigextend = int( options['wig']['wigextend'] ) if wigextend >= 0: --- a/tools/peak_calling/macs_wrapper.xml Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/peak_calling/macs_wrapper.xml Wed Jul 06 09:44:56 2011 +1000 @@ -28,8 +28,7 @@ <param name="tsize" type="integer" label="Tag size" value="25"/><param name="bw" type="integer" label="Band width" value="300"/><param name="pvalue" type="float" label="Pvalue cutoff for peak detection" value="1e-5" help="default: 1e-5"/> - <param name="mfold" type="text" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model" value="10,30" - help="Range for high-confidence enrichment ratio against background for model are within this range. DEFAULT:10,30" /> + <param name="mfold" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model" value="32"/><param name="xls_to_interval" label="Parse xls files into into distinct interval files" type="boolean" truevalue="create" falsevalue="do_not_create" checked="False"/><conditional name="wig_type"><param name="wig_type_selector" type="select" label="Save shifted raw tag count at every bp into a wiggle file"> @@ -45,6 +44,7 @@ </when></conditional><param name="nolambda" label="Use fixed background lambda as local lambda for every peak region" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" help="up to 9X more time consuming"/> + <param name="lambdaset" type="text" label="3 levels of regions around the peak region to calculate the maximum lambda as local lambda" value="1000,5000,10000" size="50"/><conditional name="nomodel_type"><param name="nomodel_type_selector" type="select" label="Build Model"><option value="nomodel">Do not build the shifting model</option> @@ -95,7 +95,7 @@ <configfile name="options_file"><% import simplejson %> -#set $__options = { 'experiment_name':str( $experiment_name ), 'gsize':int( float( str( $gsize ) ) ), 'tsize':str( $tsize ), 'bw':str( $bw ), 'pvalue':str( $pvalue ), 'mfold':str( $mfold ), 'nolambda':str( $nolambda ), 'futurefdr':str( $futurefdr ) } +#set $__options = { 'experiment_name':str( $experiment_name ), 'gsize':int( float( str( $gsize ) ) ), 'tsize':str( $tsize ), 'bw':str( $bw ), 'pvalue':str( $pvalue ), 'mfold':str( $mfold ), 'nolambda':str( $nolambda ), 'lambdaset': str( $lambdaset ), 'futurefdr':str( $futurefdr ) } #if str( $xls_to_interval ) == 'create': #set $__options['xls_to_interval'] = { 'peaks_file': str( $output_xls_to_interval_peaks_file ), 'negative_peaks_file': str( $output_xls_to_interval_negative_peaks_file ) } #else: @@ -145,13 +145,14 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="10,30" /> + <param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /><param name="xls_to_interval" /><param name="wig_type_selector" value="no_wig" /><param name="nolambda"/> + <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> @@ -170,13 +171,14 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="10,30" /> + <param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /><param name="xls_to_interval" value="true" /><param name="wig_type_selector" value="no_wig" /><param name="nolambda"/> + <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> @@ -193,7 +195,7 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="10,30" /> + <param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /> @@ -202,6 +204,7 @@ <param name="wigextend" value="-1" /><param name="space" value="10" /><param name="nolambda"/> + <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> --- a/tools/plotting/histogram.py Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/plotting/histogram.py Wed Jul 06 09:44:56 2011 +1000 @@ -73,8 +73,7 @@ if skipped_lines < i: try: - #a = array( matrix ) - a=matrix + a = r.array( matrix ) r.pdf( out_fname, 8, 8 ) histogram = r.hist( a, probability=not frequency, main=title, xlab=xlab, breaks=breaks ) if density: --- a/tools/plotting/scatterplot.py Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/plotting/scatterplot.py Wed Jul 06 09:44:56 2011 +1000 @@ -19,14 +19,8 @@ title = sys.argv[5] xlab = sys.argv[6] ylab = sys.argv[7] - out_type = sys.argv[8] - out_width = int(sys.argv[9]) - out_height = int(sys.argv[10]) - point_size = float(sys.argv[11]) - - xvec=[] - yvec=[] + matrix = [] skipped_lines = 0 first_invalid_line = 0 invalid_value = '' @@ -34,19 +28,17 @@ i = 0 for i, line in enumerate( file( in_fname ) ): valid = True - vals = [] line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ): row = [] fields = line.split( "\t" ) - for c,column in enumerate(columns): + for column in columns: try: val = fields[column] if val.lower() == "na": - v = float( "nan" ) + row.append( float( "nan" ) ) else: - v = float( fields[column] ) - vals.append(val) + row.append( float( fields[column] ) ) except: valid = False skipped_lines += 1 @@ -65,19 +57,12 @@ first_invalid_line = i+1 if valid: - xvec.append(vals[0]) - yvec.append(vals[1]) + matrix.append( row ) + if skipped_lines < i: try: - if out_type == "jpg": - r.jpeg(out_fname,width=out_width,height=out_height) - elif out_type == "png": - # type="cairo" needed to be set for headless servers - r.png(out_fname,type="cairo",width=out_width,height=out_height) - else: - r.pdf(out_fname, out_width, out_height) - - r.plot(xvec,yvec, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19,cex=point_size ) + r.pdf( out_fname, 8, 8 ) + r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 ) r.dev_off() except Exception, exc: stop_err( "%s" %str( exc ) ) --- a/tools/plotting/scatterplot.xml Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/plotting/scatterplot.xml Wed Jul 06 09:44:56 2011 +1000 @@ -1,6 +1,6 @@ <tool id="scatterplot_rpy" name="Scatterplot"><description>of two numeric columns</description> - <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab" $output_format $out_width $out_height $point_size</command> + <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command><inputs><param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/><param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" /> @@ -8,26 +8,15 @@ <param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/><param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/><param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/> - <param name="output_format" type="select" label="Output format"> - <option value="pdf">pdf</option> - <option value="png">png</option> - <option value="jpg">jpg</option> - </param> - <param name="out_width" size="4" type="integer" value="8" label="Width (pdf=inches, image=pixels)"/> - <param name="out_height" size="4" type="integer" value="8" label="Height (pdf=inches, image=pixels)"/> - <param name="point_size" size="4" type="float" value="0.2" label="Point Size"/></inputs><outputs> - <data format="pdf" name="out_file1"> - <change_format> - <when input="output_format" value="png" format="png" /> - <when input="output_format" value="jpg" format="jpg" /> - </change_format> - </data> + <data format="pdf" name="out_file1" /></outputs><requirements><requirement type="python-module">rpy</requirement></requirements> + <help> --- a/tools/samtools/bam_to_sam.py Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/samtools/bam_to_sam.py Wed Jul 06 09:44:56 2011 +1000 @@ -21,6 +21,7 @@ parser = optparse.OptionParser() parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' ) parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' ) + parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' ) ( options, args ) = parser.parse_args() # output version # of tool @@ -87,7 +88,11 @@ try: # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ). - command = 'samtools view -o -h %s %s' % ( options.output1, tmp_sorted_aligns_file_name ) + if options.header: + view_options = "-h" + else: + view_options = "" + command = 'samtools view %s -o %s %s' % ( view_options, options.output1, tmp_sorted_aligns_file_name ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) --- a/tools/samtools/sam_bitwise_flag_filter.py Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/samtools/sam_bitwise_flag_filter.py Wed Jul 06 09:44:56 2011 +1000 @@ -1,6 +1,6 @@ #!/usr/bin/env python # Refactored on 11/13/2010 by Kanwei Li -# Added drop_header option - default is now keep headers for downstream sanity by ross lazarus + import sys import optparse @@ -14,11 +14,7 @@ options (listed below) default to 'None' if omitted """ parser = optparse.OptionParser(usage=usage) - parser.add_option('--drop_header', - action = 'store_true', - dest='drop_header', - help="Remove sam header - you probably NEVER want this for fussy downstream tools") - + parser.add_option( '--0x0001','--is_paired', choices = ( '0','1' ), @@ -133,24 +129,21 @@ opt_map = { '0': False, '1': True } used_indices = [(index, opt_map[opt]) for index, opt in enumerate(opt_ary) if opt is not None] flag_col = int( options.flag_col ) - 1 + for line in infile: line = line.rstrip( '\r\n' ) - if line: - if line.startswith('@'): - if not options.drop_header: - print line # usually want these so add -h if you don't want headers - elif not line.startswith( '#' ) : - fields = line.split( '\t' ) - flags = int( fields[flag_col] ) + if line and not line.startswith( '#' ) and not line.startswith( '@' ) : + fields = line.split( '\t' ) + flags = int( fields[flag_col] ) - valid_line = True - for index, opt_bool in used_indices: - if bool(flags & 0x0001 << index) != opt_bool: - valid_line = False - break + valid_line = True + for index, opt_bool in used_indices: + if bool(flags & 0x0001 << index) != opt_bool: + valid_line = False + break - if valid_line: - print line + if valid_line: + print line if __name__ == "__main__": main() --- a/tools/samtools/sam_bitwise_flag_filter.xml Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/samtools/sam_bitwise_flag_filter.xml Wed Jul 06 09:44:56 2011 +1000 @@ -1,11 +1,8 @@ -<tool id="sam_bw_filter" name="Filter SAM" version="1.0.1"> +<tool id="sam_bw_filter" name="Filter SAM" version="1.0.0"><description>on bitwise flag values</description><parallelism method="basic"></parallelism><command interpreter="python"> sam_bitwise_flag_filter.py - #if $drop_header == "1": - --drop_header - #end if --input_sam_file=$input1 --flag_column=2 #for $bit in $bits @@ -15,11 +12,6 @@ </command><inputs><param format="sam" name="input1" type="data" label="Select dataset to filter"/> - <param name="drop_header" type="select" display="radio" label="DROP sam headers" - help="Set this if you REALLY want to throw away existing sam header metadata - downstream (eg Picard) tools often demand it" > - <option value="0" selected="true">Keep headers (default)</option> - <option value="1">Drop headers</option> - </param><repeat name="bits" title="Flag"><param name="flags" type="select" label="Type"><option value="--0x0001">Read is paired</option> --- a/tools/samtools/sam_to_bam.py Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/samtools/sam_to_bam.py Wed Jul 06 09:44:56 2011 +1000 @@ -68,7 +68,7 @@ # and the equCab2.fa file will contain fasta sequences. seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) tmp_dir = tempfile.mkdtemp() - if options.ref_file == 'None': + if not options.ref_file or options.ref_file == 'None': # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ). # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai @@ -125,9 +125,7 @@ tmp_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir ) tmp_aligns_file_name = tmp_aligns_file.name tmp_aligns_file.close() - # IMPORTANT NOTE: for some reason the samtools view command gzips the resulting bam file without warning, - # and the docs do not currently state that this occurs ( very bad ). - command = 'samtools view -h -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) + command = 'samtools view -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) @@ -147,8 +145,6 @@ tmp_stderr.close() if returncode != 0: raise Exception, stderr - if len( open( tmp_aligns_file_name ).read() ) == 0: - raise Exception, 'Initial BAM file empty' except Exception, e: #clean up temp files if os.path.exists( tmp_dir ): @@ -188,11 +184,6 @@ stop_err( 'Error sorting alignments from (%s), %s' % ( tmp_aligns_file_name, str( e ) ) ) # Move tmp_aligns_file_name to our output dataset location sorted_bam_file = '%s.bam' % tmp_sorted_aligns_file_name - if os.path.getsize( sorted_bam_file ) == 0: - #clean up temp files - if os.path.exists( tmp_dir ): - shutil.rmtree( tmp_dir ) - stop_err( 'Error creating sorted version of BAM file' ) shutil.move( sorted_bam_file, options.output1 ) #clean up temp files if os.path.exists( tmp_dir ): @@ -201,6 +192,6 @@ if os.path.getsize( options.output1 ) > 0: sys.stdout.write( 'SAM file converted to BAM' ) else: - stop_err( 'The output file is empty, there may be an error with your input file or settings.' ) + stop_err( 'Error creating sorted version of BAM file.' ) if __name__=="__main__": __main__() http://bitbucket.org/galaxy/galaxy-central/changeset/f37951db86e6/ changeset: f37951db86e6 user: fubar date: 2011-07-06 01:45:41 summary: committing backout from 5765 which included reversions from a broken galaxy-central repository affected #: 251 files (5.7 KB) --- a/lib/galaxy/security/__init__.py Tue Jul 05 11:42:56 2011 -0400 +++ b/lib/galaxy/security/__init__.py Wed Jul 06 09:45:41 2011 +1000 @@ -1005,8 +1005,7 @@ ucsc_main = ( 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', 'hgw4.cse.ucsc.edu', 'hgw5.cse.ucsc.edu', 'hgw6.cse.ucsc.edu', 'hgw7.cse.ucsc.edu', 'hgw8.cse.ucsc.edu' ), ucsc_test = ( 'hgwdev.cse.ucsc.edu', ), - ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ), - ucsc_bhri = ('ucsc.omics.bhri.internal','galaxy.omics.bhri.internal'), + ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ) ) def __init__( self, model, permitted_actions=None ): self.model = model @@ -1037,7 +1036,7 @@ # We're going to search in order, but if the remote site is load # balancing their connections (as UCSC does), this is okay. try: - if socket.gethostbyname( server ) == addr or server == '127.0.0.1' or server == '172.16.0.38': + if socket.gethostbyname( server ) == addr: break # remote host is in the server list except ( socket.error, socket.gaierror ): pass # can't resolve, try next --- a/lib/galaxy/tools/__init__.py Tue Jul 05 11:42:56 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Wed Jul 06 09:45:41 2011 +1000 @@ -922,8 +922,6 @@ if not self.check_values: return for input in self.inputs.itervalues(): - if input.name not in value: - value[input.name] = input.get_initial_value( None, value ) if isinstance( input, ToolParameter ): callback( "", input, value[input.name] ) else: --- a/lib/galaxy/tools/parameters/basic.py Tue Jul 05 11:42:56 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Wed Jul 06 09:45:41 2011 +1000 @@ -748,6 +748,9 @@ # Dependency on a value that does not yet exist if isinstance( dep_value, RuntimeValue ): return True + #dataset not ready yet + if hasattr( self, 'ref_input' ) and isinstance( dep_value, self.tool.app.model.HistoryDatasetAssociation ) and ( dep_value.is_pending or not isinstance( dep_value.datatype, self.ref_input.formats ) ): + return True # Dynamic, but all dependenceis are known and have values return False def get_initial_value( self, trans, context ): @@ -878,6 +881,7 @@ self.force_select = string_as_bool( elem.get( "force_select", True )) self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) + self.ref_input = None self.default_value = elem.get( "default_value", None ) self.is_dynamic = True def from_html( self, value, trans=None, context={} ): @@ -973,7 +977,7 @@ if not dataset.metadata.columns: # Only allow late validation if the dataset is not yet ready # (since we have reason to expect the metadata to be ready eventually) - if dataset.is_pending: + if dataset.is_pending or not isinstance( dataset.datatype, self.ref_input.formats ): return True # No late validation return False @@ -1353,7 +1357,7 @@ selected = ( value and ( hda in value ) ) field.add_option( "%s: %s" % ( hid, hda_name ), hda.id, selected ) else: - target_ext, converted_dataset = hda.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) ) + target_ext, converted_dataset = hda.find_conversion_destination( self.formats ) if target_ext: if converted_dataset: hda = converted_dataset @@ -1402,13 +1406,22 @@ pass #no valid options def dataset_collector( datasets ): def is_convertable( dataset ): - target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = self.converter_safe( context, trans ) ) + target_ext, converted_dataset = dataset.find_conversion_destination( self.formats ) if target_ext is not None: return True return False for i, data in enumerate( datasets ): - if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): - if self.options and self._options_filter_attribute( data ) != filter_value: + if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED]: + is_valid = False + if isinstance( data.datatype, self.formats ): + is_valid = True + else: + target_ext, converted_dataset = data.find_conversion_destination( self.formats ) + if target_ext: + is_valid = True + if converted_dataset: + data = converted_dataset + if not is_valid or ( self.options and self._options_filter_attribute( data ) != filter_value ): continue most_recent_dataset[0] = data # Also collect children via association object --- a/lib/galaxy/web/framework/middleware/remoteuser.py Tue Jul 05 11:42:56 2011 -0400 +++ b/lib/galaxy/web/framework/middleware/remoteuser.py Wed Jul 06 09:45:41 2011 +1000 @@ -36,7 +36,6 @@ """ UCSC_MAIN_SERVERS = ( - 'omics.bhri.internal', 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', @@ -50,7 +49,6 @@ 'lowepub.cse.ucsc.edu', ) - class RemoteUser( object ): def __init__( self, app, maildomain=None, ucsc_display_sites=[], admin_users=[] ): self.app = app @@ -58,7 +56,7 @@ self.allow_ucsc_main = False self.allow_ucsc_archaea = False self.admin_users = admin_users - if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites or 'bhri' in ucsc_display_sites: + if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites: self.allow_ucsc_main = True if 'archaea' in ucsc_display_sites: self.allow_ucsc_archaea = True --- a/scripts/cleanup_datasets/purge_libraries.sh Tue Jul 05 11:42:56 2011 -0400 +++ b/scripts/cleanup_datasets/purge_libraries.sh Wed Jul 06 09:45:41 2011 +1000 @@ -1,5 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -#python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 2 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log --- a/tool-data/shared/ucsc/ucsc_build_sites.txt Tue Jul 05 11:42:56 2011 -0400 +++ b/tool-data/shared/ucsc/ucsc_build_sites.txt Wed Jul 06 09:45:41 2011 +1000 @@ -1,6 +1,5 @@ #Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,felCat3,apiMel2,monDom4,apiMel1,ce2 -bhri http://ucsc.omics.bhri.internal/cgi-bin/hgTracks? hg18,hg19,mm8,mm9,rn4 #Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 #Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn --- a/tool_conf.xml.sample Tue Jul 05 11:42:56 2011 -0400 +++ b/tool_conf.xml.sample Wed Jul 06 09:45:41 2011 +1000 @@ -368,7 +368,6 @@ </section><section name="NGS: Simulation" id="ngs-simulation"><tool file="ngs_simulation/ngs_simulation.xml" /> - <tool file="rgenetics/EpiD.xml" /></section><section name="SNP/WGA: Data; Filters" id="rgdat"><label text="Data: Import and upload" id="rgimport" /> --- a/tools/data_source/ucsc_tablebrowser.xml Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/data_source/ucsc_tablebrowser.xml Wed Jul 06 09:45:41 2011 +1000 @@ -5,27 +5,27 @@ initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed. --><tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source"> - <description>table browser</description> - <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://ucsc.omics.bhri.internal/cgi-bin/hgTables" check_values="false" method="get"> - <display>go to UCSC Table Browser $GALAXY_URL</display> - <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> - <param name="tool_id" type="hidden" value="ucsc_table_direct1" /> - <param name="sendToGalaxy" type="hidden" value="1" /> - <param name="hgta_compressType" type="hidden" value="none" /> - <param name="hgta_outputType" type="hidden" value="bed" /> - </inputs> - <request_param_translation> + <description>table browser</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get"> + <display>go to UCSC Table Browser $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> + <param name="tool_id" type="hidden" value="ucsc_table_direct1" /> + <param name="sendToGalaxy" type="hidden" value="1" /> + <param name="hgta_compressType" type="hidden" value="none" /> + <param name="hgta_outputType" type="hidden" value="bed" /> + </inputs> + <request_param_translation><request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /><request_param galaxy_name="URL" remote_name="URL" missing="" /><request_param galaxy_name="dbkey" remote_name="db" missing="?" /><request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> - <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> - <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" > + <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> + <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="auto" ><value_translation> - <value galaxy_value="tabular" remote_value="primaryTable" /> - <value galaxy_value="tabular" remote_value="selectedFields" /> + <value galaxy_value="auto" remote_value="primaryTable" /> + <value galaxy_value="auto" remote_value="selectedFields" /><value galaxy_value="wig" remote_value="wigData" /><value galaxy_value="interval" remote_value="tab" /><value galaxy_value="html" remote_value="hyperlinks" /> @@ -33,10 +33,10 @@ <value galaxy_value="gtf" remote_value="gff" /></value_translation></request_param> - </request_param_translation> - <uihints minwidth="800"/> - <outputs> - <data name="output" format="tabular" /> - </outputs> - <options sanitize="False" refresh="True"/> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/> + </outputs> + <options sanitize="False" refresh="True"/></tool> --- a/tools/meme/meme.xml Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/meme/meme.xml Wed Jul 06 09:45:41 2011 +1000 @@ -304,7 +304,7 @@ </when></conditional> - <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="True"> + <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"><validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator></param> --- a/tools/peak_calling/macs_wrapper.py Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/peak_calling/macs_wrapper.py Wed Jul 06 09:45:41 2011 +1000 @@ -51,8 +51,7 @@ cmdline = "macs -t %s" % ",".join( options['input_chipseq'] ) if options['input_control']: cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) ) - cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s %s" %\ - ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['futurefdr'] ) + cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s --lambdaset='%s' %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['lambdaset'], options['futurefdr'] ) if 'wig' in options: wigextend = int( options['wig']['wigextend'] ) if wigextend >= 0: --- a/tools/peak_calling/macs_wrapper.xml Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/peak_calling/macs_wrapper.xml Wed Jul 06 09:45:41 2011 +1000 @@ -28,8 +28,7 @@ <param name="tsize" type="integer" label="Tag size" value="25"/><param name="bw" type="integer" label="Band width" value="300"/><param name="pvalue" type="float" label="Pvalue cutoff for peak detection" value="1e-5" help="default: 1e-5"/> - <param name="mfold" type="text" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model" value="10,30" - help="Range for high-confidence enrichment ratio against background for model are within this range. DEFAULT:10,30" /> + <param name="mfold" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model" value="32"/><param name="xls_to_interval" label="Parse xls files into into distinct interval files" type="boolean" truevalue="create" falsevalue="do_not_create" checked="False"/><conditional name="wig_type"><param name="wig_type_selector" type="select" label="Save shifted raw tag count at every bp into a wiggle file"> @@ -45,6 +44,7 @@ </when></conditional><param name="nolambda" label="Use fixed background lambda as local lambda for every peak region" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" help="up to 9X more time consuming"/> + <param name="lambdaset" type="text" label="3 levels of regions around the peak region to calculate the maximum lambda as local lambda" value="1000,5000,10000" size="50"/><conditional name="nomodel_type"><param name="nomodel_type_selector" type="select" label="Build Model"><option value="nomodel">Do not build the shifting model</option> @@ -95,7 +95,7 @@ <configfile name="options_file"><% import simplejson %> -#set $__options = { 'experiment_name':str( $experiment_name ), 'gsize':int( float( str( $gsize ) ) ), 'tsize':str( $tsize ), 'bw':str( $bw ), 'pvalue':str( $pvalue ), 'mfold':str( $mfold ), 'nolambda':str( $nolambda ), 'futurefdr':str( $futurefdr ) } +#set $__options = { 'experiment_name':str( $experiment_name ), 'gsize':int( float( str( $gsize ) ) ), 'tsize':str( $tsize ), 'bw':str( $bw ), 'pvalue':str( $pvalue ), 'mfold':str( $mfold ), 'nolambda':str( $nolambda ), 'lambdaset': str( $lambdaset ), 'futurefdr':str( $futurefdr ) } #if str( $xls_to_interval ) == 'create': #set $__options['xls_to_interval'] = { 'peaks_file': str( $output_xls_to_interval_peaks_file ), 'negative_peaks_file': str( $output_xls_to_interval_negative_peaks_file ) } #else: @@ -145,13 +145,14 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="10,30" /> + <param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /><param name="xls_to_interval" /><param name="wig_type_selector" value="no_wig" /><param name="nolambda"/> + <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> @@ -170,13 +171,14 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="10,30" /> + <param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /><param name="xls_to_interval" value="true" /><param name="wig_type_selector" value="no_wig" /><param name="nolambda"/> + <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> @@ -193,7 +195,7 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="10,30" /> + <param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /> @@ -202,6 +204,7 @@ <param name="wigextend" value="-1" /><param name="space" value="10" /><param name="nolambda"/> + <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> --- a/tools/plotting/histogram.py Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/plotting/histogram.py Wed Jul 06 09:45:41 2011 +1000 @@ -73,8 +73,7 @@ if skipped_lines < i: try: - #a = array( matrix ) - a=matrix + a = r.array( matrix ) r.pdf( out_fname, 8, 8 ) histogram = r.hist( a, probability=not frequency, main=title, xlab=xlab, breaks=breaks ) if density: --- a/tools/plotting/scatterplot.py Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/plotting/scatterplot.py Wed Jul 06 09:45:41 2011 +1000 @@ -19,14 +19,8 @@ title = sys.argv[5] xlab = sys.argv[6] ylab = sys.argv[7] - out_type = sys.argv[8] - out_width = int(sys.argv[9]) - out_height = int(sys.argv[10]) - point_size = float(sys.argv[11]) - - xvec=[] - yvec=[] + matrix = [] skipped_lines = 0 first_invalid_line = 0 invalid_value = '' @@ -34,19 +28,17 @@ i = 0 for i, line in enumerate( file( in_fname ) ): valid = True - vals = [] line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ): row = [] fields = line.split( "\t" ) - for c,column in enumerate(columns): + for column in columns: try: val = fields[column] if val.lower() == "na": - v = float( "nan" ) + row.append( float( "nan" ) ) else: - v = float( fields[column] ) - vals.append(val) + row.append( float( fields[column] ) ) except: valid = False skipped_lines += 1 @@ -65,19 +57,12 @@ first_invalid_line = i+1 if valid: - xvec.append(vals[0]) - yvec.append(vals[1]) + matrix.append( row ) + if skipped_lines < i: try: - if out_type == "jpg": - r.jpeg(out_fname,width=out_width,height=out_height) - elif out_type == "png": - # type="cairo" needed to be set for headless servers - r.png(out_fname,type="cairo",width=out_width,height=out_height) - else: - r.pdf(out_fname, out_width, out_height) - - r.plot(xvec,yvec, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19,cex=point_size ) + r.pdf( out_fname, 8, 8 ) + r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 ) r.dev_off() except Exception, exc: stop_err( "%s" %str( exc ) ) --- a/tools/plotting/scatterplot.xml Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/plotting/scatterplot.xml Wed Jul 06 09:45:41 2011 +1000 @@ -1,6 +1,6 @@ <tool id="scatterplot_rpy" name="Scatterplot"><description>of two numeric columns</description> - <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab" $output_format $out_width $out_height $point_size</command> + <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command><inputs><param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/><param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" /> @@ -8,26 +8,15 @@ <param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/><param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/><param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/> - <param name="output_format" type="select" label="Output format"> - <option value="pdf">pdf</option> - <option value="png">png</option> - <option value="jpg">jpg</option> - </param> - <param name="out_width" size="4" type="integer" value="8" label="Width (pdf=inches, image=pixels)"/> - <param name="out_height" size="4" type="integer" value="8" label="Height (pdf=inches, image=pixels)"/> - <param name="point_size" size="4" type="float" value="0.2" label="Point Size"/></inputs><outputs> - <data format="pdf" name="out_file1"> - <change_format> - <when input="output_format" value="png" format="png" /> - <when input="output_format" value="jpg" format="jpg" /> - </change_format> - </data> + <data format="pdf" name="out_file1" /></outputs><requirements><requirement type="python-module">rpy</requirement></requirements> + <help> --- a/tools/samtools/bam_to_sam.py Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/samtools/bam_to_sam.py Wed Jul 06 09:45:41 2011 +1000 @@ -21,6 +21,7 @@ parser = optparse.OptionParser() parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' ) parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' ) + parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' ) ( options, args ) = parser.parse_args() # output version # of tool @@ -87,7 +88,11 @@ try: # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ). - command = 'samtools view -o -h %s %s' % ( options.output1, tmp_sorted_aligns_file_name ) + if options.header: + view_options = "-h" + else: + view_options = "" + command = 'samtools view %s -o %s %s' % ( view_options, options.output1, tmp_sorted_aligns_file_name ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) --- a/tools/samtools/sam_bitwise_flag_filter.py Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/samtools/sam_bitwise_flag_filter.py Wed Jul 06 09:45:41 2011 +1000 @@ -1,6 +1,6 @@ #!/usr/bin/env python # Refactored on 11/13/2010 by Kanwei Li -# Added drop_header option - default is now keep headers for downstream sanity by ross lazarus + import sys import optparse @@ -14,11 +14,7 @@ options (listed below) default to 'None' if omitted """ parser = optparse.OptionParser(usage=usage) - parser.add_option('--drop_header', - action = 'store_true', - dest='drop_header', - help="Remove sam header - you probably NEVER want this for fussy downstream tools") - + parser.add_option( '--0x0001','--is_paired', choices = ( '0','1' ), @@ -133,24 +129,21 @@ opt_map = { '0': False, '1': True } used_indices = [(index, opt_map[opt]) for index, opt in enumerate(opt_ary) if opt is not None] flag_col = int( options.flag_col ) - 1 + for line in infile: line = line.rstrip( '\r\n' ) - if line: - if line.startswith('@'): - if not options.drop_header: - print line # usually want these so add -h if you don't want headers - elif not line.startswith( '#' ) : - fields = line.split( '\t' ) - flags = int( fields[flag_col] ) + if line and not line.startswith( '#' ) and not line.startswith( '@' ) : + fields = line.split( '\t' ) + flags = int( fields[flag_col] ) - valid_line = True - for index, opt_bool in used_indices: - if bool(flags & 0x0001 << index) != opt_bool: - valid_line = False - break + valid_line = True + for index, opt_bool in used_indices: + if bool(flags & 0x0001 << index) != opt_bool: + valid_line = False + break - if valid_line: - print line + if valid_line: + print line if __name__ == "__main__": main() --- a/tools/samtools/sam_bitwise_flag_filter.xml Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/samtools/sam_bitwise_flag_filter.xml Wed Jul 06 09:45:41 2011 +1000 @@ -1,11 +1,8 @@ -<tool id="sam_bw_filter" name="Filter SAM" version="1.0.1"> +<tool id="sam_bw_filter" name="Filter SAM" version="1.0.0"><description>on bitwise flag values</description><parallelism method="basic"></parallelism><command interpreter="python"> sam_bitwise_flag_filter.py - #if $drop_header == "1": - --drop_header - #end if --input_sam_file=$input1 --flag_column=2 #for $bit in $bits @@ -15,11 +12,6 @@ </command><inputs><param format="sam" name="input1" type="data" label="Select dataset to filter"/> - <param name="drop_header" type="select" display="radio" label="DROP sam headers" - help="Set this if you REALLY want to throw away existing sam header metadata - downstream (eg Picard) tools often demand it" > - <option value="0" selected="true">Keep headers (default)</option> - <option value="1">Drop headers</option> - </param><repeat name="bits" title="Flag"><param name="flags" type="select" label="Type"><option value="--0x0001">Read is paired</option> --- a/tools/samtools/sam_to_bam.py Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/samtools/sam_to_bam.py Wed Jul 06 09:45:41 2011 +1000 @@ -68,7 +68,7 @@ # and the equCab2.fa file will contain fasta sequences. seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) tmp_dir = tempfile.mkdtemp() - if options.ref_file == 'None': + if not options.ref_file or options.ref_file == 'None': # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ). # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai @@ -125,9 +125,7 @@ tmp_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir ) tmp_aligns_file_name = tmp_aligns_file.name tmp_aligns_file.close() - # IMPORTANT NOTE: for some reason the samtools view command gzips the resulting bam file without warning, - # and the docs do not currently state that this occurs ( very bad ). - command = 'samtools view -h -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) + command = 'samtools view -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) @@ -147,8 +145,6 @@ tmp_stderr.close() if returncode != 0: raise Exception, stderr - if len( open( tmp_aligns_file_name ).read() ) == 0: - raise Exception, 'Initial BAM file empty' except Exception, e: #clean up temp files if os.path.exists( tmp_dir ): @@ -188,11 +184,6 @@ stop_err( 'Error sorting alignments from (%s), %s' % ( tmp_aligns_file_name, str( e ) ) ) # Move tmp_aligns_file_name to our output dataset location sorted_bam_file = '%s.bam' % tmp_sorted_aligns_file_name - if os.path.getsize( sorted_bam_file ) == 0: - #clean up temp files - if os.path.exists( tmp_dir ): - shutil.rmtree( tmp_dir ) - stop_err( 'Error creating sorted version of BAM file' ) shutil.move( sorted_bam_file, options.output1 ) #clean up temp files if os.path.exists( tmp_dir ): @@ -201,6 +192,6 @@ if os.path.getsize( options.output1 ) > 0: sys.stdout.write( 'SAM file converted to BAM' ) else: - stop_err( 'The output file is empty, there may be an error with your input file or settings.' ) + stop_err( 'Error creating sorted version of BAM file.' ) 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: add infrastructure for getting data iteratively but, for now, still fetch all data when getting more data. Use Galaxy button styles as well.
by Bitbucket 05 Jul '11

05 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9a5c403bb2e5/ changeset: 9a5c403bb2e5 user: jgoecks date: 2011-07-05 17:42:56 summary: Trackster: add infrastructure for getting data iteratively but, for now, still fetch all data when getting more data. Use Galaxy button styles as well. affected #: 1 file (2.2 KB) --- a/static/scripts/trackster.js Tue Jul 05 16:46:21 2011 +1000 +++ b/static/scripts/trackster.js Tue Jul 05 11:42:56 2011 -0400 @@ -305,10 +305,8 @@ // Look for entry and return if found. var mode = this.track.mode, - entry = this.get(this.gen_key(low, high, mode)); - if (entry) { - return entry; - } + entry = this.get_data_from_cache(low, high, mode); + if (entry) { return entry; } // // If data supports subsetting: @@ -348,6 +346,69 @@ this.set_data(low, high, mode, entry); return entry }, + /** "Deep" data request; used as a parameter for DataManager.get_more_data() */ + DEEP_DATA_REQ: "deep", + /** "Broad" data request; used as a parameter for DataManager.get_more_data() */ + BROAD_DATA_REQ: "breadth", + /** + * Gets more data for a region using either a depth-first or a breadth-first approach. + */ + get_more_data: function(low, high, resolution, extra_params, req_type) { + // + // Get current data from cache and mark as stale. + // + var + mode = this.track.mode, + cur_data = this.get_data_from_cache(low, high, mode); + if (!cur_data) { + console.log("ERROR: no current data for: ", this.track, low, high, resolution, extra_params); + return; + } + cur_data.stale = true; + + // + // Set parameters based on request type. + // + if (req_type === this.DEEP_DATA_REQ) { + // HACK: for now, just up the max vals and request all data; in the future, + // need server to recognize min_vals and max_vals to specify range of data to + // return. + $.extend(extra_params, {max_vals: cur_data.data.length * 2}); + } + else if (req_type === this.BROAD_DATA_REQ) { + // Set low to be past the last feature returned. + low = cur_data.data[cur_data.length-1][2] + 1; + } + + // + // Get additional data, append to current data, and set new data. Use a custom deferred object + // to signal when new data is available. + // + var + data_manager = this, + new_data_request = this.load_data(low, high, resolution, extra_params) + new_data_available = $.Deferred(); + // load_data sets cache to new_data_request, but use custom deferred object so that signal and data + // is all data, not just new data. + this.set_data(low, high, mode, new_data_available); + $.when(new_data_request).then(function(result) { + if (result.data) { + //result.data.append(cur_data.data); + } + data_manager.set_data(low, high, mode, result); + new_data_available.resolve(result); + }); + return new_data_available; + }, + /** + * Gets data from the cache. + */ + get_data_from_cache: function(low, high, mode) { + return this.get(this.gen_key(low, high, mode)); + }, + /** + * Sets data in the cache. + */ set_data: function(low, high, mode, result) { //console.log("set_data", low, high, mode, result); return this.set(this.gen_key(low, high, mode), result); @@ -2150,18 +2211,15 @@ message_div = $("<div/>").addClass("tile-message").text(tile.message). // -1 to account for border. css({'height': ERROR_PADDING-1, 'width': tile.canvas.width}).appendTo(container_div), - show_more_data_btn = $("<button/>").text("Show more").css("margin-left", "0.5em").appendTo(message_div); + show_more_data_btn = $("<div/>").text("Show more").addClass("action-button").css({'padding-top': 0, 'padding-bottom':0}).appendTo(message_div); container_div.append(canvas); tile_element = container_div; // Set up actions for button. show_more_data_btn.click(function() { - // Mark data, tile as stale, request more data, and redraw track. - // HACK: get_data used will return object that can be marked as stale, but a better way to this is needed. - var cur_data = track.data_manager.get_data(tile.low, tile.high, tile.resolution); - cur_data.stale = true; + // Mark tile as stale, request more data, and redraw track. tile.stale = true; - track.data_manager.get_data(tile.low, tile.high, tile.resolution, {max_vals: cur_data.data.length * 2}); + track.data_manager.get_more_data(tile.low, tile.high, tile.resolution, {}, track.data_manager.DEEP_DATA_REQ); track.draw(); }).dblclick(function(e) { // Do not propogate as this would normal zoom in. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 05 Jul '11

05 Jul '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/48bbe32beefe/ changeset: 48bbe32beefe user: galaxy galaxy date: 2011-07-05 04:40:43 summary: branch merge affected #: 250 files (5.2 KB) --- a/lib/galaxy/security/__init__.py Mon Jul 04 11:06:04 2011 -0400 +++ b/lib/galaxy/security/__init__.py Tue Jul 05 12:40:43 2011 +1000 @@ -1005,7 +1005,8 @@ ucsc_main = ( 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', 'hgw4.cse.ucsc.edu', 'hgw5.cse.ucsc.edu', 'hgw6.cse.ucsc.edu', 'hgw7.cse.ucsc.edu', 'hgw8.cse.ucsc.edu' ), ucsc_test = ( 'hgwdev.cse.ucsc.edu', ), - ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ) + ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ), + ucsc_bhri = ('ucsc.omics.bhri.internal','galaxy.omics.bhri.internal'), ) def __init__( self, model, permitted_actions=None ): self.model = model @@ -1036,7 +1037,7 @@ # We're going to search in order, but if the remote site is load # balancing their connections (as UCSC does), this is okay. try: - if socket.gethostbyname( server ) == addr: + if socket.gethostbyname( server ) == addr or server == '127.0.0.1' or server == '172.16.0.38': break # remote host is in the server list except ( socket.error, socket.gaierror ): pass # can't resolve, try next --- a/lib/galaxy/tools/__init__.py Mon Jul 04 11:06:04 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Tue Jul 05 12:40:43 2011 +1000 @@ -922,6 +922,8 @@ if not self.check_values: return for input in self.inputs.itervalues(): + if input.name not in value: + value[input.name] = input.get_initial_value( None, value ) if isinstance( input, ToolParameter ): callback( "", input, value[input.name] ) else: --- a/lib/galaxy/tools/parameters/basic.py Mon Jul 04 11:06:04 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Tue Jul 05 12:40:43 2011 +1000 @@ -748,9 +748,6 @@ # Dependency on a value that does not yet exist if isinstance( dep_value, RuntimeValue ): return True - #dataset not ready yet - if hasattr( self, 'ref_input' ) and isinstance( dep_value, self.tool.app.model.HistoryDatasetAssociation ) and ( dep_value.is_pending or not isinstance( dep_value.datatype, self.ref_input.formats ) ): - return True # Dynamic, but all dependenceis are known and have values return False def get_initial_value( self, trans, context ): @@ -881,7 +878,6 @@ self.force_select = string_as_bool( elem.get( "force_select", True )) self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) - self.ref_input = None self.default_value = elem.get( "default_value", None ) self.is_dynamic = True def from_html( self, value, trans=None, context={} ): @@ -977,7 +973,7 @@ if not dataset.metadata.columns: # Only allow late validation if the dataset is not yet ready # (since we have reason to expect the metadata to be ready eventually) - if dataset.is_pending or not isinstance( dataset.datatype, self.ref_input.formats ): + if dataset.is_pending: return True # No late validation return False @@ -1357,7 +1353,7 @@ selected = ( value and ( hda in value ) ) field.add_option( "%s: %s" % ( hid, hda_name ), hda.id, selected ) else: - target_ext, converted_dataset = hda.find_conversion_destination( self.formats ) + target_ext, converted_dataset = hda.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) ) if target_ext: if converted_dataset: hda = converted_dataset @@ -1406,22 +1402,13 @@ pass #no valid options def dataset_collector( datasets ): def is_convertable( dataset ): - target_ext, converted_dataset = dataset.find_conversion_destination( self.formats ) + target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = self.converter_safe( context, trans ) ) if target_ext is not None: return True return False for i, data in enumerate( datasets ): - if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED]: - is_valid = False - if isinstance( data.datatype, self.formats ): - is_valid = True - else: - target_ext, converted_dataset = data.find_conversion_destination( self.formats ) - if target_ext: - is_valid = True - if converted_dataset: - data = converted_dataset - if not is_valid or ( self.options and self._options_filter_attribute( data ) != filter_value ): + if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): + if self.options and self._options_filter_attribute( data ) != filter_value: continue most_recent_dataset[0] = data # Also collect children via association object --- a/lib/galaxy/web/framework/middleware/remoteuser.py Mon Jul 04 11:06:04 2011 -0400 +++ b/lib/galaxy/web/framework/middleware/remoteuser.py Tue Jul 05 12:40:43 2011 +1000 @@ -36,6 +36,7 @@ """ UCSC_MAIN_SERVERS = ( + 'omics.bhri.internal', 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', @@ -49,6 +50,7 @@ 'lowepub.cse.ucsc.edu', ) + class RemoteUser( object ): def __init__( self, app, maildomain=None, ucsc_display_sites=[], admin_users=[] ): self.app = app @@ -56,7 +58,7 @@ self.allow_ucsc_main = False self.allow_ucsc_archaea = False self.admin_users = admin_users - if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites: + if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites or 'bhri' in ucsc_display_sites: self.allow_ucsc_main = True if 'archaea' in ucsc_display_sites: self.allow_ucsc_archaea = True --- a/scripts/cleanup_datasets/purge_libraries.sh Mon Jul 04 11:06:04 2011 -0400 +++ b/scripts/cleanup_datasets/purge_libraries.sh Tue Jul 05 12:40:43 2011 +1000 @@ -1,4 +1,5 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log +#python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 2 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log --- a/tool-data/shared/ucsc/ucsc_build_sites.txt Mon Jul 04 11:06:04 2011 -0400 +++ b/tool-data/shared/ucsc/ucsc_build_sites.txt Tue Jul 05 12:40:43 2011 +1000 @@ -1,5 +1,6 @@ #Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,felCat3,apiMel2,monDom4,apiMel1,ce2 +bhri http://ucsc.omics.bhri.internal/cgi-bin/hgTracks? hg18,hg19,mm8,mm9,rn4 #Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 #Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn --- a/tool_conf.xml.sample Mon Jul 04 11:06:04 2011 -0400 +++ b/tool_conf.xml.sample Tue Jul 05 12:40:43 2011 +1000 @@ -368,6 +368,7 @@ </section><section name="NGS: Simulation" id="ngs-simulation"><tool file="ngs_simulation/ngs_simulation.xml" /> + <tool file="rgenetics/EpiD.xml" /></section><section name="SNP/WGA: Data; Filters" id="rgdat"><label text="Data: Import and upload" id="rgimport" /> --- a/tools/data_source/ucsc_tablebrowser.xml Mon Jul 04 11:06:04 2011 -0400 +++ b/tools/data_source/ucsc_tablebrowser.xml Tue Jul 05 12:40:43 2011 +1000 @@ -5,27 +5,27 @@ initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed. --><tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source"> - <description>table browser</description> - <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get"> - <display>go to UCSC Table Browser $GALAXY_URL</display> - <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> - <param name="tool_id" type="hidden" value="ucsc_table_direct1" /> - <param name="sendToGalaxy" type="hidden" value="1" /> - <param name="hgta_compressType" type="hidden" value="none" /> - <param name="hgta_outputType" type="hidden" value="bed" /> - </inputs> - <request_param_translation> + <description>table browser</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://ucsc.omics.bhri.internal/cgi-bin/hgTables" check_values="false" method="get"> + <display>go to UCSC Table Browser $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> + <param name="tool_id" type="hidden" value="ucsc_table_direct1" /> + <param name="sendToGalaxy" type="hidden" value="1" /> + <param name="hgta_compressType" type="hidden" value="none" /> + <param name="hgta_outputType" type="hidden" value="bed" /> + </inputs> + <request_param_translation><request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /><request_param galaxy_name="URL" remote_name="URL" missing="" /><request_param galaxy_name="dbkey" remote_name="db" missing="?" /><request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> - <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> - <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="auto" > + <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> + <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" ><value_translation> - <value galaxy_value="auto" remote_value="primaryTable" /> - <value galaxy_value="auto" remote_value="selectedFields" /> + <value galaxy_value="tabular" remote_value="primaryTable" /> + <value galaxy_value="tabular" remote_value="selectedFields" /><value galaxy_value="wig" remote_value="wigData" /><value galaxy_value="interval" remote_value="tab" /><value galaxy_value="html" remote_value="hyperlinks" /> @@ -33,10 +33,10 @@ <value galaxy_value="gtf" remote_value="gff" /></value_translation></request_param> - </request_param_translation> - <uihints minwidth="800"/> - <outputs> - <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/> - </outputs> - <options sanitize="False" refresh="True"/> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <options sanitize="False" refresh="True"/></tool> --- a/tools/meme/meme.xml Mon Jul 04 11:06:04 2011 -0400 +++ b/tools/meme/meme.xml Tue Jul 05 12:40:43 2011 +1000 @@ -304,7 +304,7 @@ </when></conditional> - <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"> + <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="True"><validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator></param> --- a/tools/peak_calling/macs_wrapper.py Mon Jul 04 11:06:04 2011 -0400 +++ b/tools/peak_calling/macs_wrapper.py Tue Jul 05 12:40:43 2011 +1000 @@ -51,7 +51,8 @@ cmdline = "macs -t %s" % ",".join( options['input_chipseq'] ) if options['input_control']: cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) ) - cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s --lambdaset='%s' %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['lambdaset'], options['futurefdr'] ) + cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s %s" %\ + ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['futurefdr'] ) if 'wig' in options: wigextend = int( options['wig']['wigextend'] ) if wigextend >= 0: --- a/tools/peak_calling/macs_wrapper.xml Mon Jul 04 11:06:04 2011 -0400 +++ b/tools/peak_calling/macs_wrapper.xml Tue Jul 05 12:40:43 2011 +1000 @@ -28,7 +28,8 @@ <param name="tsize" type="integer" label="Tag size" value="25"/><param name="bw" type="integer" label="Band width" value="300"/><param name="pvalue" type="float" label="Pvalue cutoff for peak detection" value="1e-5" help="default: 1e-5"/> - <param name="mfold" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model" value="32"/> + <param name="mfold" type="text" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model" value="10,30" + help="Range for high-confidence enrichment ratio against background for model are within this range. DEFAULT:10,30" /><param name="xls_to_interval" label="Parse xls files into into distinct interval files" type="boolean" truevalue="create" falsevalue="do_not_create" checked="False"/><conditional name="wig_type"><param name="wig_type_selector" type="select" label="Save shifted raw tag count at every bp into a wiggle file"> @@ -44,7 +45,6 @@ </when></conditional><param name="nolambda" label="Use fixed background lambda as local lambda for every peak region" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" help="up to 9X more time consuming"/> - <param name="lambdaset" type="text" label="3 levels of regions around the peak region to calculate the maximum lambda as local lambda" value="1000,5000,10000" size="50"/><conditional name="nomodel_type"><param name="nomodel_type_selector" type="select" label="Build Model"><option value="nomodel">Do not build the shifting model</option> @@ -95,7 +95,7 @@ <configfile name="options_file"><% import simplejson %> -#set $__options = { 'experiment_name':str( $experiment_name ), 'gsize':int( float( str( $gsize ) ) ), 'tsize':str( $tsize ), 'bw':str( $bw ), 'pvalue':str( $pvalue ), 'mfold':str( $mfold ), 'nolambda':str( $nolambda ), 'lambdaset': str( $lambdaset ), 'futurefdr':str( $futurefdr ) } +#set $__options = { 'experiment_name':str( $experiment_name ), 'gsize':int( float( str( $gsize ) ) ), 'tsize':str( $tsize ), 'bw':str( $bw ), 'pvalue':str( $pvalue ), 'mfold':str( $mfold ), 'nolambda':str( $nolambda ), 'futurefdr':str( $futurefdr ) } #if str( $xls_to_interval ) == 'create': #set $__options['xls_to_interval'] = { 'peaks_file': str( $output_xls_to_interval_peaks_file ), 'negative_peaks_file': str( $output_xls_to_interval_negative_peaks_file ) } #else: @@ -145,14 +145,13 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="13" /> + <param name="mfold" value="10,30" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /><param name="xls_to_interval" /><param name="wig_type_selector" value="no_wig" /><param name="nolambda"/> - <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> @@ -171,14 +170,13 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="13" /> + <param name="mfold" value="10,30" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /><param name="xls_to_interval" value="true" /><param name="wig_type_selector" value="no_wig" /><param name="nolambda"/> - <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> @@ -195,7 +193,7 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="13" /> + <param name="mfold" value="10,30" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /> @@ -204,7 +202,6 @@ <param name="wigextend" value="-1" /><param name="space" value="10" /><param name="nolambda"/> - <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> --- a/tools/plotting/histogram.py Mon Jul 04 11:06:04 2011 -0400 +++ b/tools/plotting/histogram.py Tue Jul 05 12:40:43 2011 +1000 @@ -73,7 +73,8 @@ if skipped_lines < i: try: - a = r.array( matrix ) + #a = array( matrix ) + a=matrix r.pdf( out_fname, 8, 8 ) histogram = r.hist( a, probability=not frequency, main=title, xlab=xlab, breaks=breaks ) if density: --- a/tools/plotting/scatterplot.py Mon Jul 04 11:06:04 2011 -0400 +++ b/tools/plotting/scatterplot.py Tue Jul 05 12:40:43 2011 +1000 @@ -19,8 +19,14 @@ title = sys.argv[5] xlab = sys.argv[6] ylab = sys.argv[7] + out_type = sys.argv[8] + out_width = int(sys.argv[9]) + out_height = int(sys.argv[10]) + point_size = float(sys.argv[11]) - matrix = [] + + xvec=[] + yvec=[] skipped_lines = 0 first_invalid_line = 0 invalid_value = '' @@ -28,17 +34,19 @@ i = 0 for i, line in enumerate( file( in_fname ) ): valid = True + vals = [] line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ): row = [] fields = line.split( "\t" ) - for column in columns: + for c,column in enumerate(columns): try: val = fields[column] if val.lower() == "na": - row.append( float( "nan" ) ) + v = float( "nan" ) else: - row.append( float( fields[column] ) ) + v = float( fields[column] ) + vals.append(val) except: valid = False skipped_lines += 1 @@ -57,12 +65,19 @@ first_invalid_line = i+1 if valid: - matrix.append( row ) - + xvec.append(vals[0]) + yvec.append(vals[1]) if skipped_lines < i: try: - r.pdf( out_fname, 8, 8 ) - r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 ) + if out_type == "jpg": + r.jpeg(out_fname,width=out_width,height=out_height) + elif out_type == "png": + # type="cairo" needed to be set for headless servers + r.png(out_fname,type="cairo",width=out_width,height=out_height) + else: + r.pdf(out_fname, out_width, out_height) + + r.plot(xvec,yvec, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19,cex=point_size ) r.dev_off() except Exception, exc: stop_err( "%s" %str( exc ) ) --- a/tools/plotting/scatterplot.xml Mon Jul 04 11:06:04 2011 -0400 +++ b/tools/plotting/scatterplot.xml Tue Jul 05 12:40:43 2011 +1000 @@ -1,6 +1,6 @@ <tool id="scatterplot_rpy" name="Scatterplot"><description>of two numeric columns</description> - <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command> + <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab" $output_format $out_width $out_height $point_size</command><inputs><param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/><param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" /> @@ -8,15 +8,26 @@ <param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/><param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/><param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/> + <param name="output_format" type="select" label="Output format"> + <option value="pdf">pdf</option> + <option value="png">png</option> + <option value="jpg">jpg</option> + </param> + <param name="out_width" size="4" type="integer" value="8" label="Width (pdf=inches, image=pixels)"/> + <param name="out_height" size="4" type="integer" value="8" label="Height (pdf=inches, image=pixels)"/> + <param name="point_size" size="4" type="float" value="0.2" label="Point Size"/></inputs><outputs> - <data format="pdf" name="out_file1" /> + <data format="pdf" name="out_file1"> + <change_format> + <when input="output_format" value="png" format="png" /> + <when input="output_format" value="jpg" format="jpg" /> + </change_format> + </data></outputs><requirements><requirement type="python-module">rpy</requirement></requirements> - <help> --- a/tools/samtools/bam_to_sam.py Mon Jul 04 11:06:04 2011 -0400 +++ b/tools/samtools/bam_to_sam.py Tue Jul 05 12:40:43 2011 +1000 @@ -21,7 +21,6 @@ parser = optparse.OptionParser() parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' ) parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' ) - parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' ) ( options, args ) = parser.parse_args() # output version # of tool @@ -88,11 +87,7 @@ try: # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ). - if options.header: - view_options = "-h" - else: - view_options = "" - command = 'samtools view %s -o %s %s' % ( view_options, options.output1, tmp_sorted_aligns_file_name ) + command = 'samtools view -o -h %s %s' % ( options.output1, tmp_sorted_aligns_file_name ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) --- a/tools/samtools/sam_bitwise_flag_filter.py Mon Jul 04 11:06:04 2011 -0400 +++ b/tools/samtools/sam_bitwise_flag_filter.py Tue Jul 05 12:40:43 2011 +1000 @@ -1,6 +1,6 @@ #!/usr/bin/env python # Refactored on 11/13/2010 by Kanwei Li - +# Added drop_header option - default is now keep headers for downstream sanity by ross lazarus import sys import optparse @@ -14,7 +14,11 @@ options (listed below) default to 'None' if omitted """ parser = optparse.OptionParser(usage=usage) - + parser.add_option('--drop_header', + action = 'store_true', + dest='drop_header', + help="Remove sam header - you probably NEVER want this for fussy downstream tools") + parser.add_option( '--0x0001','--is_paired', choices = ( '0','1' ), @@ -129,21 +133,24 @@ opt_map = { '0': False, '1': True } used_indices = [(index, opt_map[opt]) for index, opt in enumerate(opt_ary) if opt is not None] flag_col = int( options.flag_col ) - 1 - for line in infile: line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and not line.startswith( '@' ) : - fields = line.split( '\t' ) - flags = int( fields[flag_col] ) + if line: + if line.startswith('@'): + if not options.drop_header: + print line # usually want these so add -h if you don't want headers + elif not line.startswith( '#' ) : + fields = line.split( '\t' ) + flags = int( fields[flag_col] ) - valid_line = True - for index, opt_bool in used_indices: - if bool(flags & 0x0001 << index) != opt_bool: - valid_line = False - break + valid_line = True + for index, opt_bool in used_indices: + if bool(flags & 0x0001 << index) != opt_bool: + valid_line = False + break - if valid_line: - print line + if valid_line: + print line if __name__ == "__main__": main() --- a/tools/samtools/sam_bitwise_flag_filter.xml Mon Jul 04 11:06:04 2011 -0400 +++ b/tools/samtools/sam_bitwise_flag_filter.xml Tue Jul 05 12:40:43 2011 +1000 @@ -1,8 +1,11 @@ -<tool id="sam_bw_filter" name="Filter SAM" version="1.0.0"> +<tool id="sam_bw_filter" name="Filter SAM" version="1.0.1"><description>on bitwise flag values</description><parallelism method="basic"></parallelism><command interpreter="python"> sam_bitwise_flag_filter.py + #if $drop_header == "1": + --drop_header + #end if --input_sam_file=$input1 --flag_column=2 #for $bit in $bits @@ -12,6 +15,11 @@ </command><inputs><param format="sam" name="input1" type="data" label="Select dataset to filter"/> + <param name="drop_header" type="select" display="radio" label="DROP sam headers" + help="Set this if you REALLY want to throw away existing sam header metadata - downstream (eg Picard) tools often demand it" > + <option value="0" selected="true">Keep headers (default)</option> + <option value="1">Drop headers</option> + </param><repeat name="bits" title="Flag"><param name="flags" type="select" label="Type"><option value="--0x0001">Read is paired</option> --- a/tools/samtools/sam_to_bam.py Mon Jul 04 11:06:04 2011 -0400 +++ b/tools/samtools/sam_to_bam.py Tue Jul 05 12:40:43 2011 +1000 @@ -68,7 +68,7 @@ # and the equCab2.fa file will contain fasta sequences. seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) tmp_dir = tempfile.mkdtemp() - if not options.ref_file or options.ref_file == 'None': + if options.ref_file == 'None': # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ). # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai @@ -125,7 +125,9 @@ tmp_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir ) tmp_aligns_file_name = tmp_aligns_file.name tmp_aligns_file.close() - command = 'samtools view -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) + # IMPORTANT NOTE: for some reason the samtools view command gzips the resulting bam file without warning, + # and the docs do not currently state that this occurs ( very bad ). + command = 'samtools view -h -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) @@ -145,6 +147,8 @@ tmp_stderr.close() if returncode != 0: raise Exception, stderr + if len( open( tmp_aligns_file_name ).read() ) == 0: + raise Exception, 'Initial BAM file empty' except Exception, e: #clean up temp files if os.path.exists( tmp_dir ): @@ -184,6 +188,11 @@ stop_err( 'Error sorting alignments from (%s), %s' % ( tmp_aligns_file_name, str( e ) ) ) # Move tmp_aligns_file_name to our output dataset location sorted_bam_file = '%s.bam' % tmp_sorted_aligns_file_name + if os.path.getsize( sorted_bam_file ) == 0: + #clean up temp files + if os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + stop_err( 'Error creating sorted version of BAM file' ) shutil.move( sorted_bam_file, options.output1 ) #clean up temp files if os.path.exists( tmp_dir ): @@ -192,6 +201,6 @@ if os.path.getsize( options.output1 ) > 0: sys.stdout.write( 'SAM file converted to BAM' ) else: - stop_err( 'Error creating sorted version of BAM file.' ) + stop_err( 'The output file is empty, there may be an error with your input file or settings.' ) if __name__=="__main__": __main__() http://bitbucket.org/galaxy/galaxy-central/changeset/100080d818fa/ changeset: 100080d818fa user: galaxy galaxy date: 2011-07-05 08:46:21 summary: Added new test and optional x axis unit alternatives (bits/probability/kcal etc) to weblogo as suggested by Assaf Gordon affected #: 3 files (28.9 KB) Binary file test-data/rgWebLogo3_test2.png has changed --- a/tools/rgenetics/rgWebLogo3.py Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/rgenetics/rgWebLogo3.py Tue Jul 05 16:46:21 2011 +1000 @@ -1,10 +1,13 @@ """ +# modified june 2 ross lazarus to add units option at Assaf Gordon's suggestion # rgWebLogo3.py # wrapper to check that all fasta files are same length """ import optparse, os, sys, subprocess, tempfile +WEBLOGO = 'weblogo' # executable name for weblogo3 - confusing isn't it? + class WL3: """ simple wrapper class to check fasta sequence lengths are all identical @@ -18,10 +21,21 @@ self.fastaf = file(self.opts.input,'r') self.clparams = {} + def whereis(self,program): + for path in os.environ.get('PATH', '').split(':'): + if os.path.exists(os.path.join(path, program)) and not os.path.isdir(os.path.join(path, program)): + return os.path.join(path, program) + return None + def runCL(self): """ construct and run a command line """ - cll = ['weblogo',] + wl = self.whereis(WEBLOGO) + if not wl: + print >> sys.stderr, '## rgWebLogo3.py error - cannot locate the weblogo binary %s on the current path' % WEBLOGO + print >> sys.stderr, '## Please ensure it is installed and working from http://code.google.com/p/weblogo' + sys.exit(1) + cll = [WEBLOGO,] cll += [' '.join(it) for it in list(self.clparams.items())] cl = ' '.join(cll) assert cl > '', 'runCL needs a command line as clparms' @@ -59,8 +73,13 @@ sys.exit(1) else: seqname = row[1:].strip() - else: - aseq.append(row.strip()) + else: # sequence row + if seqname == None: + print >> sys.stderr,'Invalid fasta file %s - does not start with %s - please read the tool documentation carefully' % (self.opts.input,self.FASTASTARTSYM) + sys.exit(1) + else: + aseq.append(row.strip()) + if seqname <> None: # last one l = len(''.join(aseq)) yield (seqname,l) @@ -74,7 +93,7 @@ lasti = None f = self.iter_fasta() for i,(seqname,seqlen) in enumerate(f): - lasti = i + lasti = i if i == 0: flen = seqlen else: @@ -98,6 +117,8 @@ self.clparams['-u'] = self.opts.upper if self.opts.colours <> None: self.clparams['-c'] = self.opts.colours + if self.opts.units <> None: + self.clparams['-U'] = self.opts.units s = self.runCL() return check,s @@ -122,6 +143,7 @@ op.add_option('-c', '--colours', default=None) op.add_option('-l', '--lower', default=None) op.add_option('-u', '--upper', default=None) + op.add_option('-U', '--units', default=None) opts, args = op.parse_args() assert opts.input <> None,'weblogo3 needs a -i parameter with a fasta input file - cannot open' assert os.path.isfile(opts.input),'weblogo3 needs a valid fasta input file - cannot open %s' % opts.input --- a/tools/rgenetics/rgWebLogo3.xml Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/rgenetics/rgWebLogo3.xml Tue Jul 05 16:46:21 2011 +1000 @@ -1,7 +1,7 @@ -<tool id="rgweblogo3" name="Sequence Logo" version="0.2"> +<tool id="rgweblogo3" name="Sequence Logo" version="0.3"><description>generator for fasta (eg Clustal alignments)</description><command interpreter="python"> - rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" + rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units" #if $range.mode == 'part' -l "$range.seqstart" -u "$range.seqend" #end if @@ -18,6 +18,15 @@ <option value="eps">EPS</option><option value="txt">Text (shows the detailed calculations for each position - no image)</option></param> + <param name="units" type="select" label="Display Units" + help="What the height of each logo element depicts - eg bits of entropy (default)"> + <option value="bits" selected="True">Entropy (bits)</option> + <option value="probability">Probability</option> + <option value="nats">Nats</option> + <option value="kT">kT</option> + <option value="kJ/mol">kJ/mol</option> + <option value="kcal/mol">kcal/mol</option> + </param><param name="colours" type="select" label="Colour scheme for output Sequence Logo" help="Note that some of these only make sense for protein sequences!"><option value="auto" selected="True">Default automatic colour selection</option> @@ -28,6 +37,7 @@ <option value="hydrophobicity">Hydrophobicity</option><option value="monochrome">monochrome</option></param> + <conditional name="range"><param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use"> @@ -63,17 +73,26 @@ </data></outputs><tests> - <test> - + <test><param name="input" value="rgClustal_testout.fasta" /><param name = "logoname" value="Galaxy/Rgenetics weblogo" /><param name = "outformat" value="jpeg" /><param name = "mode" value="complete" /><param name = "size" value="medium" /><param name = "colours" value="auto" /> + <param name = "units" value="bits" /><output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" compare="sim_size" delta="10000" /></test> - + <test> + <param name="input" value="rgClustal_testout.fasta" /> + <param name = "logoname" value="Galaxy/Rgenetics weblogo" /> + <param name = "outformat" value="png" /> + <param name = "mode" value="complete" /> + <param name = "size" value="medium" /> + <param name = "colours" value="auto" /> + <param name = "units" value="probability" /> + <output name="output" file="rgWebLogo3_test2.png" ftype="png" compare="sim_size" delta="10000" /> + </test></tests><help> @@ -92,7 +111,8 @@ **Warning about input Fasta format files** -The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. +The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. The tool will provide a warning +and refuse to call the weblogo3 executable if irregular length sequences are detected. Fasta alignments from the companion ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta 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 refactoring: (a) change data_cache attributes to data_manager to reflect attribute type; (b) automatically use track mode and track view's chrom when getting data from the manager; and (c) calculate and store low, high for Tiles to facilitate reuse.
by Bitbucket 04 Jul '11

04 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ffa23ea969e6/ changeset: ffa23ea969e6 user: jgoecks date: 2011-07-04 17:06:04 summary: Trackster refactoring: (a) change data_cache attributes to data_manager to reflect attribute type; (b) automatically use track mode and track view's chrom when getting data from the manager; and (c) calculate and store low, high for Tiles to facilitate reuse. affected #: 1 file (64 bytes) --- a/static/scripts/trackster.js Sun Jul 03 15:05:25 2011 -0400 +++ b/static/scripts/trackster.js Mon Jul 04 11:06:04 2011 -0400 @@ -263,9 +263,12 @@ /** * Load data from server; returns AJAX object so that use of Deferred is possible. */ - load_data: function(chrom, low, high, mode, resolution, extra_params) { + load_data: function(low, high, resolution, extra_params) { // Setup data request params. - var params = {"chrom": chrom, "low": low, "high": high, "mode": mode, + var + chrom = this.track.view.chrom, + mode = this.track.mode, + params = {"chrom": chrom, "low": low, "high": high, "mode": mode, "resolution": resolution, "dataset_id" : this.track.dataset_id, "hda_ldda": this.track.hda_ldda}; $.extend(params, extra_params); @@ -289,7 +292,7 @@ /** * Get track data. */ - get_data: function(chrom, low, high, mode, resolution, extra_params) { + get_data: function(low, high, resolution, extra_params) { // Debugging: //console.log("get_data", low, high, mode); /* @@ -300,7 +303,9 @@ */ // Look for entry and return if found. - var entry = this.get(this.gen_key(low, high, mode)); + var + mode = this.track.mode, + entry = this.get(this.gen_key(low, high, mode)); if (entry) { return entry; } @@ -315,6 +320,7 @@ // /* Disabling for now, more detailed data is never loaded for line tracks + TODO: can using resolution in the key solve this problem? if (this.subset) { var key, split_key, entry_low, entry_high, mode, entry; for (var i = 0; i < this.key_ary.length; i++) { @@ -338,7 +344,7 @@ // Load data from server. The deferred is immediately saved until the // data is ready, it then replaces itself with the actual data - entry = this.load_data(chrom, low, high, mode, resolution, extra_params); + entry = this.load_data(low, high, resolution, extra_params); this.set_data(low, high, mode, entry); return entry }, @@ -349,6 +355,8 @@ /** * Generate key for cache. */ + // TODO: use chrom in key so that (a) data is not thrown away when changing chroms and (b) + // manager does not need to be cleared when changing chroms. gen_key: function(low, high, mode) { var key = low + "_" + high + "_" + mode; return key; @@ -1504,6 +1512,8 @@ */ var Tile = function(index, resolution, canvas) { this.index = index; + this.low = index * DENSITY * resolution; + this.high = (index + 1) * DENSITY * resolution; this.resolution = resolution; // Wrap element in div for background. this.canvas = $("<div class='track-tile'/>").append(canvas); @@ -1598,7 +1608,7 @@ var track = this; track.enabled = false; track.tile_cache.clear(); - track.data_cache.clear(); + track.data_manager.clear(); track.initial_canvas = undefined; track.content_div.css("height", "auto"); /* @@ -1935,7 +1945,7 @@ var tile_high = tile_low + DENSITY * this.view.resolution; if (!force && cached) { drawn_tiles[drawn_tiles.length] = cached; - this.show_tile(cached, parent_element, tile_low, tile_high, w_scale); + this.show_tile(cached, parent_element, w_scale); } else { this.delayed_draw(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles); } @@ -2087,7 +2097,7 @@ if (tile === undefined) { return; } - track.show_tile(tile, parent_element, tile_low, tile_high, w_scale); + track.show_tile(tile, parent_element, w_scale); drawn_tiles[drawn_tiles.length] = tile; }; // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data @@ -2096,21 +2106,19 @@ // Show/draw tile: check cache for tile; if tile not in cache, draw it. var tile = (force ? undefined : track.tile_cache.get(key)); if (tile) { - track.show_tile(tile, parent_element, tile_low, tile_high, w_scale); + track.show_tile(tile, parent_element, w_scale); drawn_tiles[drawn_tiles.length] = tile; } else { // // Really draw tile: get data, seq data if available, and draw tile. // - $.when(track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, - resolution, track.data_url_extra_params)).then(function(tile_data) { + $.when(track.data_manager.get_data(tile_low, tile_high, resolution, track.data_url_extra_params)).then(function(tile_data) { extend(tile_data, more_tile_data); // If sequence data needed, get that and draw. Otherwise draw. if (view.reference_track && w_scale > view.canvas_manager.char_width_px) { - $.when(view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high, - track.mode, resolution, - view.reference_track.data_url_extra_params)).then(function(seq_data) { + $.when(view.reference_track.data_manager.get_data(tile_low, tile_high, resolution, + view.reference_track.data_url_extra_params)).then(function(seq_data) { draw_and_show_tile(id, tile_data, resolution, tile_index, parent_element, w_scale, seq_data); }); } @@ -2125,7 +2133,7 @@ /** * Show track tile and perform associated actions. */ - show_tile: function(tile, parent_element, tile_low, tile_high, w_scale) { + show_tile: function(tile, parent_element, w_scale) { // Readability. var track = this, @@ -2150,10 +2158,10 @@ show_more_data_btn.click(function() { // Mark data, tile as stale, request more data, and redraw track. // HACK: get_data used will return object that can be marked as stale, but a better way to this is needed. - var cur_data = track.data_cache.get_data(track.view.chrom, tile_low, tile_high, track.mode, tile.resolution); + var cur_data = track.data_manager.get_data(tile.low, tile.high, tile.resolution); cur_data.stale = true; tile.stale = true; - track.data_cache.get_data(track.view.chrom, tile_low, tile_high, track.mode, tile.resolution, {max_vals: cur_data.data.length * 2}); + track.data_manager.get_data(tile.low, tile.high, tile.resolution, {max_vals: cur_data.data.length * 2}); track.draw(); }).dblclick(function(e) { // Do not propogate as this would normal zoom in. @@ -2167,7 +2175,7 @@ // Position tile element, recalculate left position at display time var range = this.view.high - this.view.low, - left = (tile_low - this.view.low) * w_scale; + left = (tile.low - this.view.low) * w_scale; if (this.left_offset) { left -= this.left_offset; } @@ -2259,13 +2267,13 @@ view.reference_track = this; this.left_offset = 200; this.height_px = 12; - this.container_div.addClass( "reference-track" ); + 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: view.dbkey}; - this.data_cache = new ReferenceTrackDataManager(CACHED_DATA, this, false); + this.data_manager = new ReferenceTrackDataManager(CACHED_DATA, this, false); this.tile_cache = new Cache(CACHED_TILES_LINE); }; extend(ReferenceTrack.prototype, TiledTrack.prototype, { @@ -2283,7 +2291,7 @@ } var canvas = this.view.canvas_manager.new_canvas(); var ctx = canvas.getContext("2d"); - canvas.width = Math.ceil( tile_length * w_scale + track.left_offset); + canvas.width = Math.ceil(tile_length * w_scale + track.left_offset); canvas.height = track.height_px; ctx.font = ctx.canvas.manager.default_font; ctx.textAlign = "center"; @@ -2310,7 +2318,7 @@ this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; - this.data_cache = new DataManager(CACHED_DATA, this); + this.data_manager = new DataManager(CACHED_DATA, this); this.tile_cache = new Cache(CACHED_TILES_LINE); // Define track configuration @@ -2426,11 +2434,10 @@ // Paint line onto full canvas var ctx = canvas.getContext("2d"); - var painter = new painters.LinePainter( result.data, tile_low, tile_low + tile_length, - this.prefs, this.mode ); + var painter = new painters.LinePainter(result.data, tile_low, tile_low + tile_length, this.prefs, this.mode); painter.draw(ctx, width, height); - return new Tile(tile_length, resolution, canvas); + return new Tile(tile_index, resolution, canvas); } }); @@ -2475,7 +2482,7 @@ this.inc_slots = {}; this.start_end_dct = {}; this.tile_cache = new Cache(CACHED_TILES_FEATURE); - this.data_cache = new DataManager(20, this); + this.data_manager = new DataManager(20, this); this.left_offset = 200; this.painter = painters.LinkedFeaturePainter; @@ -2600,9 +2607,9 @@ draw_tile: function(result, resolution, tile_index, w_scale, ref_seq) { var track = this, tile_low = tile_index * DENSITY * resolution, - tile_high = ( tile_index + 1 ) * DENSITY * resolution, + tile_high = (tile_index + 1) * DENSITY * resolution, tile_span = tile_high - tile_low, - width = Math.ceil( tile_span * w_scale ), + width = Math.ceil(tile_span * w_scale), mode = this.mode, min_height = 25, left_offset = this.left_offset, @@ -2703,7 +2710,7 @@ // Create painter, and canvas of sufficient size to contain all features // 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, ref_seq); var required_height = painter.get_required_height(slots_required); var canvas = this.view.canvas_manager.new_canvas(); @@ -2786,7 +2793,7 @@ // Postdraw init: once data has been fetched, reset data url, wait time and start indexing. var track = this; var post_init = function() { - if (track.data_cache.size() === 0) { + if (track.data_manager.size() === 0) { // Track still drawing initial data, so do nothing. setTimeout(post_init, 300); } 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: provide option to fetch additional data when not all data initially fetched for a tile. For now, all data is refetched rather than iterative fetching. As part of this functionality: (a) enable data providers to accept a max_vals parameter that is used to fetch a particular number of values; and (b) Trackster caches now ignore items with stale=true.
by Bitbucket 04 Jul '11

04 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ee846dba409f/ changeset: ee846dba409f user: jgoecks date: 2011-07-03 21:05:25 summary: Trackster: provide option to fetch additional data when not all data initially fetched for a tile. For now, all data is refetched rather than iterative fetching. As part of this functionality: (a) enable data providers to accept a max_vals parameter that is used to fetch a particular number of values; and (b) Trackster caches now ignore items with stale=true. affected #: 4 files (2.3 KB) --- a/lib/galaxy/visualization/tracks/data_providers.py Thu Jun 30 16:13:52 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Sun Jul 03 15:05:25 2011 -0400 @@ -24,8 +24,7 @@ from pysam import csamtools, ctabix -MAX_VALS = 5000 # only display first MAX_VALS features -ERROR_MAX_VALS = "Only the first " + str(MAX_VALS) + " %s in the region denoted by the red line are displayed." +ERROR_MAX_VALS = "Only the first %i %s in this region are displayed." # Return None instead of NaN to pass jQuery 1.4's strict JSON def float_nan(n): @@ -73,8 +72,11 @@ # Override. pass - def get_data( self, chrom, start, end, **kwargs ): - """ Returns data in region defined by chrom, start, and end. """ + def get_data( self, chrom, start, end, max_vals=None, **kwargs ): + """ + Returns data in region defined by chrom, start, and end. If max_vals + is set, returns at most max_vals. + """ # Override. pass @@ -213,14 +215,26 @@ # Cleanup. bamfile.close() - def get_data( self, chrom, start, end, **kwargs ): + def get_data( self, chrom, start, end, max_vals=sys.maxint, **kwargs ): """ - Fetch intervals in the region + Fetch reads in the region. + + Each read is a list with the format + [<guid>, <start>, <end>, <name>, <read_1>, <read_2>] + where <read_1> has the format + [<start>, <end>, <cigar>, ?<read_seq>?] + and <read_2> has the format + [<start>, <end>, <cigar>, ?<read_seq>?] + For single-end reads, read has format: + [<guid>, <start>, <end>, <name>, cigar, seq] + NOTE: read end and sequence data are not valid for reads outside of + requested region and should not be used. """ start, end = int(start), int(end) orig_data_filename = self.original_dataset.file_name index_filename = self.converted_dataset.file_name no_detail = "no_detail" in kwargs + # Attempt to open the BAM file with index bamfile = csamtools.Samfile( filename=orig_data_filename, mode='rb', index_filename=index_filename ) message = None @@ -235,21 +249,13 @@ return None else: return None - # Encode reads as list of lists; each read is a list with the format - # [<guid>, <start>, <end>, <name>, <read_1>, <read_2>] - # where <read_1> has the format - # [<start>, <end>, <cigar>, ?<read_seq>?] - # and <read_2> has the format - # [<start>, <end>, <cigar>, ?<read_seq>?] - # For single-end reads, read has format: - # [<guid>, <start>, <end>, <name>, cigar, seq] - # NOTE: read end and sequence data are not valid for reads outside of - # requested region and should not be used. + + # Encode reads as list of lists. results = [] paired_pending = {} for read in data: - if len(results) > MAX_VALS: - message = ERROR_MAX_VALS % "reads" + if len(results) > max_vals: + message = ERROR_MAX_VALS % ( max_vals, "reads" ) break qname = read.qname seq = read.seq @@ -273,7 +279,9 @@ paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read_len, 'seq': seq, 'mate_start': read.mpos, 'rlen': read_len, 'cigar': read.cigar } else: results.append( [ "%i_%s" % ( read.pos, qname ), read.pos, read.pos + read_len, qname, read.cigar, read.seq] ) + # Take care of reads whose mates are out of range. + # TODO: count paired reads when adhering to max_vals? for qname, read in paired_pending.iteritems(): if read['mate_start'] < read['start']: # Mate is before read. @@ -311,7 +319,7 @@ f.close() return all_dat is not None - def get_data( self, chrom, start, end, **kwargs ): + def get_data( self, chrom, start, end, max_vals=None, **kwargs ): # Bigwig has the possibility of it being a standalone bigwig file, in which case we use # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset f, bbi = self._get_dataset() @@ -473,9 +481,9 @@ return tabix.fetch(reference=chrom, start=start, end=end) - def get_data( self, chrom, start, end, **kwargs ): + def get_data( self, chrom, start, end, max_vals=None, **kwargs ): iterator = self.get_iterator( chrom, start, end ) - return self.process_data(iterator, **kwargs) + return self.process_data( iterator, max_vals, **kwargs ) class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ): col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } @@ -493,7 +501,7 @@ out.write(interval.raw_line + '\n') out.close() - def get_data( self, chrom, start, end, **kwargs ): + def get_data( self, chrom, start, end, max_vals=sys.maxint, **kwargs ): start, end = int(start), int(end) source = open( self.original_dataset.file_name ) index = Indexes( self.converted_dataset.file_name ) @@ -518,8 +526,8 @@ filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) no_detail = ( "no_detail" in kwargs ) for start, end, offset in index.find(chrom, start, end): - if count >= MAX_VALS: - message = ERROR_MAX_VALS % "features" + if count >= max_vals: + message = ERROR_MAX_VALS % ( max_vals, "features" ) break count += 1 source.seek( offset ) @@ -541,7 +549,7 @@ Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ - def process_data( self, iterator, **kwargs ): + def process_data( self, iterator, max_vals=sys.maxint, **kwargs ): # # Build data to return. Payload format is: # [ <guid/offset>, <start>, <end>, <name>, <score>, <strand>, <thick_start>, @@ -555,8 +563,8 @@ rval = [] message = None for line in iterator: - if count >= MAX_VALS: - message = ERROR_MAX_VALS % "features" + if count >= max_vals: + message = ERROR_MAX_VALS % ( max_vals, "features" ) break count += 1 # TODO: can we use column metadata to fill out payload? @@ -617,14 +625,14 @@ col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } - def process_data( self, iterator, **kwargs ): + def process_data( self, iterator, max_vals=sys.maxint, **kwargs ): rval = [] count = 0 message = None for line in iterator: - if count >= MAX_VALS: - message = ERROR_MAX_VALS % "features" + if count >= max_vals: + message = ERROR_MAX_VALS % ( "max_vals", "features" ) break count += 1 @@ -649,7 +657,7 @@ NOTE: this data provider does not use indices, and hence will be very slow for large datasets. """ - def get_data( self, chrom, start, end, **kwargs ): + def get_data( self, chrom, start, end, max_vals=sys.maxint, **kwargs ): start, end = int( start ), int( end ) source = open( self.original_dataset.file_name ) results = [] @@ -661,8 +669,8 @@ feature_start, feature_end = convert_gff_coords_to_bed( [ feature.start, feature.end ] ) if feature.chrom != chrom or feature_start < start or feature_end > end: continue - if count >= MAX_VALS: - message = ERROR_MAX_VALS % "features" + if count >= max_vals: + message = ERROR_MAX_VALS % ( max_vals, "features" ) break count += 1 payload = package_gff_feature( feature ) --- a/lib/galaxy/web/controllers/tracks.py Thu Jun 30 16:13:52 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Sun Jul 03 15:05:25 2011 -0400 @@ -168,13 +168,7 @@ histories_grid = HistorySelectionGrid() history_datasets_grid = HistoryDatasetsSelectionGrid() tracks_grid = TracksterSelectionGrid() - - # - # TODO: need to encode dataset id and use - # UsesHistoryDatasetAssociation.get_dataset - # for better dataset security. - # - + available_tracks = None available_genomes = None @@ -475,9 +469,9 @@ return { "status": messages.DATA, "valid_chroms": valid_chroms } @web.json - def data( self, trans, hda_ldda, dataset_id, chrom, low, high, **kwargs ): + def data( self, trans, hda_ldda, dataset_id, chrom, low, high, max_vals=5000, **kwargs ): """ - Called by the browser to request a block of data + Provides a block of data from a dataset. """ # Parameter check. @@ -532,7 +526,7 @@ data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps ) # Get and return data from data_provider. - data = data_provider.get_data( chrom, low, high, **kwargs ) + data = data_provider.get_data( chrom, low, high, max_vals, **kwargs ) message = None if isinstance(data, dict) and 'message' in data: message = data['message'] --- a/static/scripts/packed/trackster.js Thu Jun 30 16:13:52 2011 -0400 +++ b/static/scripts/packed/trackster.js Sun Jul 03 15:05:25 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=15,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. 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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()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});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()}).bind("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},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,function(ae){ad.dataset_id=ae.dataset_id;ad.content_div.text("Running job.");ad.init()})},run:function(ab,ac){$.extend(ab,this.get_param_values_dict());var aa=function(){$.getJSON(rerun_tool_url,ab,function(ad){if(ad==="no converter"){new_track.container_div.addClass("error");new_track.content_div.text(G)}else{if(ad.error){new_track.container_div.addClass("error");new_track.content_div.text(v+ad.message)}else{if(ad==="pending"){new_track.container_div.addClass("pending");new_track.content_div.text("Converting input data so that it can be easily reused.");setTimeout(aa,2000)}else{ac(ad)}}}})};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.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(){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()}).bind("click",function(ao){ao.stopPropagation()}).bind("dblclick",function(ao){ao.stopPropagation()}).bind("keydown",function(ao){ao.stopPropagation()});var ae=this;$.each(this.filters,function(av,ap){var ar=$("<div/>").addClass("slider-row").appendTo(ae.parent_div);var ao=$("<div/>").addClass("slider-label").appendTo(ar);var ax=$("<span/>").addClass("slider-name").text(ap.name+" ").appendTo(ao);var aq=$("<span/>");var at=$("<span/>").addClass("slider-value").appendTo(ao).append("[").append(aq).append("]");var aw=$("<div/>").addClass("slider").appendTo(ar);ap.control_element=$("<div/>").attr("id",ap.name+"-filter-control").appendTo(aw);var au=[0,0];ap.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ay,az){au=az.values;aq.text(az.values[0]+"-"+az.values[1]);setTimeout(function(){if(az.values[0]==au[0]&&az.values[1]==au[1]){var aA=az.values;aq.text(aA[0]+"-"+aA[1]);ap.low=aA[0];ap.high=aA[1];ae.track.draw(true,true)}},50)},change:function(ay,az){ap.control_element.slider("option","slide").call(ap.control_element,ay,az)}});ap.slider=ap.control_element;ap.slider_label=aq;aj(at,aq,ap.control_element);$("<div style='clear: both;'/>").appendTo(ar)});if(this.filters.length!=0){var am=$("<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;$.each(this.params,function(ad,af){if(!af.hidden){var ag="param_"+ad;var ae=aa.find("#"+ag).val();if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae)}else{if(af.type==="bool"){ae=aa.find("#"+ag).is(":checked")}}}if(ae!==ac.values[af.key]){ac.values[af.key]=ae;ab=true}}});if(ab){this.onchange()}}});var b=function(ac,ab,aa){this.index=ac;this.resolution=ab;this.canvas=$("<div class='track-tile'/>").append(aa)};var l=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.max_val=ad};var L=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);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=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Q){return"ToolDataFeatureTrack"}else{if(this instanceof P){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_cache.clear();aa.initial_canvas=undefined;aa.content_div.css("height","auto");aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}$.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=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.content_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.content_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text(q);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.make_name_popup_menu()}aa.content_div.text(U);if(aa.view.chrom){aa.content_div.text("");aa.content_div.css("height",aa.height_px+"px");aa.enabled=true;$.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.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["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(){$("#no-tracks").show()};if(this.parent_track){ac=this.parent_track;ad=function(){}}aa.Remove=function(){ac.remove_track(ab);if(ac.num_tracks===0){ad()}};make_popupmenu(ab.name_div,aa)},draw:function(aa,ac){if(!this.dataset_id){return}var au=this.view.low,ag=this.view.high,ai=ag-au,ak=this.view.container.width(),ae=ak/ai,al=this.view.resolution,ad=$("<div style='position: relative;'></div>"),am=function(aw,ax,av){return aw+"_"+ax+"_"+av};if(!ac){this.content_div.children().remove()}this.content_div.append(ad);this.max_height=0;var ao=Math.floor(au/al/M);var af=[];var ap=0;while((ao*M*al)<ag){var at=am(ak,ae,ao);var ah=this.tile_cache.get(at);var aq=ao*M*this.view.resolution;var ab=aq+M*this.view.resolution;if(!aa&&ah){af[af.length]=ah;this.show_tile(ah,ad,aq,ae)}else{this.delayed_draw(aa,at,ao,al,ad,ae,af)}ao+=1;ap++}var aj=this;var ar=setInterval(function(){if(af.length===ap){clearInterval(ar);if(ac){var aA=aj.content_div.children();var aB=false;for(var az=aA.length-1,aF=0;az>=aF;az--){var ay=$(aA[az]);if(aB){ay.remove()}else{if(ay.children().length!==0){aB=true}}}}if(aj instanceof e&&aj.mode=="Histogram"){var aE=-1;for(var az=0;az<af.length;az++){var aH=af[az].max_val;if(aH>aE){aE=aH}}for(var az=0;az<af.length;az++){if(af[az].max_val!==aE){var aG=af[az];aG.canvas.remove();aj.delayed_draw(true,am(ak,ae,aG.index),aG.index,aG.resolution,ad,ae,[],{max:aE})}}}if(aj.filters_manager){var ax=aj.filters_manager.filters;for(var aD=0;aD<ax.length;aD++){ax[aD].update_ui_elt()}var aC=false;if(aj.example_feature){for(var aD=0;aD<ax.length;aD++){if(ax[aD].applies_to(aj.example_feature)){aC=true;break}}}if(aj.filters_available!==aC){aj.filters_available=aC;if(!aj.filters_available){aj.filters_div.hide()}aj.make_name_popup_menu()}}var av=false;for(var aw=0;aw<af.length;aw++){if(af[aw].message){av=true;break}}if(av){for(var aw=0;aw<af.length;aw++){aG=af[aw];if(!aG.message){aG.canvas.css("padding-top",A)}}}}},50);for(var an=0;an<this.child_tracks.length;an++){this.child_tracks[an].draw(aa,ac)}},delayed_draw:function(ab,ai,ac,ae,aj,am,ak,af){var ad=this,ag=ac*M*ae,al=ag+M*ae;var ah=function(av,an,ap,ao,at,au,aq){var ar=ad.draw_tile(an,ap,ao,au,aq);ad.tile_cache.set(ai,ar);if(ar===undefined){return}ad.show_tile(ar,at,ag,au);ak[ak.length]=ar};var aa=setTimeout(function(){if(ag<=ad.view.high&&al>=ad.view.low){var an=(ab?undefined:ad.tile_cache.get(ai));if(an){ad.show_tile(an,aj,ag,am);ak[ak.length]=an}else{$.when(ad.data_cache.get_data(view.chrom,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){$.when(view.reference_track.data_cache.get_data(view.chrom,ag,al,ad.mode,ae,view.reference_track.data_url_extra_params)).then(function(ap){ah(aa,ao,ae,ac,aj,am,ap)})}else{ah(aa,ao,ae,ac,aj,am)}})}}},50)},show_tile:function(ad,ag,ae,ah){var ab=this;var ac=this.view.high-this.view.low,af=(ae-this.view.low)*ah;if(this.left_offset){af-=this.left_offset}var aa=ad.canvas;aa.css({position:"absolute",top:0,left:af,height:""});ag.append(aa);ab.max_height=Math.max(ab.max_height,aa.height());ab.content_div.css("height",ab.max_height+"px");ag.children().css("height",ab.max_height+"px")},set_overview:function(){var aa=this.view;if(this.initial_canvas&&this.is_overview){aa.overview_close.show();aa.overview_viewport.append(this.initial_canvas);aa.overview_highlight.show().height(this.initial_canvas.height());aa.overview_viewport.height(this.initial_canvas.height()+aa.overview_box.height())}$(window).trigger("resize")},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_cache=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)}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_cache=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(ad,ae,ac)}});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_cache=new N(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{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){var at=this,aC=aA*M*aw,ab=(aA+1)*M*aw,ap=ab-aC,au=Math.ceil(ap*aj),aq=this.mode,aH=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 aG=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+O;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 aE=new I.SummaryTreePainter(an,aC,ab,this.prefs);var av=ac.getContext("2d");av.translate(ae,O);aE.draw(av,au,af);return new l(aA,aw,ac,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,aF=al.length;aB<aF;aB++){am=al[aB];am.update_attrs(ag);if(!am.keep(ag)){ay=true;break}}if(!ay){ai.push(ag)}}}var aE=new (this.painter)(ai,aC,ab,this.prefs,aq,ad);var af=aE.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){this.example_feature=(an.data.length?an.data[0]:undefined);av.translate(ae,0);aE.draw(av,au,af,ao)}if(an.message){var ar=$("<div/>");var aD=$("<div/>").addClass("tile-message").text(an.message).css("width",ac.width);aD.css({position:"absolute",top:0});$(ac).css("top",15);ar.append(aD);ar.append(ac);ac=ar}return new L(aA,aw,ac,an.message)}});var P=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.painter=I.VariantPainter};n(P.prototype,J.prototype,e.prototype);var S=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ac,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.painter=I.ReadPainter;this.make_name_popup_menu()};n(S.prototype,J.prototype,e.prototype);var Q=function(ae,ac,ag,aa,ad,af,ab){e.call(this,ae,ac,ag,aa,ad,af,{},ab);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(Q.prototype,J.prototype,e.prototype,{predraw_init:function(){var ab=this;var aa=function(){if(ab.data_cache.size()===0){setTimeout(aa,300)}else{ab.data_url=default_data_url;ab.data_query_wait=H;ab.dataset_state_url=converted_datasets_state_url;$.getJSON(ab.dataset_state_url,{dataset_id:ab.dataset_id,hda_ldda:ab.hda_ldda},function(ac){})}};aa()}});T.View=Y;T.LineTrack=k;T.FeatureTrack=e;T.ReadTrack=S};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(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 C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var m=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};m.prototype.default_prefs={};var u=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.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(x,B,D,E,z){m.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var 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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 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, 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/>").click(function(){aa.zoom_in();aa.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ad);this.chrom_select.bind("change",function(){aa.change_chrom(aa.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(ae){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ae){aa.zoom_in(ae.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ae,af){this.current_x=af.offsetX}).bind("drag",function(ae,ag){var ah=ag.offsetX-this.current_x;this.current_x=ag.offsetX;var af=Math.round(ah/aa.viewport_container.width()*(aa.max_high-aa.max_low));aa.move_delta(-af)});this.overview_close.bind("click",function(){for(var af=0,ae=aa.tracks.length;af<ae;af++){aa.tracks[af].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",aa.overview_box.height());aa.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(ae,af){if(ae.clientX>aa.viewport_container.width()-16){return false}}).bind("dragstart",function(ae,af){af.original_low=aa.low;af.current_height=ae.clientY;af.current_x=af.offsetX}).bind("drag",function(ag,ai){var ae=$(this);var aj=ai.offsetX-ai.current_x;var af=ae.scrollTop()-(ag.clientY-ai.current_height);ae.scrollTop(af);ai.current_height=ag.clientY;ai.current_x=ai.offsetX;var ah=Math.round(aj/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}).bind("mousewheel",function(ag,ai,af,ae){if(af){var ah=Math.round(-af/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}});this.top_labeltrack.bind("dragstart",function(ae,af){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(ai,aj){$(aj.proxy).css({left:Math.min(ai.pageX,aj.startX),width:Math.abs(ai.pageX-aj.startX)});var af=Math.min(ai.pageX,aj.startX)-aa.container.offset().left,ae=Math.max(ai.pageX,aj.startX)-aa.container.offset().left,ah=(aa.high-aa.low),ag=aa.viewport_container.width();aa.update_location(Math.round(af/ag*ah)+aa.low,Math.round(ae/ag*ah)+aa.low)}).bind("dragend",function(aj,ak){var af=Math.min(aj.pageX,ak.startX),ae=Math.max(aj.pageX,ak.startX),ah=(aa.high-aa.low),ag=aa.viewport_container.width(),ai=aa.low;aa.low=Math.round(af/ag*ah)+ai;aa.high=Math.round(ae/ag*ah)+ai;$(ak.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();$(window).trigger("resize")},update_location:function(aa,ab){this.location_span.text(commatize(aa)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(aa)+"-"+commatize(ab))},load_chroms:function(ab,ac){ab.num=t;$.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;if(!ad.chrom){ad.intro_div.show()}else{ad.intro_div.hide()}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},add_label_track:function(aa){aa.view=this;this.label_tracks.push(aa)},remove_track:function(aa){this.has_changes=true;aa.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(aa)];this.num_tracks-=1},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()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});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 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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=$(this).val();if(ac){ab[ab.length]=ad}});return ab},run_on_dataset:function(){var aa=this;aa.run({dataset_id:this.track.original_dataset_id,tool_id:aa.name},function(ab){show_modal(aa.name+" is Running",aa.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ac=this.track,ab=aa.tool_id+ac.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),ad;if(ac instanceof e){ad=new Q(ab,view,ac.hda_ldda,undefined,{},{},ac);ad.change_mode(ac.mode)}this.track.add_track(ad);ad.content_div.text("Starting job.");this.run(aa,function(ae){ad.dataset_id=ae.dataset_id;ad.content_div.text("Running job.");ad.init()})},run:function(ab,ac){$.extend(ab,this.get_param_values_dict());var aa=function(){$.getJSON(rerun_tool_url,ab,function(ad){if(ad==="no converter"){new_track.container_div.addClass("error");new_track.content_div.text(G)}else{if(ad.error){new_track.container_div.addClass("error");new_track.content_div.text(v+ad.message)}else{if(ad==="pending"){new_track.container_div.addClass("pending");new_track.content_div.text("Converting input data so that it can be easily reused.");setTimeout(aa,2000)}else{ac(ad)}}}})};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.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(){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()}).bind("click",function(ao){ao.stopPropagation()}).bind("dblclick",function(ao){ao.stopPropagation()}).bind("keydown",function(ao){ao.stopPropagation()});var ae=this;$.each(this.filters,function(av,ap){var ar=$("<div/>").addClass("slider-row").appendTo(ae.parent_div);var ao=$("<div/>").addClass("slider-label").appendTo(ar);var ax=$("<span/>").addClass("slider-name").text(ap.name+" ").appendTo(ao);var aq=$("<span/>");var at=$("<span/>").addClass("slider-value").appendTo(ao).append("[").append(aq).append("]");var aw=$("<div/>").addClass("slider").appendTo(ar);ap.control_element=$("<div/>").attr("id",ap.name+"-filter-control").appendTo(aw);var au=[0,0];ap.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ay,az){au=az.values;aq.text(az.values[0]+"-"+az.values[1]);setTimeout(function(){if(az.values[0]==au[0]&&az.values[1]==au[1]){var aA=az.values;aq.text(aA[0]+"-"+aA[1]);ap.low=aA[0];ap.high=aA[1];ae.track.draw(true,true)}},50)},change:function(ay,az){ap.control_element.slider("option","slide").call(ap.control_element,ay,az)}});ap.slider=ap.control_element;ap.slider_label=aq;aj(at,aq,ap.control_element);$("<div style='clear: both;'/>").appendTo(ar)});if(this.filters.length!=0){var am=$("<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;$.each(this.params,function(ad,af){if(!af.hidden){var ag="param_"+ad;var ae=aa.find("#"+ag).val();if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae)}else{if(af.type==="bool"){ae=aa.find("#"+ag).is(":checked")}}}if(ae!==ac.values[af.key]){ac.values[af.key]=ae;ab=true}}});if(ab){this.onchange()}}});var b=function(ac,ab,aa){this.index=ac;this.resolution=ab;this.canvas=$("<div class='track-tile'/>").append(aa);this.stale=false};var l=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.max_val=ad};var L=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);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=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Q){return"ToolDataFeatureTrack"}else{if(this instanceof P){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_cache.clear();aa.initial_canvas=undefined;aa.content_div.css("height","auto");aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}$.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=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.content_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.content_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text(q);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.make_name_popup_menu()}aa.content_div.text(U);if(aa.view.chrom){aa.content_div.text("");aa.content_div.css("height",aa.height_px+"px");aa.enabled=true;$.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.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["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(){$("#no-tracks").show()};if(this.parent_track){ac=this.parent_track;ad=function(){}}aa.Remove=function(){ac.remove_track(ab);if(ac.num_tracks===0){ad()}};make_popupmenu(ab.name_div,aa)},draw:function(aa,ac){if(!this.dataset_id){return}var au=this.view.low,ag=this.view.high,ai=ag-au,ak=this.view.container.width(),ae=ak/ai,al=this.view.resolution,ad=$("<div style='position: relative;'></div>"),am=function(aw,ax,av){return aw+"_"+ax+"_"+av};if(!ac){this.content_div.children().remove()}this.content_div.append(ad);this.max_height=0;var ao=Math.floor(au/al/M);var af=[];var ap=0;while((ao*M*al)<ag){var at=am(ak,ae,ao);var ah=this.tile_cache.get(at);var aq=ao*M*this.view.resolution;var ab=aq+M*this.view.resolution;if(!aa&&ah){af[af.length]=ah;this.show_tile(ah,ad,aq,ab,ae)}else{this.delayed_draw(aa,at,ao,al,ad,ae,af)}ao+=1;ap++}var aj=this;var ar=setInterval(function(){if(af.length===ap){clearInterval(ar);if(ac){var aA=aj.content_div.children();var aB=false;for(var az=aA.length-1,aF=0;az>=aF;az--){var ay=$(aA[az]);if(aB){ay.remove()}else{if(ay.children().length!==0){aB=true}}}}if(aj instanceof e&&aj.mode=="Histogram"){var aE=-1;for(var az=0;az<af.length;az++){var aH=af[az].max_val;if(aH>aE){aE=aH}}for(var az=0;az<af.length;az++){if(af[az].max_val!==aE){var aG=af[az];aG.canvas.remove();aj.delayed_draw(true,am(ak,ae,aG.index),aG.index,aG.resolution,ad,ae,[],{max:aE})}}}if(aj.filters_manager){var ax=aj.filters_manager.filters;for(var aD=0;aD<ax.length;aD++){ax[aD].update_ui_elt()}var aC=false;if(aj.example_feature){for(var aD=0;aD<ax.length;aD++){if(ax[aD].applies_to(aj.example_feature)){aC=true;break}}}if(aj.filters_available!==aC){aj.filters_available=aC;if(!aj.filters_available){aj.filters_div.hide()}aj.make_name_popup_menu()}}var av=false;for(var aw=0;aw<af.length;aw++){if(af[aw].message){av=true;break}}if(av){for(var aw=0;aw<af.length;aw++){aG=af[aw];if(!aG.message){aG.canvas.css("padding-top",A)}}}}},50);for(var an=0;an<this.child_tracks.length;an++){this.child_tracks[an].draw(aa,ac)}},delayed_draw:function(ab,ai,ac,ae,aj,am,ak,af){var ad=this,ag=ac*M*ae,al=ag+M*ae;var ah=function(av,an,ap,ao,at,au,aq){var ar=ad.draw_tile(an,ap,ao,au,aq);ad.tile_cache.set(ai,ar);if(ar===undefined){return}ad.show_tile(ar,at,ag,al,au);ak[ak.length]=ar};var aa=setTimeout(function(){if(ag<=ad.view.high&&al>=ad.view.low){var an=(ab?undefined:ad.tile_cache.get(ai));if(an){ad.show_tile(an,aj,ag,al,am);ak[ak.length]=an}else{$.when(ad.data_cache.get_data(view.chrom,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){$.when(view.reference_track.data_cache.get_data(view.chrom,ag,al,ad.mode,ae,view.reference_track.data_url_extra_params)).then(function(ap){ah(aa,ao,ae,ac,aj,am,ap)})}else{ah(aa,ao,ae,ac,aj,am)}})}}},50)},show_tile:function(ah,aj,ae,ak,am){var ab=this,aa=ah.canvas,af=aa;if(ah.message){var al=$("<div/>"),ai=$("<div/>").addClass("tile-message").text(ah.message).css({height:A-1,width:ah.canvas.width}).appendTo(al),ag=$("<button/>").text("Show more").css("margin-left","0.5em").appendTo(ai);al.append(aa);af=al;ag.click(function(){var an=ab.data_cache.get_data(ab.view.chrom,ae,ak,ab.mode,ah.resolution);an.stale=true;ah.stale=true;ab.data_cache.get_data(ab.view.chrom,ae,ak,ab.mode,ah.resolution,{max_vals:an.data.length*2});ab.draw()}).dblclick(function(an){an.stopPropagation()})}var ad=this.view.high-this.view.low,ac=(ae-this.view.low)*am;if(this.left_offset){ac-=this.left_offset}af.css({position:"absolute",top:0,left:ac,height:""});aj.append(af);ab.max_height=Math.max(ab.max_height,af.height());ab.content_div.css("height",ab.max_height+"px");aj.children().css("height",ab.max_height+"px")},set_overview:function(){var aa=this.view;if(this.initial_canvas&&this.is_overview){aa.overview_close.show();aa.overview_viewport.append(this.initial_canvas);aa.overview_highlight.show().height(this.initial_canvas.height());aa.overview_viewport.height(this.initial_canvas.height()+aa.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(ac,aa,ad){var ab=this,ae=(ac!==undefined&&aa!==undefined&&ad!==undefined?ac+":"+aa+"-"+ad:"all");return" - region=["+ae+"], parameters=["+ab.tool.get_param_values().join(", ")+"]"},add_track:function(aa){aa.track_id=this.track_id+"_"+this.child_tracks.length;aa.container_div.attr("id","track_"+aa.track_id);this.child_tracks_container.append(aa.container_div);C(aa.container_div,".child-track-icon");if(!$(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_cache=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)}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_cache=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(ad,ae,ac)}});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_cache=new N(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{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,av,az,aj,ad){var ar=this,aB=az*M*av,ab=(az+1)*M*av,ap=ab-aB,at=Math.ceil(ap*aj),aq=this.mode,aF=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 aE=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=at+ae;ac.height=af+O;if(an.dataset_type!="summary_tree"){var ak=this.get_summary_tree_data(an.data,aB,ab,200);if(an.max){ak.max=an.max}an=ak}var aC=new I.SummaryTreePainter(an,aB,ab,this.prefs);var au=ac.getContext("2d");au.translate(ae,O);aC.draw(au,at,af);return new l(az,av,ac,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 aw=0,ay=an.data.length;aw<ay;aw++){var ag=an.data[aw];var ax=false;var am;for(var aA=0,aD=al.length;aA<aD;aA++){am=al[aA];am.update_attrs(ag);if(!am.keep(ag)){ax=true;break}}if(!ax){ai.push(ag)}}}var aC=new (this.painter)(ai,aB,ab,this.prefs,aq,ad);var af=aC.get_required_height(ah);var ac=this.view.canvas_manager.new_canvas();ac.width=at+ae;ac.height=af;var au=ac.getContext("2d");au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";this.container_div.find(".yaxislabel").remove();if(an.data){this.example_feature=(an.data.length?an.data[0]:undefined);au.translate(ae,0);aC.draw(au,at,af,ao)}return new L(az,av,ac,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 Q=function(ae,ac,ag,aa,ad,af,ab){e.call(this,ae,ac,ag,aa,ad,af,{},ab);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(Q.prototype,J.prototype,e.prototype,{predraw_init:function(){var ab=this;var aa=function(){if(ab.data_cache.size()===0){setTimeout(aa,300)}else{ab.data_url=default_data_url;ab.data_query_wait=H;ab.dataset_state_url=converted_datasets_state_url;$.getJSON(ab.dataset_state_url,{dataset_id:ab.dataset_id,hda_ldda:ab.hda_ldda},function(ac){})}};aa()}});T.View=Y;T.LineTrack=k;T.FeatureTrack=e;T.ReadTrack=S};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(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 C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var m=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};m.prototype.default_prefs={};var u=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.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(x,B,D,E,z){m.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var T=Math.round(J+G/I*J);if(H!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,T,L,1)}M.beginPath();var Q,D,B;if(S.length>1){B=Math.ceil((S[1][0]-S[0][0])*A)}else{B=10}for(var N=0,O=S.length;N<O;N++){M.fillStyle=this.prefs.color;Q=Math.round((S[N][0]-z)*A);D=S[N][1];var P=false,F=false;if(D===null){if(E&&H==="Filled"){M.lineTo(Q,x)}E=false;continue}if(D<G){F=true;D=G}else{if(D>C){P=true;D=C}}if(H==="Histogram"){D=Math.round(D/I*x);M.fillRect(Q,T,B,-D)}else{if(H==="Intensity"){D=255-Math.floor((D-G)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(Q,0,B,x)}else{D=Math.round(x-(D-G)/I*x);if(E){M.lineTo(Q,D)}else{E=true;if(H==="Filled"){M.moveTo(Q,x);M.lineTo(Q,D)}else{M.moveTo(Q,D)}}}}M.fillStyle=this.prefs.overflow_color;if(P||F){var R;if(H==="Histogram"||H==="Intensity"){R=B}else{Q-=2;R=4}if(P){M.fillRect(Q,0,R,3)}if(F){M.fillRect(Q,x-3,R,3)}}M.fillStyle=this.prefs.color}if(H==="Filled"){if(E){M.lineTo(Q,T);M.lineTo(0,T)}M.fill()}else{M.stroke()}M.restore()};var n=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};t(n.prototype,{get_required_height:function(y){var x=y_scale=this.get_row_height(),z=this.mode;if(z==="no_detail"||z==="Squish"||z==="Pack"){x=y*y_scale}return x+Math.max(Math.round(y_scale/2),5)},draw:function(J,A,I,F){var D=this.data,G=this.view_start,K=this.view_end;J.save();J.fillStyle=this.prefs.block_color;J.textAlign="right";var N=this.view_end-this.view_start,M=A/N,z=this.get_row_height();for(var C=0,E=D.length;C<E;C++){var L=D[C],B=L[0],x=L[1],y=L[2],H=(F&&F[B]!==undefined?F[B]:null);if((x<K&&y>G)&&(this.mode=="Dense"||H!==null)){this.draw_element(J,this.mode,L,H,G,K,M,z,A)}}J.restore()}});var d=10,h=3,l=5,v=10,f=1,r=3,e=3,a=9,k=2,g="#ccc";var q=function(z,B,x,y,A){n.call(this,z,B,x,y,A)};t(q.prototype,n.prototype,{get_row_height:function(){var y=this.mode,x;if(y==="Dense"){x=d}else{if(y==="no_detail"){x=h}else{if(y==="Squish"){x=l}else{x=v}}}return x},draw_element:function(J,C,R,E,L,ab,af,ag,x){var O=R[0],ad=R[1],V=R[2],M=R[3],W=Math.floor(Math.max(0,(ad-L)*af)),K=Math.ceil(Math.min(x,Math.max(0,(V-L)*af))),U=(C==="Dense"?0:(0+E))*ag,I,Z,N=null,ah=null,A=this.prefs.block_color,Y=this.prefs.label_color;if(C=="Dense"){E=1}if(C==="no_detail"){J.fillStyle=A;J.fillRect(W,U+5,K-W,f)}else{var H=R[4],T=R[5],X=R[6],B=R[7];if(T&&X){N=Math.floor(Math.max(0,(T-L)*af));ah=Math.ceil(Math.min(x,Math.max(0,(X-L)*af)))}var ae,P;if(C==="Squish"||C==="Dense"){ae=1;P=e}else{ae=5;P=a}if(!B){if(R.strand){if(R.strand==="+"){J.fillStyle=J.canvas.manager.get_pattern("right_strand_inv")}else{if(R.strand==="-"){J.fillStyle=J.canvas.manager.get_pattern("left_strand_inv")}}}else{J.fillStyle=A}J.fillRect(W,U,K-W,P)}else{var G,Q;if(C==="Squish"||C==="Dense"){J.fillStyle=g;G=U+Math.floor(e/2)+1;Q=1}else{if(H){var G=U;var Q=P;if(H==="+"){J.fillStyle=J.canvas.manager.get_pattern("right_strand")}else{if(H==="-"){J.fillStyle=J.canvas.manager.get_pattern("left_strand")}}}else{J.fillStyle=g;G+=(e/2)+1;Q=1}}J.fillRect(W,G,K-W,Q);for(var ac=0,z=B.length;ac<z;ac++){var D=B[ac],y=Math.floor(Math.max(0,(D[0]-L)*af)),S=Math.ceil(Math.min(x,Math.max((D[1]-L)*af)));if(y>S){continue}J.fillStyle=A;J.fillRect(y,U+(P-ae)/2+1,S-y,ae);if(N!==undefined&&X>T&&!(y>ah||S<N)){var aa=Math.max(y,N),F=Math.min(S,ah);J.fillRect(aa,U+1,F-aa,P);if(B.length==1&&C=="Pack"){if(H==="+"){J.fillStyle=J.canvas.manager.get_pattern("right_strand_inv")}else{if(H==="-"){J.fillStyle=J.canvas.manager.get_pattern("left_strand_inv")}}if(aa+14<F){aa+=2;F-=2}J.fillRect(aa,U+1,F-aa,P)}}}}if(C==="Pack"&&ad>L){J.fillStyle=Y;if(L===0&&W-J.measureText(M).width<0){J.textAlign="left";J.fillText(M,K+k,U+8)}else{J.textAlign="right";J.fillText(M,W-k,U+8)}J.fillStyle=A}}}});var 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 aa=0,x=P.length;aa<x;aa++){if(this.prefs.show_differences&&ref_seq){var J=ref_seq[F-Y+aa];if(!J||J.toLowerCase()===P[aa].toLowerCase()){continue}}if(F+aa>=Y&&F+aa<=z){var ab=Math.floor(Math.max(0,(F+aa-Y)*K));T.fillText(P[aa],ab,D+9)}}}else{T.fillStyle=this.prefs.block_color;T.fillRect(ac,D+4,G-ac,e)}}U+=M;N+=M;break;case"N":T.fillStyle=g;T.fillRect(ac-Q,D+5,G-ac,1);N+=M;break;case"D":T.fillStyle="red";T.fillRect(ac-Q,D+4,G-ac,3);N+=M;break;case"P":break;case"I":var X=ac-Q;if(is_overlap([F,F+M],y)){var P=E.slice(U,U+M);if(this.prefs.show_insertions){var C=ac-(G-ac)/2;if((O==="Pack"||this.mode==="Auto")&&E!==undefined&&K>char_width_px){T.fillStyle="yellow";T.fillRect(C-Q,D-9,G-ac,9);ad[ad.length]={type:"triangle",data:[X,D+4,5]};T.fillStyle=g;switch(seq_tile_overlap){case (OVERLAP_START):P=P.slice(Y-F);break;case (OVERLAP_END):P=P.slice(0,F-z);break;case (CONTAINED_BY):break;case (CONTAINS):P=P.slice(Y-F,F-z);break}for(var aa=0,x=P.length;aa<x;aa++){var 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 --- a/static/scripts/trackster.js Thu Jun 30 16:13:52 2011 -0400 +++ b/static/scripts/trackster.js Sun Jul 03 15:05:25 2011 -0400 @@ -172,7 +172,7 @@ // height of individual features within tracks. Feature height, then, should always be less // than track height. CHAR_HEIGHT_PX = 9, // FIXME: font size may not be static - ERROR_PADDING = 15, // Padding at the top of tracks for error messages + ERROR_PADDING = 18, // Padding at the top of tracks for error messages SUMMARY_TREE_TOP_PADDING = CHAR_HEIGHT_PX + 2, // Maximum number of rows un a slotted track MAX_FEATURE_DEPTH = 100, @@ -212,7 +212,14 @@ get: function(key) { var index = this.key_ary.indexOf(key); if (index !== -1) { - this.move_key_to_end(key, index); + if (this.obj_cache[key].stale) { + // Object is stale, so remove key and object. + this.key_ary.splice(index, 1); + delete this.obj_cache[key]; + } + else { + this.move_key_to_end(key, index); + } } return this.obj_cache[key]; }, @@ -280,7 +287,7 @@ }); }, /** - * Get data and do callback. + * Get track data. */ get_data: function(chrom, low, high, mode, resolution, extra_params) { // Debugging: @@ -332,7 +339,7 @@ // Load data from server. The deferred is immediately saved until the // data is ready, it then replaces itself with the actual data entry = this.load_data(chrom, low, high, mode, resolution, extra_params); - this.set_data( low, high, mode, entry ); + this.set_data(low, high, mode, entry); return entry }, set_data: function(low, high, mode, result) { @@ -1500,6 +1507,7 @@ this.resolution = resolution; // Wrap element in div for background. this.canvas = $("<div class='track-tile'/>").append(canvas); + this.stale = false; }; var SummaryTreeTile = function(index, resolution, canvas, max_val) { @@ -1925,9 +1933,9 @@ var cached = this.tile_cache.get(key); var tile_low = tile_index * DENSITY * this.view.resolution; var tile_high = tile_low + DENSITY * this.view.resolution; - if ( !force && cached ) { + if (!force && cached) { drawn_tiles[drawn_tiles.length] = cached; - this.show_tile(cached, parent_element, tile_low, w_scale); + this.show_tile(cached, parent_element, tile_low, tile_high, w_scale); } else { this.delayed_draw(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles); } @@ -2079,7 +2087,7 @@ if (tile === undefined) { return; } - track.show_tile(tile, parent_element, tile_low, w_scale); + track.show_tile(tile, parent_element, tile_low, tile_high, w_scale); drawn_tiles[drawn_tiles.length] = tile; }; // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data @@ -2088,7 +2096,7 @@ // Show/draw tile: check cache for tile; if tile not in cache, draw it. var tile = (force ? undefined : track.tile_cache.get(key)); if (tile) { - track.show_tile(tile, parent_element, tile_low, w_scale); + track.show_tile(tile, parent_element, tile_low, tile_high, w_scale); drawn_tiles[drawn_tiles.length] = tile; } else { @@ -2117,9 +2125,41 @@ /** * Show track tile and perform associated actions. */ - show_tile: function(tile, parent_element, tile_low, w_scale) { + show_tile: function(tile, parent_element, tile_low, tile_high, w_scale) { // Readability. - var track = this; + var + track = this, + canvas = tile.canvas, + tile_element = canvas; + + // + // If tile has message, display message and button to show more data. + // TODO: need to handle other messages, not assume message === show more data. + // + if (tile.message) { + var + container_div = $("<div/>"), + message_div = $("<div/>").addClass("tile-message").text(tile.message). + // -1 to account for border. + css({'height': ERROR_PADDING-1, 'width': tile.canvas.width}).appendTo(container_div), + show_more_data_btn = $("<button/>").text("Show more").css("margin-left", "0.5em").appendTo(message_div); + container_div.append(canvas); + tile_element = container_div; + + // Set up actions for button. + show_more_data_btn.click(function() { + // Mark data, tile as stale, request more data, and redraw track. + // HACK: get_data used will return object that can be marked as stale, but a better way to this is needed. + var cur_data = track.data_cache.get_data(track.view.chrom, tile_low, tile_high, track.mode, tile.resolution); + cur_data.stale = true; + tile.stale = true; + track.data_cache.get_data(track.view.chrom, tile_low, tile_high, track.mode, tile.resolution, {max_vals: cur_data.data.length * 2}); + track.draw(); + }).dblclick(function(e) { + // Do not propogate as this would normal zoom in. + e.stopPropagation(); + }); + } // // Show tile element. @@ -2131,7 +2171,6 @@ if (this.left_offset) { left -= this.left_offset; } - var tile_element = tile.canvas; tile_element.css({ position: 'absolute', top: 0, left: left, height: '' }); parent_element.append(tile_element); @@ -2389,7 +2428,7 @@ var ctx = canvas.getContext("2d"); var painter = new painters.LinePainter( result.data, tile_low, tile_low + tile_length, this.prefs, this.mode ); - painter.draw( ctx, width, height ); + painter.draw(ctx, width, height); return new Tile(tile_length, resolution, canvas); } @@ -2680,6 +2719,7 @@ if (result.data) { // Set example feature. This is needed so that track can update its UI based on feature attributes. + // TODO: use tile data rather than example feature? this.example_feature = (result.data.length ? result.data[0] : undefined); // Draw features. @@ -2687,17 +2727,6 @@ painter.draw(ctx, width, required_height, slots); } - // If tile has a message, create container div with both a message div and the canvas. - if (result.message) { - var container_div = $("<div/>"); - var message_div = $("<div/>").addClass("tile-message").text(result.message).css('width', canvas.width); - message_div.css({position: 'absolute', top: 0}); - $(canvas).css("top", 15); - container_div.append(message_div); - container_div.append(canvas); - canvas = container_div; - } - return new FeatureTrackTile(tile_index, resolution, canvas, result.message); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits July 2011