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galaxy-dist commit 9d9f0de20f4f: Make default initial value for Integer and Float parameters None.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan(a)bx.psu.edu> # Date 1287683139 14400 # Node ID 9d9f0de20f4f9da28d53be38411b1ee1075201a1 # Parent 151d007da2f4709ba546cd5cc76738e28b64e05d Make default initial value for Integer and Float parameters None. --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -212,7 +212,7 @@ class IntegerToolParameter( TextToolPara if self.value: return int( self.value ) else: - return 0 + return None class FloatToolParameter( TextToolParameter ): """ @@ -254,7 +254,7 @@ class FloatToolParameter( TextToolParame try: return float( self.value ) except: - return float( 0 ) + return None class BooleanToolParameter( ToolParameter ): """

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galaxy-dist commit 8cc9544dd81d: Fix traceback encountered if you try to access the admin job management interface from a server with job running disabled.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1287678598 14400 # Node ID 8cc9544dd81d6c53e7c79a24b5fb30f58854e45b # Parent 423e72ab19901de8dc8f5e4e2d2e7524921380bc Fix traceback encountered if you try to access the admin job management interface from a server with job running disabled. --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1491,6 +1491,8 @@ class Admin( object ): deleted = [] msg = None status = None + if not trans.app.config.get_bool( "enable_job_running", True ): + return trans.show_error_message( 'This Galaxy instance is not configured to run jobs. If using multiple servers, please directly access the job running instance to manage jobs.' ) job_ids = util.listify( stop ) if job_ids and stop_msg in [ None, '' ]: msg = 'Please enter an error message to display to the user describing why the job was terminated'

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galaxy-dist commit 5f9d6d9582e5: Read zipfiles in chunks when uncompressing in the upload tool. And I continue to wish zipfile was a lot more like tarfile...
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1287608406 14400 # Node ID 5f9d6d9582e50f134c97e8523a015f210dd3af70 # Parent 7afd79d131e40f5f9a61125ec159552dc7c3fabd Read zipfiles in chunks when uncompressing in the upload tool. And I continue to wish zipfile was a lot more like tarfile... --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -258,6 +258,9 @@ def add_file( dataset, registry, json_fi # See if we have a zip archive is_zipped = check_zip( dataset.path ) if is_zipped: + CHUNK_SIZE = 2**20 # 1Mb + uncompressed = None + uncompressed_name = None unzipped = False z = zipfile.ZipFile( dataset.path ) for name in z.namelist(): @@ -267,18 +270,28 @@ def add_file( dataset, registry, json_fi stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.' break fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_zip_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ), text=False ) - try: - outfile = open( uncompressed, 'wb' ) - outfile.write( z.read( name ) ) - outfile.close() - shutil.move( uncompressed, dataset.path ) - dataset.name = name - unzipped = True - except IOError: - os.close( fd ) - os.remove( uncompressed ) - file_err( 'Problem decompressing zipped data', dataset, json_file ) - return + zipped_file = z.open( name ) + while 1: + try: + chunk = zipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing zipped data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + zipped_file.close() + uncompressed_name = name + unzipped = True + z.close() + # Replace the zipped file with the decompressed file + if uncompressed is not None: + shutil.move( uncompressed, dataset.path ) + dataset.name = uncompressed_name + data_type = 'zip' if not data_type: if check_binary( dataset.path ): # We have a binary dataset, but it is not Bam, Sff or Pdf

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galaxy-dist commit c375c4a8e4e4: Fix more unicode issues when listing and running workflows.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287605437 14400 # Node ID c375c4a8e4e42e5e29e996f3472aacdbdc3d22e0 # Parent 647ca0049221bcadde31559d6a99a6ccf236d134 Fix more unicode issues when listing and running workflows. --- a/templates/workflow/list_for_run.mako +++ b/templates/workflow/list_for_run.mako @@ -36,7 +36,7 @@ %for i, workflow in enumerate( workflows ): <tr><td> - <a href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a> + <a href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">${h.to_unicode( workflow.name )}</a><a id="wf-${i}-popup" class="popup-arrow" style="display: none;">▼</a></td><td>${len(workflow.latest_workflow.steps)}</td> --- a/templates/workflow/run.mako +++ b/templates/workflow/run.mako @@ -119,7 +119,7 @@ from galaxy.jobs.actions.post import Act </div></%def> -<h2>Running workflow "${workflow.name}"</h2> +<h2>Running workflow "${h.to_unicode( workflow.name )}"</h2> %if has_upgrade_messages: <div class="warningmessage"> @@ -130,7 +130,7 @@ from galaxy.jobs.actions.post import Act %endif <form id="tool_form" name="tool_form" method="POST"> -## <input type="hidden" name="workflow_name" value="${workflow.name | h}" /> +## <input type="hidden" name="workflow_name" value="${h.to_unicode( workflow.name ) | h}" /> %for i, step in enumerate( steps ): %if step.type == 'tool' or step.type is None: <% tool = app.toolbox.tools_by_id[step.tool_id] %> @@ -153,7 +153,7 @@ from galaxy.jobs.actions.post import Act % if step.annotations: <hr/><div class='form-row'> - <label>Annotation:</label> ${step.annotations[0].annotation} + <label>Annotation:</label> ${h.to_unicode( step.annotations[0].annotation )} </div> % endif </div>

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galaxy-dist commit 423e72ab1990: trackster: Don't index bottom level for summary_tree, greatly reducing computation time (>5x speedup) while not sacrificing usability
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1287612031 14400 # Node ID 423e72ab19901de8dc8f5e4e2d2e7524921380bc # Parent 5f9d6d9582e50f134c97e8523a015f210dd3af70 trackster: Don't index bottom level for summary_tree, greatly reducing computation time (>5x speedup) while not sacrificing usability --- a/lib/galaxy/visualization/tracks/summary.py +++ b/lib/galaxy/visualization/tracks/summary.py @@ -1,12 +1,15 @@ ''' 2010, Kanwei Li Summary tree data structure for aggregation + +10/20/2010: Changed version to 2 as we no longer look at bottom level, for better performance ''' import sys, os import cPickle -VERSION = 1 +VERSION = 2 +MIN_LEVEL = 2 class SummaryTree: def __init__(self, block_size, levels, draw_cutoff, detail_cutoff): @@ -27,11 +30,11 @@ class SummaryTree: else: blocks = self.chrom_blocks[chrom] = {} self.chrom_stats[chrom] = {} - for level in range(1, self.levels+1): + for level in range(MIN_LEVEL, self.levels+1): blocks[level] = {} - for level in range(1, self.levels+1): + for level in range(MIN_LEVEL, self.levels+1): block_level = blocks[level] starting_block = self.find_block(start, level) ending_block = self.find_block(end, level) @@ -45,7 +48,7 @@ class SummaryTree: ''' Checks for cutoff and only stores levels above it ''' for chrom, blocks in self.chrom_blocks.iteritems(): cur_best = 999 - for level in range(self.levels, 0, -1): + for level in range(self.levels, MIN_LEVEL-1, -1): max_val = max(blocks[level].values()) if max_val < self.draw_cutoff: if "draw_level" not in self.chrom_stats[chrom]:

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galaxy-dist commit 647ca0049221: Enable display of unicode characters in history and workflow annotations.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287604356 14400 # Node ID 647ca0049221bcadde31559d6a99a6ccf236d134 # Parent b3763f7ecec7082e76a5ff407091fa7f0bffb7df Enable display of unicode characters in history and workflow annotations. --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -1038,7 +1038,7 @@ <label>Annotation / Notes:</label><div id="workflow-annotation" class="tooltip editable-text" original-title="Click to edit annotation"> %if annotation: - ${annotation | h} + ${h.to_unicode( annotation ) | h} %else: <em>Describe or add notes to workflow</em> %endif --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -378,7 +378,7 @@ div.form-row { <div id="history-annotation-container"><div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation"> %if annotation: - ${annotation | h} + ${h.to_unicode( annotation ) | h} %else: <em>Describe or add notes to history</em> %endif

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galaxy-dist commit b3763f7ecec7: added more zoom levels for mutation viz tool
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287603271 14400 # Node ID b3763f7ecec7082e76a5ff407091fa7f0bffb7df # Parent e226033419a91100e657f6880562dc50ae01ef98 added more zoom levels for mutation viz tool --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -30,6 +30,11 @@ <option value="3">3x</option><option value="4">4x</option><option value="5">5x</option> + <option value="6">6x</option> + <option value="7">7x</option> + <option value="8">8x</option> + <option value="9">9x</option> + <option value="10">10x</option><option value="interactive">Interactive</option></param> --- a/tools/mutation/visualize.py +++ b/tools/mutation/visualize.py @@ -263,8 +263,8 @@ def mainsvg(opts, args): # display legend for i, b in enumerate( bases ): bt = svg.SVG("tspan", b, style="font-family:Verdana;font-size:20%") - s.append(svg.SVG("text", bt, x=12+(i*10), y=4, stroke="none", fill="black")) - s.append(svg.SVG("rect", x=14+(i*10), y=1, width=4, height=3, + s.append(svg.SVG("text", bt, x=12+(i*10), y=3, stroke="none", fill="black")) + s.append(svg.SVG("rect", x=14+(i*10), y=0, width=4, height=3, stroke="none", fill=colors[b], fill_opacity=0.5)) reader = open(opts.input_file, 'U')

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galaxy-dist commit 73c4c66ff3dd: Add RNA-seq tools -- Tophat + Cufflinks suite -- to main.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287602065 14400 # Node ID 73c4c66ff3dd8101a0e6126077f4f8fc897c71fe # Parent 14fd007fc550092df7ea23f1019ab2d99ba03ce2 Add RNA-seq tools -- Tophat + Cufflinks suite -- to main. --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -288,7 +288,7 @@ <tool file="indels/indel_table.xml" />" <tool file="indels/indel_analysis.xml" /></section> - <section name="NGS: Expression Analysis" id="ngs-rna-tools"> + <section name="NGS: RNA Analysis" id="ngs-rna-tools"><label text="RNA-seq" id="rna_seq" /><tool file="ngs_rna/tophat_wrapper.xml" /><tool file="ngs_rna/cufflinks_wrapper.xml" /> --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -370,6 +370,15 @@ <tool file="genetrack/genetrack_indexer.xml" /><tool file="genetrack/genetrack_peak_prediction.xml" /></section> + <section name="NGS: RNA Analysis" id="ngs-rna-tools"> + <label text="RNA-seq" id="rna_seq" /> + <tool file="ngs_rna/tophat_wrapper.xml" /> + <tool file="ngs_rna/cufflinks_wrapper.xml" /> + <tool file="ngs_rna/cuffcompare_wrapper.xml" /> + <tool file="ngs_rna/cuffdiff_wrapper.xml" /> + <label text="Filtering" id="filtering" /> + <tool file="ngs_rna/filter_transcripts_via_tracking.xml" /> + </section><label text="RGENETICS" id="rgenetics" /><section name="SNP/WGA: Data; Filters" id="rgdat"><label text="Data: Import and upload" id="rgimport" />

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galaxy-dist commit 35b379691524: Add dynamic attribute filtering framework for trackster and enable dynamic filtering of VCF quality values and BED score values. Framework enables users to interactively filter a visualized dataset within trackster; for example, a BED file of peaks can be filtering so that only peaks with a score greater than 100 are shown.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287519951 14400 # Node ID 35b379691524c768ec84f86477f1ab49859afec2 # Parent 6372b67c9e370b3a80159bcc719e13d50ddc018f Add dynamic attribute filtering framework for trackster and enable dynamic filtering of VCF quality values and BED score values. Framework enables users to interactively filter a visualized dataset within trackster; for example, a BED file of peaks can be filtering so that only peaks with a score greater than 100 are shown. Individual changes include: (a) improvements to datatypes and data providers to support BED score filtering and VCF quality filtering; (b) addition of jQueryUI theme for slider; (c) modifications to trackster to show, update, and apply filters. --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -469,7 +469,7 @@ class Vcf( Tabular ): MetadataElement( name="columns", default=10, desc="Number of columns", readonly=True, visible=False ) MetadataElement( name="column_types", default=['str','int','str','str','str','int','str','list','str','str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) - MetadataElement( name="viz_filter_columns", default=[5] ) + MetadataElement( name="viz_filter_cols", default=[5], param=metadata.ColumnParameter, multiple=True ) def sniff( self, filename ): try: --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -function 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h=d.attr("refresh_on_change_values"),l=d.attr("last_selected_value");if(h!==undefined){h=h.split(",")}var j=function(){var n=i[c.attr("value")];if(n!==null&&n!==undefined){if($.inArray(n,h)===-1&&$.inArray(l,h)===-1){return}c.attr("value",n);$(window).trigger("refresh_on_change");c.parents("form").submit()}};c.bind("result",j);c.keyup(function(n){if(n.keyCode===13){j()}});c.keydown(function(n){if(n.keyCode===13){return false}})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m 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lass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false 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Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function() {RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new 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f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(d){this.origin al_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a. low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g i n c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.reset_overview();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this .tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=this.low/(this.max_high-this.max_low)*this.overview_viewport.width();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_locatio n(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);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 Track=function(b,a,c){this.name=b;this.parent_ element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<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=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name)}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("e rror");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined ){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configuration"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},j=function(){d.update_options(d.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){j()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:l,OK :j})};b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};make_popupmenu(d.name_div,b)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){if(!c.initial_canvas){c.initial_ca nvas=$(tile_element).clone();var l=tile_element.get(0).getContext("2d");var j=c.initial_canvas.get(0).getContext("2d");var k=l.getImageData(0,0,l.canvas.width,l.canvas.height);j.putImageData(k,0,0);c.set_overview()}c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10 )))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey: this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,l,p){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),o=e.get(0).getContext("2d"),k=f+"_"+b;if(p>PX_PER_CHAR){if(this.data_cache.get(k)===undefined){this.get_data(f,b);return}var n=this.data_cache.get(k);if(n===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*p+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*p-this.left_offset});for(var h=0,m=n.length;h<m;h++){var a=Math.round(h*p),j=Math.round(p/2);o.fillText(n[h],a+this.left_offset+j,10)}l.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_ px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;a.container_div.find(".yaxislabel").remove();var e=$("<div />").addCl ass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,s,c,e){if(this.vertical_range===undefined){return}var t=s*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),w=p+"_"+s;if(this.data_cache.get(w)===undefined){this.get_data(p,s);return}v ar j=this.data_cache.get(w);if(j===null){return}b.css({position:"absolute",top:0,left:(t-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,u=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();o.fillStyle=this.prefs.color;if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var v,h;for(var q=0,r=data.length;q<r;q++){v=Math.round((data[q][0]-t)*e);h=data[q][1];if(h===null){if(k&&m==="Filled"){o.lineTo(v,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(d-(h-l)/n*d);o.fillRect(v,h,f,d-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(v,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(v,h)}else{k=true;if(m==="Filled"){o.moveTo(v,d);o.lineTo(v,h)}else{o.moveTo(v,h)}}}}}if(m==="Filled"){if(k){o.lineTo(v,d)}o.fill()}else {o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div />").addClass("form-row");var e="track_"+n+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+n+"_minval",m=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),l=$("<input></input>").attr("id",h).val(d),k="track_"+n+"_maxval",g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j);return a.append(m).append(l).append(g).append(f).append(b).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();color=$("#track_"+c+"_color").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value||color!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.prefs.color=color;this.vert ical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_colo r!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_ slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefine d&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(ad,n,r,aq){var M=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,L=ai-M;var ak=(!this.initial_canvas?"initial":M+"_"+ai);var H=this.data_cache.get(ak);var e;if(H===undefined||(this.mode!=="Auto"&&H.dataset_type==="summary_tree")){this.data_queue[[M,ai]]=true;this.get_data(M,ai);return}var a=Math.ceil(L*aq),R=$("<canvas class='tile'></canvas>"),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,w=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(H.extra_info==="no_detail")),V=this.left_offset,ap,C,ar;if(H.dataset_type==="summary_tree"){C=this.summary_draw_height}else{if(q==="Dense"){C=w;ar=10}else{ar=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var z=(aq<0.0001?1/view.zoom_res:aq);C=this.incremental_slots(z,H.data,ab,q)*ar+w;ap=this.inc_slots[z]}}R.css({position:"absolute",top:0,left:(M-this.view.low)*aq-V});R.get(0).width=a+V;R.get(0).height=C;r.parent().css("height",Math.max(this.height_px,C)+"px");var I=R.get(0).getContext("2d");I.fillStyle=h;I.font=this.default_font;I.textAlign="right";this.container_div.find(".yaxislabel").remove();if(H.dataset_type=="summary_tree"){var X=H.data,K=H.max,p=H.avg,b=Math.ceil(H.delta*aq);var o=$("<div />").addClass("yaxislabel").text(K);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,G=X.length;am<G;am++){var Z=Math.floor((X[am][0]-M)*aq);var Y=X[am][1];if(!Y){continue}var aj=Y/K*this.summary_draw_height;I.fillStyle="black";I.fillRect(Z+V,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&I.measureText(Y).width<b){I.fillStyle="#bbb";I.textAlign="center";I.fillText(Y,Z+V+(b/2),this.summary_draw_height-5)}}e="Summary";r.append (R);return R}if(H.message){R.css({border:"solid red","border-width":"2px 2px 2px 0px"});I.fillStyle="red";I.textAlign="left";I.fillText(H.message,100+V,ar)}var ao=H.data;var al=0;for(var am=0,G=ao.length;am<G;am++){var S=ao[am],Q=S[0],an=S[1],aa=S[2],N=S[3];if(an<=ai&&aa>=M){var ac=Math.floor(Math.max(0,(an-M)*aq)),J=Math.ceil(Math.min(a,Math.max(0,(aa-M)*aq))),W=(q==="Dense"?1:(1+ap[Q]))*ar;if(H.dataset_type==="bai"){var u=S[4];I.fillStyle=h;if(S[5] instanceof Array){var D=Math.floor(Math.max(0,(S[5][0]-M)*aq)),P=Math.ceil(Math.min(a,Math.max(0,(S[5][1]-M)*aq))),B=Math.floor(Math.max(0,(S[6][0]-M)*aq)),v=Math.ceil(Math.min(a,Math.max(0,(S[6][1]-M)*aq)));if(S[5][1]>=M&&S[5][0]<=ai){this.rect_or_text(I,aq,M,ai,S[5][0],S[5][2],D+V,P-D,W)}if(S[6][1]>=M&&S[6][0]<=ai){this.rect_or_text(I,aq,M,ai,S[6][0],S[6][2],B+V,v-B,W)}if(B>P){I.fillStyle="#999";I.fillRect(P+V,W+5,B-P,1)}}else{I.fillStyle=h;this.rect_or_text(I,aq,M,ai,an,N,ac+V,J-ac,W)}if(q!=="Dense"&&!ab&&an>M){I.fillStyle=th is.prefs.label_color;if(n===0&&ac-I.measureText(N).width<0){I.textAlign="left";I.fillText(Q,J+2+V,W+8)}else{I.textAlign="right";I.fillText(Q,ac-2+V,W+8)}I.fillStyle=h}}else{if(H.dataset_type==="interval_index"){if(ab){I.fillStyle=h;I.fillRect(ac+V,W+5,J-ac,1)}else{var F=S[4],U=S[5],ae=S[6],g=S[7];var E,ag,O=null,at=null;if(U&&ae){O=Math.floor(Math.max(0,(U-M)*aq));at=Math.ceil(Math.min(a,Math.max(0,(ae-M)*aq)))}if(q!=="Dense"&&N!==undefined&&an>M){I.fillStyle=af;if(n===0&&ac-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+V,W+8)}else{I.textAlign="right";I.fillText(N,ac-2+V,W+8)}I.fillStyle=h}if(g){if(F){if(F=="+"){I.fillStyle=RIGHT_STRAND}else{if(F=="-"){I.fillStyle=LEFT_STRAND}}I.fillRect(ac+V,W,J-ac,10);I.fillStyle=h}for(var ak=0,f=g.length;ak<f;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-M)*aq)),T=Math.ceil(Math.min(a,Math.max((t[1]-M)*aq)));if(d>T){continue}E=5;ag=3;I.fillRect(d+V,W+ag,T-d,E);if(O!==undefined&&!(d>at||T<O)){E=9;ag=1;var ah=Math.max(d,O) ,A=Math.min(T,at);I.fillRect(ah+V,W+ag,A-ah,E)}}}else{E=9;ag=1;I.fillRect(ac+V,W+ag,J-ac,E);if(S.strand){if(S.strand=="+"){I.fillStyle=RIGHT_STRAND_INV}else{if(S.strand=="-"){I.fillStyle=LEFT_STRAND_INV}}I.fillRect(ac+V,W,J-ac,10);I.fillStyle=h}}}}else{if(H.dataset_type==="vcf"){if(ab){I.fillStyle=h;I.fillRect(ac+V,W+5,J-ac,1)}else{var s=S[4],m=S[5],c=S[6];E=9;ag=1;I.fillRect(ac+V,W,J-ac,E);if(q!=="Dense"&&N!==undefined&&an>M){I.fillStyle=af;if(n===0&&ac-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+V,W+8)}else{I.textAlign="right";I.fillText(N,ac-2+V,W+8)}I.fillStyle=h}var l=s+" / "+m;if(an>M&&I.measureText(l).width<(J-ac)){I.fillStyle="white";I.textAlign="center";I.fillText(l,V+ac+(J-ac)/2,W+8);I.fillStyle=h}}}}}al++}}r.append(R);return R},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k ="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vert ical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";r ight_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_coun ter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Ove rview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div />").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack (a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("drag start",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.contai ner.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.rese t();c.redraw(true);for(var g in c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.reset_overview();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remo ve()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=this.low/(this.max_high-this.max_low)*this.overview_viewport.width();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a ,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);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 Filter=function( b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=Number.MIN_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=Number.MIN_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[th is.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<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=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.filte ring_div.hide();this.filtering_div.bind("drag",function(k){k.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(var e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);d.text("[0-2]");var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(h);a.control_element.slider({range:true,min:0,max:1,values:[0,1],slide:function(l,m){var k=m.values;d.text("["+k[0]+"-"+k[1]+"]");a.low=k[0];a.high=k[1];c.draw(true)},change:function(k,l){a.control_element.slider("option","slide").call(a.control_element,k,l)}});a.slider=a.control_element;a.slider_label=d}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},i nit_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div. addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configurat ion"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},j=function(){d.update_options(d.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){j()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:l,OK:j})};if(d.filters.length>0){b["Show filters"]=function(){var j;if(!d.filtering_div.is(":visible")){j="Hide filters";d.filters_visible=true}else{j="Show filters";d.filters_visible=false}$("#"+d.name_div.attr("id")+"-menu").find("li").eq(2).text(j);d.filtering_div.toggle()}}b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};d.popup_menu=make_popupmenu(d.name_div,b);show_hide_popupmenu_options(d.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,h=g-m,f=this.view.res olution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h,k;this.content_div.append(p),this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=new Object();while((a*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+a;var e=this.tile_cache.get(n);if(!b&&e){var j=a*DENSITY*f;var d=(j-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(this,n,m,g,a,f,p,q,l)}a+=1}var c=this;var o=setInterval(function(){if(l.length!=0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var r=0;r<c.filters.length;r++){c.filters[r].update_ui_elt()}clearInterval(o)}},50)},delayed_draw:function(c,h,g,e,b,d,j,k,f){var a=setTimeout(function(){if(!(g>c.view.high||e<c.view.low)){tile_element=c.draw_tile(d,b,j,k);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var n=tile_element.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n. getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,tile_element);c.show_tile(tile_element,j)}}delete f.id},50);f.id=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a ,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_da ta:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,l,p){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),o=e.get(0).getContext("2d"),k=f+"_"+b;if(p>PX_PER_CHAR){if(this.data_cache.get(k)===undefined){this.get_data(f,b);return}var n=this.data_cache.get(k);if(n===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*p+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*p-this.left_offset});for(var h=0,m=n.length;h<m;h++){var a=Math.round(h*p),j=Math.round(p/2);o.fillText(n[h],a+this.left_offset+j,10)}l.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=func tion(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#trac k_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;a.container_div.find(".yaxislabel").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:func tion(p,s,c,e){if(this.vertical_range===undefined){return}var t=s*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),w=p+"_"+s;if(this.data_cache.get(w)===undefined){this.get_data(p,s);return}var j=this.data_cache.get(w);if(j===null){return}b.css({position:"absolute",top:0,left:(t-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,u=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();o.fillStyle=this.prefs.color;if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var v,h;for(var q=0,r=data.length;q<r;q++){v=Math.round((data[q][0]-t)*e);h=data[q][1];if(h===null){if(k&&m==="Filled"){o.lineTo(v,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(d-(h-l)/n*d);o.fillRect(v,h,f,d-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")"; o.fillRect(v,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(v,h)}else{k=true;if(m==="Filled"){o.moveTo(v,d);o.lineTo(v,h)}else{o.moveTo(v,h)}}}}}if(m==="Filled"){if(k){o.lineTo(v,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div />").addClass("form-row");var e="track_"+n+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+n+"_minval",m=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),l=$("<input></input>").attr("id",h).val(d),k="track_"+n+"_maxval",g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j);return a.append(m).append(l).append(g).append(f).append(b).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();color=$("#track_"+ c+"_color").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value||color!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.prefs.color=color;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE );this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};th is.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e, f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(ah,o,s,aw){var N=o*DENSITY*ah,am=(o+1)*DENSITY*ah,M=am-N;var ao=(!this.initial_canvas?"initial":N+"_"+am);var I=this.data_cache.get(ao);var e;if(I===undefined||(this.mode!=="Auto"&&I.dataset_type==="summary_tree")){this.data_queue[[N,am]]=true;this.get_data(N,am);return}var a=Math.ceil(M*aw),S=$("<canvas class='tile'></canvas>"),aj=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,z=25,af=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(I.extra_inf o==="no_detail")),X=this.left_offset,av,D,ax;if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;ax=10}else{ax=(af?this.vertical_nodetail_px:this.vertical_detail_px);var A=(aw<0.0001?1/view.zoom_res:aw);D=this.incremental_slots(A,I.data,af,r)*ax+z;av=this.inc_slots[A]}}S.css({position:"absolute",top:0,left:(N-this.view.low)*aw-X});S.get(0).width=a+X;S.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=S.get(0).getContext("2d");J.fillStyle=l;J.font=this.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Z=I.data,L=I.max,q=I.avg,b=Math.ceil(I.delta*aw);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var aq=0,H=Z.length;aq<H;aq++){var ab=Math.floor((Z[aq][0]-N)*aw);var aa=Z[aq][1];if(!aa){continue}var an=aa/L*this.summary_draw_height;J.fillStyle="black";J.fil lRect(ab+X,this.summary_draw_height-an,b,an);if(this.prefs.show_counts&&J.measureText(aa).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(aa,ab+X+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(S);return S}if(I.message){S.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fillStyle="red";J.textAlign="left";J.fillText(I.message,100+X,ax)}var ae=false;if(I.data.length!=0){ae=true;for(var at=0;at<this.filters.length;at++){if(!this.filters[at].applies_to(I.data[0])){ae=false}}}if(ae){S.addClass(FILTERABLE_CLASS)}var au=I.data;var ap=0;for(var aq=0,H=au.length;aq<H;aq++){var T=au[aq],R=T[0],ar=T[1],ad=T[2],O=T[3];var ac=false;var V;for(var at=0;at<this.filters.length;at++){V=this.filters[at];V.update_attrs(T);if(!V.keep(T)){ac=true;break}}if(ac){continue}if(ar<=am&&ad>=N){var ag=Math.floor(Math.max(0,(ar-N)*aw)),K=Math.ceil(Math.min(a,Math.max(0,(ad-N)*aw))),Y=(r==="Dense"?1:(1+av[R]))*ax;if(I.dataset_type==="bai"){var v=T[4];J.fillStyle=l;if(T[5] in stanceof Array){var E=Math.floor(Math.max(0,(T[5][0]-N)*aw)),Q=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-N)*aw))),C=Math.floor(Math.max(0,(T[6][0]-N)*aw)),w=Math.ceil(Math.min(a,Math.max(0,(T[6][1]-N)*aw)));if(T[5][1]>=N&&T[5][0]<=am){this.rect_or_text(J,aw,N,am,T[5][0],T[5][2],E+X,Q-E,Y)}if(T[6][1]>=N&&T[6][0]<=am){this.rect_or_text(J,aw,N,am,T[6][0],T[6][2],C+X,w-C,Y)}if(C>Q){J.fillStyle="#999";J.fillRect(Q+X,Y+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,aw,N,am,ar,O,ag+X,K-ag,Y)}if(r!=="Dense"&&!af&&ar>N){J.fillStyle=this.prefs.label_color;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(R,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(R,ag-2+X,Y+8)}J.fillStyle=l}}else{if(I.dataset_type==="interval_index"){if(af){J.fillStyle=l;J.fillRect(ag+X,Y+5,K-ag,1)}else{var G=T[4],W=T[5],ai=T[6],h=T[7];var F,ak,P=null,ay=null;if(W&&ai){P=Math.floor(Math.max(0,(W-N)*aw));ay=Math.ceil(Math.min(a,Math.max(0,(ai-N)*aw)))}if(r!=="Dense"&&O!==undefined&&ar>N){J.fil lStyle=aj;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(O,ag-2+X,Y+8)}J.fillStyle=l}if(h){if(G){if(G=="+"){J.fillStyle=RIGHT_STRAND}else{if(G=="-"){J.fillStyle=LEFT_STRAND}}J.fillRect(ag+X,Y,K-ag,10);J.fillStyle=l}for(var ao=0,g=h.length;ao<g;ao++){var u=h[ao],d=Math.floor(Math.max(0,(u[0]-N)*aw)),U=Math.ceil(Math.min(a,Math.max((u[1]-N)*aw)));if(d>U){continue}F=5;ak=3;J.fillRect(d+X,Y+ak,U-d,F);if(P!==undefined&&!(d>ay||U<P)){F=9;ak=1;var al=Math.max(d,P),B=Math.min(U,ay);J.fillRect(al+X,Y+ak,B-al,F)}}}else{F=9;ak=1;J.fillRect(ag+X,Y+ak,K-ag,F);if(T.strand){if(T.strand=="+"){J.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){J.fillStyle=LEFT_STRAND_INV}}J.fillRect(ag+X,Y,K-ag,10);J.fillStyle=l}}}}else{if(I.dataset_type==="vcf"){if(af){J.fillStyle=l;J.fillRect(ag+X,Y+5,K-ag,1)}else{var t=T[4],n=T[5],c=T[6];F=9;ak=1;J.fillRect(ag+X,Y,K-ag,F);if(r!=="Dense"&&O!==undefined&&ar>N){J.fillStyle=aj;if(o===0&&a g-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(O,ag-2+X,Y+8)}J.fillStyle=l}var m=t+" / "+n;if(ar>N&&J.measureText(m).width<(K-ag)){J.fillStyle="white";J.textAlign="center";J.fillText(m,X+ag+(K-ag)/2,Y+8);J.fillStyle=l}}}}}ap++}}return S},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_opti ons:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -10,6 +10,7 @@ var DENSITY = 200, DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", DATA_LOADING = "Loading data...", + FILTERABLE_CLASS = "filterable", CACHED_TILES_FEATURE = 10, CACHED_TILES_LINE = 30, CACHED_DATA = 5, @@ -448,10 +449,100 @@ var View = function( container, chrom, t } }); -var Track = function (name, view, parent_element) { +// Generic filter. +var Filter = function( name, index, value ) { this.name = name; + this.index = index; + this.value = value; +}; + +// Number filter for a track. +var NumberFilter = function( name, index ) { + this.name = name; + // Index into payload to filter. + this.index = index; + // Filter low/high. These values are used to filter elements. + this.low = Number.MIN_VALUE; + this.high = Number.MAX_VALUE; + // Slide min/max. These values are used to set/update slider. + this.slider_min = Number.MAX_VALUE; + this.slider_max = Number.MIN_VALUE; + // UI Slider element and label that is associated with filter. + this.slider = null; + this.slider_label = null; +}; +$.extend( NumberFilter.prototype, { + // Returns true if filter can be applied to element. + applies_to: function( element ) { + if ( element.length > this.index ) + return true; + return false; + }, + // Returns true iff element is in [low, high]; range is inclusive. + keep: function( element ) { + if ( !this.applies_to( element ) ) + // No element to filter on. + return true; + return ( element[this.index] >= this.low && element[this.index] <= this.high ); + }, + // Update filter's min and max values based on element's values. + update_attrs: function( element ) { + var updated = false; + if ( !this.applies_to( element ) ) { + return updated; + } + + // Update filter's min, max based on element values. + if ( element[this.index] < this.slider_min ) { + this.slider_min = element[this.index]; + updated = true; + } + if ( element[this.index] > this.slider_max ) { + this.slider_max = element[this.index]; + updated = false; + } + return updated; + }, + // Update filter's slider. + update_ui_elt: function () { + var + slider_min = this.slider.slider( "option", "min" ), + slider_max = this.slider.slider( "option", "max" ); + if (this.slider_min < slider_min || this.slider_max > slider_max) { + // Need to update slider. + this.slider.slider( "option", "min", this.slider_min ); + this.slider.slider( "option", "max", this.slider_max ); + // Refresh slider: + // TODO: do we want to keep current values or reset to min/max? + // Currently we reset values: + this.slider.slider( "option", "values", [ this.slider_min, this.slider_max ] ); + // To use the current values. + //var values = this.slider.slider( "option", "values" ); + //this.slider.slider( "option", "values", values ); + } + } +}); + +// Parse filters dict and return filters. +var get_filters = function( filters_dict ) { + var filters = [] + for (var i = 0; i < filters_dict.length; i++) { + var filter_dict = filters_dict[i]; + var name = filter_dict['name'], type = filter_dict['type'], index = filter_dict['index']; + if ( type == 'int' || type == 'float' ) { + filters[i] = new NumberFilter( name, index ); + } + else + filters[i] = new Filter( name, index, type ); + } + return filters; +}; + +var Track = function (name, view, parent_element, filters) { + this.name = name; + this.view = view; this.parent_element = parent_element; - this.view = view; + this.filters = (filters !== undefined ? get_filters( filters ) : []); this.init_global(); }; $.extend( Track.prototype, { @@ -462,7 +553,51 @@ var Track = function (name, view, parent 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() ); } + // Create track filtering div. + this.filtering_div = $("<div class='track-filters'>").appendTo(this.container_div); + this.filtering_div.hide(); + // Dragging is disabled on div so that actions on slider do not impact viz. + this.filtering_div.bind( "drag", function(e) { + e.stopPropagation(); + }); + var filters_table = $("<table class='filters'>").appendTo(this.filtering_div); + var track = this; + for (var i = 0; i < this.filters.length; i++) { + var filter = this.filters[i]; + var table_row = $("<tr>").appendTo(filters_table); + var filter_th = $("<th class='filter-info'>").appendTo(table_row); + var name_span = $("<span class='name'>").appendTo(filter_th); + name_span.text(filter.name + " "); // Extra spacing to separate name and values + var values_span = $("<span class='values'>").appendTo(filter_th); + values_span.text("[0-2]"); + // TODO: generate custom interaction elements based on filter type. + var table_data = $("<td>").appendTo(table_row); + filter.control_element = $("<div id='" + filter.name + "-filter-control' style='width: 200px; position: relative'>").appendTo(table_data); + filter.control_element.slider({ + range: true, + min: 0, + max: 1, + values: [0, 1], + slide: function( event, ui ) { + var values = ui.values; + // Set new values in UI. + values_span.text( "[" + values[0] + "-" + values[1] + "]" ); + // Set new values in filter. + filter.low = values[0]; + filter.high = values[1]; + // Redraw track. + track.draw( true ); + }, + change: function( event, ui ) { + filter.control_element.slider( "option", "slide" ).call( filter.control_element, event, ui ); + } + }); + filter.slider = filter.control_element; + filter.slider_label = values_span; + } + this.content_div = $("<div class='track-content'>").appendTo(this.container_div); this.parent_element.append(this.container_div); }, @@ -478,7 +613,7 @@ var Track = function (name, view, parent track.content_div.text(DATA_LOADING); } track.container_div.removeClass("nodata error pending"); - + if (track.view.chrom) { $.getJSON( data_url, params, function (result) { if (!result || result === "error" || result.kind === "error") { @@ -577,14 +712,30 @@ var TiledTrack = function() { "OK": ok_fn }); }; + if (track.filters.length > 0) { + track_dropdown["Show filters"] = function() { + // Set option text and toggle filtering div. + var menu_option_text; + if (!track.filtering_div.is(":visible")) { + menu_option_text = "Hide filters"; + track.filters_visible = true; + } + else { + menu_option_text = "Show filters"; + track.filters_visible = false; + } + $("#" + track.name_div.attr("id") + "-menu").find("li").eq(2).text(menu_option_text); + track.filtering_div.toggle(); + }; + } track_dropdown["Remove"] = function() { view.remove_track(track); if (view.num_tracks === 0) { $("#no-tracks").show(); } }; - make_popupmenu(track.name_div, track_dropdown); - + track.popup_menu = make_popupmenu(track.name_div, track_dropdown); + show_hide_popupmenu_options(track.popup_menu, "(Show|Hide) filters", false); /* if (track.overview_check_div === undefined) { track.overview_check_div = $("<div class='right-float' />").css("margin-top", "-3px").appendTo(track.header_div); @@ -604,7 +755,7 @@ var TiledTrack = function() { */ }; $.extend( TiledTrack.prototype, Track.prototype, { - draw: function() { + draw: function( force ) { var low = this.view.low, high = this.view.high, range = high - low, @@ -614,35 +765,54 @@ var TiledTrack = function() { w_scale = this.content_div.width() / range, tile_element; - this.content_div.children( ":first" ).remove(); this.content_div.append( parent_element ), this.max_height = 0; // Index of first tile that overlaps visible region var tile_index = Math.floor( low / resolution / DENSITY ); + // A list of setTimeout() ids used when drawing tiles. + var draw_tile_ids = new Object(); while ( ( tile_index * DENSITY * resolution ) < high ) { // Check in cache var key = this.content_div.width() + '_' + w_scale + '_' + tile_index; var cached = this.tile_cache.get(key); - if ( cached ) { - // console.log("cached tile " + tile_index); + if ( !force && cached ) { var tile_low = tile_index * DENSITY * resolution; var left = ( tile_low - low ) * w_scale; if (this.left_offset) { left -= this.left_offset; } cached.css({ left: left }); - // Our responsibility to move the element to the new parent - parent_element.append( cached ); - this.max_height = Math.max( this.max_height, cached.height() ); - this.content_div.css("height", this.max_height + "px"); + this.show_tile( cached, parent_element ); } else { - this.delayed_draw(this, key, low, high, tile_index, resolution, parent_element, w_scale); + this.delayed_draw(this, key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids); } tile_index += 1; } - }, delayed_draw: function(track, key, low, high, tile_index, resolution, parent_element, w_scale) { + + // + // Actions to take after new tiles have been loaded/drawn: + // (1) remove old tile(s); + // (2) update filtering UI elements. + // + var track = this; + var intervalId = setInterval(function() { + if ( draw_tile_ids.length != 0 ) { + // Add drawing has finished; if there is more than one child in the content div, + // remove the first one, which is the oldest. + if ( track.content_div.children().length > 1 ) { + track.content_div.children( ":first" ).remove(); + } + + // Update filtering UI. + for (var f = 0; f < track.filters.length; f++) + track.filters[f].update_ui_elt(); + // Method complete; do not call it again. + clearInterval(intervalId); + } + }, 50); + }, delayed_draw: function(track, key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids) { // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data - setTimeout(function() { + var id = setTimeout(function() { if ( !(low > track.view.high || high < track.view.low) ) { tile_element = track.draw_tile( resolution, tile_index, parent_element, w_scale ); if (tile_element) { @@ -655,12 +825,36 @@ var TiledTrack = function() { tgt_ctx.putImageData(data, 0, 0); track.set_overview(); } + // Add tile to cache and show tile. track.tile_cache.set(key, tile_element); - track.max_height = Math.max( track.max_height, tile_element.height() ); - track.content_div.css("height", track.max_height + "px"); + track.show_tile( tile_element, parent_element ) } } + // Remove setTimeout id. + delete draw_tile_ids.id; }, 50); + draw_tile_ids.id = true; + }, + // Show track tile and perform associated actions. + show_tile: function( tile_element, parent_element ) { + // Readability. + var track = this; + + // Setup and show tile element. + parent_element.append( tile_element ); + track.max_height = Math.max( track.max_height, tile_element.height() ); + track.content_div.css("height", track.max_height + "px"); + + // Show/hide filters based on whether tile is filterable. + if ( tile_element.hasClass(FILTERABLE_CLASS) ) { + show_hide_popupmenu_options(track.popup_menu, "(Show|Hide) filters"); + if (track.filters_visible) + track.filtering_div.show(); + } + else { + show_hide_popupmenu_options(track.popup_menu, "(Show|Hide) filters", false); + track.filtering_div.hide(); + } }, set_overview: function() { var view = this.view; @@ -986,10 +1180,10 @@ var LineTrack = function ( name, view, d } }); -var FeatureTrack = function ( name, view, dataset_id, prefs ) { +var FeatureTrack = function ( name, view, dataset_id, filters, prefs ) { this.track_type = "FeatureTrack"; this.display_modes = ["Auto", "Dense", "Squish", "Pack"]; - Track.call( this, name, view, view.viewport_container ); + Track.call( this, name, view, view.viewport_container, filters ); TiledTrack.call( this ); this.height_px = 0; @@ -1245,6 +1439,24 @@ var FeatureTrack = function ( name, view ctx.fillText(result.message, 100 + left_offset, y_scale); } + // + // We're now working at the level of individual data points. + // + + // See if tile is filterable. If so, add class. + var filterable = false; + if ( result.data.length != 0 ) { + filterable = true; + for (var f = 0; f < this.filters.length; f++) + if ( !this.filters[f].applies_to( result.data[0] ) ) { + filterable = false; + } + } + if ( filterable ) { + new_canvas.addClass(FILTERABLE_CLASS); + } + + // Draw data points. var data = result.data; var j = 0; for (var i = 0, len = data.length; i < len; i++) { @@ -1254,6 +1466,20 @@ var FeatureTrack = function ( name, view feature_end = feature[2], feature_name = feature[3]; + // Apply filters to feature. + var hide_feature = false; + var filter; + for (var f = 0; f < this.filters.length; f++) { + filter = this.filters[f]; + filter.update_attrs( feature ); + if ( !filter.keep( feature ) ) { + hide_feature = true; + break; + } + } + if ( hide_feature ) + continue; + if (feature_start <= tile_high && feature_end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), @@ -1374,6 +1600,7 @@ var FeatureTrack = function ( name, view } } } else if (result.dataset_type === 'vcf') { + // VCF track. if (no_detail) { ctx.fillStyle = block_color; ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, 1); @@ -1414,7 +1641,6 @@ var FeatureTrack = function ( name, view j++; } } - parent_element.append(new_canvas); return new_canvas; }, gen_options: function(track_id) { var container = $("<div />").addClass("form-row"); @@ -1446,8 +1672,8 @@ var FeatureTrack = function ( name, view } }); -var ReadTrack = function ( name, view, dataset_id, prefs ) { - FeatureTrack.call( this, name, view, dataset_id, prefs ); +var ReadTrack = function ( name, view, dataset_id, filters, prefs ) { + FeatureTrack.call( this, name, view, dataset_id, filters, prefs ); this.track_type = "ReadTrack"; this.vertical_detail_px = 10; this.vertical_nodetail_px = 5; --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -90,6 +90,20 @@ function make_popupmenu( button_element, .appendTo( "body" ) .hide(); attach_popupmenu( button_element, wrapper ); + return menu_element; +} + +// Toggle popup menu options using regular expression on option names. +function show_hide_popupmenu_options( menu, option_name_re, show ) { + var show = (show === undefined ? true : show ); + var re = new RegExp(option_name_re); + $(menu).find("li").each( function() { + if ( re.exec( $(this).text() ) ) + if (show) + $(this).show(); + else + $(this).hide(); + }); } function make_popup_menus() { Binary file static/june_2007_style/blue/overcast/images/ui-bg_inset-soft_50_c9c9c9_1x100.png has changed --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -19,10 +19,13 @@ class TracksDataProvider( object ): """ Base class for tracks data providers. """ """ - Mapping from column name to index in data. This mapping is used to create - filters. + Mapping from column name to payload data; this mapping is used to create + filters. Key is column name, value is a dict with mandatory key 'index' and + optional key 'name'. E.g. this defines column 4 + + col_name_data_attr_mapping = {4 : { index: 5, name: 'Score' } } """ - col_name_data_index_mapping = {} + col_name_data_attr_mapping = {} def __init__( self, converted_dataset=None, original_dataset=None ): """ Create basic data provider. """ @@ -37,7 +40,7 @@ class TracksDataProvider( object ): def get_filters( self ): """ Returns filters for provider's data. Return value is a list of - filters; each filter is a dictionary with the keys 'name', 'index', 'value'. + filters; each filter is a dictionary with the keys 'name', 'index', 'type'. NOTE: This method uses the original dataset's datatype and metadata to create the filters. """ @@ -58,17 +61,17 @@ class TracksDataProvider( object ): # Create and return filters. filters = [] - if self.original_dataset.metadata.viz_filter_columns: - for viz_col_index in self.original_dataset.metadata.viz_filter_columns: + if self.original_dataset.metadata.viz_filter_cols: + for viz_col_index in self.original_dataset.metadata.viz_filter_cols: col_name = column_names[ viz_col_index ] # Make sure that column has a mapped index. If not, do not add filter. try: - index = self.col_name_data_index_mapping[ col_name ] + attrs = self.col_name_data_attr_mapping[ col_name ] except KeyError: continue filters.append( - { 'name' : col_name, 'value' : column_types[viz_col_index], \ - 'index' : index } ) + { 'name' : attrs[ 'name' ], 'type' : column_types[viz_col_index], \ + 'index' : attrs[ 'index' ] } ) return filters class SummaryTreeDataProvider( TracksDataProvider ): @@ -119,7 +122,7 @@ class VcfDataProvider( TracksDataProvide [ uid (offset), start, end, ID, reference base(s), alternate base(s), quality score] """ - col_name_data_index_mapping = { 'Qual' : 6 } + col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } def get_data( self, chrom, start, end, **kwargs ): """ Returns data in region defined by chrom, start, and end. """ @@ -153,7 +156,7 @@ class VcfDataProvider( TracksDataProvide # alternative base(s) feature[4], \ # phred quality score - feature[5] ] + int( feature[5] )] results.append(payload) return { 'data_type' : 'vcf', 'data': results, 'message': message } @@ -306,6 +309,9 @@ class IntervalIndexDataProvider( TracksD Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ + + col_name_data_attr_mapping = { 4 : { 'index': 8 , 'name' : 'Score' } } + def get_data( self, chrom, start, end, **kwargs ): start, end = int(start), int(end) source = open( self.original_dataset.file_name ) @@ -355,6 +361,9 @@ class IntervalIndexDataProvider( TracksD block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] blocks = zip(block_sizes, block_starts) payload.append( [ (start + block[1], start + block[1] + block[0]) for block in blocks] ) + + if length >= 5: + payload.append( int(feature[4]) ) # score results.append(payload) @@ -375,7 +384,7 @@ dataset_type_name_to_data_provider = { } dataset_type_to_data_provider = { - Vcf : VcfDataProvider + Vcf : VcfDataProvider, } def get_data_provider( name=None, original_dataset=None ): @@ -395,11 +404,16 @@ def get_data_provider( name=None, origin # Look for data provider in mapping. data_provider = dataset_type_to_data_provider.get( original_dataset.datatype.__class__, None ) if not data_provider: - # If get_track_type is available, then dataset can be added to trackster - # and hence has at least a generic data provider. + # Look up data provider from datatype's informaton. try: - original_dataset.datatype.get_track_type() - data_provider = TracksDataProvider + # Get data provider mapping and data provider for 'data'. If + # provider available, use it; otherwise use generic provider. + _ , data_provider_mapping = original_dataset.datatype.get_track_type() + data_provider_name = data_provider_mapping[ 'data' ] + if data_provider_name: + data_provider = get_data_provider( name=data_provider_name, original_dataset=original_dataset ) + else: + data_provider = TracksDataProvider except: pass return data_provider --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -12,7 +12,7 @@ <%def name="stylesheets()"> ${parent.stylesheets()} -${h.css( "history", "autocomplete_tagging", "trackster" )} +${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom" )} <style type="text/css"> #center { @@ -34,6 +34,17 @@ left: 0; bottom: 0; } + # Styles for filters. + .filter-name { + float: left; + } + table.filters { + border-collapse: separate; + border-spacing: 7px 0px; + } + .values { + padding-right: 1em; + } </style></%def> @@ -67,7 +78,7 @@ view.editor = true; %for track in config.get('tracks'): view.add_track( - new ${track["track_type"]}( "${track['name'] | h}", view, ${track['dataset_id']}, ${track['prefs']} ) + new ${track["track_type"]}( "${track['name'] | h}", view, ${track['dataset_id']}, ${track['filters']}, ${track['prefs']} ) ); %endfor init(); @@ -134,7 +145,7 @@ var add_async_success = function(track_data) { var td = track_data, track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack }, - new_track = new track_types[track_data.track_type]( track_data.name, view, track_data.dataset_id, track_data.prefs); + new_track = new track_types[track_data.track_type]( track_data.name, view, track_data.dataset_id, track_data.filters, track_data.prefs); view.add_track(new_track); view.has_changes = true; Binary file static/june_2007_style/blue/overcast/images/ui-bg_glass_35_dddddd_1x400.png has changed --- /dev/null +++ b/static/june_2007_style/blue/overcast/jquery-ui-1.8.5.custom.css @@ -0,0 +1,318 @@ +/* + * jQuery UI CSS Framework @VERSION + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Theming/API + */ + +/* Layout helpers +----------------------------------*/ +.ui-helper-hidden { display: none; } +.ui-helper-hidden-accessible { position: absolute; left: -99999999px; } +.ui-helper-reset { margin: 0; padding: 0; border: 0; outline: 0; line-height: 1.3; text-decoration: none; font-size: 100%; list-style: none; } +.ui-helper-clearfix:after { content: "."; display: block; height: 0; clear: both; visibility: hidden; } +.ui-helper-clearfix { display: inline-block; } +/* required comment for clearfix to work in Opera \*/ +* html .ui-helper-clearfix { height:1%; } +.ui-helper-clearfix { display:block; } +/* end clearfix */ +.ui-helper-zfix { width: 100%; height: 100%; top: 0; left: 0; position: absolute; opacity: 0; filter:Alpha(Opacity=0); } + + +/* Interaction Cues +----------------------------------*/ +.ui-state-disabled { cursor: default !important; } + + +/* Icons +----------------------------------*/ + +/* states and images */ +.ui-icon { display: block; text-indent: -99999px; overflow: hidden; background-repeat: no-repeat; } + + +/* Misc visuals +----------------------------------*/ + +/* Overlays */ +.ui-widget-overlay { position: absolute; top: 0; left: 0; width: 100%; height: 100%; } + + +/* + * jQuery UI CSS Framework @VERSION + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Theming/API + * + * To view and modify this theme, visit http://jqueryui.com/themeroller/?ffDefault=Trebuchet%20MS,%20Helvetica,%20A… Highlight=444444&iconColorHighlight=3383bb&bgColorError=c0402a&bgTextureError=01_flat.png&bgImgOpacityError=55&borderColorError=c0402a&fcError=ffffff&iconColorError=fbc856&bgColorOverlay=eeeeee&bgTextureOverlay=01_flat.png&bgImgOpacityOverlay=0&opacityOverlay=80&bgColorShadow=aaaaaa&bgTextureShadow=01_flat.png&bgImgOpacityShadow=0&opacityShadow=60&thicknessShadow=4px&offsetTopShadow=-4px&offsetLeftShadow=-4px&cornerRadiusShadow=0pxdow=0px + */ + + +/* Component containers +----------------------------------*/ +.ui-widget { font-family: Trebuchet MS, Helvetica, Arial, sans-serif; font-size: 1.1em; } +.ui-widget .ui-widget { font-size: 1em; } +.ui-widget input, .ui-widget select, .ui-widget textarea, .ui-widget button { font-family: Trebuchet MS, Helvetica, Arial, sans-serif; font-size: 1em; } +.ui-widget-content { border: 1px solid #aaaaaa; background: #c9c9c9 url(images/ui-bg_inset-soft_50_c9c9c9_1x100.png) 50% bottom repeat-x; color: #333333; } +.ui-widget-content a { color: #333333; } +.ui-widget-header { border: 1px solid #bbbbbb; background: #dddddd url(images/ui-bg_glass_35_dddddd_1x400.png) 50% 50% repeat-x; color: #444444; font-weight: bold; } +.ui-widget-header a { color: #444444; } + +/* Interaction states +----------------------------------*/ +.ui-state-default, .ui-widget-content .ui-state-default, .ui-widget-header .ui-state-default { border: 1px solid #cccccc; background: #eeeeee url(images/ui-bg_glass_60_eeeeee_1x400.png) 50% 50% repeat-x; font-weight: bold; color: #3383bb; } +.ui-state-default a, .ui-state-default a:link, .ui-state-default a:visited { color: #3383bb; text-decoration: none; } +.ui-state-hover, .ui-widget-content .ui-state-hover, .ui-widget-header .ui-state-hover, .ui-state-focus, .ui-widget-content .ui-state-focus, .ui-widget-header .ui-state-focus { border: 1px solid #bbbbbb; background: #f8f8f8 url(images/ui-bg_glass_100_f8f8f8_1x400.png) 50% 50% repeat-x; font-weight: bold; color: #599fcf; } +.ui-state-hover a, .ui-state-hover a:hover { color: #599fcf; text-decoration: none; } +.ui-state-active, .ui-widget-content .ui-state-active, .ui-widget-header .ui-state-active { border: 1px solid #999999; background: #999999 url(images/ui-bg_inset-hard_75_999999_1x100.png) 50% 50% repeat-x; font-weight: bold; color: #ffffff; } +.ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited { color: #ffffff; text-decoration: none; } +.ui-widget :active { outline: none; } + +/* Interaction Cues +----------------------------------*/ +.ui-state-highlight, .ui-widget-content .ui-state-highlight, .ui-widget-header .ui-state-highlight {border: 1px solid #ffffff; background: #eeeeee url(images/ui-bg_flat_55_eeeeee_40x100.png) 50% 50% repeat-x; color: #444444; } +.ui-state-highlight a, .ui-widget-content .ui-state-highlight a,.ui-widget-header .ui-state-highlight a { color: #444444; } +.ui-state-error, .ui-widget-content .ui-state-error, .ui-widget-header .ui-state-error {border: 1px solid #c0402a; background: #c0402a url(images/ui-bg_flat_55_c0402a_40x100.png) 50% 50% repeat-x; color: #ffffff; } +.ui-state-error a, .ui-widget-content .ui-state-error a, .ui-widget-header .ui-state-error a { color: #ffffff; } +.ui-state-error-text, .ui-widget-content .ui-state-error-text, .ui-widget-header .ui-state-error-text { color: #ffffff; } +.ui-priority-primary, .ui-widget-content .ui-priority-primary, .ui-widget-header .ui-priority-primary { font-weight: bold; } +.ui-priority-secondary, .ui-widget-content .ui-priority-secondary, .ui-widget-header .ui-priority-secondary { opacity: .7; filter:Alpha(Opacity=70); font-weight: normal; } +.ui-state-disabled, .ui-widget-content .ui-state-disabled, .ui-widget-header .ui-state-disabled { opacity: .35; filter:Alpha(Opacity=35); background-image: none; } + +/* Icons +----------------------------------*/ + +/* states and images */ +.ui-icon { width: 16px; height: 16px; background-image: url(images/ui-icons_999999_256x240.png); } +.ui-widget-content .ui-icon {background-image: url(images/ui-icons_999999_256x240.png); } +.ui-widget-header .ui-icon {background-image: url(images/ui-icons_999999_256x240.png); } +.ui-state-default .ui-icon { background-image: url(images/ui-icons_70b2e1_256x240.png); } +.ui-state-hover .ui-icon, .ui-state-focus .ui-icon {background-image: url(images/ui-icons_3383bb_256x240.png); } +.ui-state-active .ui-icon {background-image: url(images/ui-icons_454545_256x240.png); } +.ui-state-highlight .ui-icon {background-image: url(images/ui-icons_3383bb_256x240.png); } +.ui-state-error .ui-icon, .ui-state-error-text .ui-icon {background-image: url(images/ui-icons_fbc856_256x240.png); } + +/* positioning */ +.ui-icon-carat-1-n { background-position: 0 0; } +.ui-icon-carat-1-ne { background-position: -16px 0; } +.ui-icon-carat-1-e { background-position: -32px 0; } +.ui-icon-carat-1-se { background-position: -48px 0; } +.ui-icon-carat-1-s { background-position: -64px 0; } +.ui-icon-carat-1-sw { background-position: -80px 0; } +.ui-icon-carat-1-w { background-position: -96px 0; } +.ui-icon-carat-1-nw { background-position: -112px 0; } +.ui-icon-carat-2-n-s { background-position: -128px 0; } +.ui-icon-carat-2-e-w { background-position: -144px 0; } +.ui-icon-triangle-1-n { background-position: 0 -16px; } +.ui-icon-triangle-1-ne { background-position: -16px -16px; } +.ui-icon-triangle-1-e { background-position: -32px -16px; } +.ui-icon-triangle-1-se { background-position: -48px -16px; } +.ui-icon-triangle-1-s { background-position: -64px -16px; } +.ui-icon-triangle-1-sw { background-position: -80px -16px; } +.ui-icon-triangle-1-w { background-position: -96px -16px; } +.ui-icon-triangle-1-nw { background-position: -112px -16px; } +.ui-icon-triangle-2-n-s { background-position: -128px -16px; } +.ui-icon-triangle-2-e-w { background-position: -144px -16px; } +.ui-icon-arrow-1-n { background-position: 0 -32px; } +.ui-icon-arrow-1-ne { background-position: -16px -32px; } +.ui-icon-arrow-1-e { background-position: -32px -32px; } +.ui-icon-arrow-1-se { background-position: -48px -32px; } +.ui-icon-arrow-1-s { background-position: -64px -32px; } +.ui-icon-arrow-1-sw { background-position: -80px -32px; } +.ui-icon-arrow-1-w { background-position: -96px -32px; } +.ui-icon-arrow-1-nw { background-position: -112px -32px; } +.ui-icon-arrow-2-n-s { background-position: -128px -32px; } +.ui-icon-arrow-2-ne-sw { background-position: -144px -32px; } +.ui-icon-arrow-2-e-w { background-position: -160px -32px; } +.ui-icon-arrow-2-se-nw { background-position: -176px -32px; } +.ui-icon-arrowstop-1-n { background-position: -192px -32px; } +.ui-icon-arrowstop-1-e { background-position: -208px -32px; } +.ui-icon-arrowstop-1-s { background-position: -224px -32px; } +.ui-icon-arrowstop-1-w { background-position: -240px -32px; } +.ui-icon-arrowthick-1-n { background-position: 0 -48px; } +.ui-icon-arrowthick-1-ne { background-position: -16px -48px; } +.ui-icon-arrowthick-1-e { background-position: -32px -48px; } +.ui-icon-arrowthick-1-se { background-position: -48px -48px; } +.ui-icon-arrowthick-1-s { background-position: -64px -48px; } +.ui-icon-arrowthick-1-sw { background-position: -80px -48px; } +.ui-icon-arrowthick-1-w { background-position: -96px -48px; } +.ui-icon-arrowthick-1-nw { background-position: -112px -48px; } +.ui-icon-arrowthick-2-n-s { background-position: -128px -48px; } +.ui-icon-arrowthick-2-ne-sw { background-position: -144px -48px; } +.ui-icon-arrowthick-2-e-w { background-position: -160px -48px; } +.ui-icon-arrowthick-2-se-nw { background-position: -176px -48px; } +.ui-icon-arrowthickstop-1-n { background-position: -192px -48px; } +.ui-icon-arrowthickstop-1-e { background-position: -208px -48px; } +.ui-icon-arrowthickstop-1-s { background-position: -224px -48px; } +.ui-icon-arrowthickstop-1-w { background-position: -240px -48px; } +.ui-icon-arrowreturnthick-1-w { background-position: 0 -64px; } +.ui-icon-arrowreturnthick-1-n { background-position: -16px -64px; } +.ui-icon-arrowreturnthick-1-e { background-position: -32px -64px; } +.ui-icon-arrowreturnthick-1-s { background-position: -48px -64px; } +.ui-icon-arrowreturn-1-w { background-position: -64px -64px; } +.ui-icon-arrowreturn-1-n { background-position: -80px -64px; } +.ui-icon-arrowreturn-1-e { background-position: -96px -64px; } +.ui-icon-arrowreturn-1-s { background-position: -112px -64px; } +.ui-icon-arrowrefresh-1-w { background-position: -128px -64px; } +.ui-icon-arrowrefresh-1-n { background-position: -144px -64px; } +.ui-icon-arrowrefresh-1-e { background-position: -160px -64px; } +.ui-icon-arrowrefresh-1-s { background-position: -176px -64px; } +.ui-icon-arrow-4 { background-position: 0 -80px; } +.ui-icon-arrow-4-diag { background-position: -16px -80px; } +.ui-icon-extlink { background-position: -32px -80px; } +.ui-icon-newwin { background-position: -48px -80px; } +.ui-icon-refresh { background-position: -64px -80px; } +.ui-icon-shuffle { background-position: -80px -80px; } +.ui-icon-transfer-e-w { background-position: -96px -80px; } +.ui-icon-transferthick-e-w { background-position: -112px -80px; } +.ui-icon-folder-collapsed { background-position: 0 -96px; } +.ui-icon-folder-open { background-position: -16px -96px; } +.ui-icon-document { background-position: -32px -96px; } +.ui-icon-document-b { background-position: -48px -96px; } +.ui-icon-note { background-position: -64px -96px; } +.ui-icon-mail-closed { background-position: -80px -96px; } +.ui-icon-mail-open { background-position: -96px -96px; } +.ui-icon-suitcase { background-position: -112px -96px; } +.ui-icon-comment { background-position: -128px -96px; } +.ui-icon-person { background-position: -144px -96px; } +.ui-icon-print { background-position: -160px -96px; } +.ui-icon-trash { background-position: -176px -96px; } +.ui-icon-locked { background-position: -192px -96px; } +.ui-icon-unlocked { background-position: -208px -96px; } +.ui-icon-bookmark { background-position: -224px -96px; } +.ui-icon-tag { background-position: -240px -96px; } +.ui-icon-home { background-position: 0 -112px; } +.ui-icon-flag { background-position: -16px -112px; } +.ui-icon-calendar { background-position: -32px -112px; } +.ui-icon-cart { background-position: -48px -112px; } +.ui-icon-pencil { background-position: -64px -112px; } +.ui-icon-clock { background-position: -80px -112px; } +.ui-icon-disk { background-position: -96px -112px; } +.ui-icon-calculator { background-position: -112px -112px; } +.ui-icon-zoomin { background-position: -128px -112px; } +.ui-icon-zoomout { background-position: -144px -112px; } +.ui-icon-search { background-position: -160px -112px; } +.ui-icon-wrench { background-position: -176px -112px; } +.ui-icon-gear { background-position: -192px -112px; } +.ui-icon-heart { background-position: -208px -112px; } +.ui-icon-star { background-position: -224px -112px; } +.ui-icon-link { background-position: -240px -112px; } +.ui-icon-cancel { background-position: 0 -128px; } +.ui-icon-plus { background-position: -16px -128px; } +.ui-icon-plusthick { background-position: -32px -128px; } +.ui-icon-minus { background-position: -48px -128px; } +.ui-icon-minusthick { background-position: -64px -128px; } +.ui-icon-close { background-position: -80px -128px; } +.ui-icon-closethick { background-position: -96px -128px; } +.ui-icon-key { background-position: -112px -128px; } +.ui-icon-lightbulb { background-position: -128px -128px; } +.ui-icon-scissors { background-position: -144px -128px; } +.ui-icon-clipboard { background-position: -160px -128px; } +.ui-icon-copy { background-position: -176px -128px; } +.ui-icon-contact { background-position: -192px -128px; } +.ui-icon-image { background-position: -208px -128px; } +.ui-icon-video { background-position: -224px -128px; } +.ui-icon-script { background-position: -240px -128px; } +.ui-icon-alert { background-position: 0 -144px; } +.ui-icon-info { background-position: -16px -144px; } +.ui-icon-notice { background-position: -32px -144px; } +.ui-icon-help { background-position: -48px -144px; } +.ui-icon-check { background-position: -64px -144px; } +.ui-icon-bullet { background-position: -80px -144px; } +.ui-icon-radio-off { background-position: -96px -144px; } +.ui-icon-radio-on { background-position: -112px -144px; } +.ui-icon-pin-w { background-position: -128px -144px; } +.ui-icon-pin-s { background-position: -144px -144px; } +.ui-icon-play { background-position: 0 -160px; } +.ui-icon-pause { background-position: -16px -160px; } +.ui-icon-seek-next { background-position: -32px -160px; } +.ui-icon-seek-prev { background-position: -48px -160px; } +.ui-icon-seek-end { background-position: -64px -160px; } +.ui-icon-seek-start { background-position: -80px -160px; } +/* ui-icon-seek-first is deprecated, use ui-icon-seek-start instead */ +.ui-icon-seek-first { background-position: -80px -160px; } +.ui-icon-stop { background-position: -96px -160px; } +.ui-icon-eject { background-position: -112px -160px; } +.ui-icon-volume-off { background-position: -128px -160px; } +.ui-icon-volume-on { background-position: -144px -160px; } +.ui-icon-power { background-position: 0 -176px; } +.ui-icon-signal-diag { background-position: -16px -176px; } +.ui-icon-signal { background-position: -32px -176px; } +.ui-icon-battery-0 { background-position: -48px -176px; } +.ui-icon-battery-1 { background-position: -64px -176px; } +.ui-icon-battery-2 { background-position: -80px -176px; } +.ui-icon-battery-3 { background-position: -96px -176px; } +.ui-icon-circle-plus { background-position: 0 -192px; } +.ui-icon-circle-minus { background-position: -16px -192px; } +.ui-icon-circle-close { background-position: -32px -192px; } +.ui-icon-circle-triangle-e { background-position: -48px -192px; } +.ui-icon-circle-triangle-s { background-position: -64px -192px; } +.ui-icon-circle-triangle-w { background-position: -80px -192px; } +.ui-icon-circle-triangle-n { background-position: -96px -192px; } +.ui-icon-circle-arrow-e { background-position: -112px -192px; } +.ui-icon-circle-arrow-s { background-position: -128px -192px; } +.ui-icon-circle-arrow-w { background-position: -144px -192px; } +.ui-icon-circle-arrow-n { background-position: -160px -192px; } +.ui-icon-circle-zoomin { background-position: -176px -192px; } +.ui-icon-circle-zoomout { background-position: -192px -192px; } +.ui-icon-circle-check { background-position: -208px -192px; } +.ui-icon-circlesmall-plus { background-position: 0 -208px; } +.ui-icon-circlesmall-minus { background-position: -16px -208px; } +.ui-icon-circlesmall-close { background-position: -32px -208px; } +.ui-icon-squaresmall-plus { background-position: -48px -208px; } +.ui-icon-squaresmall-minus { background-position: -64px -208px; } +.ui-icon-squaresmall-close { background-position: -80px -208px; } +.ui-icon-grip-dotted-vertical { background-position: 0 -224px; } +.ui-icon-grip-dotted-horizontal { background-position: -16px -224px; } +.ui-icon-grip-solid-vertical { background-position: -32px -224px; } +.ui-icon-grip-solid-horizontal { background-position: -48px -224px; } +.ui-icon-gripsmall-diagonal-se { background-position: -64px -224px; } +.ui-icon-grip-diagonal-se { background-position: -80px -224px; } + + +/* Misc visuals +----------------------------------*/ + +/* Corner radius */ +.ui-corner-tl { -moz-border-radius-topleft: 6px; -webkit-border-top-left-radius: 6px; border-top-left-radius: 6px; } +.ui-corner-tr { -moz-border-radius-topright: 6px; -webkit-border-top-right-radius: 6px; border-top-right-radius: 6px; } +.ui-corner-bl { -moz-border-radius-bottomleft: 6px; -webkit-border-bottom-left-radius: 6px; border-bottom-left-radius: 6px; } +.ui-corner-br { -moz-border-radius-bottomright: 6px; -webkit-border-bottom-right-radius: 6px; border-bottom-right-radius: 6px; } +.ui-corner-top { -moz-border-radius-topleft: 6px; -webkit-border-top-left-radius: 6px; border-top-left-radius: 6px; -moz-border-radius-topright: 6px; -webkit-border-top-right-radius: 6px; border-top-right-radius: 6px; } +.ui-corner-bottom { -moz-border-radius-bottomleft: 6px; -webkit-border-bottom-left-radius: 6px; border-bottom-left-radius: 6px; -moz-border-radius-bottomright: 6px; -webkit-border-bottom-right-radius: 6px; border-bottom-right-radius: 6px; } +.ui-corner-right { -moz-border-radius-topright: 6px; -webkit-border-top-right-radius: 6px; border-top-right-radius: 6px; -moz-border-radius-bottomright: 6px; -webkit-border-bottom-right-radius: 6px; border-bottom-right-radius: 6px; } +.ui-corner-left { -moz-border-radius-topleft: 6px; -webkit-border-top-left-radius: 6px; border-top-left-radius: 6px; -moz-border-radius-bottomleft: 6px; -webkit-border-bottom-left-radius: 6px; border-bottom-left-radius: 6px; } +.ui-corner-all { -moz-border-radius: 6px; -webkit-border-radius: 6px; border-radius: 6px; } + +/* Overlays */ +.ui-widget-overlay { background: #eeeeee url(images/ui-bg_flat_0_eeeeee_40x100.png) 50% 50% repeat-x; opacity: .80;filter:Alpha(Opacity=80); } +.ui-widget-shadow { margin: -4px 0 0 -4px; padding: 4px; background: #aaaaaa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x; opacity: .60;filter:Alpha(Opacity=60); -moz-border-radius: 0pxdow=0px; -webkit-border-radius: 0pxdow=0px; border-radius: 0pxdow=0px; }/* + * jQuery UI Slider @VERSION + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Slider#theming + */ +.ui-slider { position: relative; text-align: left; } +.ui-slider .ui-slider-handle { position: absolute; z-index: 2; width: 1.2em; height: 1.2em; cursor: default; } +.ui-slider .ui-slider-range { position: absolute; z-index: 1; font-size: .7em; display: block; border: 0; background-position: 0 0; } + +.ui-slider-horizontal { height: .8em; } +.ui-slider-horizontal .ui-slider-handle { top: -.3em; margin-left: -.6em; } +.ui-slider-horizontal .ui-slider-range { top: 0; height: 100%; } +.ui-slider-horizontal .ui-slider-range-min { left: 0; } +.ui-slider-horizontal .ui-slider-range-max { right: 0; } + +.ui-slider-vertical { width: .8em; height: 100px; } +.ui-slider-vertical .ui-slider-handle { left: -.3em; margin-left: 0; margin-bottom: -.6em; } +.ui-slider-vertical .ui-slider-range { left: 0; width: 100%; } +.ui-slider-vertical .ui-slider-range-min { bottom: 0; } +.ui-slider-vertical .ui-slider-range-max { top: 0; } --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -406,6 +406,7 @@ class Bed( Interval ): MetadataElement( name="endCol", default=3, desc="End column", param=metadata.ColumnParameter ) MetadataElement( name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 ) MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False ) + MetadataElement( name="viz_filter_cols", default=[4], param=metadata.ColumnParameter, multiple=True ) ###do we need to repeat these? they are the same as should be inherited from interval type def set_meta( self, dataset, overwrite = True, **kwd ): Binary file static/june_2007_style/blue/overcast/images/ui-bg_glass_100_f8f8f8_1x400.png has changed Binary file static/june_2007_style/blue/overcast/images/ui-bg_glass_60_eeeeee_1x400.png has changed

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galaxy-dist commit ad9bb65d2d15: mutation viz tool help cleanup
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287520820 14400 # Node ID ad9bb65d2d153af5db0ae497930eb35d17f63057 # Parent 35b379691524c768ec84f86477f1ab49859afec2 mutation viz tool help cleanup --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -20,7 +20,7 @@ <repeat name="sample_chooser" title="Sample"><param name="name" type="text" label="Label" help="Optional" /> - <param name="a_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="A Column" help="" /> + <param name="a_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Base A Column" help="" /><param name="totals_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Totals Column" help="" /></repeat> @@ -60,27 +60,42 @@ </test></tests><help> - -**Example** +**What it does** This tool allows you to visualize mutations described in a tabular input file. It generates an SVG image which can be viewed in any web browser. +You will need to specify the position and reference columns in the input file. Then click on the 'Add new Sample' to add samples in the input file that you would like to visualize. For each sample you select, specify the column for base 'A', the totals column and enter a name. +This tool assumes the columns specifying bases A, C, G, T are placed consecutively and in that order in an input file. + +Interactivity: If interactive zoom option is selected, then the resultant image can be zoomed in or out using the scroll mouse wheel and can be panned by dragging the image using left mouse button. + +----- + +**General Example** + Given the input file:: - gm blood gm cheek chrM 72 73 G 26394 4 49 0 26447 26398 1 23389 3 45 0 23437 23392 1 chrM 149 150 T 11 50422 2 96 50531 50435 1 4 45417 1 65 45487 45422 1 -You will need to specify the position and reference columns in the input file. Then click on the 'Add new Sample' to add samples in the input file that you would like to visualize. For each sample you select, specify the column for base 'A' and the totals column. -This tool assumes the columns specifying bases A, C, G, T are placed consecutively and in that order in an input file. +To visualize the two samples in the input file, the following parameters are selected before running the tool:: + + Position column: 2 + Reference Base column: 4 + Sample 1 Label: gm blood + Sample 1 Base A column: 5 + Sample 1 Totals column: 9 + Sample 2 Label: gm cheek + Sample 2 Base A column: 12 + Sample 2 Totals column: 16 -Visualization: +Visualization output: .. image:: ../static/images/mutation_visualization_example.png :width: 150 -Interactivity:: - If interactive zoom option is selected, then the resultant image can be zoomed in or out using the scroll mouse wheel and can be panned by dragging the image using left mouse button. +Here the left-most column represents the position and the background color is the reference base color. Each column on its right describe each sample. +In the output above, the blue bar is the longest, which means that base A is maximum in position 72 for both the samples. </help></tool>

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