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commit/galaxy-central: kellyv: Modified add_manual_builds script so that it will include the build in parentheses after the name even if there are no chromosome lengths listed (previously would not because of line break after name); also added a couple of new manual builds
by Bitbucket 29 Mar '11

29 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c761ea39e3c9/ changeset: r5280:c761ea39e3c9 user: kellyv date: 2011-03-29 19:59:07 summary: Modified add_manual_builds script so that it will include the build in parentheses after the name even if there are no chromosome lengths listed (previously would not because of line break after name); also added a couple of new manual builds affected #: 2 files (454 bytes) --- a/cron/add_manual_builds.py Tue Mar 29 13:43:24 2011 -0400 +++ b/cron/add_manual_builds.py Tue Mar 29 13:59:07 2011 -0400 @@ -21,12 +21,12 @@ build_file_out = open(build_file,'a') for line in open(input_file): try: - fields = line.split("\t") + fields = line.replace("\n","").replace("\r","").split("\t") build = fields.pop(0) if build in existing_builds: continue # if build exists, leave alone name = fields.pop(0) try: # get chrom lens if included in file, otherwise still add build - chrs = fields.pop(0).replace("\n","").replace("\r","").split(",") + chrs = fields.pop(0).split(",") except: chrs = [] print>>build_file_out, build+"\t"+name+" ("+build+")" --- a/tool-data/shared/ucsc/manual_builds.txt Tue Mar 29 13:43:24 2011 -0400 +++ b/tool-data/shared/ucsc/manual_builds.txt Tue Mar 29 13:59:07 2011 -0400 @@ -698,3 +698,5 @@ Hydra_JCVI Hydra magnipapillata str. 105 Araly1 Arabidopsis lyrata Zea_mays_B73_RefGen_v2 Maize (Zea mays) chr1=301354135,chr2=237068928,chr3=232140222,chr4=241473566,chr5=217872898,chr6=169174371,chr7=176764813,chr8=175793772,chr9=156750718,chr10=150189513,chr11=7140224 +Homo_sapiens_AK1 Korean Man chrM=16571,chr1=247249719,chr2=242951149,chr3=199501827,chr4=191273063,chr5=180857866,chr6=170899992,chr7=158821424,chr8=146274826,chr9=140273252,chr10=135374737,chr11=134452384,chr12=132349534,chr13=114142980,chr14=106368585,chr15=100338915,chr16=88827254,chr17=78774742,chr18=76117153,chr19=63811651,chr20=62435964,chr21=46944323,chr22=49691432,chrX=154913754,chrY=57772954 +Tcas_3.0 Red Flour Beetle (Tribolium castaneum) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: use gap to correctly position read connector in Pack mode. Also some code cleanup and commenting.
by Bitbucket 29 Mar '11

29 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/96ada6a6b2d8/ changeset: r5279:96ada6a6b2d8 user: jgoecks date: 2011-03-29 19:43:24 summary: Trackster: use gap to correctly position read connector in Pack mode. Also some code cleanup and commenting. affected #: 1 file (26 bytes) --- a/static/scripts/trackster.js Tue Mar 29 08:18:49 2011 -0400 +++ b/static/scripts/trackster.js Tue Mar 29 13:43:24 2011 -0400 @@ -1594,10 +1594,10 @@ high = this.view.high, range = high - low, width = this.view.container.width(), - resolution = this.view.resolution; - - var parent_element = $("<div style='position: relative;'></div>"), - w_scale = width / range; + // w_scale units are pixels per base. + w_scale = width / range, + resolution = this.view.resolution, + parent_element = $("<div style='position: relative;'></div>"); if (!clear_after) { this.content_div.children().remove(); } this.content_div.append( parent_element ); @@ -3029,8 +3029,7 @@ */ draw_element: function(ctx, tile_index, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width, left_offset, ref_seq) { // All features need a start, end, and vertical center. - var - feature_uid = feature[0], + var feature_uid = feature[0], feature_start = feature[1], feature_end = feature[2], feature_name = feature[3], @@ -3038,8 +3037,14 @@ f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), y_center = (mode === "Dense" ? 1 : (1 + slot)) * y_scale, block_color = this.prefs.block_color, - label_color = this.prefs.label_color; - gap = 0; // Left-gap for label text since we align chrom text to the position tick + label_color = this.prefs.label_color, + // Left-gap for label text since we align chrom text to the position tick. + gap = 0; + + // TODO: fix gap usage; also see note on gap in draw_read. + if ((mode === "Pack" || this.mode === "Auto") && w_scale > CHAR_WIDTH_PX) { + var gap = Math.round(w_scale/2); + } // Draw read. ctx.fillStyle = block_color; @@ -3061,8 +3066,7 @@ // Draw connector. if (b2_start > b1_end) { ctx.fillStyle = CONNECTOR_COLOR; - //ctx.fillRect(b1_end + left_offset, y_center + 5, b2_start - b1_end, 1); - ctx.dashedLine(b1_end + left_offset, y_center + 5, left_offset + b2_start, y_center + 5); + ctx.dashedLine(b1_end + left_offset - gap, y_center + 5, left_offset + b2_start - gap, y_center + 5); } } else { // Read is single. @@ -3072,9 +3076,6 @@ if (mode === "Pack" && feature_start > tile_low) { // Draw label. ctx.fillStyle = this.prefs.label_color; - if ( (mode === "Pack" || this.mode === "Auto") && w_scale > CHAR_WIDTH_PX) { - var gap = Math.round(w_scale/2); - } if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) { ctx.textAlign = "left"; ctx.fillText(feature_name, f_end + left_offset + LABEL_SPACING - gap, y_center + 8); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Use new_file_path as tempfile's tempdir, obviates the need for $TEMP in the environment.
by Bitbucket 29 Mar '11

29 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2be2b8e0e916/ changeset: r5278:2be2b8e0e916 user: natefoo date: 2011-03-29 14:18:49 summary: Use new_file_path as tempfile's tempdir, obviates the need for $TEMP in the environment. affected #: 1 file (56 bytes) --- a/lib/galaxy/config.py Mon Mar 28 15:27:14 2011 -0400 +++ b/lib/galaxy/config.py Tue Mar 29 08:18:49 2011 -0400 @@ -2,7 +2,7 @@ Universe configuration builder. """ -import sys, os +import sys, os, tempfile import logging, logging.config import ConfigParser from galaxy.util import string_as_bool @@ -39,6 +39,7 @@ # Where dataset files are stored self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) + tempfile.tempdir = self.new_file_path self.openid_consumer_cache_path = resolve_path( kwargs.get( "openid_consumer_cache_path", "database/openid_consumer_cache" ), self.root ) self.cookie_path = kwargs.get( "cookie_path", "/" ) # web API Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Another pass on Trackster filtering. Filtering now supports (a) score columns in BED and GFF and (b) GTF attributes. Refactoring so that slider behavior for dynamic tools and filters are the same.
by Bitbucket 28 Mar '11

28 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9af3a7580efa/ changeset: r5277:9af3a7580efa user: jgoecks date: 2011-03-28 21:27:14 summary: Another pass on Trackster filtering. Filtering now supports (a) score columns in BED and GFF and (b) GTF attributes. Refactoring so that slider behavior for dynamic tools and filters are the same. affected #: 6 files (6.3 KB) --- a/lib/galaxy/visualization/tracks/data_providers.py Fri Mar 25 13:26:40 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Mon Mar 28 15:27:14 2011 -0400 @@ -11,13 +11,16 @@ pkg_resources.require( "pysam" ) pkg_resources.require( "numpy" ) from galaxy.datatypes.util.gff_util import * +from galaxy.util.json import from_json_string from bx.interval_index_file import Indexes from bx.arrays.array_tree import FileArrayTreeDict from bx.bbi.bigwig_file import BigWigFile from galaxy.util.lrucache import LRUCache from galaxy.visualization.tracks.summary import * from galaxy.datatypes.tabular import Vcf -from galaxy.datatypes.interval import Bed, Gff +from galaxy.datatypes.interval import Bed, Gff, Gtf +from galaxy.datatypes.util.gff_util import parse_gff_attributes + from pysam import csamtools MAX_VALS = 5000 # only display first MAX_VALS features @@ -126,7 +129,7 @@ return st.chrom_blocks.keys() - def get_summary( self, chrom, start, end, **kwargs): + def get_summary( self, chrom, start, end, **kwargs ): filename = self.converted_dataset.file_name st = self.CACHE[filename] if st is None: @@ -170,7 +173,7 @@ self.CACHE[filename] = st # Check for data. - return st.chrom_blocks.get(chrom, None) is not None or st.chrom_blocks.get(chrom[3:], None) is not None + return st.chrom_blocks.get(chrom, None) is not None or (chrom and st.chrom_blocks.get(chrom[3:], None) is not None) class VcfDataProvider( TracksDataProvider ): """ @@ -486,7 +489,63 @@ def write_data_to_file( self, chrom, start, end, filename ): # TODO: write function. pass - + + def get_filters( self ): + """ Returns a dataset's filters. """ + + # is_ functions taken from Tabular.set_meta + def is_int( column_text ): + try: + int( column_text ) + return True + except: + return False + def is_float( column_text ): + try: + float( column_text ) + return True + except: + if column_text.strip().lower() == 'na': + return True #na is special cased to be a float + return False + + # + # Get filters. + # TODOs: + # (a) might be useful to move this into each datatype's set_meta method; + # (b) could look at first N lines to ensure GTF attribute types are consistent. + # + filters = [] + # HACK: first 8 fields are for drawing, so start filter column index at 9. + filter_col = 8 + if isinstance( self.original_dataset.datatype, Gff ): + # Can filter by score and GTF attributes. + filters = [ { 'name': 'Score', 'type': 'int', 'index': filter_col } ] + filter_col += 1 + if isinstance( self.original_dataset.datatype, Gtf ): + for i, line in enumerate( open(self.original_dataset.file_name) ): + if not line.startswith('#'): + # Look at first line for attributes and types. + attributes = parse_gff_attributes( line.split('\t')[8] ) + for attr, value in attributes.items(): + # Get attribute type. + if is_int( value ): + attr_type = 'int' + elif is_float( value ): + attr_type = 'float' + else: + attr_type = 'str' + # Add to filters. + if attr_type is not 'str': + filters.append( { 'name': attr, 'type': attr_type, 'index': filter_col } ) + filter_col += 1 + break + elif isinstance( self.original_dataset.datatype, Bed ): + # Can filter by score column only. + filters = [ { 'name': 'Score', 'type': 'int', 'index': filter_col } ] + + return filters + def get_data( self, chrom, start, end, **kwargs ): start, end = int(start), int(end) source = open( self.original_dataset.file_name ) @@ -509,6 +568,7 @@ # # First three entries are mandatory, others are optional. # + filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) no_detail = ( "no_detail" in kwargs ) for start, end, offset in index.find(chrom, start, end): if count >= MAX_VALS: @@ -522,7 +582,7 @@ # GFF dataset. reader = GFFReaderWrapper( source, fix_strand=True ) feature = reader.next() - payload = package_gff_feature( feature, no_detail ) + payload = package_gff_feature( feature, no_detail, filter_cols ) payload.insert( 0, offset ) elif isinstance( self.original_dataset.datatype, Bed ): # BED dataset. @@ -536,15 +596,11 @@ #end = min( len( feature ), 8 ) #payload.extend( feature[ 3:end ] ) - # Name, score, strand, thick start, thick end. + # Name, strand, thick start, thick end. if length >= 4: payload.append(feature[3]) - if length >= 5: - payload.append( float(feature[4]) ) if length >= 6: payload.append(feature[5]) - - # Thick start, end. if length >= 8: payload.append(int(feature[6])) payload.append(int(feature[7])) @@ -555,7 +611,11 @@ 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 ] ) - + + # Score (filter data) + if length >= 5 and filter_cols and filter_cols[0] == "Score": + payload.append( float(feature[4]) ) + results.append( payload ) return { 'data': results, 'message': message } @@ -644,7 +704,7 @@ pass return data_provider -def package_gff_feature( feature, no_detail=False ): +def package_gff_feature( feature, no_detail=False, filter_cols=[] ): """ Package a GFF feature in an array for data providers. """ feature = convert_gff_coords_to_bed( feature ) @@ -656,7 +716,6 @@ payload = [ feature.start, feature.end, feature.name(), - feature.score, feature.strand, # No notion of thick start, end in GFF, so make everything # thick. @@ -677,4 +736,13 @@ blocks = zip( block_sizes, block_starts ) payload.append( [ ( feature.start + block[1], feature.start + block[1] + block[0] ) for block in blocks ] ) + # Add filter data to payload. + for col in filter_cols: + if col == "Score": + payload.append( feature.score ) + elif col in feature.attributes: + payload.append( feature.attributes[col] ) + else: + # Dummy value. + payload.append( "na" ) return payload --- a/static/june_2007_style/blue/trackster.css Fri Mar 25 13:26:40 2011 -0400 +++ b/static/june_2007_style/blue/trackster.css Mon Mar 28 15:27:14 2011 -0400 @@ -38,7 +38,6 @@ .top-labeltrack{position:relative;border-bottom:solid #999 1px;} .nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #333 1px;} input{font:10px verdana;} -.values{padding-left:0.25em;} .dynamic-tool,.filters{width:400px;margin-left:0.25em;padding-bottom:0.5em;} .slider-row{margin-top:0.4em;margin-left:1em;} .slider-label{float:left;font-weight:bold;} --- a/static/june_2007_style/trackster.css.tmpl Fri Mar 25 13:26:40 2011 -0400 +++ b/static/june_2007_style/trackster.css.tmpl Mon Mar 28 15:27:14 2011 -0400 @@ -228,9 +228,6 @@ input { font: 10px verdana; } -.values { - padding-left: 0.25em; -} .dynamic-tool, .filters { width: 400px; margin-left: 0.25em; --- a/static/scripts/packed/trackster.js Fri Mar 25 13:26:40 2011 -0400 +++ b/static/scripts/packed/trackster.js Mon Mar 28 15:27:14 2011 -0400 @@ -1,1 +1,1 @@ -CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();var c;for(c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c===f.length){if(this!==f.get(c-1)){g.append(this)}}else{if(this!==f.get(c)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!==NO_OVERLAP)}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,ERROR_PADDING=10,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",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_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;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 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.move_key_to_end(b,a)}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},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataManager=function(b,a,c){Cache.call(this,b);this.track=a;this.subset=(c!==undefined?c:true)};$.extend(DataManager.prototype,Cache.prototype,{load_data:function(d,a,f,h,b,e){var g={chrom:d,low:a,high:f,mode:h,resolution:b,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(g,e);var c=this;return $.getJSON(this.track.data_url,g,function(j){c.set_data(a,f,h,j)})},get_data:function(j,k,c,h,b,f){var l=this.get(this.gen_key(k,c,h));if(l){return l}if(this.subset){var m,g,a,e,h,l;for(var d=0;d<this.key_ary.length;d++){m=this.key_ary[d];g=this.split_key(m);a=g[0];e=g[1];if(k>=a&&c<=e){l=this.obj_cache[m];if(l.dataset_type!=="summary_tree"&&l.extra_info!=="no_detail"){this.move_key_to_end(m,d);return l}}}}return this.load_data(j,k,c,h,b,f)},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();$(this).val("");a.location_span.show();a.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",b).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.val(a.chrom+":"+a.low+"-"+a.high);a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var j=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(j/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,k){var f=$(this);var l=k.offsetX-k.current_x;var g=f.scrollTop()-(h.clientY-k.current_height);f.scrollTop(g);k.current_height=h.clientY;k.current_x=k.offsetX;var j=Math.round(l/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}).bind("mousewheel",function(h,k,g,f){if(g){var j=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(k,l){$(l.proxy).css({left:Math.min(k.pageX,l.startX),width:Math.abs(k.pageX-l.startX)});var g=Math.min(k.pageX,l.startX)-a.container.offset().left,f=Math.max(k.pageX,l.startX)-a.container.offset().left,j=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*j)+a.low,Math.round(f/h*j)+a.low)}).bind("dragend",function(l,m){var g=Math.min(l.pageX,m.startX),f=Math.max(l.pageX,m.startX),j=(a.high-a.low),h=a.viewport_container.width(),k=a.low;a.low=Math.round(g/h*j)+k;a.high=Math.round(f/h*j)+k;$(m.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.chrom_info.length===0){alert("Invalid chromosome: "+b.chrom);return}if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e==="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e==="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len-1;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var k=this,a,d,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}k.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},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);sortable(a.container_div,".draghandle");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())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;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(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()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)===0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};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.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_url_extra_params={};this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.make_name_popup_menu()}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(b,j,n){var c=this,o=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(j!==undefined?get_tool_from_dict(j):undefined);this.parent_track=n;this.child_tracks=[];if(c.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});$.each(this.filters,function(t,w){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var v=$("<div/>").addClass("slider-label").appendTo(u);var s=$("<span/>").addClass("name").appendTo(v);s.text(w.name+" ");var r=$("<span/>").addClass("values").appendTo(v);var q=$("<div/>").addClass("slider").appendTo(u);w.control_element=$("<div/>").attr("id",w.name+"-filter-control").appendTo(q);w.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(y,z){var x=z.values;r.text("["+x[0]+"-"+x[1]+"]");w.low=x[0];w.high=x[1];c.draw(true,true)},change:function(x,y){w.control_element.slider("option","slide").call(w.control_element,x,y)}});w.slider=w.control_element;w.slider_label=r;$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(q){q.stopPropagation()}).bind("click",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});var m=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var l=this.tool.params;var c=this;$.each(this.tool.params,function(x,s){var v=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(v);var z=$("<span class='param-name'>").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var w=$("<span class='param-value'>").appendTo(u).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(v);var q=$("<div id='"+s.name+"-param-control'>").appendTo(y);var r=(s.max<=1?0.01:(s.max<=1000?1:5));q.slider({min:s.min,max:s.max,step:r,value:s.value,slide:function(A,C){var B=C.value;s.value=B;if(0<B&&B<1){B=parseFloat(B).toFixed(2)}t.text(B)},change:function(A,B){s.value=B.value}});w.click(function(){var C=t,B=C.text(),A=(s.max<=1?4:s.max.length);C.text("");$("<input type='text'/>").attr("size",A).attr("maxlength",A).attr("value",B).appendTo(C).focus().select().click(function(D){D.stopPropagation()}).blur(function(){$(this).remove();C.text(B)}).keyup(function(F){if(F.keyCode===27){$(this).trigger("blur")}else{if(F.keyCode===13){var D=$(this),E=parseFloat(D.val());if(isNaN(E)||E>s.max||E<s.min){alert("Parameter value must be in the range ["+s.min+"-"+s.max+"]");return $(this)}C.text(E);q.slider("value",E);s.value=E}}})});$("<div style='clear: both;'/>").appendTo(v)});var p=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var k=$("<input type='submit'>").attr("value","Run").appendTo(p);var c=this;k.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(q){c.mode_div.text(q);c.mode=q;c.track_config.values.mode=q;c.tile_cache.clear();c.draw()};var a={};for(var f=0,h=c.display_modes.length;f<h;f++){var g=c.display_modes[f];a[g]=function(q){return function(){d(q)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide Tool":"Show Tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},draw:function(a,d){var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),m=this.view.resolution;var e=$("<div style='position: relative;'></div>"),f=l/j;if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}if(d){var k=this;var q=setInterval(function(){if(obj_length(c)===0){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var x=$(v[w]);if(u){x.remove()}else{if(x.children().length!==0){u=true}}}clearInterval(q)}},50)}for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,g,l,c,e,k,m,f){var d=this;var h=function(u,n,p,o,s,t,q){returned_tile=d.draw_tile(n,p,o,s,t,q);var r=$("<div class='track-tile'>").prepend(returned_tile);tile_element=r;d.tile_cache.set(j,tile_element);d.show_tile(tile_element,s,g,t);delete f[u]};var a=setTimeout(function(){if(g<=d.view.high&&l>=d.view.low){var n=(b?undefined:d.tile_cache.get(j));if(n){d.show_tile(n,k,g,m);delete f[a]}else{$.when(d.data_cache.get_data(view.chrom,g,l,d.mode,e,d.data_url_extra_params)).then(function(){var o=d.data_cache.get_data(view.chrom,g,l,d.mode,e,d.data_url_extra_params);if(view.reference_track&&m>CHAR_WIDTH_PX){$.when(view.reference_track.data_cache.get_data(view.chrom,g,l,d.mode,e,view.reference_track.data_url_extra_params)).then(function(){var p=view.reference_track.data_cache.get_data(view.chrom,g,l,d.mode,e,view.reference_track.data_url_extra_params);h(a,o,e,c,k,m,p)})}else{h(a,o,e,c,k,m)}})}}},50);f[a]=true},show_tile:function(h,j,e,k){var a=this;var c=this.view.high-this.view.low,b=(e-this.view.low)*k;if(this.left_offset){b-=this.left_offset}h.css({position:"absolute",top:0,left:b,height:""});j.append(h);a.max_height=Math.max(a.max_height,h.height());a.content_div.css("height",a.max_height+"px");j.children().css("height",a.max_height+"px");if(a.hidden){return}for(var g=0;g<a.filters.length;g++){a.filters[g].update_ui_elt()}var d=false;if(a.example_feature){for(var g=0;g<a.filters.length;g++){if(a.filters[g].applies_to(a.example_feature)){d=true;break}}}if(a.filters_available!==d){a.filters_available=d;if(!a.filters_available){a.filters_div.hide()}a.make_name_popup_menu()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:a.dbkey};this.data_cache=new DataManager(CACHED_DATA,this,false);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{draw_tile:function(m,g,b,j,n){var f=this,d=DENSITY*g;if(n>CHAR_WIDTH_PX){if(m===null){f.content_div.css("height","0px");return}var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var l=e.get(0).getContext("2d");e.get(0).width=Math.ceil(d*n+f.left_offset);e.get(0).height=f.height_px;l.font=DEFAULT_FONT;l.textAlign="center";for(var h=0,k=m.length;h<k;h++){var a=Math.round(h*n);l.fillText(m[h],a+f.left_offset,10)}return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataManager(CACHED_DATA,this);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var k=false;var j=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){k=true;h.show()},function(){k=false;if(!j){h.hide()}});h.hide().bind("dragstart",function(l,m){j=true;m.original_height=$(g.content_div).height()}).bind("drag",function(m,n){var l=Math.min(Math.max(n.original_height+n.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",l);g.height_px=l;g.draw(true)}).bind("dragend",function(l,m){g.tile_cache.clear();j=false;if(!k){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(j,q,t,c,e){if(this.vertical_range===undefined){return}var o=this,u=t*DENSITY*q,a=DENSITY*q,B=q+"_"+t,v={hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution};var b=document.createElement("canvas"),z=j.data;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);b.get(0).width=Math.ceil(a*e);b.get(0).height=o.height_px;var p=b.get(0).getContext("2d"),k=false,l=o.prefs.min_value,g=o.prefs.max_value,n=o.vertical_range,w=o.total_frequency,d=o.height_px,m=o.mode;var A=Math.round(d+l/n*d);p.beginPath();p.moveTo(0,A);p.lineTo(a*e,A);p.fillStyle="#aaa";p.stroke();p.beginPath();p.fillStyle=o.prefs.color;var x,h,f;if(z.length>1){f=Math.ceil((z[1][0]-z[0][0])*e)}else{f=10}for(var r=0,s=z.length;r<s;r++){x=Math.round((z[r][0]-u)*e);h=z[r][1];if(h===null){if(k&&m==="Filled"){p.lineTo(x,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(h/n*d);p.fillRect(x,A,f,-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);p.fillStyle="rgb("+h+","+h+","+h+")";p.fillRect(x,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){p.lineTo(x,h)}else{k=true;if(m==="Filled"){p.moveTo(x,d);p.lineTo(x,h)}else{p.moveTo(x,h)}}}}}if(m==="Filled"){if(k){p.lineTo(x,A);p.lineTo(0,A)}p.fill()}else{p.stroke()}return b}});var FeatureTrack=function(a,f,e,j,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=j;this.original_dataset_id=j;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataManager(20,this);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j+1},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<div />").addClass("yaxislabel");h.text(l);h.css({position:"absolute",top:"22px",left:"10px"});h.prependTo(this.container_div);var q=b.get(0).getContext("2d");for(var d=0,g=o.length;d<g;d++){var m=Math.floor((o[d][0]-f)*r);var k=o[d][1];if(!k){continue}var p=k/l*j;q.fillStyle="black";q.fillRect(m+e,c-p,delta_x_px,p);var a=4;if(this.prefs.show_counts&&(q.measureText(k).width+a)<delta_x_px){q.fillStyle="#666";q.textAlign="center";q.fillText(k,m+e+(delta_x_px/2),10)}}},draw_element:function(p,f,g,x,j,r,I,M,N,a,A){var u=x[0],K=x[1],C=x[2]-1,s=x[3],D=Math.floor(Math.max(0,(K-r)*M)),q=Math.ceil(Math.min(a,Math.max(0,(C-r)*M))),B=ERROR_PADDING+(g==="Dense"?0:(0+j))*N,o,G,t=null,O=null,d=this.prefs.block_color,F=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(D+A,B,q-D,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(D+A,B+5,q-D,DENSE_FEATURE_HEIGHT)}else{var n=x[5],z=x[6],E=x[7],e=x[8];if(z&&E){t=Math.floor(Math.max(0,(z-r)*M));O=Math.ceil(Math.min(a,Math.max(0,(E-r)*M)))}var L,v;if(g==="Squish"){L=1;v=SQUISH_FEATURE_HEIGHT}else{L=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(D+A,B,q-D,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=B+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=B;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(D+A,m,q-D,w);for(var J=0,c=e.length;J<c;J++){var h=e[J],b=Math.floor(Math.max(0,(h[0]-r)*M)),y=Math.ceil(Math.min(a,Math.max((h[1]-1-r)*M)));if(b>y){continue}p.fillStyle=d;p.fillRect(b+A,B+(v-L)/2+1,y-b,L);if(t!==undefined&&!(b>O||y<t)){var H=Math.max(b,t),l=Math.min(y,O);p.fillRect(H+A,B+1,l-H,v)}}}if(g==="Pack"&&K>r){p.fillStyle=F;if(f===0&&D-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+A+LABEL_SPACING,B+8)}else{p.textAlign="right";p.fillText(s,D+A-LABEL_SPACING,B+8)}p.fillStyle=d}}}},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(o,x,C,k,m,d){var t=this;var E=C*DENSITY*x,a=(C+1)*DENSITY*x,q=a-E,F={hda_ldda:t.hda_ldda,dataset_id:t.dataset_id,resolution:this.view.resolution,mode:this.mode};var v=Math.ceil(q*m),s=this.mode,H=25,g=this.left_offset,p,h;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(s==="Auto"){if(o.dataset_type==="summary_tree"){s=o.dataset_type}else{if(o.extra_info==="no_detail"){s="no_detail"}else{var G=o.data;if((G.length&&G.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){s="Squish"}else{s="Pack"}}}}var y=this.get_y_scale(s);if(s==="summary_tree"){h=this.summary_draw_height}if(s==="Dense"){h=H}else{if(s==="no_detail"||s==="Squish"||s==="Pack"){h=this.incremental_slots(m,o.data,s)*y+H;p=this.inc_slots[m]}}c.get(0).width=v+g;c.get(0).height=h;if(o.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}k.parent().css("height",Math.max(this.height_px,h)+"px");var w=c.get(0).getContext("2d");w.fillStyle=this.prefs.block_color;w.font=this.default_font;w.textAlign="right";this.container_div.find(".yaxislabel").remove();if(s==="summary_tree"){this.draw_summary_tree(c,o.data,o.delta,o.max,m,h,E,g);return c}if(o.message){c.css({"border-top":"1px solid red"});w.fillStyle="red";w.textAlign="left";var r=w.textBaseline;w.textBaseline="top";w.fillText(o.message,g,0);w.textBaseline=r;if(!o.data){return c}}this.example_feature=(o.data.length?o.data[0]:undefined);var G=o.data;for(var z=0,B=G.length;z<B;z++){var j=G[z],l=j[0],u=j[1],b=j[2],e=(p&&p[l]!==undefined?p[l]:null);var A=false;var n;for(var D=0;D<this.filters.length;D++){n=this.filters[D];n.update_attrs(j);if(!n.keep(j)){A=true;break}}if(A){continue}if(is_overlap([u,b],[E,a])&&(s=="Dense"||e!==null)){this.draw_element(w,C,s,j,e,E,a,m,y,v,g,d)}}return c}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=ERROR_PADDING+(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:c,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.track_config.values.show_insertions){a*=2}}}return a},draw_read:function(m,d,J,n,D,G,e,o,y,a){m.textAlign="center";var l=this,u=[n,D],C=0,z=0,f=0;var r=[];if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){f=Math.round(J/2)}if(!e){e=[[0,o.length]]}for(var h=0,k=e.length;h<k;h++){var b=e[h],g="MIDNSHP=X"[b[0]],v=b[1];if(g==="H"||g==="S"){C-=v}var x=G+C,B=Math.floor(Math.max(0,(x-n)*J)),E=Math.floor(Math.max(0,(x+v-n)*J));switch(g){case"H":break;case"S":case"M":case"=":var p=compute_overlap([x,x+v],u);if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(f>0){m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset-f,y+1,E-B,9);m.fillStyle=CONNECTOR_COLOR;for(var I=0,j=q.length;I<j;I++){if(this.track_config.values.show_differences&&a){var s=a[x-n+I];if(!s||s.toLowerCase()===q[I].toLowerCase()){continue}}if(x+I>=n&&x+I<=D){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset,y+9)}}}else{m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset,y+(this.mode!=="Dense"?4:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}z+=v;C+=v;break;case"N":m.fillStyle=CONNECTOR_COLOR;m.fillRect(B+this.left_offset-f,y+5,E-B,1);C+=v;break;case"D":m.fillStyle="red";m.fillRect(B+this.left_offset-f,y+4,E-B,3);C+=v;break;case"P":break;case"I":var p=compute_overlap([x,x+v],u),K=this.left_offset+B-f;if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(this.track_config.values.show_insertions){var w=this.left_offset+B-(E-B)/2;if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){m.fillStyle="yellow";m.fillRect(w-f,y-9,E-B,9);r[r.length]={type:"triangle",data:[K,y+4,5]};m.fillStyle=CONNECTOR_COLOR;switch(p){case (OVERLAP_START):q=q.slice(n-x);break;case (OVERLAP_END):q=q.slice(0,x-D);break;case (CONTAINED_BY):break;case (CONTAINS):q=q.slice(n-x,x-D);break}for(var I=0,j=q.length;I<j;I++){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset-(E-B)/2,y)}}else{m.fillStyle="yellow";m.fillRect(w,y+(this.mode!=="Dense"?2:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){r[r.length]={type:"text",data:[q.length,K,y+9]}}else{}}}z+=v;break;case"X":z+=v;break}}m.fillStyle="yellow";var t,L,H;for(var F=0;F<r.length;F++){t=r[F];L=t.type;H=t.data;if(L==="text"){m.font="bold "+DEFAULT_FONT;m.fillText(H[0],H[1],H[2]);m.font=DEFAULT_FONT}else{if(L=="triangle"){m.drawDownwardEquilateralTriangle(H[0],H[1],H[2])}}}},draw_element:function(w,y,r,k,e,A,b,n,x,u,f,c){var m=k[0],v=k[1],d=k[2],o=k[3],h=Math.floor(Math.max(0,(v-A)*n)),j=Math.ceil(Math.min(u,Math.max(0,(d-A)*n))),g=(r==="Dense"?1:(1+e))*x,z=this.prefs.block_color,l=this.prefs.label_color;t=0;w.fillStyle=z;if(k[5] instanceof Array){var s=Math.floor(Math.max(0,(k[4][0]-A)*n)),q=Math.ceil(Math.min(u,Math.max(0,(k[4][1]-A)*n))),p=Math.floor(Math.max(0,(k[5][0]-A)*n)),a=Math.ceil(Math.min(u,Math.max(0,(k[5][1]-A)*n)));if(k[4][1]>=A&&k[4][0]<=b&&k[4][2]){this.draw_read(w,r,n,A,b,k[4][0],k[4][2],k[4][3],g,c)}if(k[5][1]>=A&&k[5][0]<=b&&k[5][2]){this.draw_read(w,r,n,A,b,k[5][0],k[5][2],k[5][3],g,c)}if(p>q){w.fillStyle=CONNECTOR_COLOR;w.dashedLine(q+f,g+5,f+p,g+5)}}else{w.fillStyle=z;this.draw_read(w,r,n,A,b,v,k[4],k[5],g,c)}if(r==="Pack"&&v>A){w.fillStyle=this.prefs.label_color;if((r==="Pack"||this.mode==="Auto")&&n>CHAR_WIDTH_PX){var t=Math.round(n/2)}if(y===0&&h-w.measureText(o).width<0){w.textAlign="left";w.fillText(o,j+f+LABEL_SPACING-t,g+8)}else{w.textAlign="right";w.fillText(o,h+f-LABEL_SPACING-t,g+8)}w.fillStyle=z}}});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}}); \ No newline at end of file +CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();var c;for(c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c===f.length){if(this!==f.get(c-1)){g.append(this)}}else{if(this!==f.get(c)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!==NO_OVERLAP)}function get_slider_step(c,a){var b=a-c;return(b<=1?0.01:(b<=1000?1:5))}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,ERROR_PADDING=10,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",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_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;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 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()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!==-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataManager=function(b,a,c){Cache.call(this,b);this.track=a;this.subset=(c!==undefined?c:true)};$.extend(DataManager.prototype,Cache.prototype,{load_data:function(h,j,d,g,a,f){var c={chrom:h,low:j,high:d,mode:g,resolution:a,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(c,f);var k=[];for(var e=0;e<this.track.filters.length;e++){k[k.length]=this.track.filters[e].name}c.filter_cols=JSON.stringify(k);var b=this;return $.getJSON(this.track.data_url,c,function(l){b.set_data(j,d,g,l)})},get_data:function(j,k,c,h,b,f){var l=this.get(this.gen_key(k,c,h));if(l){return l}if(this.subset){var m,g,a,e,h,l;for(var d=0;d<this.key_ary.length;d++){m=this.key_ary[d];g=this.split_key(m);a=g[0];e=g[1];if(k>=a&&c<=e){l=this.obj_cache[m];if(l.dataset_type!=="summary_tree"&&l.extra_info!=="no_detail"){this.move_key_to_end(m,d);return l}}}}return this.load_data(j,k,c,h,b,f)},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();$(this).val("");a.location_span.show();a.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",b).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.val(a.chrom+":"+a.low+"-"+a.high);a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var j=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(j/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,k){var f=$(this);var l=k.offsetX-k.current_x;var g=f.scrollTop()-(h.clientY-k.current_height);f.scrollTop(g);k.current_height=h.clientY;k.current_x=k.offsetX;var j=Math.round(l/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}).bind("mousewheel",function(h,k,g,f){if(g){var j=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(k,l){$(l.proxy).css({left:Math.min(k.pageX,l.startX),width:Math.abs(k.pageX-l.startX)});var g=Math.min(k.pageX,l.startX)-a.container.offset().left,f=Math.max(k.pageX,l.startX)-a.container.offset().left,j=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*j)+a.low,Math.round(f/h*j)+a.low)}).bind("dragend",function(l,m){var g=Math.min(l.pageX,m.startX),f=Math.max(l.pageX,m.startX),j=(a.high-a.low),h=a.viewport_container.width(),k=a.low;a.low=Math.round(g/h*j)+k;a.high=Math.round(f/h*j)+k;$(m.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.chrom_info.length===0){alert("Invalid chromosome: "+b.chrom);return}if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e==="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e==="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len-1;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var k=this,a,d,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}k.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},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);sortable(a.container_div,".draghandle");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())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;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(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()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)===0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};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.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.min){this.min=Math.floor(b[this.index]);a=true}if(b[this.index]>this.max){this.max=Math.ceil(b[this.index]);a=true}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.min<b||this.max>a){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_url_extra_params={};this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.make_name_popup_menu()}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(b,j,o){var c=this,p=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(j!==undefined?get_tool_from_dict(j):undefined);this.parent_track=o;this.child_tracks=[];if(c.hidden){return}var k=function(r,s,t){r.click(function(){var u=s.text();max=parseFloat(t.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(t.slider("option","values")){input_size=2*input_size+1;multi_value=true}s.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",u).appendTo(s).focus().select().click(function(v){v.stopPropagation()}).blur(function(){$(this).remove();s.text(u)}).keyup(function(z){if(z.keyCode===27){$(this).trigger("blur")}else{if(z.keyCode===13){var x=t.slider("option","min"),v=t.slider("option","max"),y=function(A){return(isNaN(A)||A>v||A<x)},w=$(this).val();if(!multi_value){w=parseFloat(w);if(y(w)){alert("Parameter value must be in the range ["+x+"-"+v+"]");return $(this)}}else{w=w.split("-");w=[parseFloat(w[0]),parseFloat(w[1])];if(y(w[0])||y(w[1])){alert("Parameter value must be in the range ["+x+"-"+v+"]");return $(this)}}t.slider((multi_value?"values":"value"),w)}}})})};if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(r){r.stopPropagation()}).bind("click",function(r){r.stopPropagation()}).bind("dblclick",function(r){r.stopPropagation()});$.each(this.filters,function(x,s){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var r=$("<div/>").addClass("slider-label").appendTo(u);var z=$("<span/>").addClass("slider-name").text(s.name+" ").appendTo(r);var t=$("<span/>");var v=$("<span/>").addClass("slider-value").appendTo(r).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(u);s.control_element=$("<div/>").attr("id",s.name+"-filter-control").appendTo(y);var w=[0,0];s.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(A,B){w=B.values;t.text(B.values[0]+"-"+B.values[1]);setTimeout(function(){if(B.values[0]==w[0]&&B.values[1]==w[1]){var C=B.values;t.text(C[0]+"-"+C[1]);s.low=C[0];s.high=C[1];c.draw(true,true)}},50)},change:function(A,B){s.control_element.slider("option","slide").call(s.control_element,A,B)}});s.slider=s.control_element;s.slider_label=t;k(v,t,s.control_element);$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(r){r.stopPropagation()}).bind("click",function(r){r.stopPropagation()}).bind("dblclick",function(r){r.stopPropagation()});var n=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var m=this.tool.params;var c=this;$.each(this.tool.params,function(x,s){var v=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(v);var z=$("<span/>").addClass("slider-name").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var w=$("<span/>").addClass("slider-value").appendTo(u).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(v);var r=$("<div id='"+s.name+"-param-control'>").appendTo(y);r.slider({min:s.min,max:s.max,step:get_slider_step(s.min,s.max),value:s.value,slide:function(A,C){var B=C.value;s.value=B;if(0<B&&B<1){B=parseFloat(B).toFixed(2)}t.text(B)},change:function(A,B){r.slider("option","slide").call(r,A,B)}});k(w,t,r);$("<div style='clear: both;'/>").appendTo(v)});var q=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var l=$("<input type='submit'>").attr("value","Run").appendTo(q);var c=this;l.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(r){c.mode_div.text(r);c.mode=r;c.track_config.values.mode=r;c.tile_cache.clear();c.draw()};var a={};for(var f=0,h=c.display_modes.length;f<h;f++){var g=c.display_modes[f];a[g]=function(r){return function(){d(r)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},draw:function(a,d){var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),m=this.view.resolution;var e=$("<div style='position: relative;'></div>"),f=l/j;if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}var k=this;var q=setInterval(function(){if(obj_length(c)===0){clearInterval(q);if(d){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var z=$(v[w]);if(u){z.remove()}else{if(z.children().length!==0){u=true}}}}for(var y=0;y<k.filters.length;y++){k.filters[y].update_ui_elt()}var x=false;if(k.example_feature){for(var y=0;y<k.filters.length;y++){if(k.filters[y].applies_to(k.example_feature)){x=true;break}}}if(k.filters_available!==x){k.filters_available=x;if(!k.filters_available){k.filters_div.hide()}k.make_name_popup_menu()}}},50);for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,g,l,c,e,k,m,f){var d=this;var h=function(u,n,p,o,s,t,q){returned_tile=d.draw_tile(n,p,o,s,t,q);var r=$("<div class='track-tile'>").prepend(returned_tile);tile_element=r;d.tile_cache.set(j,tile_element);d.show_tile(tile_element,s,g,t);delete f[u]};var a=setTimeout(function(){if(g<=d.view.high&&l>=d.view.low){var n=(b?undefined:d.tile_cache.get(j));if(n){d.show_tile(n,k,g,m);delete f[a]}else{$.when(d.data_cache.get_data(view.chrom,g,l,d.mode,e,d.data_url_extra_params)).then(function(){var o=d.data_cache.get_data(view.chrom,g,l,d.mode,e,d.data_url_extra_params);if(view.reference_track&&m>CHAR_WIDTH_PX){$.when(view.reference_track.data_cache.get_data(view.chrom,g,l,d.mode,e,view.reference_track.data_url_extra_params)).then(function(){var p=view.reference_track.data_cache.get_data(view.chrom,g,l,d.mode,e,view.reference_track.data_url_extra_params);h(a,o,e,c,k,m,p)})}else{h(a,o,e,c,k,m)}})}}},50);f[a]=true},show_tile:function(a,f,d,g){var b=this;var c=this.view.high-this.view.low,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px")},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:a.dbkey};this.data_cache=new DataManager(CACHED_DATA,this,false);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{draw_tile:function(m,g,b,j,n){var f=this,d=DENSITY*g;if(n>CHAR_WIDTH_PX){if(m===null){f.content_div.css("height","0px");return}var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var l=e.get(0).getContext("2d");e.get(0).width=Math.ceil(d*n+f.left_offset);e.get(0).height=f.height_px;l.font=DEFAULT_FONT;l.textAlign="center";for(var h=0,k=m.length;h<k;h++){var a=Math.round(h*n);l.fillText(m[h],a+f.left_offset,10)}return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataManager(CACHED_DATA,this);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var k=false;var j=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){k=true;h.show()},function(){k=false;if(!j){h.hide()}});h.hide().bind("dragstart",function(l,m){j=true;m.original_height=$(g.content_div).height()}).bind("drag",function(m,n){var l=Math.min(Math.max(n.original_height+n.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",l);g.height_px=l;g.draw(true)}).bind("dragend",function(l,m){g.tile_cache.clear();j=false;if(!k){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(j,q,t,c,e){if(this.vertical_range===undefined){return}var o=this,u=t*DENSITY*q,a=DENSITY*q,B=q+"_"+t,v={hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution};var b=document.createElement("canvas"),z=j.data;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);b.get(0).width=Math.ceil(a*e);b.get(0).height=o.height_px;var p=b.get(0).getContext("2d"),k=false,l=o.prefs.min_value,g=o.prefs.max_value,n=o.vertical_range,w=o.total_frequency,d=o.height_px,m=o.mode;var A=Math.round(d+l/n*d);p.beginPath();p.moveTo(0,A);p.lineTo(a*e,A);p.fillStyle="#aaa";p.stroke();p.beginPath();p.fillStyle=o.prefs.color;var x,h,f;if(z.length>1){f=Math.ceil((z[1][0]-z[0][0])*e)}else{f=10}for(var r=0,s=z.length;r<s;r++){x=Math.round((z[r][0]-u)*e);h=z[r][1];if(h===null){if(k&&m==="Filled"){p.lineTo(x,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(h/n*d);p.fillRect(x,A,f,-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);p.fillStyle="rgb("+h+","+h+","+h+")";p.fillRect(x,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){p.lineTo(x,h)}else{k=true;if(m==="Filled"){p.moveTo(x,d);p.lineTo(x,h)}else{p.moveTo(x,h)}}}}}if(m==="Filled"){if(k){p.lineTo(x,A);p.lineTo(0,A)}p.fill()}else{p.stroke()}return b}});var FeatureTrack=function(a,f,e,j,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=j;this.original_dataset_id=j;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataManager(20,this);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j+1},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<div />").addClass("yaxislabel");h.text(l);h.css({position:"absolute",top:"22px",left:"10px"});h.prependTo(this.container_div);var q=b.get(0).getContext("2d");for(var d=0,g=o.length;d<g;d++){var m=Math.floor((o[d][0]-f)*r);var k=o[d][1];if(!k){continue}var p=k/l*j;q.fillStyle="black";q.fillRect(m+e,c-p,delta_x_px,p);var a=4;if(this.prefs.show_counts&&(q.measureText(k).width+a)<delta_x_px){q.fillStyle="#666";q.textAlign="center";q.fillText(k,m+e+(delta_x_px/2),10)}}},draw_element:function(p,f,g,x,j,r,I,M,N,a,A){var u=x[0],K=x[1],C=x[2]-1,s=x[3],D=Math.floor(Math.max(0,(K-r)*M)),q=Math.ceil(Math.min(a,Math.max(0,(C-r)*M))),B=ERROR_PADDING+(g==="Dense"?0:(0+j))*N,o,G,t=null,O=null,d=this.prefs.block_color,F=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(D+A,B,q-D,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(D+A,B+5,q-D,DENSE_FEATURE_HEIGHT)}else{var n=x[4],z=x[5],E=x[6],e=x[7];if(z&&E){t=Math.floor(Math.max(0,(z-r)*M));O=Math.ceil(Math.min(a,Math.max(0,(E-r)*M)))}var L,v;if(g==="Squish"){L=1;v=SQUISH_FEATURE_HEIGHT}else{L=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(D+A,B,q-D,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=B+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=B;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(D+A,m,q-D,w);for(var J=0,c=e.length;J<c;J++){var h=e[J],b=Math.floor(Math.max(0,(h[0]-r)*M)),y=Math.ceil(Math.min(a,Math.max((h[1]-1-r)*M)));if(b>y){continue}p.fillStyle=d;p.fillRect(b+A,B+(v-L)/2+1,y-b,L);if(t!==undefined&&!(b>O||y<t)){var H=Math.max(b,t),l=Math.min(y,O);p.fillRect(H+A,B+1,l-H,v)}}}if(g==="Pack"&&K>r){p.fillStyle=F;if(f===0&&D-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+A+LABEL_SPACING,B+8)}else{p.textAlign="right";p.fillText(s,D+A-LABEL_SPACING,B+8)}p.fillStyle=d}}}},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(o,x,C,k,m,d){var t=this;var E=C*DENSITY*x,a=(C+1)*DENSITY*x,q=a-E,F={hda_ldda:t.hda_ldda,dataset_id:t.dataset_id,resolution:this.view.resolution,mode:this.mode};var v=Math.ceil(q*m),s=this.mode,H=25,g=this.left_offset,p,h;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(s==="Auto"){if(o.dataset_type==="summary_tree"){s=o.dataset_type}else{if(o.extra_info==="no_detail"){s="no_detail"}else{var G=o.data;if((G.length&&G.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){s="Squish"}else{s="Pack"}}}}var y=this.get_y_scale(s);if(s==="summary_tree"){h=this.summary_draw_height}if(s==="Dense"){h=H}else{if(s==="no_detail"||s==="Squish"||s==="Pack"){h=this.incremental_slots(m,o.data,s)*y+H;p=this.inc_slots[m]}}c.get(0).width=v+g;c.get(0).height=h;if(o.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}k.parent().css("height",Math.max(this.height_px,h)+"px");var w=c.get(0).getContext("2d");w.fillStyle=this.prefs.block_color;w.font=this.default_font;w.textAlign="right";this.container_div.find(".yaxislabel").remove();if(s==="summary_tree"){this.draw_summary_tree(c,o.data,o.delta,o.max,m,h,E,g);return c}if(o.message){c.css({"border-top":"1px solid red"});w.fillStyle="red";w.textAlign="left";var r=w.textBaseline;w.textBaseline="top";w.fillText(o.message,g,0);w.textBaseline=r;if(!o.data){return c}}this.example_feature=(o.data.length?o.data[0]:undefined);var G=o.data;for(var z=0,B=G.length;z<B;z++){var j=G[z],l=j[0],u=j[1],b=j[2],e=(p&&p[l]!==undefined?p[l]:null);var A=false;var n;for(var D=0;D<this.filters.length;D++){n=this.filters[D];n.update_attrs(j);if(!n.keep(j)){A=true;break}}if(A){continue}if(is_overlap([u,b],[E,a])&&(s=="Dense"||e!==null)){this.draw_element(w,C,s,j,e,E,a,m,y,v,g,d)}}return c}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=ERROR_PADDING+(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:c,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.track_config.values.show_insertions){a*=2}}}return a},draw_read:function(m,d,J,n,D,G,e,o,y,a){m.textAlign="center";var l=this,u=[n,D],C=0,z=0,f=0;var r=[];if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){f=Math.round(J/2)}if(!e){e=[[0,o.length]]}for(var h=0,k=e.length;h<k;h++){var b=e[h],g="MIDNSHP=X"[b[0]],v=b[1];if(g==="H"||g==="S"){C-=v}var x=G+C,B=Math.floor(Math.max(0,(x-n)*J)),E=Math.floor(Math.max(0,(x+v-n)*J));switch(g){case"H":break;case"S":case"M":case"=":var p=compute_overlap([x,x+v],u);if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(f>0){m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset-f,y+1,E-B,9);m.fillStyle=CONNECTOR_COLOR;for(var I=0,j=q.length;I<j;I++){if(this.track_config.values.show_differences&&a){var s=a[x-n+I];if(!s||s.toLowerCase()===q[I].toLowerCase()){continue}}if(x+I>=n&&x+I<=D){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset,y+9)}}}else{m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset,y+(this.mode!=="Dense"?4:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}z+=v;C+=v;break;case"N":m.fillStyle=CONNECTOR_COLOR;m.fillRect(B+this.left_offset-f,y+5,E-B,1);C+=v;break;case"D":m.fillStyle="red";m.fillRect(B+this.left_offset-f,y+4,E-B,3);C+=v;break;case"P":break;case"I":var p=compute_overlap([x,x+v],u),K=this.left_offset+B-f;if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(this.track_config.values.show_insertions){var w=this.left_offset+B-(E-B)/2;if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){m.fillStyle="yellow";m.fillRect(w-f,y-9,E-B,9);r[r.length]={type:"triangle",data:[K,y+4,5]};m.fillStyle=CONNECTOR_COLOR;switch(p){case (OVERLAP_START):q=q.slice(n-x);break;case (OVERLAP_END):q=q.slice(0,x-D);break;case (CONTAINED_BY):break;case (CONTAINS):q=q.slice(n-x,x-D);break}for(var I=0,j=q.length;I<j;I++){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset-(E-B)/2,y)}}else{m.fillStyle="yellow";m.fillRect(w,y+(this.mode!=="Dense"?2:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){r[r.length]={type:"text",data:[q.length,K,y+9]}}else{}}}z+=v;break;case"X":z+=v;break}}m.fillStyle="yellow";var t,L,H;for(var F=0;F<r.length;F++){t=r[F];L=t.type;H=t.data;if(L==="text"){m.font="bold "+DEFAULT_FONT;m.fillText(H[0],H[1],H[2]);m.font=DEFAULT_FONT}else{if(L=="triangle"){m.drawDownwardEquilateralTriangle(H[0],H[1],H[2])}}}},draw_element:function(w,y,r,k,e,A,b,n,x,u,f,c){var m=k[0],v=k[1],d=k[2],o=k[3],h=Math.floor(Math.max(0,(v-A)*n)),j=Math.ceil(Math.min(u,Math.max(0,(d-A)*n))),g=(r==="Dense"?1:(1+e))*x,z=this.prefs.block_color,l=this.prefs.label_color;t=0;w.fillStyle=z;if(k[5] instanceof Array){var s=Math.floor(Math.max(0,(k[4][0]-A)*n)),q=Math.ceil(Math.min(u,Math.max(0,(k[4][1]-A)*n))),p=Math.floor(Math.max(0,(k[5][0]-A)*n)),a=Math.ceil(Math.min(u,Math.max(0,(k[5][1]-A)*n)));if(k[4][1]>=A&&k[4][0]<=b&&k[4][2]){this.draw_read(w,r,n,A,b,k[4][0],k[4][2],k[4][3],g,c)}if(k[5][1]>=A&&k[5][0]<=b&&k[5][2]){this.draw_read(w,r,n,A,b,k[5][0],k[5][2],k[5][3],g,c)}if(p>q){w.fillStyle=CONNECTOR_COLOR;w.dashedLine(q+f,g+5,f+p,g+5)}}else{w.fillStyle=z;this.draw_read(w,r,n,A,b,v,k[4],k[5],g,c)}if(r==="Pack"&&v>A){w.fillStyle=this.prefs.label_color;if((r==="Pack"||this.mode==="Auto")&&n>CHAR_WIDTH_PX){var t=Math.round(n/2)}if(y===0&&h-w.measureText(o).width<0){w.textAlign="left";w.fillText(o,j+f+LABEL_SPACING-t,g+8)}else{w.textAlign="right";w.fillText(o,h+f-LABEL_SPACING-t,g+8)}w.fillStyle=z}}});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}}); \ No newline at end of file --- a/static/scripts/trackster.js Fri Mar 25 13:26:40 2011 -0400 +++ b/static/scripts/trackster.js Mon Mar 28 15:27:14 2011 -0400 @@ -121,6 +121,14 @@ } /** + * Calculates step for slider with a given min, max. + */ +function get_slider_step(min, max) { + var range = max - min; + return (range <= 1 ? 0.01 : (range <= 1000 ? 1 : 5)); +} + +/** * Init constants & functions used throughout trackster. */ var @@ -255,10 +263,20 @@ * Load data from server; returns AJAX object so that use of Deferred is possible. */ load_data: function(chrom, low, high, mode, resolution, extra_params) { + // Setup data request params. var params = {"chrom": chrom, "low": low, "high": high, "mode": mode, "resolution": resolution, "dataset_id" : this.track.dataset_id, "hda_ldda": this.track.hda_ldda}; $.extend(params, extra_params); + + // Add track filters to params. + var filter_names = []; + for (var i = 0; i < this.track.filters.length; i++) { + filter_names[filter_names.length] = this.track.filters[i].name; + } + params.filter_cols = JSON.stringify(filter_names); + + // Do request. var manager = this; return $.getJSON(this.track.data_url, params, function (result) { manager.set_data(low, high, mode, result); @@ -864,6 +882,9 @@ this.index = index; this.value = value; }; +/** + * Number filters have a min, max as well as a low, high; low and high are used + */ var NumberFilter = function(name, index) { this.name = name; // Index into payload to filter. @@ -872,21 +893,25 @@ this.low = -Number.MAX_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.MAX_VALUE; + this.min = Number.MAX_VALUE; + this.max = -Number.MAX_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. + /** + * 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. + /** + * Returns true iff element is in [low, high]; range is inclusive. + */ keep: function(element) { if ( !this.applies_to( element ) ) { // No element to filter on. @@ -894,7 +919,9 @@ } return (element[this.index] >= this.low && element[this.index] <= this.high); }, - // Update filter's min and max values based on element's values. + /** + * Update filter's min and max values based on element's values. + */ update_attrs: function(element) { var updated = false; if (!this.applies_to(element) ) { @@ -902,29 +929,32 @@ } // Update filter's min, max based on element values. - if (element[this.index] < this.slider_min) { - this.slider_min = element[this.index]; + if (element[this.index] < this.min) { + this.min = Math.floor(element[this.index]); updated = true; } - if (element[this.index] > this.slider_max) { - this.slider_max = element[this.index]; - updated = false; + if (element[this.index] > this.max) { + this.max = Math.ceil(element[this.index]); + updated = true; } return updated; }, - // Update filter's slider. + /** + * 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); + if (this.min < slider_min || this.max > slider_max) { + // Update slider min, max, step. + this.slider.slider("option", "min", this.min); + this.slider.slider("option", "max", this.max); + this.slider.slider("option", "step", get_slider_step(this.min, this.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]); + this.slider.slider("option", "values", [this.min, this.max]); // To use the current values. //var values = this.slider.slider( "option", "values" ); //this.slider.slider( "option", "values", values ); @@ -932,7 +962,9 @@ } }); -// Parse filters dict and return filters. +/** + * Parse filters dict and return filters. + */ var get_filters_from_dict = function(filters_dict) { var filters = []; for (var i = 0; i < filters_dict.length; i++) { @@ -947,6 +979,9 @@ return filters; }; +/** + * Container for track configuration data. + */ var TrackConfig = function( options ) { this.track = options.track; this.params = options.params; @@ -1185,6 +1220,66 @@ // Init HTML elements for tool, filters. // + // Function that supports inline text editing of slider values for tools, filters. + // Enable users to edit parameter's value via a text box. + var edit_slider_values = function(container, span, slider) { + container.click(function() { + var cur_value = span.text(); + max = parseFloat(slider.slider("option", "max")), + input_size = (max <= 1 ? 4 : max <= 1000000 ? max.toString().length : 6), + multi_value = false; + // Increase input size if there are two values. + if (slider.slider("option", "values")) { + input_size = 2*input_size + 1; + multi_value = true; + } + span.text(""); + // Temporary input for changing value. + $("<input type='text'/>").attr("size", input_size).attr("maxlength", input_size) + .attr("value", cur_value).appendTo(span).focus().select() + .click(function(e) { + // Don't want click to propogate up to values_span and restart everything. + e.stopPropagation(); + }).blur(function() { + $(this).remove(); + span.text(cur_value); + }).keyup(function(e) { + if (e.keyCode === 27) { + // Escape key. + $(this).trigger("blur"); + } else if (e.keyCode === 13) { + // + // Enter/return key initiates callback. If new value(s) are in slider range, + // change value (which calls slider's change() function). + // + var slider_min = slider.slider("option", "min"), + slider_max = slider.slider("option", "max"), + invalid = function(a_val) { + return (isNaN(a_val) || a_val > slider_max || a_val < slider_min); + }, + new_value = $(this).val(); + if (!multi_value) { + new_value = parseFloat(new_value); + if (invalid(new_value)) { + alert("Parameter value must be in the range [" + slider_min + "-" + slider_max + "]"); + return $(this); + } + } + else { // Multi value. + new_value = new_value.split("-"); + new_value = [parseFloat(new_value[0]), parseFloat(new_value[1])]; + if (invalid(new_value[0]) || invalid(new_value[1])) { + alert("Parameter value must be in the range [" + slider_min + "-" + slider_max + "]"); + return $(this); + } + } + slider.slider((multi_value ? "values" : "value"), new_value); + } + }); + }); + }; + + // If track has parent: // -replace drag handle with child-track icon button; (TODO: eventually, we'll want to be able // to make a set of child tracks dragable.) @@ -1201,6 +1296,8 @@ // Disable dragging, double clicking on div so that actions on slider do not impact viz. this.filters_div.bind("drag", function(e) { e.stopPropagation(); + }).bind("click", function( e ) { + e.stopPropagation(); }).bind("dblclick", function(e) { e.stopPropagation(); }); @@ -1209,36 +1306,49 @@ // Set up filter label (name, values). var filter_label = $("<div/>").addClass("slider-label").appendTo(filter_div) - var name_span = $("<span/>").addClass("name").appendTo(filter_label); - name_span.text(filter.name + " "); // Extra spacing to separate name and values - var values_span = $("<span/>").addClass("values").appendTo(filter_label); + var name_span = $("<span/>").addClass("slider-name").text(filter.name + " ").appendTo(filter_label); + var values_span = $("<span/>"); + var values_span_container = $("<span/>").addClass("slider-value").appendTo(filter_label).append("[").append(values_span).append("]"); // Set up slider for filter. - // TODO: generate custom interaction elements based on filter type. var slider_div = $("<div/>").addClass("slider").appendTo(filter_div); filter.control_element = $("<div/>").attr("id", filter.name + "-filter-control").appendTo(slider_div); + var prev_values = [0,0]; filter.control_element.slider({ range: true, min: Number.MAX_VALUE, max: -Number.MIN_VALUE, values: [0, 0], 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, true); + // + // Always update UI values, but set timeout for doing more--especially drawing-- + // so that viz is more responsive. + // + prev_values = ui.values; + values_span.text(ui.values[0] + "-" + ui.values[1]); + setTimeout(function() { + if (ui.values[0] == prev_values[0] && ui.values[1] == prev_values[1]) { + var values = ui.values; + // Set new values in UI. + values_span.text(values[0] + "-" + values[1]); + // Set new values in filter. + filter.low = values[0]; + filter.high = values[1]; + // Redraw track. + track.draw(true, true); + } + }, 50); }, - change: function( event, ui ) { - filter.control_element.slider("option", "slide").call( filter.control_element, event, ui ); + 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; + // Enable users to edit slider values via text box. + edit_slider_values(values_span_container, values_span, filter.control_element); + // Add to clear floating layout. $("<div style='clear: both;'/>").appendTo(filter_div); }); @@ -1266,19 +1376,17 @@ // Slider label. var label_div = $("<div>").addClass("slider-label").appendTo(param_div); - var name_span = $("<span class='param-name'>").text(param.label + " ").appendTo(label_div); + var name_span = $("<span/>").addClass("slider-name").text(param.label + " ").appendTo(label_div); var values_span = $("<span/>").text(param.value); - var values_span_container = $("<span class='param-value'>").appendTo(label_div).append("[").append(values_span).append("]"); + var values_span_container = $("<span/>").addClass("slider-value").appendTo(label_div).append("[").append(values_span).append("]"); // Slider. var slider_div = $("<div/>").addClass("slider").appendTo(param_div); var slider = $("<div id='" + param.name + "-param-control'>").appendTo(slider_div); - // Make step reasonable. - var step = (param.max <= 1 ? 0.01 : (param.max <= 1000 ? 1 : 5)); slider.slider({ min: param.min, max: param.max, - step: step, + step: get_slider_step(param.min, param.max), value: param.value, slide: function(event, ui) { var value = ui.value; @@ -1290,47 +1398,12 @@ values_span.text(value); }, change: function(event, ui) { - param.value = ui.value; + slider.slider("option", "slide").call(slider, event, ui); } }); - // Enable users to edit parameter's value via a text box. - values_span_container.click(function() { - var span = values_span, - cur_value = span.text(), - // TODO: is there a better way to handle input size when param max is <= 1? - input_size = (param.max <= 1 ? 4 : param.max.length); - span.text(""); - // Temporary input for changing value. - $("<input type='text'/>").attr("size", input_size).attr("maxlength", input_size) - .attr("value", cur_value).appendTo(span).focus().select() - .click(function(e) { - // Don't want click to propogate up to values_span and restart everything. - e.stopPropagation(); - }).blur(function() { - $(this).remove(); - span.text(cur_value); - }).keyup(function(e) { - if ( e.keyCode === 27 ) { - // Escape key. - $(this).trigger("blur"); - } else if ( e.keyCode === 13 ) { - // Enter/return key sets new value. - var input = $(this), - new_value = parseFloat(input.val()); - if (isNaN(new_value) || new_value > param.max || new_value < param.min) { - // TODO: display popup menu instead of alert? - alert("Parameter value must be in the range [" + param.min + "-" + param.max + "]"); - return $(this); - } - // Update value in three places; update param value last b/c slider updates param value - // as well and slider may round values depending on its settings. - span.text(new_value); - slider.slider('value', new_value); - param.value = new_value; - } - }); - }); + // Enable users to edit parameter's value via text box. + edit_slider_values(values_span_container, values_span, slider); // Add to clear floating layout. $("<div style='clear: both;'/>").appendTo(param_div); @@ -1467,7 +1540,7 @@ // if (track.tool) { // Show/hide dynamic tool menu item. - var text = (track.dynamic_tool_div.is(":visible") ? "Hide Tool" : "Show Tool"); + var text = (track.dynamic_tool_div.is(":visible") ? "Hide tool" : "Show tool"); track_dropdown[text] = function() { // Set track name, toggle tool div, and remake menu. if (!track.dynamic_tool_div.is(":visible")) { @@ -1551,15 +1624,17 @@ } // - // Actions to take after tiles have been drawn: - // (1) remove old tile(s); - // (2) update filtering UI elements. + // Post-draw actions: // - if (clear_after) { - var track = this; - var intervalId = setInterval(function() { - if (obj_length(draw_tile_dict) === 0) { - // All tiles have been drawn; clear out track content in order to show the most recent content. + var track = this; + var intervalId = setInterval(function() { + if (obj_length(draw_tile_dict) === 0) { + // All tiles have been drawn. + clearInterval(intervalId); + + // Clear tiles? + if (clear_after) { + // Clear out track content in order to show the most recent content. // Most recent content is the div with children (tiles) most recently appended to track. // However, do not delete recently-appended empty content as calls to draw() may still be active // and using these divs. @@ -1575,12 +1650,38 @@ remove = true; } } + } + + // + // Update filter attributes, UI. + // - // Method complete; do not call it again. - clearInterval(intervalId); + // Update filtering UI. + for (var f = 0; f < track.filters.length; f++) { + track.filters[f].update_ui_elt(); } - }, 50); - } + + // Determine if filters are available; this is based on the example feature. + var filters_available = false; + if (track.example_feature) { + for (var f = 0; f < track.filters.length; f++) { + if (track.filters[f].applies_to(track.example_feature)) { + filters_available = true; + break; + } + } + } + + // If filter availability changed, hide filter div if necessary and update menu. + if (track.filters_available !== filters_available) { + track.filters_available = filters_available; + if (!track.filters_available) { + track.filters_div.hide(); + } + track.make_name_popup_menu(); + } + } + }, 50); // // Draw child tracks. @@ -1678,40 +1779,7 @@ 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"); - parent_element.children().css("height", track.max_height + "px"); - - if (track.hidden) { return; } - - // - // Update filter attributes, UI. - // TODO: this could be done after all tiles are drawn, but there's no reliable way to detect - // that right now. - // - - // Update filtering UI. - for (var f = 0; f < track.filters.length; f++) { - track.filters[f].update_ui_elt(); - } - - // Determine if filters are available; this is based on the example feature. - var filters_available = false; - if (track.example_feature) { - for (var f = 0; f < track.filters.length; f++) { - if (track.filters[f].applies_to(track.example_feature)) { - filters_available = true; - break; - } - } - } - - // If filter availability changed, hide filter div if necessary and update menu. - if (track.filters_available !== filters_available) { - track.filters_available = filters_available; - if (!track.filters_available) { - track.filters_div.hide(); - } - track.make_name_popup_menu(); - } + parent_element.children().css("height", track.max_height + "px"); }, // Set track as the overview track in the visualization. set_overview: function() { @@ -2376,10 +2444,10 @@ } else { // Mode is either Squish or Pack: // Feature details. - var feature_strand = feature[5], - feature_ts = feature[6], - feature_te = feature[7], - feature_blocks = feature[8]; + var feature_strand = feature[4], + feature_ts = feature[5], + feature_te = feature[6], + feature_blocks = feature[7]; if (feature_ts && feature_te) { thick_start = Math.floor( Math.max(0, (feature_ts - tile_low) * w_scale) ); @@ -2642,15 +2710,15 @@ var filter; for (var f = 0; f < this.filters.length; f++) { filter = this.filters[f]; - filter.update_attrs( feature ); - if ( !filter.keep( feature ) ) { + filter.update_attrs(feature); + if (!filter.keep(feature)) { hide_feature = true; break; } } if (hide_feature) { continue; - } + } // Draw feature if there's overlap and mode is dense or feature is slotted (as it must be for all non-dense modes). if (is_overlap([feature_start, feature_end], [tile_low, tile_high]) && (mode == "Dense" || slot !== null)) { @@ -3051,7 +3119,7 @@ track.data_url = default_data_url; track.data_query_wait = DEFAULT_DATA_QUERY_WAIT; track.dataset_state_url = converted_datasets_state_url; - $.getJSON(track.dataset_state_url, { dataset_id : track.dataset_id, hda_ldda: track.hda_ldda }, function(track_data) {}); + $.getJSON(track.dataset_state_url, {dataset_id : track.dataset_id, hda_ldda: track.hda_ldda}, function(track_data) {}); } }; post_init(); --- a/templates/tracks/browser.mako Fri Mar 25 13:26:40 2011 -0400 +++ b/templates/tracks/browser.mako Mon Mar 28 15:27:14 2011 -0400 @@ -69,6 +69,7 @@ chrom_url = "${h.url_for( action='chroms' )}", dataset_state_url = "${h.url_for( action='dataset_state' )}", converted_datasets_state_url = "${h.url_for( action='converted_datasets_state' )}", + filters_url = "${h.url_for( action='filters' )}", addable_track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack }, view; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: fubar: Remove bogus makeGFF from rgutils
by Bitbucket 25 Mar '11

25 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9d6a34b0a4fa/ changeset: r5276:9d6a34b0a4fa user: fubar date: 2011-03-25 18:26:40 summary: Remove bogus makeGFF from rgutils affected #: 1 file (1 byte) --- a/tools/rgenetics/rgutils.py Fri Mar 25 13:21:13 2011 -0400 +++ b/tools/rgenetics/rgutils.py Fri Mar 25 13:26:40 2011 -0400 @@ -62,6 +62,7 @@ chr1 67065090 67065317 - CCDS635.1_cds_2_0_chr1_67065091_r chr1 67066082 67066181 - CCDS635.1_cds_3_0_chr1_67066083_r + see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 we need to add 1 to start coordinates on the way through - but length calculations are easier """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 25 Mar '11

25 Mar '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c25c8055e608/ changeset: r5274:c25c8055e608 user: fubar date: 2011-03-25 18:12:21 summary: Revised rgenetics tools to remove post job hooks affected #: 35 files (21.8 KB) --- a/test-data/rgCaCotest1_CaCo_topTable.gff Thu Mar 24 20:29:40 2011 -0400 +++ b/test-data/rgCaCotest1_CaCo_topTable.gff Fri Mar 25 13:12:21 2011 -0400 @@ -1,26 +1,26 @@ -track name=rgGLM_TopTable description="rgCaCotest1" visibility=2 useScore=1 color=0,60,120 -chr22 rgGLM variation 21784622 21784822 0 . . rs2283802 logp=-0.00 -chr22 rgGLM variation 21785266 21785466 42 . . rs2267000 logp=0.05 -chr22 rgGLM variation 21794654 21794854 249 . . rs16997606 logp=0.29 -chr22 rgGLM variation 21794710 21794910 493 . . rs4820537 logp=0.58 -chr22 rgGLM variation 21797704 21797904 237 . . rs3788347 logp=0.28 -chr22 rgGLM variation 21799818 21800018 61 . . rs756632 logp=0.07 -chr22 rgGLM variation 21807870 21808070 153 . . rs4820539 logp=0.18 -chr22 rgGLM variation 21820235 21820435 44 . . rs2283804 logp=0.05 -chr22 rgGLM variation 21820890 21821090 44 . . rs2267006 logp=0.05 -chr22 rgGLM variation 21820900 21821100 184 . . rs4822363 logp=0.22 -chr22 rgGLM variation 21827574 21827774 317 . . rs5751592 logp=0.37 -chr22 rgGLM variation 21832608 21832808 0 . . rs5759608 logp=-0.00 -chr22 rgGLM variation 21833070 21833270 0 . . rs5759612 logp=-0.00 -chr22 rgGLM variation 21860068 21860268 0 . . rs2267009 logp=-0.00 -chr22 rgGLM variation 21864266 21864466 117 . . rs2267010 logp=0.14 -chr22 rgGLM variation 21868598 21868798 571 . . rs5759636 logp=0.67 -chr22 rgGLM variation 21871388 21871588 0 . . rs2071436 logp=-0.00 -chr22 rgGLM variation 21875779 21875979 249 . . rs2267013 logp=0.29 -chr22 rgGLM variation 21889706 21889906 378 . . rs6003566 logp=0.44 -chr22 rgGLM variation 21892791 21892991 249 . . rs2256725 logp=0.29 -chr22 rgGLM variation 21892825 21893025 193 . . rs12160770 logp=0.23 -chr22 rgGLM variation 21895919 21896119 42 . . rs5751611 logp=0.05 -chr22 rgGLM variation 21898758 21898958 40 . . rs762601 logp=0.05 -chr22 rgGLM variation 21898963 21899163 40 . . rs2156921 logp=0.05 -chr22 rgGLM variation 21905542 21905742 40 . . rs4822375 logp=0.05 +track name=rgCaCo_TopTable description="rgCaCotest1" visibility=2 useScore=1 color=0,60,120 +chr22 rgCaCo variation 21784622 21784822 0 . . rs2283802 logp=-0.00 +chr22 rgCaCo variation 21785266 21785466 42 . . rs2267000 logp=0.05 +chr22 rgCaCo variation 21794654 21794854 249 . . rs16997606 logp=0.29 +chr22 rgCaCo variation 21794710 21794910 493 . . rs4820537 logp=0.58 +chr22 rgCaCo variation 21797704 21797904 237 . . rs3788347 logp=0.28 +chr22 rgCaCo variation 21799818 21800018 61 . . rs756632 logp=0.07 +chr22 rgCaCo variation 21807870 21808070 153 . . rs4820539 logp=0.18 +chr22 rgCaCo variation 21820235 21820435 44 . . rs2283804 logp=0.05 +chr22 rgCaCo variation 21820890 21821090 44 . . rs2267006 logp=0.05 +chr22 rgCaCo variation 21820900 21821100 184 . . rs4822363 logp=0.22 +chr22 rgCaCo variation 21827574 21827774 317 . . rs5751592 logp=0.37 +chr22 rgCaCo variation 21832608 21832808 0 . . rs5759608 logp=-0.00 +chr22 rgCaCo variation 21833070 21833270 0 . . rs5759612 logp=-0.00 +chr22 rgCaCo variation 21860068 21860268 0 . . rs2267009 logp=-0.00 +chr22 rgCaCo variation 21864266 21864466 117 . . rs2267010 logp=0.14 +chr22 rgCaCo variation 21868598 21868798 571 . . rs5759636 logp=0.67 +chr22 rgCaCo variation 21871388 21871588 0 . . rs2071436 logp=-0.00 +chr22 rgCaCo variation 21875779 21875979 249 . . rs2267013 logp=0.29 +chr22 rgCaCo variation 21889706 21889906 378 . . rs6003566 logp=0.44 +chr22 rgCaCo variation 21892791 21892991 249 . . rs2256725 logp=0.29 +chr22 rgCaCo variation 21892825 21893025 193 . . rs12160770 logp=0.23 +chr22 rgCaCo variation 21895919 21896119 42 . . rs5751611 logp=0.05 +chr22 rgCaCo variation 21898758 21898958 40 . . rs762601 logp=0.05 +chr22 rgCaCo variation 21898963 21899163 40 . . rs2156921 logp=0.05 +chr22 rgCaCo variation 21905542 21905742 40 . . rs4822375 logp=0.05 --- a/test-data/rgTDTtest1_TDT_topTable.gff Thu Mar 24 20:29:40 2011 -0400 +++ b/test-data/rgTDTtest1_TDT_topTable.gff Fri Mar 25 13:12:21 2011 -0400 @@ -1,25 +1,25 @@ track name=rgTDT_Top_Table description="rgTDTtest1" visibility=2 useScore=1 color=0,60,120 -chr22 rgGLM variation 21784622 21784822 0 . . rs2283802 logp=-0.00 -chr22 rgGLM variation 21785266 21785466 120 . . rs2267000 logp=0.13 -chr22 rgGLM variation 21794654 21794854 0 . . rs16997606 logp=-0.00 -chr22 rgGLM variation 21794710 21794910 457 . . rs4820537 logp=0.50 -chr22 rgGLM variation 21797704 21797904 120 . . rs3788347 logp=0.13 -chr22 rgGLM variation 21799818 21800018 228 . . rs756632 logp=0.25 -chr22 rgGLM variation 21807870 21808070 120 . . rs4820539 logp=0.13 -chr22 rgGLM variation 21820235 21820435 292 . . rs2283804 logp=0.32 -chr22 rgGLM variation 21820890 21821090 292 . . rs2267006 logp=0.32 -chr22 rgGLM variation 21820900 21821100 0 . . rs4822363 logp=-0.00 -chr22 rgGLM variation 21827574 21827774 541 . . rs5751592 logp=0.59 -chr22 rgGLM variation 21832608 21832808 400 . . rs5759608 logp=0.44 -chr22 rgGLM variation 21833070 21833270 400 . . rs5759612 logp=0.44 -chr22 rgGLM variation 21860068 21860268 0 . . rs2267009 logp=-0.00 -chr22 rgGLM variation 21864266 21864466 0 . . rs2267010 logp=-0.00 -chr22 rgGLM variation 21868598 21868798 457 . . rs5759636 logp=0.50 -chr22 rgGLM variation 21871388 21871588 0 . . rs2071436 logp=-0.00 -chr22 rgGLM variation 21875779 21875979 457 . . rs2267013 logp=0.50 -chr22 rgGLM variation 21889706 21889906 168 . . rs6003566 logp=0.18 -chr22 rgGLM variation 21892791 21892991 457 . . rs2256725 logp=0.50 -chr22 rgGLM variation 21895919 21896119 359 . . rs5751611 logp=0.39 -chr22 rgGLM variation 21898758 21898958 400 . . rs762601 logp=0.44 -chr22 rgGLM variation 21898963 21899163 400 . . rs2156921 logp=0.44 -chr22 rgGLM variation 21905542 21905742 400 . . rs4822375 logp=0.44 +chr22 rgTDT variation 21784622 21784822 0 . . rs2283802 logp=-0.00 +chr22 rgTDT variation 21785266 21785466 120 . . rs2267000 logp=0.13 +chr22 rgTDT variation 21794654 21794854 0 . . rs16997606 logp=-0.00 +chr22 rgTDT variation 21794710 21794910 457 . . rs4820537 logp=0.50 +chr22 rgTDT variation 21797704 21797904 120 . . rs3788347 logp=0.13 +chr22 rgTDT variation 21799818 21800018 228 . . rs756632 logp=0.25 +chr22 rgTDT variation 21807870 21808070 120 . . rs4820539 logp=0.13 +chr22 rgTDT variation 21820235 21820435 292 . . rs2283804 logp=0.32 +chr22 rgTDT variation 21820890 21821090 292 . . rs2267006 logp=0.32 +chr22 rgTDT variation 21820900 21821100 0 . . rs4822363 logp=-0.00 +chr22 rgTDT variation 21827574 21827774 541 . . rs5751592 logp=0.59 +chr22 rgTDT variation 21832608 21832808 400 . . rs5759608 logp=0.44 +chr22 rgTDT variation 21833070 21833270 400 . . rs5759612 logp=0.44 +chr22 rgTDT variation 21860068 21860268 0 . . rs2267009 logp=-0.00 +chr22 rgTDT variation 21864266 21864466 0 . . rs2267010 logp=-0.00 +chr22 rgTDT variation 21868598 21868798 457 . . rs5759636 logp=0.50 +chr22 rgTDT variation 21871388 21871588 0 . . rs2071436 logp=-0.00 +chr22 rgTDT variation 21875779 21875979 457 . . rs2267013 logp=0.50 +chr22 rgTDT variation 21889706 21889906 168 . . rs6003566 logp=0.18 +chr22 rgTDT variation 21892791 21892991 457 . . rs2256725 logp=0.50 +chr22 rgTDT variation 21895919 21896119 359 . . rs5751611 logp=0.39 +chr22 rgTDT variation 21898758 21898958 400 . . rs762601 logp=0.44 +chr22 rgTDT variation 21898963 21899163 400 . . rs2156921 logp=0.44 +chr22 rgTDT variation 21905542 21905742 400 . . rs4822375 logp=0.44 --- a/tools/rgenetics/rgCaCo.py Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgCaCo.py Fri Mar 25 13:12:21 2011 -0400 @@ -20,7 +20,6 @@ import sys,math,shutil,subprocess,os,time,tempfile,string from os.path import abspath from rgutils import timenow, plinke - imagedir = '/static/rg' # if needed for images myversion = 'V000.1 April 2007' verbose = False @@ -82,7 +81,7 @@ outres = [] # need to resort into chrom offset order for i,lrow in enumerate(resfl): chrom,snp,offset,p, = [lrow[x] for x in wewant] - gff = ('chr%s' % chrom,'rgGLM','variation','%d' % (int(offset)-halfwidth), + gff = ('chr%s' % chrom,'rgCaCo','variation','%d' % (int(offset)-halfwidth), '%d' % (int(offset)+halfwidth),p,'.','.','%s logp=%1.2f' % (snp,pvals[i])) outres.append(gff) outres = [(x[0],int(x[3]),x) for x in outres] # decorate @@ -94,7 +93,6 @@ outf.close() - def plink_assocToGG(plinkout="hm",tag='test'): """ plink --assoc output looks like this # CHR SNP A1 F_A F_U A2 CHISQ P OR @@ -170,14 +168,8 @@ else: headl = headl.split() delim = None - chrpos = headl.index('CHR') - rspos = headl.index('SNP') - testpos = headl.index('TEST') - naffpos = headl.index('AFF') - nuaffpos = headl.index('UNAFF') - chisqpos = headl.index('CHISQ') - ppos = headl.index('P') - wewant = [chrpos,rspos,testpos,naffpos,nuaffpos,chisqpos,ppos] + whatwewant = ['CHR','SNP','TEST','AFF','UNAFF','CHISQ','P'] + wewant = [headl.index(x) for x in whatwewant] llen = len(headl) lnum = anum = 0 lastsnp = None # so we know when to write out a gg line @@ -273,7 +265,7 @@ retval = p.wait() resf = '%s.model' % tname # plink output is here we hope xformModel(bfname,resf,outfname,name,amapf,flog) # leaves the desired summary file - makeGFF(resf=outfname,outfname=gffout,logf=flog,twd=twd,name='rgGLM_TopTable',description=name,topn=topn) + makeGFF(resf=outfname,outfname=gffout,logf=flog,twd=twd,name='rgCaCo_TopTable',description=name,topn=topn) flog.write('\n'.join(logme)) flog.close() # close the log used #shutil.copytree(twd,logoutdir) --- a/tools/rgenetics/rgCaCo.xml Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgCaCo.xml Fri Mar 25 13:12:21 2011 -0400 @@ -1,25 +1,19 @@ <tool id="rgCaCo1" name="Case Control:"> - <code file="listFiles.py"/> - <code file="rgCaCo_code.py"/> - <description>for unrelated subjects</description> - <command interpreter="python"> - rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$name" - '$out_file1' '$logf' '$logf.files_path' '$gffout' + rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$title" '$out_file1' '$logf' '$logf.files_path' '$gffout' </command> - <inputs><param name="i" type="data" label="RGenetics genotype data from your current history" format="pbed" /> - <param name='name' type='text' size="132" value='CaseControl' label="Title for this job"/> + <param name='title' type='text' size="132" value='CaseControl' label="Title for this job"/></inputs><outputs> - <data format="tabular" name="out_file1" /> - <data format="txt" name="logf" /> - <data format="gff" name="gffout" /> + <data format="tabular" name="out_file1" label="${title}_rgCaCo.xls" /> + <data format="txt" name="logf" label="${title}_rgCaCo.log"/> + <data format="gff" name="gffout" label="${title}_rgCaCoTop.gff" /></outputs><tests><test> @@ -30,7 +24,7 @@ <composite_data value='tinywga.fam' /><edit_attributes type='name' value='tinywga' /></param> - <param name='name' value='rgCaCotest1' /> + <param name='title' value='rgCaCotest1' /><output name='out_file1' file='rgCaCotest1_CaCo.xls' ftype='tabular' compare='diff' /><output name='logf' file='rgCaCotest1_CaCo_log.txt' ftype='txt' compare='diff' lines_diff='20' /><output name='gffout' file='rgCaCotest1_CaCo_topTable.gff' ftype='gff' compare='diff' /> @@ -79,24 +73,31 @@ spreadsheet data, choose the .xls tab delimited format. It's not a stupid binary excel file. Just a plain old tab delimited one with a header. Fortunately excel is dumb enough to open these without much protest. + ----- +.. class:: infomark + **Attribution** -When you click 'execute', this Galaxy tool will run Plink (from Shaun Purcell) for you (which is GPL, so this must be too I guess) for calculations. For full Plink -attribution, source code and documentation, please see http://pngu.mgh.harvard.edu/~purcell/plink/ +This Galaxy tool relies on Plink (see Plinksrc_) to test Casae Control association models. -The Plink output files will be adjusted into UCSC compatible tracks - gg or wig, or else as tab delimited -for you spreadsheet junkies out there. Python is used for all glue and data format yoga. -Originally designed and written for the Rgenetics Galaxy tools by -ross lazarus (ross spot lazarus ate gmail spot com), who didn't write -either Galaxy or Plink but wishes he had. +So, we rely on the author (Shaun Purcell) for the documentation you need specific to those settings - they are very nicely documented - see +DOC_ -copyright Ross Lazarus 2007 -Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html -but is about as useful as a chocolate teapot without Plink which is GPL. +Tool and Galaxy datatypes originally designed and written for the Rgenetics +series of whole genome scale statistical genetics tools by ross lazarus (ross.lazarus(a)gmail.com) + +Copyright Ross Lazarus March 2007 +This Galaxy wrapper is released licensed under the LGPL_ but is about as useful as a chocolate teapot without Plink which is GPL. I'm no lawyer, but it looks like you got GPL if you use this software. Good luck. +.. _Plinksrc: http://pngu.mgh.harvard.edu/~purcell/plink/ + +.. _LGPL: http://www.gnu.org/copyleft/lesser.html + +.. _DOC: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#cc + </help></tool> --- a/tools/rgenetics/rgCaCo_code.py Thu Mar 24 20:29:40 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,45 +0,0 @@ -# for caco -# called as plinkCaCo.py $i $name $test $outformat $out_file1 $logf $map -from galaxy import datatypes -import time,string,sys - -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - """Sets the name of the data""" - job_name = param_dict.get( 'name', 'RgCaCo' ).encode() - killme = string.punctuation + string.whitespace - trantab = string.maketrans(killme,'_'*len(killme)) - title = job_name.translate(trantab) - indatname = inp_data['i'].name - outxls = ['tabular','%s_CaCo.xls' % job_name] - logtxt = ['txt','%s_CaCo_log.txt' % job_name] - ggout = ['gff','%s_CaCo_topTable.gff' % job_name] - lookup={} - lookup['out_file1'] = outxls - lookup['logf'] = logtxt - lookup['gffout'] = ggout - info = '%s rgCaCo from %s at %s' % (job_name,indatname,timenow()) - for name in lookup.keys(): - data = out_data[name] - data_type,newname = lookup[name] - data.name = newname - data.info = info - out_data[name] = data - app.model.context.flush() - - -def get_test_opts(): - """return test options""" - dat = [('Armitage test for trend chisq. Does NOT assume HWE!','TREND',True), - ('Allelic (A vs a) chisq. assumes HWE','ALLELIC',False), - ('Genotype (AA vs Aa vs aa)chisq. assumes HWE','GENO',False), - ('Dominant model (AA/Aa vs aa) chisq. assumesWE','DOM',False), - ('Recessive (AA vs Aa/aa) chisq. assumes HWE','REC',False)] - dat.reverse() - return dat - - --- a/tools/rgenetics/rgClean.xml Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgClean.xml Fri Mar 25 13:12:21 2011 -0400 @@ -1,6 +1,4 @@ <tool id="rgClean1" name="Clean genotypes:"> - <code file="rgClean_code.py"/> - <description>filter markers, subjects</description><command interpreter="python"> @@ -47,7 +45,7 @@ </inputs><outputs> - <data format="pbed" name="out_file1" metadata_source="input_file" /> + <data format="pbed" name="out_file1" metadata_source="input_file" label="${title}_rgClean.pbed" /></outputs><tests> --- a/tools/rgenetics/rgClean_code.py Thu Mar 24 20:29:40 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -from galaxy import app -import os, string, time - -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - - - -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - name,data = out_data.items()[0] - basename = param_dict['title'] - basename = basename.encode() - killme = string.punctuation + string.whitespace - trantab = string.maketrans(killme,'_'*len(killme)) - title = basename.translate(trantab) - info = '%s filtered by rgClean.py at %s' % (title,timenow()) - data.change_datatype('pbed') - #data.file_name = data.file_name - data.metadata.base_name = title - data.name = '%s.pbed' % title - data.info = info - data.readonly = True - app.model.context.flush() - - - --- a/tools/rgenetics/rgEigPCA.xml Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgEigPCA.xml Fri Mar 25 13:12:21 2011 -0400 @@ -1,5 +1,4 @@ <tool id="rgEigPCA1" name="Eigensoft:"> - <code file="rgEigPCA_code.py"/><description>PCA Ancestry using SNP</description><command interpreter="python"> @@ -27,12 +26,10 @@ </inputs><outputs> - <data name="out_file1" format="html" /> - <data name="pca" format="txt" /> + <data name="out_file1" format="html" label="${title}_rgEig.html"/> + <data name="pca" format="txt" label="${title}_rgEig.txt"/></outputs> - - <tests><test><param name='i' value='tinywga' ftype='ldindep' > @@ -59,17 +56,45 @@ **Syntax** -- **Genotype data** is the input genotype file chosen from available library files. -- **Title** is used to name the output files -- **Tuning parameters** documented in the Eigensoft documentation - see below +- **Genotype data** is an input genotype dataset in Plink lped (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) format. See below for notes +- **Title** is used to name the output files so you can remember what the outputs are for +- **Tuning parameters** are documented in the Eigensoft (http://genepath.med.harvard.edu/~reich/Software.htm) documentation - see below -(Note that you may need to convert an existing genotype file into that format to use this tool) ----- **Summary** +Eigensoft requires ld-reduced genotype data. +Galaxy has an automatic converter for genotype data in Plink linkage pedigree (lped) format. +For details of this generic genotype format, please see the Plink documentation at +http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml + +Reading that documentation, you'll see that the linkage pedigree format is really two related files with the same +file base name - a map and ped file - eg 'mygeno.ped' and 'mygeno.map'. +The map file has the chromosome, offset, genetic offset and snp name corresponding to each +genotype stored as separate alleles in the ped file. The ped file has family id, individual id, father id (or 0), mother id +(or 0), gender (1=male, 2=female, 0=unknown) and affection (1=unaffected, 2=affected, 0=unknown), +then two separate allele columns for each genotype. + +Once you have your data in the right format, you can upload those into your Galaxy history using the "upload" tool. + +To upload your lped data in the upload tool, choose 'lped' as the 'file format'. The tool form will change to +allow you to navigate to and select each member of the pair of ped and map files stored on your local computer +(or available at a public URL for Galaxy to grab). +Give the dataset a meaningful name (replace rgeneticsData with something more useful!) and click execute. + +When the upload is done, your new lped format dataset will appear in your history and then, +when you choose the ancestry tool, that history dataset will be available as input. + +**Warning for the Impatient** + +When you execute the tool, it will look like it has not started running for a while as the automatic converter +reduces the amount of LD - otherwise eigenstrat gives biased results. + + **Attribution** + This tool runs and relies on the work of many others, including the maintainers of the Eigensoft program, and the R and Bioconductor projects. For full attribution, source code and documentation, please see @@ -84,7 +109,7 @@ Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html but is about as useful as a sponge boat without EIGENSOFT pca code. -**README from eigensoft2** +**README from eigensoft2 distribution at http://genepath.med.harvard.edu/~reich/Software.htm** [rerla@beast eigensoft2]$ cat README EIGENSOFT version 2.0, January 2008 (for Linux only) --- a/tools/rgenetics/rgEigPCA_code.py Thu Mar 24 20:29:40 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -from galaxy import datatypes,model -import sys,time,string,shutil,os - -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - """Sets the name of the html output file - if we created a set of ldreduced files, we need to move them into the input files_path - so it doesn't need to be done again - """ - indat = inp_data['i'] - indatname = indat.name - base_name = indat.metadata.base_name - todir = indat.extra_files_path # where the ldreduced stuff should be - job_name = param_dict.get( 'title', 'Eigenstrat run' ) - job_name = job_name.encode() - killme = string.punctuation + string.whitespace - trantab = string.maketrans(killme,'_'*len(killme)) - job_name = job_name.translate(trantab) - info = '%s rgEigPCA2 on %s at %s' % (job_name,indatname,timenow()) - exts = ['html','txt'] - for i,ofname in enumerate(['out_file1','pca']): - data = out_data[ofname] - ext = exts[i] - newname = '%s.%s' % (job_name,ext) - data.name = newname - data.info = info - out_data[ofname] = data - if i == 0: - fromdir = data.extra_files_path - ldfname = '%s_INDEP_THIN' % base_name # we store ld reduced and thinned data - ldout = os.path.join(todir,ldfname) - ldin = os.path.join(fromdir,ldfname) - if os.path.exists('%s.bed' % ldin) and not os.path.exists('%s.bed' % ldout): # copy ldreduced to input for next time - for ext in ['bim','bed','fam']: - src = '%s.%s' % (ldin,ext) - dest = '%s.%s' % (ldout,ext) - shutil.copy(src,dest) - app.model.context.flush() --- a/tools/rgenetics/rgGLM.py Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgGLM.py Fri Mar 25 13:12:21 2011 -0400 @@ -95,6 +95,7 @@ outf.close() + def xformQassoc(resf='',outfname='',logf=None,twd='.'): """ plink.assoc.linear to gg file from the docs --- a/tools/rgenetics/rgGLM.xml Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgGLM.xml Fri Mar 25 13:12:21 2011 -0400 @@ -1,18 +1,15 @@ <tool id="rgGLM1" name="Linear Models:" version="0.2"> - <code file="listFiles.py"/> + <description>for genotype data</description><code file="rgGLM_code.py"/> - - <description>for genotype data</description> - <command interpreter="python"> rgGLM.py '$i.extra_files_path/$i.metadata.base_name' '$phef.extra_files_path/$phef.metadata.base_name' - "$title1" '$predvar' '$covar' '$out_file1' '$logf' '$i.metadata.base_name' + "$title" '$predvar' '$covar' '$out_file1' '$logf' '$i.metadata.base_name' '$inter' '$cond' '$gender' '$mind' '$geno' '$maf' '$logistic' '$gffout' </command><inputs><page> - <param name='title1' label='Title for outputs' type='text' value='GLM' size="80" /> + <param name='title' label='Title for outputs' type='text' value='GLM' size="80" /><param name="i" type="data" format="pbed" label="Genotype file" size="80" /><param name="phef" type="data" format="pphe" label="Phenotype file" size="80" help="Dependent variable and covariates will be chosen from this file on the next page"/> @@ -41,9 +38,9 @@ </inputs><outputs> - <data format="tabular" name="out_file1" /> - <data format="txt" name="logf" /> - <data format="gff" name="gffout" /> + <data format="tabular" name="out_file1" label="${title}_rgGLM.xls"/> + <data format="txt" name="logf" label="${title}_rgGLMlog.txt" /> + <data format="gff" name="gffout" label="${title}_rgGLM.gff"/></outputs><tests><test> @@ -59,7 +56,7 @@ <composite_data value='tinywga.pphe' /><edit_attributes type='name' value='tinywga' /></param> - <param name='title1' value='rgGLMtest1' /> + <param name='title' value='rgGLMtest1' /><param name='predvar' value='c1' /><param name='covar' value='None' /><param name='inter' value='0' /> @@ -124,18 +121,26 @@ **Attribution** -This tool allows you to control settings for models using Plink linear models. So, we rely on the author (Shaun Purcell) -for the documentation you need specific to those settings - they are very nicely documented at -http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#glm +This Galaxy tool relies on Plink (see Plinksrc_) to test GLM models. + +So, we rely on the author (Shaun Purcell) for the documentation you need specific to those settings - they are very nicely documented - see +DOC_ Tool and Galaxy datatypes originally designed and written for the Rgenetics series of whole genome scale statistical genetics tools by ross lazarus (ross.lazarus(a)gmail.com) -supported by NIH grant -Shaun Purcell created and maintains Plink -Please acknowledge your use of this tool, Galaxy and Plink in your publications and let -us know so we can keep track. These tools all rely on highly competitive grant funding -so your letting us know about publications is important to our ongoing support. +Copyright Ross Lazarus March 2007 +This Galaxy wrapper is released licensed under the LGPL_ but is about as useful as a chocolate teapot without Plink which is GPL. + +I'm no lawyer, but it looks like you got GPL if you use this software. Good luck. + +.. _Plinksrc: http://pngu.mgh.harvard.edu/~purcell/plink/ + +.. _LGPL: http://www.gnu.org/copyleft/lesser.html + +.. _DOC: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#glm + </help></tool> + --- a/tools/rgenetics/rgGLM_code.py Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgGLM_code.py Fri Mar 25 13:12:21 2011 -0400 @@ -2,17 +2,6 @@ import os,string,time from galaxy import datatypes -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - -def get_out_formats(): - """return options for formats""" - dat = [['ucsc track','wig'],['ucsc genome graphs','gg'],['tab delimited','xls']] - dat = [(x[0],x[1],False) for x in dat] - dat.reverse() - return dat def get_phecols(phef='',selectOne=0): """return column names """ @@ -32,28 +21,3 @@ res = [('None','no phenotype columns found',False),] return res - -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - """Sets the name of the data""" - killme=string.punctuation+string.whitespace - trantab = string.maketrans(killme,'_'*len(killme)) - job_name = param_dict.get( 'title1', 'GLM' ) - job_name = job_name.encode().translate(trantab) - outxls = ['tabular','%s_GLM.xls' % job_name] - logtxt = ['txt','%s_GLM_log.txt' % job_name] - ggout = ['gg','%s_GLM_topTable.gff' % job_name] - lookup={} - lookup['out_file1'] = outxls - lookup['logf'] = logtxt - lookup['gffout'] = ggout - info = '%s GLM output by rgGLM created at %s' % (job_name,timenow()) - for name in lookup.keys(): - data = out_data[name] - data_type,newname = lookup.get(name,(None,None)) - if data_type <> None: - data.name = newname - data.info = info - out_data[name] = data - else: - print >> stdout,'no output matching %s in exec after hook for rgGLM' % name - app.model.context.flush() --- a/tools/rgenetics/rgGRR.xml Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgGRR.xml Fri Mar 25 13:12:21 2011 -0400 @@ -1,20 +1,19 @@ <tool id="rgGRR1" name="GRR:"> - <code file="rgGRR_code.py"/><description>Pairwise Allele Sharing</description><command interpreter="python"> rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name" - '$out_file1' '$out_file1.files_path' "$title1" '$n' '$Z' + '$out_file1' '$out_file1.files_path' "$title" '$n' '$Z' </command><inputs><param name="i" type="data" label="Genotype data file from your current history" format="ldindep" /> - <param name='title1' type='text' size="80" value='rgGRR' label="Title for this job"/> + <param name='title' type='text' size="80" value='rgGRR' label="Title for this job"/><param name="n" type="integer" label="N snps to use (0=all)" value="5000" /><param name="Z" type="float" label="Z score cutoff for outliers (eg 2)" value="6" help="2 works but for very large numbers of pairs, you might want to see less than 5%" /></inputs><outputs> - <data format="html" name="out_file1" /> + <data format="html" name="out_file1" label="${title}_rgGRR.html"/></outputs><tests> @@ -26,7 +25,7 @@ <composite_data value='tinywga.fam' /><edit_attributes type='name' value='tinywga' /></param> - <param name='title1' value='rgGRRtest1' /> + <param name='title' value='rgGRRtest1' /><param name='n' value='100' /><param name='Z' value='6' /><param name='force' value='true' /> --- a/tools/rgenetics/rgGRR_code.py Thu Mar 24 20:29:40 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -from galaxy import datatypes,model -import sys,time,string,os,shutil - -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - """Sets the name of the html output file - """ - killme = string.punctuation + string.whitespace - trantab = string.maketrans(killme,'_'*len(killme)) - job_name = param_dict.get( 'title1', 'rgGRR' ) - job_name = job_name.encode() - newname = '%s.html' % job_name.translate(trantab) - indatname = inp_data['i'].name - info = '%s Mean allele sharing on %s at %s' % (job_name,indatname,timenow()) - ofname = 'out_file1' - data = out_data[ofname] - data.name = newname - data.info = info - out_data[ofname] = data - fromdir = data.extra_files_path - indat = inp_data['i'] - indatname = indat.name - base_name = indat.metadata.base_name - todir = indat.extra_files_path # where the ldreduced stuff should be - ldfname = '%s_INDEP_THIN' % base_name # we store ld reduced and thinned data - ldout = os.path.join(todir,ldfname) - ldin = os.path.join(fromdir,ldfname) - if os.path.exists('%s.bed' % ldin) and not os.path.exists('%s.bed' % ldout): # copy ldreduced to input for next time - for ext in ['bim','bed','fam']: - src = '%s.%s' % (ldin,ext) - dest = '%s.%s' % (ldout,ext) - shutil.copy(src,dest) - app.model.context.flush() --- a/tools/rgenetics/rgGTOOL.xml Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgGTOOL.xml Fri Mar 25 13:12:21 2011 -0400 @@ -1,6 +1,5 @@ <tool id="rgGTOOL1" name="Converter"> - <code file="listFiles.py"/> - <code file="rgGTOOL_code.py"/> + <description>from linkage format to SNPTEST Marchini files</description> --- a/tools/rgenetics/rgGTOOL_code.py Thu Mar 24 20:29:40 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -# for GTOOL linkage ped to marchini snptest format -from galaxy import datatypes - - -def exec_before_job(app, inp_data, out_data, param_dict, tool=None): - """Sets the name of the data""" - job_name = param_dict.get( 'o', 'Marchini' ) - log = ['txt','%s_rgGTOOL_report.log' % job_name,'txt'] - lookup={} - lookup['logf'] = log - for name in lookup.keys(): - data = out_data[name] - data_type,newname,ext = lookup[name] - data = app.datatypes_registry.change_datatype(data, data_type) - data.name = newname - out_data[name] = data - - - --- a/tools/rgenetics/rgHaploView.py Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgHaploView.py Fri Mar 25 13:12:21 2011 -0400 @@ -105,15 +105,8 @@ self.lf = file(self.log_file,'w') s = 'PATH=%s\n' % os.environ.get('PATH','?') self.lf.write(s) - - def setupRegions(self): - """ - """ - chromosome = '' - spos = epos = -9 - rslist = [] - rsdict = {} + def getRs(self): if self.region > '': useRs = [] useRsdict={} @@ -138,6 +131,20 @@ else: useRs = self.orslist.split() # galaxy replaces newlines with XX - go figure useRsdict = dict(zip(useRs,useRs)) + return useRs, useRsdict + + + def setupRegions(self): + """ + This turns out to be complex because we allow the user + flexibility - paste a list of rs or give a region. + In most cases, some subset has to be generated correctly before running Haploview + """ + chromosome = '' + spos = epos = -9 + rslist = [] + rsdict = {} + useRs,useRsdict = self.getRs() self.useTemp = False try: dfile = open(self.DATA_FILE, 'r') @@ -284,7 +291,60 @@ self.lf.write(s) print >> sys.stdout,s sys.exit(1) - + + def run(self,vcl): + """ + """ + p=subprocess.Popen(vcl,shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) + retval = p.wait() + self.lf.write('## executing %s returned %d\n' % (vcl,retval)) + + def plotHmPanels(self,ste): + """ + """ + sp = '%d' % (self.spos/1000.) # hapmap wants kb + ep = '%d' % (self.epos/1000.) + fnum=0 + for panel in self.hmpanels: + if panel > '' and panel.lower() <> 'none': # in case someone checks that option too :) + ptran = panel.strip() + ptran = ptran.replace('+','_') + fnum += 1 # preserve an order or else we get sorted + vcl = [javabin,'-jar',self.hvbin,'-n','-memory','%d' % self.memSize, + '-chromosome',self.chromosome, '-panel',panel.strip(), + '-hapmapDownload','-startpos',sp,'-endpos',ep, + '-ldcolorscheme',self.ldType] + if self.minMaf: + vcl += ['-minMaf','%f' % self.minMaf] + if self.maxDist: + vcl += ['-maxDistance',self.maxDist] + if self.hiRes: + vcl.append('-png') + else: + vcl.append('-compressedpng') + if self.infotrack: + vcl.append('-infoTrack') + p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=ste,stdout=self.lf) + retval = p.wait() + inpng = 'Chromosome%s%s.LD.PNG' % (self.chromosome,panel) + inpng = inpng.replace(' ','') # mysterious spaces! + outpng = '%d_HapMap_%s_%s.png' % (fnum,ptran,self.chromosome) + # hack for stupid chb+jpt + outpng = outpng.replace(' ','') + tmppng = '%s.tmp.png' % self.title + tmppng = tmppng.replace(' ','') + outpng = os.path.split(outpng)[-1] + vcl = [self.convert, '-resize 800x400!', inpng, tmppng] + self.run(' '.join(vcl)) + s = "text 10,300 'HapMap %s'" % ptran.strip() + vcl = [self.convert, '-pointsize 25','-fill maroon', + '-draw "%s"' % s, tmppng, outpng] + self.run(' '.join(vcl)) + try: + os.remove(os.path.join(self.outfpath,tmppng)) + except: + pass + def doPlots(self): """ """ @@ -308,15 +368,9 @@ vcl += ['-chromosome',self.chromosome] if self.infotrack: vcl.append('-infoTrack') - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=ste,stdout=self.lf) - retval = p.wait() - s = '## executing %s returned %d\n' % (' '.join(vcl),retval) - self.lf.write(s) + self.run(' '.join(vcl)) vcl = [self.mogrify, '-resize 800x400!', '*.PNG'] - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) - retval = p.wait() - s = '## executing %s returned %d\n' % (' '.join(vcl),retval) - self.lf.write(s) + self.run(' '.join(vcl)) inpng = '%s.LD.PNG' % DATA_FILE # stupid but necessary - can't control haploview name mangle inpng = inpng.replace(' ','') inpng = os.path.split(inpng)[-1] @@ -326,89 +380,29 @@ outpng = outpng.replace(' ','') outpng = os.path.split(outpng)[-1] vcl = [self.convert, '-resize 800x400!', inpng, tmppng] - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) - retval = p.wait() - s = '## executing %s returned %d\n' % (' '.join(vcl),retval) - self.lf.write(s) + self.run(' '.join(vcl)) s = "text 10,300 '%s'" % self.title[:40] vcl = [self.convert, '-pointsize 25','-fill maroon', '-draw "%s"' % s, tmppng, outpng] - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) - retval = p.wait() - s = '## executing %s returned %d\n' % (' '.join(vcl),retval) - self.lf.write(s) + self.run(' '.join(vcl)) try: os.remove(os.path.join(self.outfpath,tmppng)) except: pass # label all the plots then delete all the .PNG files before munging fnum=1 if self.hmpanels: - sp = '%d' % (self.spos/1000.) # hapmap wants kb - ep = '%d' % (self.epos/1000.) - for panel in self.hmpanels: - if panel > '' and panel.lower() <> 'none': # in case someone checks that option too :) - ptran = panel.strip() - ptran = ptran.replace('+','_') - fnum += 1 # preserve an order or else we get sorted - vcl = [javabin,'-jar',self.hvbin,'-n','-memory','%d' % self.memSize, - '-chromosome',self.chromosome, '-panel',panel.strip(), - '-hapmapDownload','-startpos',sp,'-endpos',ep, - '-ldcolorscheme',self.ldType] - if self.minMaf: - vcl += ['-minMaf','%f' % self.minMaf] - if self.maxDist: - vcl += ['-maxDistance',self.maxDist] - if self.hiRes: - vcl.append('-png') - else: - vcl.append('-compressedpng') - if self.infotrack: - vcl.append('-infoTrack') - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=ste,stdout=self.lf) - retval = p.wait() - inpng = 'Chromosome%s%s.LD.PNG' % (self.chromosome,panel) - inpng = inpng.replace(' ','') # mysterious spaces! - outpng = '%d_HapMap_%s_%s.png' % (fnum,ptran,self.chromosome) - # hack for stupid chb+jpt - outpng = outpng.replace(' ','') - tmppng = '%s.tmp.png' % self.title - tmppng = tmppng.replace(' ','') - outpng = os.path.split(outpng)[-1] - vcl = [self.convert, '-resize 800x400!', inpng, tmppng] - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) - retval = p.wait() - s = '## executing %s returned %d\n' % (' '.join(vcl),retval) - self.lf.write(s) - s = "text 10,300 'HapMap %s'" % ptran.strip() - vcl = [self.convert, '-pointsize 25','-fill maroon', - '-draw "%s"' % s, tmppng, outpng] - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) - retval = p.wait() - s = '## executing %s returned %d\n' % (' '.join(vcl),retval) - self.lf.write(s) - try: - os.remove(os.path.join(self.outfpath,tmppng)) - except: - pass + self.plotHmPanels(ste) nimages = len(glob.glob(os.path.join(self.outfpath,'*.png'))) # rely on HaploView shouting - PNG @! self.lf.write('### nimages=%d\n' % nimages) if nimages > 0: # haploview may fail? vcl = '%s -format pdf -resize 800x400! *.png' % self.mogrify - p=subprocess.Popen(vcl,shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) - retval = p.wait() - self.lf.write('## executing %s returned %d\n' % (vcl,retval)) + self.run(vcl) vcl = '%s *.pdf --fitpaper true --outfile alljoin.pdf' % self.pdfjoin - p=subprocess.Popen(vcl,shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) - retval = p.wait() - self.lf.write('## executing %s returned %d\n' % (vcl,retval)) + self.run(vcl) vcl = '%s alljoin.pdf --nup 1x%d --outfile allnup.pdf' % (self.pdfnup,nimages) - p=subprocess.Popen(vcl,shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) - retval = p.wait() - self.lf.write('## executing %s returned %d\n' % (vcl,retval)) + self.run(vcl) vcl = '%s -resize x300 allnup.pdf allnup.png' % (self.convert) - p=subprocess.Popen(vcl,shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) - retval = p.wait() - self.lf.write('## executing %s returned %d\n' % (vcl,retval)) + self.run(vcl) ste.close() # temp file used to catch haploview blather hblather = open(blog,'r').readlines() # to catch the blather os.unlink(blog) @@ -417,6 +411,10 @@ self.lf.write(''.join(hblather)) self.lf.write('\n') self.lf.close() + + def writeHtml(self): + """ + """ flist = glob.glob(os.path.join(self.outfpath, '*')) flist.sort() ts = '!"#$%&\'()*+,-/:;<=>?@[\\]^_`{|}~' + string.whitespace @@ -509,6 +507,7 @@ sys.exit(1) ld = ldPlot(argv = sys.argv) ld.doPlots() + ld.writeHtml() --- a/tools/rgenetics/rgHaploView_code.py Thu Mar 24 20:29:40 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ -from galaxy import app -import galaxy.util,string,os,glob,time - -librepos = '/usr/local/galaxy/data/rg/library' -myrepos = '/home/rerla/galaxy' - - -#Provides Upload tool with access to list of available builds - -builds = [] -#Read build names and keys from galaxy.util -for dbkey, build_name in galaxy.util.dbnames: - builds.append((build_name,dbkey,False)) - -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - -#Return available builds -def get_available_builds(defval='hg18'): - for i,x in enumerate(builds): - if x[1] == defval: - x = list(x) - x[2] = True - builds[i] = tuple(x) - return builds - -#return available datasets for build -def get_available_data( file_type_dir, build='hg18' ): - #we need to allow switching of builds, and properly set in post run hook - import_files = [('Use the History file chosen below','',True),] - flist = glob.glob(os.path.join(librepos,file_type_dir,'*.ped')) - maplist = glob.glob(os.path.join(librepos,file_type_dir,'*.map')) - maplist = [os.path.splitext(x)[0] for x in maplist] # get unique filenames - mapdict = dict(zip(maplist,maplist)) - flist = [os.path.splitext(x)[0] for x in flist] # get unique filenames - flist = list(set(flist)) # remove dupes - flist = [x for x in flist if mapdict.get(x,None)] - flist.sort() - for i, data in enumerate( flist ): - #import_files.append( (os.path.split(data)[-1], os.path.split(data)[-1], False) ) - import_files.append((data,data, False) ) - if len(import_files) < 1: - import_files = [('No %s data available - please choose a History file below' - % file_type_dir,'',True),] - return import_files - -def get_available_outexts(uid): - userId = uid - print 'userId=',userId - flib = os.path.join(librepos,userId,'fped') - plib = os.path.join(librepos,userId,'lped') - e = [('Fbat style (header row has marker names)',flib,False),('Linkage style (separate .map file)',plib,True)] - return e - -def getcols(fname="/usr/local/galaxy/data/camp2007/camp2007.xls"): - """return column names other than chr offset as a select list""" - head = open(fname,'r').next() - c = head.strip().split() - res = [(cname,'%d' % n,False) for n,cname in enumerate(c)] - for i in range(4): - x,y,z = res[i] - res[i] = (x,y,True) # set first couple as selected - return res - - -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - """Sets the name of the html output file - that's all we need - for a html file result set - """ - ts = '%s%s' % (string.punctuation,string.whitespace) - ptran = string.maketrans(ts,'_'*len(ts)) - job_name = param_dict.get( 'title', 'LD_Plot' ) - job_name = job_name.encode().translate(ptran) - ofname = 'out_file1' - data = out_data[ofname] - newname = job_name - data.name = '%s.html' % newname - info = '%s created by rgHaploView at %s' % (job_name,timenow()) - out_data[ofname] = data - app.model.context.flush() - - --- a/tools/rgenetics/rgLDIndep_code.py Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgLDIndep_code.py Fri Mar 25 13:12:21 2011 -0400 @@ -15,7 +15,7 @@ trantab = string.maketrans(killme,'_'*len(killme)) title = basename.encode().translate(trantab) info = '%s filtered by rgLDIndep.py at %s' % (title,timenow()) - #data.file_name = data.file_name + data.file_name = data.file_name data.metadata.base_name = title data.name = '%s.pbed' % title data.info = info --- a/tools/rgenetics/rgManQQ.xml Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgManQQ.xml Fri Mar 25 13:12:21 2011 -0400 @@ -44,9 +44,9 @@ <param name='grey' value='0' /><output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='60'><extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size" - delta = "10000"/> + delta = "20000"/><extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size" - delta = "10000" /> + delta = "20000" /><extra_files type="file" name='rgManQQtest1.R' value='rgtestouts/rgManQQ/rgManQQtest1.R' compare="diff" lines_diff="160"/></output></test> --- a/tools/rgenetics/rgPedSub.xml Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgPedSub.xml Fri Mar 25 13:12:21 2011 -0400 @@ -1,5 +1,4 @@ <tool id="rgPedSub1" name="Subset markers:"> - <code file="rgPedSub_code.py"/><description>region or rs list</description> @@ -44,7 +43,7 @@ </inputs><outputs> - <data format="lped" name="output1" metadata_source="input1"/> + <data format="lped" name="output1" metadata_source="input1" label="${title}.lped"/></outputs><configfiles> --- a/tools/rgenetics/rgPedSub_code.py Thu Mar 24 20:29:40 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,78 +0,0 @@ -from galaxy import app -import galaxy.util,string,os,glob,time - -#Provides Upload tool with access to list of available builds - -builds = [] -#Read build names and keys from galaxy.util -for dbkey, build_name in galaxy.util.dbnames: - builds.append((build_name,dbkey,False)) - -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - - -#Return available builds -def get_available_builds(defval='hg18'): - for i,x in enumerate(builds): - if x[1] == defval: - x = list(x) - x[2] = True - builds[i] = tuple(x) - return builds - -#return available datasets for build -def get_available_data( file_type_dir, build='hg18' ): - #we need to allow switching of builds, and properly set in post run hook - import_files = [] # [('Use the History file chosen below','',False),] - flist = glob.glob(os.path.join(librepos,file_type_dir,'*.ped')) - flist = [os.path.splitext(x)[0] for x in flist] # get unique filenames - flist = list(set(flist)) # remove dupes - flist.sort() - for i, data in enumerate( flist ): - #import_files.append( (os.path.split(data)[-1], os.path.split(data)[-1], False) ) - import_files.append((os.path.split(data)[-1],data, False) ) - if len(import_files) < 1: - import_files.append(('No %s data available - please choose a History file instead' - % file_type_dir,'',True)) - return import_files - -def get_available_outexts(uid): - userId = uid - print 'userId=',userId - flib = os.path.join(librepos,userId,'fped') - plib = os.path.join(librepos,userId,'lped') - e = [('Fbat style (header row has marker names)',flib,False),('Linkage style (separate .map file)',plib,True)] - return e - -def getcols(fname="/usr/local/galaxy/data/camp2007/camp2007.xls"): - """return column names other than chr offset as a select list""" - head = open(fname,'r').next() - c = head.strip().split() - res = [(cname,'%d' % n,False) for n,cname in enumerate(c)] - for i in range(4): - x,y,z = res[i] - res[i] = (x,y,True) # set first couple as selected - return res - - -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - """from rgConvert_code - """ - name,data = out_data.items()[0] - iname,idata = inp_data.items()[0] - basename = idata.metadata.base_name - title = param_dict.get( 'title', 'Lped Subset' ) - title = title.encode() # make str - unicode is evil here - killme = string.punctuation + string.whitespace - trantab = string.maketrans(killme,'_'*len(killme)) - title = title.translate(trantab) - info = '%s filtered by rgPedSub.py at %s' % (title,timenow()) - #data.file_name = data.file_name - data.metadata.base_name = basename - data.name = '%s.lped' % title - data.info = info - app.model.context.flush() - --- a/tools/rgenetics/rgQC.xml Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgQC.xml Fri Mar 25 13:12:21 2011 -0400 @@ -1,21 +1,20 @@ <tool id="rgQC1" name="QC reports:"> - <code file="rgQC_code.py"/><description>Marker and Subject measures</description><command interpreter="python"> - rgQC.py -i '$input_file.extra_files_path/$input_file.metadata.base_name' -o "$out_prefix" + rgQC.py -i '$input_file.extra_files_path/$input_file.metadata.base_name' -o "$title" -s '$html_file' -p '$html_file.files_path' </command><inputs><param name="input_file" type="data" label="RGenetics genotype file in compressed Plink format" size="80" format="pbed" /> - <param name="out_prefix" size="80" type="text" value="RgQC report" label="Descriptive report title"/> + <param name="title" size="80" type="text" value="RgQC report" label="Descriptive report title"/></inputs><outputs> - <data format="html" name="html_file" metadata_source="input_file"/> + <data format="html" name="html_file" metadata_source="input_file" label="${title}.html"/></outputs><tests> @@ -27,9 +26,9 @@ <composite_data value='tinywga.fam' /><edit_attributes type='name' value='tinywga' /></param> - <param name='out_prefix' value='rgQCtest1' /> - <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='280'> - <extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="sim_size" delta = "5000"/> + <param name='title' value='rgQCtest1' /> + <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='300'> + <extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="sim_size" delta = "100000"/><extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="15"/><extra_files type="file" name='tinywga.frq' value="rgtestouts/rgQC/tinywga.frq" compare="diff" /><extra_files type="file" name='tinywga.het' value="rgtestouts/rgQC/tinywga.het" compare="diff" lines_diff="90"/> @@ -38,7 +37,7 @@ <extra_files type="file" name='tinywga.imiss' value="rgtestouts/rgQC/tinywga.imiss" compare="diff" /><extra_files type="file" name='tinywga.lmendel' value="rgtestouts/rgQC/tinywga.lmendel" compare="diff" /><extra_files type="file" name='tinywga.lmiss' value="rgtestouts/rgQC/tinywga.lmiss" compare="diff" /> - <extra_files type="file" name='tinywga_All_3x3.pdf' value="rgtestouts/rgQC/tinywga_All_3x3.pdf" compare="sim_size" delta="5000"/> + <extra_files type="file" name='tinywga_All_3x3.pdf' value="rgtestouts/rgQC/tinywga_All_3x3.pdf" compare="sim_size" delta="100000"/><extra_files type="file" name='ldp_tinywga.bed' value="rgtestouts/rgQC/ldp_tinywga.bed" compare="diff" lines_diff="10" /><extra_files type="file" name='ldp_tinywga.bim' value="rgtestouts/rgQC/ldp_tinywga.bim" compare="sim_size" delta="1000" /><extra_files type="file" name='ldp_tinywga.fam' value="rgtestouts/rgQC/ldp_tinywga.fam" compare="diff" /> @@ -46,9 +45,9 @@ <extra_files type="file" name='Ranked_Marker_HWE.xls' value="rgtestouts/rgQC/Ranked_Marker_HWE.xls" compare="diff" /><extra_files type="file" name='Ranked_Marker_MAF.xls' value="rgtestouts/rgQC/Ranked_Marker_MAF.xls" compare="diff" /><extra_files type="file" name='Ranked_Marker_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Marker_Missing_Genotype.xls" compare="diff" lines_diff="5"/> - <extra_files type="file" name='Ranked_Subject_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls" compare="diff" lines_diff="10"/> + <extra_files type="file" name='Ranked_Subject_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls" compare="diff" lines_diff="40"/><extra_files type="file" name='tinywga_fracmiss_cum.jpg' value="rgtestouts/rgQC/tinywga_fracmiss_cum.jpg" compare="sim_size" delta = "20000"/> - <extra_files type="file" name='tinywga_fracmiss_cum.pdf' value="rgtestouts/rgQC/tinywga_fracmiss_cum.pdf" compare="sim_size" delta = "1000"/> + <extra_files type="file" name='tinywga_fracmiss_cum.pdf' value="rgtestouts/rgQC/tinywga_fracmiss_cum.pdf" compare="sim_size" delta = "100000"/></output></test></tests> --- a/tools/rgenetics/rgQC_code.py Thu Mar 24 20:29:40 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -""" -# after running the qc, need to rename various output files - <data format="html" name="html_file" /> - <data format="txt" name="log_file" parent="html_file" /> - <data format="tabular" name="marker_file" parent="html_file" /> - <data format="tabular" name="subject_file" parent="html_file" /> - <data format="tabular" name="freq_file" parent="html_file" /> - </outputs> -""" -from galaxy import datatypes,model -import sys,time - -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - - -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - """Change data file names - - """ - job_name = param_dict.get( 'out_prefix', 'rgQCdefault' ) - html = ['html','%s.html' % job_name] - lookup={} - lookup['html_file'] = html - info = '%s QC report by rgQC at %s' % (job_name,timenow()) - for aname in lookup.keys(): - data = out_data[aname] - data_type,newname = lookup[aname] - data = app.datatypes_registry.change_datatype(data, data_type) - data.name = newname - data.info = info - out_data[aname] = data - app.model.context.flush() - - - --- a/tools/rgenetics/rgQQ.xml Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgQQ.xml Fri Mar 25 13:12:21 2011 -0400 @@ -4,14 +4,14 @@ <description>for p values from an analysis </description><command interpreter="python"> - rgQQ.py "$input1" "$name" "$sample" "$cols" "$allqq" "$height" "$width" "$logtrans" "$allqq.id" "$__new_file_path__" + rgQQ.py "$input1" "$title" "$sample" "$cols" "$allqq" "$height" "$width" "$logtrans" "$allqq.id" "$__new_file_path__" </command><inputs><page><param name="input1" type="data" label="Choose the History dataset containing p values to QQ plot" size="80" format="tabular" help="Dataset missing? See Tip below" /> - <param name="name" type="text" size="80" label = "Descriptive title for QQ plot" value="QQ" /> + <param name="title" type="text" size="80" label = "Descriptive title for QQ plot" value="QQ" /><param name="logtrans" type="boolean" label = "Use a log scale - recommended for p values in range 0-1.0" truevalue="true" falsevalue="false"/> @@ -28,13 +28,13 @@ </inputs><outputs> - <data format="pdf" name="allqq" /> + <data format="pdf" name="allqq" label="${title}.html"/></outputs><tests><test><param name='input1' value='tinywga.pphe' /> - <param name='name' value="rgQQtest1" /> + <param name='title' value="rgQQtest1" /><param name='logtrans' value="false" /><param name='sample' value='1.0' /><param name='height' value='8' /> --- a/tools/rgenetics/rgQQ_code.py Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgQQ_code.py Fri Mar 25 13:12:21 2011 -0400 @@ -48,25 +48,3 @@ else: columns = [('?','?',False),] return columns - - -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - """Sets the name of the data - <outputs> - <data format="pdf" name="allqq" /> - <data format="pdf" name="lowqq" parent="allqq"/> - </outputs> - """ - job_name = param_dict.get( 'name', 'My rgQQplot' ) - killme = string.punctuation + string.whitespace - trantab = string.maketrans(killme,'_'*len(killme)) - newname = '%s.pdf' % job_name.translate(trantab) - lookup={} - lookup['allqq'] = newname - for aname in lookup.keys(): - data = out_data[aname] - newname = lookup[aname] - data.name = newname - out_data[aname] = data - app.model.context.flush() - --- a/tools/rgenetics/rgRegion.xml Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgRegion.xml Fri Mar 25 13:12:21 2011 -0400 @@ -1,24 +1,20 @@ <tool id="rgRegion" name="Subset:"> - <code file="rgRegion_code.py"/> - <code file="listFiles.py"/> - <description>genotypes from genomic region</description><command interpreter="python"> - rgRegion.py $infile $r $tag $out_file1 + rgRegion.py $infile $r $title $out_file1 </command><inputs><page><param name="infile" type="data" format="lped" label="Linkage ped genotype file name from current history" size="80"/> + <param name="title" type="text" size="80" label="Title for output files" optional="true" + help="Descriptive title for new genotype/map files" value="RGRegion" /><param name="r" type="text" label="Region" help="Cut and paste a UCSC browser region" size="80" value="chr9:119,506,000-122,518,000"/><param name="rslist" type="text" area="true" label="List of rs numbers" help="Type (or cut and paste) a space or newline separated list of rs numbers" size="5x20"/> - - <param name="tag" type="text" label="Output file name" value="My_favourite_region" size="80"/> - <param name="outformat" type="select" label="Output file format" dynamic_options="get_rgRegionOutFormats()" size="80"/> - <param name="dbkey" type="hidden" value="hg18" /> + <param name="outformat" type="select" label="Output file format" dynamic_options="get_rgRegionOutFormats()" size="80"/></page> @@ -26,7 +22,7 @@ </inputs><outputs> - <data format="lped" name="out_file1" /> + <data format="lped" name="out_file1" label="${title}.lped" metadata_source=infile /></outputs><help> --- a/tools/rgenetics/rgRegion_code.py Thu Mar 24 20:29:40 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,47 +0,0 @@ -from galaxy import app -import galaxy.util,string - -librepos = '/usr/local/galaxy/data/rg' -myrepos = '/home/rerla/galaxy' -marchinirepos = '/usr/local/galaxy/data/rg/snptest' - -#Provides Upload tool with access to list of available builds - - -def get_rgRegionOutFormats(): - """return options for formats""" - dat = [['ucsc track','wig',False],['Strict genome graphs (rs+floats)','gg',True],['tab delimited','xls',False]] - dat = [(x[0],x[1],x[2]) for x in dat] - return dat - - -def get_phecols(phef): - """return column names """ - head = open(phef,'r').next() - c = head.strip().split() - res = [(cname,cname,False) for cname in c] - x,y,z = res[2] # 0,1 = fid,iid - res[2] = (x,y,True) # set second selected - return res - - -def getAllcols(fname="/usr/local/galaxy/data/camp2007/camp2007.xls",outformat='gg'): - """return column names other than chr offset as a select list""" - head = open(fname,'r').next() - c = head.strip().split() - res = [(cname,'%d' % n,True) for n,cname in enumerate(c)] - - return res - - -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - """Sets the name of the data""" - data_name = param_dict.get( 'tag', 'My region' ) - outformat = param_dict.get( 'outformat', 'gg' ) - outfile = param_dict.get( 'outfile1', 'lped' ) - for name, data in out_data.items(): - if name == 'tag': - data = app.datatypes_registry.change_datatype(data, outformat) - data.name = data_name - out_data[name] = data - --- a/tools/rgenetics/rgTDT.py Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgTDT.py Fri Mar 25 13:12:21 2011 -0400 @@ -26,6 +26,7 @@ verbose = False + def makeGFF(resf='',outfname='',logf=None,twd='.',name='track name',description='track description',topn=1000): """ score must be scaled to 0-1000 @@ -84,7 +85,7 @@ outres = [] # need to resort into chrom offset order for i,lrow in enumerate(resfl): chrom,snp,offset,p, = [lrow[x] for x in wewant] - gff = ('chr%s' % chrom,'rgGLM','variation','%d' % (int(offset)-halfwidth), + gff = ('chr%s' % chrom,'rgTDT','variation','%d' % (int(offset)-halfwidth), '%d' % (int(offset)+halfwidth),p,'.','.','%s logp=%1.2f' % (snp,pvals[i])) outres.append(gff) outres = [(x[0],int(x[3]),x) for x in outres] # decorate --- a/tools/rgenetics/rgTDT.xml Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgTDT.xml Fri Mar 25 13:12:21 2011 -0400 @@ -1,23 +1,21 @@ <tool id="rgTDT1" name="Transmission Distortion:"> - <code file="rgTDT_code.py"/> - <description>for family data</description><command interpreter="python"> - rgTDT.py -i '$i.extra_files_path/$i.metadata.base_name' -o '$title1' + rgTDT.py -i '$i.extra_files_path/$i.metadata.base_name' -o '$title' -r '$out_file1' -l '$logf' -g '$gffout' </command><inputs><param name="i" type="data" label="Genotypes for analysis from your current history datasets" size="132" format="pbed" /> - <param name='title1' type='text' value='rgTDT' size="80"/> + <param name='title' type='text' value='rgTDT' label="Title for the output to remind you what you did" size="80"/></inputs><outputs> - <data format="tabular" name="out_file1" /> - <data format="gff" name="gffout" /> - <data format="txt" name="logf" /> + <data format="tabular" name="out_file1" label="${title}_rgTDT.xls"/> + <data format="gff" name="gffout" label="${title}_rgTDT.gff"/> + <data format="txt" name="logf" label="${title}_rgTDTlog.txt"/></outputs><tests> @@ -29,7 +27,7 @@ <composite_data value='tinywga.fam' /><edit_attributes type='name' value='tinywga' /></param> - <param name='title1' value='rgTDTtest1' /> + <param name='title' value='rgTDTtest1' /><output name='out_file1' file='rgTDTtest1_TDT.xls' ftype='tabular' compare="diff"/><output name='gffout' file='rgTDTtest1_TDT_topTable.gff' ftype='gff' compare="diff" /><output name='logf' file='rgTDTtest1_TDT_log.txt' ftype='txt' lines_diff='79'/> @@ -81,5 +79,30 @@ one with a header. Fortunately excel is dumb enough to open these without much protest. +---- + +.. class:: infomark + +**Attribution** + +This Galaxy tool relies on Plink (see Plinksrc_) to test TDT models. + +So, we rely on the author (Shaun Purcell) for the documentation you need specific to those settings - they are very nicely documented - see +DOC_ + +Tool and Galaxy datatypes originally designed and written for the Rgenetics +series of whole genome scale statistical genetics tools by ross lazarus (ross.lazarus(a)gmail.com) + +Copyright Ross Lazarus March 2007 +This Galaxy wrapper is released licensed under the LGPL_ but is about as useful as a chocolate teapot without Plink which is GPL. + +I'm no lawyer, but it looks like you got GPL if you use this software. Good luck. + +.. _Plinksrc: http://pngu.mgh.harvard.edu/~purcell/plink/ + +.. _LGPL: http://www.gnu.org/copyleft/lesser.html + +.. _DOC: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#tdt + </help></tool> --- a/tools/rgenetics/rgTDT_code.py Thu Mar 24 20:29:40 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ -# before running the qc, need to rename various output files -import time,string - -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - -def get_out_formats(): - """return options for formats""" - dat = [['ucsc genome graphs','gg',True],['ucsc track','wig',False],['tab delimited','xls',False]] - dat = [(x[0],x[1],x[2]) for x in dat] - return dat - - -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - """Sets the name of the data - <command interpreter="python2.4"> - rgTDT.py -i $i.extra_files_path/$i.metadata.base_name -o $title -f $outformat -r $out_file1 -l $logf - </command> - - """ - dbk = param_dict.get('dbkey','hg18') - job_name = param_dict.get( 'title1', 'rgTDTtest1' ) - killme=string.punctuation+string.whitespace - trantab = string.maketrans(killme,'_'*len(killme)) - job_name = job_name.encode().translate(trantab) - outxls = ['tabular','%s_TDT.xls' % job_name] - logtxt = ['txt','%s_TDT_log.txt' % job_name] - ggout = ['gg','%s_TDT_topTable.gff' % job_name] - lookup={} - lookup['out_file1'] = outxls - lookup['logf'] = logtxt - lookup['gffout'] = ggout - info = 'rgTDT run at %s' % timenow() - for name in lookup.keys(): - data = out_data[name] - data_type,newname = lookup[name] - data.name = newname - data.info = info - data.dbkey = dbk - out_data[name] = data - app.model.context.flush() --- a/tools/rgenetics/rgfakePed.xml Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgfakePed.xml Fri Mar 25 13:12:21 2011 -0400 @@ -1,14 +1,13 @@ <tool id="rgfakePed1" name="Null genotypes"><description>for testing</description> - <code file="rgfakePed_code.py"/> - <command interpreter="python">rgfakePed.py --title '$title1' + <command interpreter="python">rgfakePed.py --title '$title' -o '$out_file1' -p '$out_file1.files_path' -c '$ncases' -n '$ntotal' -s '$nsnp' -w '$lowmaf' -v '$missingValue' -l '$outFormat' -d '$mafdist' -m '$missingRate' -M '$mendelRate' </command><inputs><page> - <param name="title1" + <param name="title" type="text" help="Name for outputs from this job" label="Descriptive short name"/> @@ -60,11 +59,11 @@ </inputs><outputs> - <data format="lped" name="out_file1" /> + <data format="lped" name="out_file1" label="${title}.lped" /></outputs><tests><test> - <param name='title1' value='rgfakePedtest1' /> + <param name='title' value='rgfakePedtest1' /><param name="ntotal" value="40" /><param name="ncases" value="20" /><param name="nsnp" value="10" /> --- a/tools/rgenetics/rgfakePed_code.py Thu Mar 24 20:29:40 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ -import os, string, time -from galaxy import datatypes -from galaxy import app -import galaxy.util - -#Provides Upload tool with access to list of available builds -repospath = '/usr/local/galaxy/data/rg' -builds = [] -#Read build names and keys from galaxy.util -for dbkey, build_name in galaxy.util.dbnames: - builds.append((build_name,dbkey,False)) - -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - -#Return available builds -def get_available_builds(defval='hg18'): - for i,x in enumerate(builds): - if x[1] == defval: - x = list(x) - x[2] = True - builds[i] = tuple(x) - return builds - -# Create link to files here -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - base_name = param_dict.get( 'title1', 'Null_Genotypes' ) - base_name = base_name.encode() - outFormat = param_dict.get('outFormat','P') - s = string.whitespace + string.punctuation - ptran = string.maketrans(s,'_'*len(s)) - base_name = base_name.translate(ptran) - pname = "out_file1" - lookup = {'L':('linkped','lped'),'F':('FBAT','fped')} - # /usr/local/galaxy/data/rg/1/lped/ - info = 'Null phenotypes created by rgfakePhe at %s' % timenow() - data = out_data[pname] - ftype,pext = lookup[outFormat] - data.name = '%s.%s' % (base_name,pext) # that's how they've been named in rgfakePhe.py - data.change_datatype(pext) - #data.file_name = data.file_name - data.metadata.base_name = base_name - data.readonly = True - out_data[pname] = data - app.model.context.flush() - - - - - - --- a/tools/rgenetics/rgfakePhe_code.py Thu Mar 24 20:29:40 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -# before running the qc, need to rename various output files -import os, string, time -from galaxy import datatypes -from galaxy import app -import galaxy.util - -#Provides Upload tool with access to list of available builds -repospath = '/usr/local/galaxy/data/rg' -builds = [] -#Read build names and keys from galaxy.util -for dbkey, build_name in galaxy.util.dbnames: - builds.append((build_name,dbkey,False)) - -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - -#Return available builds -def get_available_builds(defval='hg18'): - for i,x in enumerate(builds): - if x[1] == defval: - x = list(x) - x[2] = True - builds[i] = tuple(x) - return builds - -# Create link to files here -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - base_name = param_dict.get( 'title1', 'Null_Phenotype' ) - base_name = base_name.encode() - info = 'Null phenotypes created by rgfakePhe at %s' % timenow() - s = string.whitespace + string.punctuation - ptran = string.maketrans(s,'_'*len(s)) - base_name = base_name.translate(ptran) - data = out_data['ppheout'] - data.name = '%s.phe' % (base_name) # that's how they've been named in rgfakePhe.py - #data.file_name = data.file_name - data.metadata.base_name = base_name - out_data['pheout'] = data - app.model.context.flush() - - - - - --- a/tools/rgenetics/rgutils.py Thu Mar 24 20:29:40 2011 -0400 +++ b/tools/rgenetics/rgutils.py Fri Mar 25 13:12:21 2011 -0400 @@ -5,6 +5,7 @@ # import subprocess, os, sys, time, tempfile,string,plinkbinJZ +import datetime galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> @@ -30,6 +31,9 @@ """ return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) +def timestamp(): + return datetime.datetime.now().strftime('%Y%m%d%H%M%S') + def fail( message ): print >> sys.stderr, message return -1 @@ -41,6 +45,401 @@ return os.path.join(path, program) return None +def makeGFF(resf='',outfname='',logf=None,twd='.',name='track name',description='track description',topn=1000,pname='LOG10ARMITAGEP',rgname='rgGLM'): + """ + score must be scaled to 0-1000 + + Want to make some wig tracks from each analysis + Best n -log10(p). Make top hit the window. + we use our tab output which has + rs chrom offset ADD_stat ADD_p ADD_log10p + rs3094315 1 792429 1.151 0.2528 0.597223 + + """ + + def is_number(s): + try: + float(s) + return True + except ValueError: + return False + header = 'track name=%s description="%s" visibility=2 useScore=1 color=0,60,120\n' % (name,description) + column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ] + halfwidth=100 + resfpath = os.path.join(twd,resf) + resf = open(resfpath,'r') + resfl = resf.readlines() # dumb but convenient for millions of rows + resfl = [x.split() for x in resfl] + headl = resfl[0] + resfl = resfl[1:] + headl = [x.strip().upper() for x in headl] + headIndex = dict(zip(headl,range(0,len(headl)))) + chrpos = headIndex.get('CHROM',None) + rspos = headIndex.get('RS',None) + offspos = headIndex.get('OFFSET',None) + ppos = headIndex.get(pname,None) + wewant = [chrpos,rspos,offspos,ppos] + if None in wewant: # missing something + logf.write('### Error missing a required header in makeGFF - headIndex=%s, wewant=%s\n' % (headIndex,wewant)) + return + resfl = [x for x in resfl if x[ppos] > ''] + resfl = [(float(x[ppos]),x) for x in resfl] # decorate + resfl.sort() + resfl.reverse() # using -log10 so larger is better + resfl = resfl[:topn] # truncate + pvals = [x[0] for x in resfl] # need to scale + resfl = [x[1] for x in resfl] # drop decoration + if len(pvals) == 0: + logf.write('### no pvalues found in resfl - %s' % (resfl[:3])) + sys.exit(1) + maxp = max(pvals) # need to scale + minp = min(pvals) + prange = abs(maxp-minp) + 0.5 # fudge + scalefact = 1000.0/prange + logf.write('###maxp=%f,minp=%f,prange=%f,scalefact=%f\n' % (maxp,minp,prange,scalefact)) + for i,row in enumerate(resfl): + row[ppos] = '%d' % (int(scalefact*pvals[i])) + resfl[i] = row # replace + outf = file(outfname,'w') + outf.write(header) + outres = [] # need to resort into chrom offset order + for i,lrow in enumerate(resfl): + chrom,snp,offset,p, = [lrow[x] for x in wewant] + gff = ('chr%s' % chrom,rgname,'variation','%d' % (int(offset)-halfwidth), + '%d' % (int(offset)+halfwidth),p,'.','.','%s logp=%1.2f' % (snp,pvals[i])) + outres.append(gff) + outres = [(x[0],int(x[3]),x) for x in outres] # decorate + outres.sort() # into chrom offset + outres=[x[2] for x in outres] # undecorate + outres = ['\t'.join(x) for x in outres] + outf.write('\n'.join(outres)) + outf.write('\n') + outf.close() + + +def bedToPicInterval(infile=None): + """ + Picard tools requiring targets want + a sam style header which incidentally, MUST be sorted in natural order - not lexicographic order: + + @SQ SN:chrM LN:16571 + @SQ SN:chr1 LN:247249719 + @SQ SN:chr2 LN:242951149 + @SQ SN:chr3 LN:199501827 + @SQ SN:chr4 LN:191273063 + added to the start of what looks like a bed style file + chr1 67052400 67052451 - CCDS635.1_cds_0_0_chr1_67052401_r + chr1 67060631 67060788 - CCDS635.1_cds_1_0_chr1_67060632_r + chr1 67065090 67065317 - CCDS635.1_cds_2_0_chr1_67065091_r + chr1 67066082 67066181 - CCDS635.1_cds_3_0_chr1_67066083_r + + see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 + we need to add 1 to start coordinates on the way through - but length calculations are easier + """ + # bedToPicard.py + # ross lazarus October 2010 + # LGPL + # for Rgenetics + + def getFlen(bedfname=None): + """ + find all features in a BED file and sum their lengths + """ + features = {} + try: + infile = open(bedfname,'r') + except: + print '###ERROR: getFlen unable to open bedfile %s' % bedfname + sys.exit(1) + for i,row in enumerate(infile): + if row[0] == '@': # shouldn't happen given a bed file! + print 'row %d=%s - should NOT start with @!' % (i,row) + sys.exit(1) + row = row.strip() + if len(row) > 0: + srow = row.split('\t') + f = srow[0] + spos = srow[1] # zero based from UCSC so no need to add 1 - eg 0-100 is 100 bases numbered 0-99 (!) + epos = srow[2] # see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 + flen = int(epos) - int(spos) + features.setdefault(f,0) + features[f] += flen + infile.close() + return features + + def keynat(string): + ''' + borrowed from http://code.activestate.com/recipes/285264-natural-string-sorting/ + A natural sort helper function for sort() and sorted() + without using regular expressions or exceptions. + + >>> items = ('Z', 'a', '10th', '1st', '9') + >>> sorted(items) + ['10th', '1st', '9', 'Z', 'a'] + >>> sorted(items, key=keynat) + ['1st', '9', '10th', 'a', 'Z'] + ''' + it = type(1) + r = [] + for c in string: + if c.isdigit(): + d = int(c) + if r and type( r[-1] ) == it: + r[-1] = r[-1] * 10 + d + else: + r.append(d) + else: + r.append(c.lower()) + return r + + def writePic(outfname=None,bedfname=None): + """ + collect header info and rewrite bed with header for picard + """ + featlen = getFlen(bedfname=bedfname) + try: + outf = open(outfname,'w') + except: + print '###ERROR: writePic unable to open output picard file %s' % outfname + sys.exit(1) + infile = open(bedfname,'r') # already tested in getFlen + k = featlen.keys() + fk = sorted(k, key=keynat) + header = ['@SQ\tSN:%s\tLN:%d' % (x,featlen[x]) for x in fk] + outf.write('\n'.join(header)) + outf.write('\n') + for row in infile: + row = row.strip() + if len(row) > 0: # convert zero based start coordinate to 1 based + srow = row.split('\t') + srow[1] = '%d' % (int(srow[1])+1) # see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 + outf.write('\t'.join(srow)) + outf.write('\n') + outf.close() + infile.close() + + + + # bedToPicInterval starts here + fd,outf = tempfile.mkstemp(prefix='rgPicardHsMetrics') + writePic(outfname=outf,bedfname=infile) + return outf + + +def getFileString(fpath, outpath): + """ + format a nice file size string + """ + size = '' + fp = os.path.join(outpath, fpath) + s = '? ?' + if os.path.isfile(fp): + n = float(os.path.getsize(fp)) + if n > 2**20: + size = ' (%1.1f MB)' % (n/2**20) + elif n > 2**10: + size = ' (%1.1f KB)' % (n/2**10) + elif n > 0: + size = ' (%d B)' % (int(n)) + s = '%s %s' % (fpath, size) + return s + + +def fixPicardOutputs(tempout=None,output_dir=None,log_file=None,html_output=None,progname=None,cl=[],transpose=True): + """ + picard produces long hard to read tab header files + make them available but present them transposed for readability + """ + rstyle="""<style type="text/css"> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style>""" + cruft = [] + dat = [] + try: + r = open(tempout,'r').readlines() + except: + r = [] + for row in r: + if row.strip() > '': + srow = row.split('\t') + if row[0] == '#': + cruft.append(row.strip()) # want strings + else: + dat.append(srow) # want lists + + res = [rstyle,] + res.append(galhtmlprefix % progname) + res.append(galhtmlattr % (progname,timenow())) + flist = os.listdir(output_dir) + pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'] + if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs + for p in pdflist: + imghref = '%s.jpg' % os.path.splitext(p)[0] # removes .pdf + res.append('<table cellpadding="10"><tr><td>\n') + res.append('<a href="%s"><img src="%s" alt="Click thumbnail to download %s" hspace="10" align="middle"></a>\n' % (p,imghref,p)) + res.append('</tr></td></table>\n') + res.append('<b>Your job produced the following output files.</b><hr/>\n') + res.append('<table>\n') + for i,f in enumerate(flist): + fn = os.path.split(f)[-1] + res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fn)) + res.append('</table><p/>\n') + if len(cruft) + len(dat) > 0: + res.append('<b>Picard on line resources</b><ul>\n') + res.append('<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>\n') + res.append('<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>\n') + if transpose: + res.append('<b>Picard output (transposed for readability)</b><hr/>\n') + else: + res.append('<b>Picard output</b><hr/>\n') + res.append('<table cellpadding="3" >\n') + if len(cruft) > 0: + cres = ['<tr class="d%d"><td>%s</td></tr>' % (i % 2,x) for i,x in enumerate(cruft)] + res += cres + if len(dat) > 0: + maxrows = 100 + if transpose: + tdat = map(None,*dat) # transpose an arbitrary list of lists + missing = len(tdat) - maxrows + tdat = ['<tr class="d%d"><td>%s</td><td>%s</td></tr>\n' % ((i+len(cruft)) % 2,x[0],x[1]) for i,x in enumerate(tdat) if i < maxrows] + if len(tdat) > maxrows: + tdat.append('<tr><td colspan="2">...WARNING: %d rows deleted for sanity...see raw files for all rows</td></tr>' % missing) + else: + tdat = ['<tr class="d%d"><td>%s</td></tr>\n' % ((i+len(cruft)) % 2,x) for i,x in enumerate(dat) if i < maxrows] + if len(dat) > maxrows: + missing = len(dat) - maxrows + tdat.append('<tr><td>...WARNING: %d rows deleted for sanity...see raw files for all rows</td></tr>' % missing) + res += tdat + res.append('</table>\n') + else: + res.append('<b>No Picard output found - please consult the Picard log above for an explanation</b>') + l = open(log_file,'r').readlines() + if len(l) > 0: + res.append('<b>Picard log</b><hr/>\n') + rlog = ['<pre>',] + rlog += l + rlog.append('</pre>') + res += rlog + else: + res.append("Odd, Picard left no log file %s - must have really barfed badly?" % log_file) + res.append('<hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n') + res.append( 'generated all outputs reported here, using this command line:<br/>\n<pre>%s</pre>\n' % ''.join(cl)) + res.append(galhtmlpostfix) + outf = open(html_output,'w') + outf.write(''.join(res)) + outf.write('\n') + outf.close() + +def keynat(string): + ''' + borrowed from http://code.activestate.com/recipes/285264-natural-string-sorting/ + A natural sort helper function for sort() and sorted() + without using regular expressions or exceptions. + + >>> items = ('Z', 'a', '10th', '1st', '9') + >>> sorted(items) + ['10th', '1st', '9', 'Z', 'a'] + >>> sorted(items, key=keynat) + ['1st', '9', '10th', 'a', 'Z'] + ''' + it = type(1) + r = [] + for c in string: + if c.isdigit(): + d = int(c) + if r and type( r[-1] ) == it: + r[-1] = r[-1] * 10 + d + else: + r.append(d) + else: + r.append(c.lower()) + return r + +def getFlen(bedfname=None): + """ + find all features in a BED file and sum their lengths + """ + features = {} + otherHeaders = [] + try: + infile = open(bedfname,'r') + except: + print '###ERROR: getFlen unable to open bedfile %s' % bedfname + sys.exit(1) + for i,row in enumerate(infile): + if row.startswith('@'): # add to headers if not @SQ + if not row.startswith('@SQ'): + otherHeaders.append(row) + else: + row = row.strip() + if row.startswith('#') or row.lower().startswith('browser') or row.lower().startswith('track'): + continue # ignore headers + srow = row.split('\t') + if len(srow) > 3: + srow = row.split('\t') + f = srow[0] + spos = srow[1] # zero based from UCSC so no need to add 1 - eg 0-100 is 100 bases numbered 0-99 (!) + epos = srow[2] # see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 + flen = int(epos) - int(spos) + features.setdefault(f,0) + features[f] += flen + infile.close() + fk = features.keys() + fk = sorted(fk, key=keynat) + return features,fk,otherHeaders + +def bedToPicInterval(infile=None,outfile=None): + """ + Picard tools requiring targets want + a sam style header which incidentally, MUST be sorted in natural order - not lexicographic order: + + @SQ SN:chrM LN:16571 + @SQ SN:chr1 LN:247249719 + @SQ SN:chr2 LN:242951149 + @SQ SN:chr3 LN:199501827 + @SQ SN:chr4 LN:191273063 + added to the start of what looks like a bed style file + chr1 67052400 67052451 - CCDS635.1_cds_0_0_chr1_67052401_r + chr1 67060631 67060788 - CCDS635.1_cds_1_0_chr1_67060632_r + chr1 67065090 67065317 - CCDS635.1_cds_2_0_chr1_67065091_r + chr1 67066082 67066181 - CCDS635.1_cds_3_0_chr1_67066083_r + + see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 + we need to add 1 to start coordinates on the way through - but length calculations are easier + """ + # bedToPicard.py + # ross lazarus October 2010 + # LGPL + # for Rgenetics + """ + collect header info and rewrite bed with header for picard + """ + featlen,fk,otherHeaders = getFlen(bedfname=infile) + try: + outf = open(outfile,'w') + except: + print '###ERROR: writePic unable to open output picard file %s' % outfile + sys.exit(1) + inf = open(infile,'r') # already tested in getFlen + header = ['@SQ\tSN:%s\tLN:%d' % (x,featlen[x]) for x in fk] + if len(otherHeaders) > 0: + header += otherHeaders + outf.write('\n'.join(header)) + outf.write('\n') + for row in inf: + row = row.strip() + if len(row) > 0: # convert zero based start coordinate to 1 based + if row.startswith('@'): + continue + else: + srow = row.split('\t') + srow[1] = '%d' % (int(srow[1])+1) # see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 + outf.write('\t'.join(srow)) + outf.write('\n') + outf.close() + inf.close() + def oRRun(rcmd=[],outdir=None,title='myR',rexe='R'): """ @@ -201,9 +600,12 @@ The fine Plink docs at http://pngu.mgh.harvard.edu/~purcell/plink/summary.shtml#prune reproduced below -Sometimes it is useful to generate a pruned subset of SNPs that are in approximate linkage equilibrium with each other. This can be achieved via two commands: --indep which prunes based on the variance inflation factor (VIF), which recursively removes SNPs within a sliding window; second, --indep-pairwise which is similar, except it is based only on pairwise genotypic correlation. +Sometimes it is useful to generate a pruned subset of SNPs that are in approximate linkage equilibrium with each other. This can be achieved via two commands: +--indep which prunes based on the variance inflation factor (VIF), which recursively removes SNPs within a sliding window; second, --indep-pairwise which is +similar, except it is based only on pairwise genotypic correlation. -Hint The output of either of these commands is two lists of SNPs: those that are pruned out and those that are not. A separate command using the --extract or --exclude option is necessary to actually perform the pruning. +Hint The output of either of these commands is two lists of SNPs: those that are pruned out and those that are not. A separate command using the --extract or +--exclude option is necessary to actually perform the pruning. The VIF pruning routine is performed: plink --file data --indep 50 5 2 @@ -217,16 +619,23 @@ a --extract or --exclude command. The parameters for --indep are: window size in SNPs (e.g. 50), the number of SNPs to shift the -window at each step (e.g. 5), the VIF threshold. The VIF is 1/(1-R^2) where R^2 is the multiple correlation coefficient for a SNP being regressed on all other SNPs simultaneously. That is, this considers the correlations between SNPs but also between linear combinations of SNPs. A VIF of 10 is often taken to represent near collinearity problems in standard multiple regression analyses (i.e. implies R^2 of 0.9). A VIF of 1 would imply that the SNP is completely independent of all other SNPs. Practically, values between 1.5 and 2 should probably be used; particularly in small samples, if this threshold is too low and/or the window size is too large, too many SNPs may be removed. +window at each step (e.g. 5), the VIF threshold. The VIF is 1/(1-R^2) where R^2 is the multiple correlation coefficient for a SNP being regressed on all other +SNPs simultaneously. That is, this considers the correlations between SNPs but also between linear combinations of SNPs. A VIF of 10 is often taken to represent +near collinearity problems in standard multiple regression analyses (i.e. implies R^2 of 0.9). A VIF of 1 would imply that the SNP is completely independent of +all other SNPs. Practically, values between 1.5 and 2 should probably be used; particularly in small samples, if this threshold is too low and/or the window +size is too large, too many SNPs may be removed. The second procedure is performed: plink --file data --indep-pairwise 50 5 0.5 This generates the same output files as the first version; the only difference is that a -simple pairwise threshold is used. The first two parameters (50 and 5) are the same as above (window size and step); the third parameter represents the r^2 threshold. Note: this represents the pairwise SNP-SNP metric now, not the multiple correlation coefficient; also note, this is based on the genotypic correlation, i.e. it does not involve phasing. +simple pairwise threshold is used. The first two parameters (50 and 5) are the same as above (window size and step); the third parameter represents the r^2 +threshold. Note: this represents the pairwise SNP-SNP metric now, not the multiple correlation coefficient; also note, this is based on the genotypic +correlation, i.e. it does not involve phasing. To give a concrete example: the command above that specifies 50 5 0.5 would a) consider a -window of 50 SNPs, b) calculate LD between each pair of SNPs in the window, b) remove one of a pair of SNPs if the LD is greater than 0.5, c) shift the window 5 SNPs forward and repeat the procedure. +window of 50 SNPs, b) calculate LD between each pair of SNPs in the window, b) remove one of a pair of SNPs if the LD is greater than 0.5, c) shift the window 5 +SNPs forward and repeat the procedure. To make a new, pruned file, then use something like (in this example, we also convert the standard PED fileset to a binary one): @@ -276,3 +685,4 @@ mfile.close() return markers,snpcols,rslist,rsdict + http://bitbucket.org/galaxy/galaxy-central/changeset/a892beeb00b4/ changeset: r5275:a892beeb00b4 user: fubar date: 2011-03-25 18:21:13 summary: Remove bogus makeGFF from rgutils affected #: 1 file (2.9 KB) --- a/tools/rgenetics/rgutils.py Fri Mar 25 13:12:21 2011 -0400 +++ b/tools/rgenetics/rgutils.py Fri Mar 25 13:21:13 2011 -0400 @@ -45,77 +45,6 @@ return os.path.join(path, program) return None -def makeGFF(resf='',outfname='',logf=None,twd='.',name='track name',description='track description',topn=1000,pname='LOG10ARMITAGEP',rgname='rgGLM'): - """ - score must be scaled to 0-1000 - - Want to make some wig tracks from each analysis - Best n -log10(p). Make top hit the window. - we use our tab output which has - rs chrom offset ADD_stat ADD_p ADD_log10p - rs3094315 1 792429 1.151 0.2528 0.597223 - - """ - - def is_number(s): - try: - float(s) - return True - except ValueError: - return False - header = 'track name=%s description="%s" visibility=2 useScore=1 color=0,60,120\n' % (name,description) - column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ] - halfwidth=100 - resfpath = os.path.join(twd,resf) - resf = open(resfpath,'r') - resfl = resf.readlines() # dumb but convenient for millions of rows - resfl = [x.split() for x in resfl] - headl = resfl[0] - resfl = resfl[1:] - headl = [x.strip().upper() for x in headl] - headIndex = dict(zip(headl,range(0,len(headl)))) - chrpos = headIndex.get('CHROM',None) - rspos = headIndex.get('RS',None) - offspos = headIndex.get('OFFSET',None) - ppos = headIndex.get(pname,None) - wewant = [chrpos,rspos,offspos,ppos] - if None in wewant: # missing something - logf.write('### Error missing a required header in makeGFF - headIndex=%s, wewant=%s\n' % (headIndex,wewant)) - return - resfl = [x for x in resfl if x[ppos] > ''] - resfl = [(float(x[ppos]),x) for x in resfl] # decorate - resfl.sort() - resfl.reverse() # using -log10 so larger is better - resfl = resfl[:topn] # truncate - pvals = [x[0] for x in resfl] # need to scale - resfl = [x[1] for x in resfl] # drop decoration - if len(pvals) == 0: - logf.write('### no pvalues found in resfl - %s' % (resfl[:3])) - sys.exit(1) - maxp = max(pvals) # need to scale - minp = min(pvals) - prange = abs(maxp-minp) + 0.5 # fudge - scalefact = 1000.0/prange - logf.write('###maxp=%f,minp=%f,prange=%f,scalefact=%f\n' % (maxp,minp,prange,scalefact)) - for i,row in enumerate(resfl): - row[ppos] = '%d' % (int(scalefact*pvals[i])) - resfl[i] = row # replace - outf = file(outfname,'w') - outf.write(header) - outres = [] # need to resort into chrom offset order - for i,lrow in enumerate(resfl): - chrom,snp,offset,p, = [lrow[x] for x in wewant] - gff = ('chr%s' % chrom,rgname,'variation','%d' % (int(offset)-halfwidth), - '%d' % (int(offset)+halfwidth),p,'.','.','%s logp=%1.2f' % (snp,pvals[i])) - outres.append(gff) - outres = [(x[0],int(x[3]),x) for x in outres] # decorate - outres.sort() # into chrom offset - outres=[x[2] for x in outres] # undecorate - outres = ['\t'.join(x) for x in outres] - outf.write('\n'.join(outres)) - outf.write('\n') - outf.close() - def bedToPicInterval(infile=None): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Add selected attribute to default value for Tophat coverage search.
by Bitbucket 25 Mar '11

25 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8edb38ab1afb/ changeset: r5273:8edb38ab1afb user: jgoecks date: 2011-03-25 01:29:40 summary: Add selected attribute to default value for Tophat coverage search. affected #: 1 file (32 bytes) --- a/tools/ngs_rna/tophat_wrapper.xml Thu Mar 24 18:26:29 2011 -0400 +++ b/tools/ngs_rna/tophat_wrapper.xml Thu Mar 24 20:29:40 2011 -0400 @@ -251,7 +251,7 @@ <conditional name="coverage_search"><param name="use_search" type="select" label="Use Coverage Search"> - <option value="Yes">Yes</option> + <option selected="true" value="Yes">Yes</option><option value="No">No</option></param><when value="Yes"> @@ -357,7 +357,7 @@ <conditional name="coverage_search"><param name="use_search" type="select" label="Use Coverage Search"> - <option value="Yes">Yes</option> + <option selected="true" value="Yes">Yes</option><option value="No">No</option></param><when value="Yes"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: kanwei: UI Tweaks and fixes:
by Bitbucket 24 Mar '11

24 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f2f29d55493e/ changeset: r5272:f2f29d55493e user: kanwei date: 2011-03-24 23:26:29 summary: UI Tweaks and fixes: - View details icon no longer tooltip; it now links to a page - Restore folder icon to data libraries - Make popupmenu link boxes smaller so that link clickthroughs don't activate popup as easily - Make popupmenu initial position lower after click affected #: 9 files (254 bytes) --- a/static/june_2007_style/base.css.tmpl Thu Mar 24 17:36:06 2011 -0400 +++ b/static/june_2007_style/base.css.tmpl Thu Mar 24 18:26:29 2011 -0400 @@ -326,40 +326,40 @@ } table.simple { - font-size: 12px; - background: #fff; - margin: 1em; - border-collapse: collapse; - text-align: left; + font-size: 12px; + background: #fff; + margin: 1em; + border-collapse: collapse; + text-align: left; } table.simple th { - font-size: 14px; - font-weight: normal; - padding: 10px 8px; - border-bottom: 2px solid #333; + font-size: 14px; + font-weight: normal; + padding: 10px 8px; + border-bottom: 2px solid #333; } table.simple td { - padding: 10px 8px 0px 8px; + padding: 10px 8px 0px 8px; } table.simple tbody tr:hover td { - color: #333; + color: #333; } table.tabletip { width: 100%; - border-collapse: collapse; - text-align: left; + border-collapse: collapse; + text-align: left; } table.tabletip th { white-space: nowrap; - border-bottom: 1px solid #444; - padding-right: 3px; + border-bottom: 1px solid #444; + padding-right: 3px; } table.tabletip td { - border-bottom: 1px solid #444; + border-bottom: 1px solid #ddd; } table.tabletip tbody tr:hover td { - background-color: #111; + background-color: #eee; } table.colored { @@ -576,12 +576,12 @@ .unselectable; border: solid transparent 1px; - -moz-border-radius: 0.5em; - -webkit-border-radius: 0.5em; - border-radius: 0.5em; + -moz-border-radius: 0.25em; + -webkit-border-radius: 0.25em; + border-radius: 0.25em; - padding: 3px 0.5em; - margin: -3px -0.5em; + padding: 1px 0.25em; + margin: -1px -0.25em; .label { position: relative; @@ -598,7 +598,7 @@ padding-right: 20px; background-image: url(../images/dropdownarrow.png); background-repeat: no-repeat; - background-position: right 8px; + background-position: right 7px; } .menubutton:hover { @@ -615,7 +615,7 @@ } .menubutton.popup.split:hover { - background: url(../images/ddarrowsplit.png) no-repeat right -38px; + background: url(../images/ddarrowsplit.png) no-repeat right -39px; } ## Popup menu styles --- a/static/june_2007_style/blue/base.css Thu Mar 24 17:36:06 2011 -0400 +++ b/static/june_2007_style/blue/base.css Thu Mar 24 18:26:29 2011 -0400 @@ -64,8 +64,8 @@ table.simple tbody tr:hover td{color:#333;} table.tabletip{width:100%;border-collapse:collapse;text-align:left;} table.tabletip th{white-space:nowrap;border-bottom:1px solid #444;padding-right:3px;} -table.tabletip td{border-bottom:1px solid #444;} -table.tabletip tbody tr:hover td{background-color:#111;} +table.tabletip td{border-bottom:1px solid #ddd;} +table.tabletip tbody tr:hover td{background-color:#eee;} table.colored{border-top:solid #d8b365 1px;border-bottom:solid #d8b365 1px;} table.colored td,table.colored th{text-align:left;padding:5px;} table.colored tr.header{background:#ebd9b2;background-image:url(form_title_bg.png);background-repeat:repeat-x;background-position:top;border-bottom:solid #d8b365 1px;font-weight:bold;} @@ -103,13 +103,13 @@ .action-button > *{vertical-align:middle;} .action-button:hover{color:black;background:#dddddd;} .action-button:active{color:white;background:#aaaaaa;} -.menubutton{display:inline-block;cursor:pointer;position:relative;user-select:none;-moz-user-select:none;-webkit-user-select:none;border:solid transparent 1px;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;padding:3px 0.5em;margin:-3px -0.5em;} +.menubutton{display:inline-block;cursor:pointer;position:relative;user-select:none;-moz-user-select:none;-webkit-user-select:none;border:solid transparent 1px;-moz-border-radius:0.25em;-webkit-border-radius:0.25em;border-radius:0.25em;padding:1px 0.25em;margin:-1px -0.25em;} .menubutton .label{position:relative;display:block;border-right:none;} .menubutton.action-button{border-color:#aaaaaa;} -.menubutton.popup,.action-button.popup{padding-right:20px;background-image:url(../images/dropdownarrow.png);background-repeat:no-repeat;background-position:right 8px;} +.menubutton.popup,.action-button.popup{padding-right:20px;background-image:url(../images/dropdownarrow.png);background-repeat:no-repeat;background-position:right 7px;} .menubutton:hover{border-color:#aaaaaa;} .menubutton.popup.split{padding-right:2em;} -.menubutton.popup.split:hover{background:url(../images/ddarrowsplit.png) no-repeat right -38px;} +.menubutton.popup.split:hover{background:url(../images/ddarrowsplit.png) no-repeat right -39px;} .overlay-border{position:absolute;top:0;left:0;height:100%;width:100%;padding:1em;margin:-1em;background-color:rgba(0,0,0,0.5);-moz-border-radius:1em;-webkit-border-radius:1em;z-index:-1;} div.popmenu-wrapper{position:absolute;top:100%;z-index:20000;} div.popmenu-wrapper ul{display:block;margin:0;padding:0;background:white;color:#333;font-weight:bold;font-style:normal;white-space:nowrap;border:solid #aaaaaa 1px;padding:3px 0;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;user-select:none;-moz-user-select:none;-webkit-user-select:none;} --- a/static/june_2007_style/blue/library.css Thu Mar 24 17:36:06 2011 -0400 +++ b/static/june_2007_style/blue/library.css Thu Mar 24 18:26:29 2011 -0400 @@ -11,9 +11,9 @@ .libraryTitle th{text-align:left;} pre.peek{background:white;color:black;width:100%;overflow:auto;} pre.peek th{color:white;background:#023858;} -span.expandLink{padding-left:20px;display:inline-block;vertical-align:middle;background:url(../images/silk/resultset_next.png) no-repeat;} +span.expandLink{padding-left:12px;display:inline-block;vertical-align:middle;background:url(../images/silk/resultset_next.png) no-repeat;} .folderRow.expanded span.expandLink{background:url(../images/silk/resultset_bottom.png) no-repeat;} -.folderRow span.rowIcon{float:left;width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/folder.png);} +.folderRow span.rowIcon{float:left;margin-right:5px;width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/folder.png);} .libraryItem-error{margin-right:2px;padding:0 2px 0 2px;border:1px solid #AA6666;background:#FFCCCC;} .libraryItem-queued{margin-right:2px;padding:0 2px 0 2px;border:1px solid #888888;background:#EEEEEE;} .libraryItem-running{margin-right:2px;padding:0 2px 0 2px;border:1px solid #AAAA66;background:#FFFFCC;} --- a/static/june_2007_style/library.css.tmpl Thu Mar 24 17:36:06 2011 -0400 +++ b/static/june_2007_style/library.css.tmpl Thu Mar 24 18:26:29 2011 -0400 @@ -31,14 +31,12 @@ } input.datasetCheckbox, -li, ul -{ +li, ul { padding: 0; margin: 0; } -.rowTitle -{ +.rowTitle { padding: 2px; } @@ -50,22 +48,20 @@ text-align: left; } -pre.peek -{ +pre.peek { background: white; color: black; width: 100%; overflow: auto; } -pre.peek th -{ +pre.peek th { color: white; background: $peek_table_header; } span.expandLink { - padding-left: 20px; + padding-left: 12px; display: inline-block; vertical-align: middle; background: url(../images/silk/resultset_next.png) no-repeat; @@ -77,6 +73,7 @@ .folderRow span.rowIcon { float: left; + margin-right: 5px; width: 16px; height: 16px; display: inline-block; --- a/static/scripts/galaxy.base.js Thu Mar 24 17:36:06 2011 -0400 +++ b/static/scripts/galaxy.base.js Thu Mar 24 18:26:29 2011 -0400 @@ -77,7 +77,7 @@ x = Math.max( x, $(document).scrollLeft() + 20 ); wrapper.css( { - top: e.pageY - 5, + top: e.pageY - 15, left: x } ); }, 10); --- a/static/scripts/packed/galaxy.base.js Thu Mar 24 17:36:06 2011 -0400 +++ b/static/scripts/packed/galaxy.base.js Thu Mar 24 18:26:29 2011 -0400 @@ -1,1 +1,1 @@ -if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul id='"+b.attr("id")+"-menu'></ul>");var 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replace_big_select_inputs(a,b){if(!jQuery().autocomplete){return}if(a===undefined){a=20}if(b===undefined){b=3000}$("select").each(function(){var d=$(this);var g=d.find("option").length;if((g<a)||(g>b)){return}if(d.attr("multiple")===true){return}if(d.hasClass("no-autocomplete")){return}var m=d.attr("value");var c=$("<input type='text' class='text-and-autocomplete-select'></input>");c.attr("size",40);c.attr("name",d.attr("name"));c.attr("id",d.attr("id"));c.click(function(){var n=$(this).val();$(this).val("Loading...");$(this).showAllInCache();$(this).val(n);$(this).select()});var e=[];var i={};d.children("option").each(function(){var o=$(this).text();var n=$(this).attr("value");e.push(o);i[o]=n;i[n]=n;if(n==m){c.attr("value",o)}});if(m===""||m==="?"){c.attr("value","Click to Search or Select")}if(d.attr("name")=="dbkey"){e=e.sort(naturalSort)}var 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failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStorage.get("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStorage.deleteKey("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id,h=$(this).children("div.historyItemBody"),i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){var k;if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){k=$.jStorage.get("history_expand_state");if(k){delete k[j];$.jStorage.set("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){k=$.jStorage.get("history_expand_state");if(!k){k={}}k[j]=true;$.jStorage.set("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};b()}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("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}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file --- a/templates/library/common/browse_library.mako Thu Mar 24 17:36:06 2011 -0400 +++ b/templates/library/common/browse_library.mako Thu Mar 24 18:26:29 2011 -0400 @@ -361,6 +361,7 @@ <span class="expandLink folder-${encoded_id}-click"><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="folder_img-${folder.id}-popup"><a class="folder-${encoded_id}-click" href="javascript:void(0);"> + <span class="rowIcon"></span> %if folder.deleted: <div class="libraryItem-error">${folder.name}</div> %else: --- a/templates/root/history.mako Thu Mar 24 17:36:06 2011 -0400 +++ b/templates/root/history.mako Thu Mar 24 18:26:29 2011 -0400 @@ -75,8 +75,8 @@ }); }); - // Show details icon - $(this).find("a.show-details").bind("mouseenter.load-detail", function(e) { + // Show details icon -- Disabled since it often gets stuck, etc + /* $(this).find("a.show-details").bind("mouseenter.load-detail", function(e) { var anchor = $(this); $.get($(this).attr("href"), function(data) { anchor.attr("title", data); @@ -86,8 +86,10 @@ }); return false; }); + // Disable clickthrough $(this).find("a.show-details").bind("click", function() { return false; }); + */ // Tag handling. $(this).find("a.icon-button.tags").each( function() { --- a/templates/show_params.mako Thu Mar 24 17:36:06 2011 -0400 +++ b/templates/show_params.mako Thu Mar 24 18:26:29 2011 -0400 @@ -1,3 +1,4 @@ +<%inherit file="/base.mako"/><% from galaxy.util import nice_size %><%def name="inputs_recursive( input_params, param_values, depth=1 )"> @@ -27,12 +28,12 @@ <tr><th colspan="2" style="font-size: 120%;">${tool.name}</th></tr></thead><tbody> - <tr><th>Created:</th><td>${history.create_time.strftime("%b %d, %Y")}</td></tr> - <tr><th>Modified:</th><td>${history.update_time.strftime("%b %d, %Y")}</td></tr> -## <tr><th>Copied from another history?</td><td>${hda.source_library_dataset}</td></tr> - <tr><th>Filesize:</th><td>${nice_size(hda.dataset.file_size)}</td></tr> - <tr><th>Dbkey:</th><td>${hda.dbkey}</td></tr> - <tr><th>Format:</th><td>${hda.ext}</td></tr> + <tr><td>Created:</th><td>${history.create_time.strftime("%b %d, %Y")}</td></tr> + <tr><td>Modified:</th><td>${history.update_time.strftime("%b %d, %Y")}</td></tr> +## <tr><td>Copied from another history?</td><td>${hda.source_library_dataset}</td></tr> + <tr><td>Filesize:</th><td>${nice_size(hda.dataset.file_size)}</td></tr> + <tr><td>Dbkey:</th><td>${hda.dbkey}</td></tr> + <tr><td>Format:</th><td>${hda.ext}</td></tr></table><br /><table class="tabletip"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Change default value for Tophat coverage search to true.
by Bitbucket 24 Mar '11

24 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0af3b79ea5ea/ changeset: r5271:0af3b79ea5ea user: jgoecks date: 2011-03-24 22:36:06 summary: Change default value for Tophat coverage search to true. affected #: 1 file (8 bytes) --- a/tools/ngs_rna/tophat_wrapper.xml Thu Mar 24 17:12:16 2011 -0400 +++ b/tools/ngs_rna/tophat_wrapper.xml Thu Mar 24 17:36:06 2011 -0400 @@ -251,8 +251,8 @@ <conditional name="coverage_search"><param name="use_search" type="select" label="Use Coverage Search"> - <option value="No">No</option> - <option value="Yes">Yes</option> + <option value="Yes">Yes</option> + <option value="No">No</option></param><when value="Yes"><param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" /> @@ -357,8 +357,8 @@ <conditional name="coverage_search"><param name="use_search" type="select" label="Use Coverage Search"> - <option value="No">No</option> - <option value="Yes">Yes</option> + <option value="Yes">Yes</option> + <option value="No">No</option></param><when value="Yes"><param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Trackster: put show_insertions and show_differences in track config and fix show_differences, which was broken in previous trackster commit.
by Bitbucket 24 Mar '11

24 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/120565d36127/ changeset: r5270:120565d36127 user: jgoecks date: 2011-03-24 22:12:16 summary: Trackster: put show_insertions and show_differences in track config and fix show_differences, which was broken in previous trackster commit. affected #: 2 files (961 bytes) --- a/static/scripts/packed/trackster.js Thu Mar 24 15:05:28 2011 -0400 +++ b/static/scripts/packed/trackster.js Thu Mar 24 17:12:16 2011 -0400 @@ -1,1 +1,1 @@ -CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();var c;for(c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c===f.length){if(this!==f.get(c-1)){g.append(this)}}else{if(this!==f.get(c)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!==NO_OVERLAP)}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,ERROR_PADDING=10,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",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_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;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 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.move_key_to_end(b,a)}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},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataManager=function(b,a){Cache.call(this,b);this.track=a};$.extend(DataManager.prototype,Cache.prototype,{load_data:function(d,a,f,h,b,e){var g={chrom:d,low:a,high:f,mode:h,resolution:b,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(g,e);var c=this;return $.getJSON(this.track.data_url,g,function(j){c.set_data(a,f,h,j)})},get_data:function(j,k,c,h,b,f){var l=this.get(this.gen_key(k,c,h));if(l){return l}var m,g,a,e,h,l;for(var d=0;d<this.key_ary.length;d++){m=this.key_ary[d];g=this.split_key(m);a=g[0];e=g[1];if(k>=a&&c<=e){l=this.obj_cache[m];if(l.dataset_type!=="summary_tree"&&l.extra_info!=="no_detail"){this.move_key_to_end(m,d);return l}}}return this.load_data(j,k,c,h,b,f)},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();$(this).val("");a.location_span.show();a.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",b).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.val(a.chrom+":"+a.low+"-"+a.high);a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var j=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(j/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,k){var f=$(this);var l=k.offsetX-k.current_x;var g=f.scrollTop()-(h.clientY-k.current_height);f.scrollTop(g);k.current_height=h.clientY;k.current_x=k.offsetX;var j=Math.round(l/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}).bind("mousewheel",function(h,k,g,f){if(g){var j=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(k,l){$(l.proxy).css({left:Math.min(k.pageX,l.startX),width:Math.abs(k.pageX-l.startX)});var g=Math.min(k.pageX,l.startX)-a.container.offset().left,f=Math.max(k.pageX,l.startX)-a.container.offset().left,j=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*j)+a.low,Math.round(f/h*j)+a.low)}).bind("dragend",function(l,m){var g=Math.min(l.pageX,m.startX),f=Math.max(l.pageX,m.startX),j=(a.high-a.low),h=a.viewport_container.width(),k=a.low;a.low=Math.round(g/h*j)+k;a.high=Math.round(f/h*j)+k;$(m.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.chrom_info.length===0){alert("Invalid chromosome: "+b.chrom);return}if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e==="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e==="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len-1;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var k=this,a,d,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}k.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},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);sortable(a.container_div,".draghandle");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())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;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(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()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)===0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};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.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_url_extra_params={};this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.make_name_popup_menu()}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(b,j,n){var c=this,o=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(j!==undefined?get_tool_from_dict(j):undefined);this.parent_track=n;this.child_tracks=[];if(c.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});$.each(this.filters,function(t,w){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var v=$("<div/>").addClass("slider-label").appendTo(u);var s=$("<span/>").addClass("name").appendTo(v);s.text(w.name+" ");var r=$("<span/>").addClass("values").appendTo(v);var q=$("<div/>").addClass("slider").appendTo(u);w.control_element=$("<div/>").attr("id",w.name+"-filter-control").appendTo(q);w.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(y,z){var x=z.values;r.text("["+x[0]+"-"+x[1]+"]");w.low=x[0];w.high=x[1];c.draw(true,true)},change:function(x,y){w.control_element.slider("option","slide").call(w.control_element,x,y)}});w.slider=w.control_element;w.slider_label=r;$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(q){q.stopPropagation()}).bind("click",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});var m=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var l=this.tool.params;var c=this;$.each(this.tool.params,function(x,s){var v=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(v);var z=$("<span class='param-name'>").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var w=$("<span class='param-value'>").appendTo(u).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(v);var q=$("<div id='"+s.name+"-param-control'>").appendTo(y);var r=(s.max<=1?0.01:(s.max<=1000?1:5));q.slider({min:s.min,max:s.max,step:r,value:s.value,slide:function(A,C){var B=C.value;s.value=B;if(0<B&&B<1){B=parseFloat(B).toFixed(2)}t.text(B)},change:function(A,B){s.value=B.value}});w.click(function(){var C=t,B=C.text(),A=(s.max<=1?4:s.max.length);C.text("");$("<input type='text'/>").attr("size",A).attr("maxlength",A).attr("value",B).appendTo(C).focus().select().click(function(D){D.stopPropagation()}).blur(function(){$(this).remove();C.text(B)}).keyup(function(F){if(F.keyCode===27){$(this).trigger("blur")}else{if(F.keyCode===13){var D=$(this),E=parseFloat(D.val());if(isNaN(E)||E>s.max||E<s.min){alert("Parameter value must be in the range ["+s.min+"-"+s.max+"]");return $(this)}C.text(E);q.slider("value",E);s.value=E}}})});$("<div style='clear: both;'/>").appendTo(v)});var p=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var k=$("<input type='submit'>").attr("value","Run").appendTo(p);var c=this;k.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(q){c.mode_div.text(q);c.mode=q;c.track_config.values.mode=q;c.tile_cache.clear();c.draw()};var a={};for(var f=0,h=c.display_modes.length;f<h;f++){var g=c.display_modes[f];a[g]=function(q){return function(){d(q)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide Tool":"Show Tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.track_type=="ReadTrack"){var e=(b.show_insertions?"Hide Insertions":"Show Insertions");a[e]=function(){b.show_insertions=!b.show_insertions;b.draw(true);b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},draw:function(a,d){console.log(this.name,a,d);var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),m=this.view.resolution;var e=$("<div style='position: relative;'></div>"),f=l/j;if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}if(d){var k=this;var q=setInterval(function(){if(obj_length(c)===0){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var x=$(v[w]);if(u){x.remove()}else{if(x.children().length!==0){u=true}}}clearInterval(q)}},50)}for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,g,l,c,e,k,m,f){var d=this;var h=function(u,n,p,o,s,t,q){returned_tile=d.draw_tile(n,p,o,s,t,q);var r=$("<div class='track-tile'>").prepend(returned_tile);tile_element=r;d.tile_cache.set(j,tile_element);d.show_tile(tile_element,s,g,t);delete f[u]};var a=setTimeout(function(){if(g<=d.view.high&&l>=d.view.low){var n=(b?undefined:d.tile_cache.get(j));if(n){d.show_tile(n,k,g,m);delete f[a]}else{$.when(d.data_cache.get_data(view.chrom,g,l,d.mode,e,d.data_url_extra_params)).then(function(){result=d.data_cache.get_data(view.chrom,g,l,d.mode,e,d.data_url_extra_params);if(view.reference_track&&m>CHAR_WIDTH_PX){$.when(view.reference_track.data_cache.get_data(view.chrom,g,l,d.mode,e,view.reference_track.data_url_extra_params)).then(function(){seq_data=view.reference_track.data_cache.get_data(view.chrom,g,l,d.mode,e,view.reference_track.data_url_extra_params);h(a,result,e,c,k,m,seq_data)})}else{h(a,result,e,c,k,m)}})}}},50);f[a]=true},show_tile:function(h,j,e,k){var a=this;var c=this.view.high-this.view.low,b=(e-this.view.low)*k;if(this.left_offset){b-=this.left_offset}h.css({position:"absolute",top:0,left:b,height:""});j.append(h);a.max_height=Math.max(a.max_height,h.height());a.content_div.css("height",a.max_height+"px");j.children().css("height",a.max_height+"px");if(a.hidden){return}for(var g=0;g<a.filters.length;g++){a.filters[g].update_ui_elt()}var d=false;if(a.example_feature){for(var g=0;g<a.filters.length;g++){if(a.filters[g].applies_to(a.example_feature)){d=true;break}}}if(a.filters_available!==d){a.filters_available=d;if(!a.filters_available){a.filters_div.hide()}a.make_name_popup_menu()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:a.dbkey};this.data_cache=new DataManager(CACHED_DATA,this);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{draw_tile:function(m,g,b,j,n){var f=this,d=DENSITY*g;if(n>CHAR_WIDTH_PX){if(m===null){f.content_div.css("height","0px");return}var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var l=e.get(0).getContext("2d");e.get(0).width=Math.ceil(d*n+f.left_offset);e.get(0).height=f.height_px;l.font=DEFAULT_FONT;l.textAlign="center";for(var h=0,k=m.length;h<k;h++){var a=Math.round(h*n);l.fillText(m[h],a+f.left_offset,10)}return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataManager(CACHED_DATA,this);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var k=false;var j=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){k=true;h.show()},function(){k=false;if(!j){h.hide()}});h.hide().bind("dragstart",function(l,m){j=true;m.original_height=$(g.content_div).height()}).bind("drag",function(m,n){var l=Math.min(Math.max(n.original_height+n.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",l);g.height_px=l;g.draw(true)}).bind("dragend",function(l,m){g.tile_cache.clear();j=false;if(!k){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(j,q,t,c,e){if(this.vertical_range===undefined){return}var o=this,u=t*DENSITY*q,a=DENSITY*q,B=q+"_"+t,v={hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution};var b=document.createElement("canvas"),z=j.data;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);b.get(0).width=Math.ceil(a*e);b.get(0).height=o.height_px;var p=b.get(0).getContext("2d"),k=false,l=o.prefs.min_value,g=o.prefs.max_value,n=o.vertical_range,w=o.total_frequency,d=o.height_px,m=o.mode;var A=Math.round(d+l/n*d);p.beginPath();p.moveTo(0,A);p.lineTo(a*e,A);p.fillStyle="#aaa";p.stroke();p.beginPath();p.fillStyle=o.prefs.color;var x,h,f;if(z.length>1){f=Math.ceil((z[1][0]-z[0][0])*e)}else{f=10}for(var r=0,s=z.length;r<s;r++){x=Math.round((z[r][0]-u)*e);h=z[r][1];if(h===null){if(k&&m==="Filled"){p.lineTo(x,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(h/n*d);p.fillRect(x,A,f,-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);p.fillStyle="rgb("+h+","+h+","+h+")";p.fillRect(x,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){p.lineTo(x,h)}else{k=true;if(m==="Filled"){p.moveTo(x,d);p.lineTo(x,h)}else{p.moveTo(x,h)}}}}}if(m==="Filled"){if(k){p.lineTo(x,A);p.lineTo(0,A)}p.fill()}else{p.stroke()}return b}});var FeatureTrack=function(a,f,e,j,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=j;this.original_dataset_id=j;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataManager(20,this);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j+1},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<div />").addClass("yaxislabel");h.text(l);h.css({position:"absolute",top:"22px",left:"10px"});h.prependTo(this.container_div);var q=b.get(0).getContext("2d");for(var d=0,g=o.length;d<g;d++){var m=Math.floor((o[d][0]-f)*r);var k=o[d][1];if(!k){continue}var p=k/l*j;q.fillStyle="black";q.fillRect(m+e,c-p,delta_x_px,p);var a=4;if(this.prefs.show_counts&&(q.measureText(k).width+a)<delta_x_px){q.fillStyle="#666";q.textAlign="center";q.fillText(k,m+e+(delta_x_px/2),10)}}},draw_element:function(p,f,g,x,j,r,I,M,N,a,A){var u=x[0],K=x[1],C=x[2]-1,s=x[3],D=Math.floor(Math.max(0,(K-r)*M)),q=Math.ceil(Math.min(a,Math.max(0,(C-r)*M))),B=ERROR_PADDING+(g==="Dense"?0:(0+j))*N,o,G,t=null,O=null,d=this.prefs.block_color,F=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(D+A,B,q-D,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(D+A,B+5,q-D,DENSE_FEATURE_HEIGHT)}else{var n=x[5],z=x[6],E=x[7],e=x[8];if(z&&E){t=Math.floor(Math.max(0,(z-r)*M));O=Math.ceil(Math.min(a,Math.max(0,(E-r)*M)))}var L,v;if(g==="Squish"){L=1;v=SQUISH_FEATURE_HEIGHT}else{L=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(D+A,B,q-D,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=B+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=B;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(D+A,m,q-D,w);for(var J=0,c=e.length;J<c;J++){var h=e[J],b=Math.floor(Math.max(0,(h[0]-r)*M)),y=Math.ceil(Math.min(a,Math.max((h[1]-1-r)*M)));if(b>y){continue}p.fillStyle=d;p.fillRect(b+A,B+(v-L)/2+1,y-b,L);if(t!==undefined&&!(b>O||y<t)){var H=Math.max(b,t),l=Math.min(y,O);p.fillRect(H+A,B+1,l-H,v)}}}if(g==="Pack"&&K>r){p.fillStyle=F;if(f===0&&D-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+A+LABEL_SPACING,B+8)}else{p.textAlign="right";p.fillText(s,D+A-LABEL_SPACING,B+8)}p.fillStyle=d}}}},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(o,x,C,k,m,d){var t=this;var E=C*DENSITY*x,a=(C+1)*DENSITY*x,q=a-E,F={hda_ldda:t.hda_ldda,dataset_id:t.dataset_id,resolution:this.view.resolution,mode:this.mode};var v=Math.ceil(q*m),s=this.mode,H=25,g=this.left_offset,p,h;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(s==="Auto"){if(o.dataset_type==="summary_tree"){s=o.dataset_type}else{if(o.extra_info==="no_detail"){s="no_detail"}else{var G=o.data;if((G.length&&G.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){s="Squish"}else{s="Pack"}}}}var y=this.get_y_scale(s);if(s==="summary_tree"){h=this.summary_draw_height}if(s==="Dense"){h=H}else{if(s==="no_detail"||s==="Squish"||s==="Pack"){h=this.incremental_slots(m,o.data,s)*y+H;p=this.inc_slots[m]}}c.get(0).width=v+g;c.get(0).height=h;if(o.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}k.parent().css("height",Math.max(this.height_px,h)+"px");var w=c.get(0).getContext("2d");w.fillStyle=this.prefs.block_color;w.font=this.default_font;w.textAlign="right";this.container_div.find(".yaxislabel").remove();if(s==="summary_tree"){this.draw_summary_tree(c,o.data,o.delta,o.max,m,h,E,g);return c}if(o.message){c.css({"border-top":"1px solid red"});w.fillStyle="red";w.textAlign="left";var r=w.textBaseline;w.textBaseline="top";w.fillText(o.message,g,0);w.textBaseline=r;if(!o.data){return c}}this.example_feature=(o.data.length?o.data[0]:undefined);var G=o.data;for(var z=0,B=G.length;z<B;z++){var j=G[z],l=j[0],u=j[1],b=j[2],e=(p&&p[l]!==undefined?p[l]:null);var A=false;var n;for(var D=0;D<this.filters.length;D++){n=this.filters[D];n.update_attrs(j);if(!n.keep(j)){A=true;break}}if(A){continue}if(is_overlap([u,b],[E,a])&&(s=="Dense"||e!==null)){this.draw_element(w,C,s,j,e,E,a,m,y,v,g,d)}}return c}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=ERROR_PADDING+(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.difference_mode=true;this.show_insertions=false;this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.show_insertions){a*=2}}}return a},draw_read:function(m,d,J,n,D,G,e,o,y,a){m.textAlign="center";var l=this,u=[n,D],C=0,z=0,f=0;var r=[];if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){f=Math.ceil(CHAR_WIDTH_PX/2+1)}if(!e){e=[[0,o.length]]}for(var h=0,k=e.length;h<k;h++){var b=e[h],g="MIDNSHP=X"[b[0]],v=b[1];if(g==="H"||g==="S"){C-=v}var x=G+C,B=Math.floor(Math.max(0,(x-n)*J)),E=Math.floor(Math.max(0,(x+v-n)*J));switch(g){case"H":break;case"S":case"M":case"=":var p=compute_overlap([x,x+v],u);if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(f>0){m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset-f,y+1,E-B,9);m.fillStyle=CONNECTOR_COLOR;for(var I=0,j=q.length;I<j;I++){if(this.difference_mode&&a){var s=a[x-n+I];if(!s||s.toLowerCase()===q[I].toLowerCase()){continue}}if(x+I>=n&&x+I<=D){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset,y+9)}}}else{m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset,y+(this.mode!=="Dense"?4:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}z+=v;C+=v;break;case"N":m.fillStyle=CONNECTOR_COLOR;m.fillRect(B+this.left_offset-f,y+5,E-B,1);C+=v;break;case"D":m.fillStyle="red";m.fillRect(B+this.left_offset-f,y+4,E-B,3);C+=v;break;case"P":break;case"I":var p=compute_overlap([x,x+v],u),K=this.left_offset+B-f;if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(this.show_insertions){var w=this.left_offset+B-(E-B)/2;if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){m.fillStyle="yellow";m.fillRect(w-f,y-9,E-B,9);r[r.length]={type:"triangle",data:[K,y+4,5]};m.fillStyle=CONNECTOR_COLOR;switch(p){case (OVERLAP_START):q=q.slice(n-x);break;case (OVERLAP_END):q=q.slice(0,x-D);break;case (CONTAINED_BY):break;case (CONTAINS):q=q.slice(n-x,x-D);break}for(var I=0,j=q.length;I<j;I++){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset-(E-B)/2,y)}}else{m.fillStyle="yellow";m.fillRect(w,y+(this.mode!=="Dense"?2:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){r[r.length]={type:"text",data:[q.length,K,y+9]}}else{}}}z+=v;break;case"X":z+=v;break}}m.fillStyle="yellow";var t,L,H;for(var F=0;F<r.length;F++){t=r[F];L=t.type;H=t.data;if(L==="text"){m.font="bold "+DEFAULT_FONT;m.fillText(H[0],H[1],H[2]);m.font=DEFAULT_FONT}else{if(L=="triangle"){m.drawDownwardEquilateralTriangle(H[0],H[1],H[2])}}}},draw_element:function(w,y,r,k,e,A,b,n,x,u,f,c){var m=k[0],v=k[1],d=k[2],o=k[3],h=Math.floor(Math.max(0,(v-A)*n)),j=Math.ceil(Math.min(u,Math.max(0,(d-A)*n))),g=(r==="Dense"?1:(1+e))*x,z=this.prefs.block_color,l=this.prefs.label_color;t=0;w.fillStyle=z;if(k[5] instanceof Array){var s=Math.floor(Math.max(0,(k[4][0]-A)*n)),q=Math.ceil(Math.min(u,Math.max(0,(k[4][1]-A)*n))),p=Math.floor(Math.max(0,(k[5][0]-A)*n)),a=Math.ceil(Math.min(u,Math.max(0,(k[5][1]-A)*n)));if(k[4][1]>=A&&k[4][0]<=b&&k[4][2]){this.draw_read(w,r,n,A,b,k[4][0],k[4][2],k[4][3],g,c)}if(k[5][1]>=A&&k[5][0]<=b&&k[5][2]){this.draw_read(w,r,n,A,b,k[5][0],k[5][2],k[5][3],g,c)}if(p>q){w.fillStyle=CONNECTOR_COLOR;w.dashedLine(q+f,g+5,f+p,g+5)}}else{w.fillStyle=z;this.draw_read(w,r,n,A,b,v,k[4],k[5],g,c)}if(r==="Pack"&&v>A){w.fillStyle=this.prefs.label_color;if((r==="Pack"||this.mode==="Auto")&&n>CHAR_WIDTH_PX){var t=Math.round(n/2)}if(y===0&&h-w.measureText(o).width<0){w.textAlign="left";w.fillText(o,j+f+LABEL_SPACING-t,g+8)}else{w.textAlign="right";w.fillText(o,h+f-LABEL_SPACING-t,g+8)}w.fillStyle=z}}});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}}); \ No newline at end of file +CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();var c;for(c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c===f.length){if(this!==f.get(c-1)){g.append(this)}}else{if(this!==f.get(c)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!==NO_OVERLAP)}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,ERROR_PADDING=10,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",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_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;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 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()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!==-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataManager=function(b,a,c){Cache.call(this,b);this.track=a;this.subset=(c!==undefined?c:true)};$.extend(DataManager.prototype,Cache.prototype,{load_data:function(d,a,f,h,b,e){var g={chrom:d,low:a,high:f,mode:h,resolution:b,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(g,e);var c=this;return $.getJSON(this.track.data_url,g,function(j){c.set_data(a,f,h,j)})},get_data:function(j,k,c,h,b,f){var l=this.get(this.gen_key(k,c,h));if(l){return l}if(this.subset){var m,g,a,e,h,l;for(var d=0;d<this.key_ary.length;d++){m=this.key_ary[d];g=this.split_key(m);a=g[0];e=g[1];if(k>=a&&c<=e){l=this.obj_cache[m];if(l.dataset_type!=="summary_tree"&&l.extra_info!=="no_detail"){this.move_key_to_end(m,d);return l}}}}return this.load_data(j,k,c,h,b,f)},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();$(this).val("");a.location_span.show();a.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",b).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.val(a.chrom+":"+a.low+"-"+a.high);a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var j=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(j/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,k){var f=$(this);var l=k.offsetX-k.current_x;var g=f.scrollTop()-(h.clientY-k.current_height);f.scrollTop(g);k.current_height=h.clientY;k.current_x=k.offsetX;var j=Math.round(l/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}).bind("mousewheel",function(h,k,g,f){if(g){var j=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(k,l){$(l.proxy).css({left:Math.min(k.pageX,l.startX),width:Math.abs(k.pageX-l.startX)});var g=Math.min(k.pageX,l.startX)-a.container.offset().left,f=Math.max(k.pageX,l.startX)-a.container.offset().left,j=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*j)+a.low,Math.round(f/h*j)+a.low)}).bind("dragend",function(l,m){var g=Math.min(l.pageX,m.startX),f=Math.max(l.pageX,m.startX),j=(a.high-a.low),h=a.viewport_container.width(),k=a.low;a.low=Math.round(g/h*j)+k;a.high=Math.round(f/h*j)+k;$(m.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.chrom_info.length===0){alert("Invalid chromosome: "+b.chrom);return}if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e==="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e==="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len-1;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var k=this,a,d,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}k.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},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);sortable(a.container_div,".draghandle");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())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;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(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()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)===0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};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.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_url_extra_params={};this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.make_name_popup_menu()}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(b,j,n){var c=this,o=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(j!==undefined?get_tool_from_dict(j):undefined);this.parent_track=n;this.child_tracks=[];if(c.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});$.each(this.filters,function(t,w){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var v=$("<div/>").addClass("slider-label").appendTo(u);var s=$("<span/>").addClass("name").appendTo(v);s.text(w.name+" ");var r=$("<span/>").addClass("values").appendTo(v);var q=$("<div/>").addClass("slider").appendTo(u);w.control_element=$("<div/>").attr("id",w.name+"-filter-control").appendTo(q);w.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(y,z){var x=z.values;r.text("["+x[0]+"-"+x[1]+"]");w.low=x[0];w.high=x[1];c.draw(true,true)},change:function(x,y){w.control_element.slider("option","slide").call(w.control_element,x,y)}});w.slider=w.control_element;w.slider_label=r;$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(q){q.stopPropagation()}).bind("click",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});var m=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var l=this.tool.params;var c=this;$.each(this.tool.params,function(x,s){var v=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(v);var z=$("<span class='param-name'>").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var w=$("<span class='param-value'>").appendTo(u).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(v);var q=$("<div id='"+s.name+"-param-control'>").appendTo(y);var r=(s.max<=1?0.01:(s.max<=1000?1:5));q.slider({min:s.min,max:s.max,step:r,value:s.value,slide:function(A,C){var B=C.value;s.value=B;if(0<B&&B<1){B=parseFloat(B).toFixed(2)}t.text(B)},change:function(A,B){s.value=B.value}});w.click(function(){var C=t,B=C.text(),A=(s.max<=1?4:s.max.length);C.text("");$("<input type='text'/>").attr("size",A).attr("maxlength",A).attr("value",B).appendTo(C).focus().select().click(function(D){D.stopPropagation()}).blur(function(){$(this).remove();C.text(B)}).keyup(function(F){if(F.keyCode===27){$(this).trigger("blur")}else{if(F.keyCode===13){var D=$(this),E=parseFloat(D.val());if(isNaN(E)||E>s.max||E<s.min){alert("Parameter value must be in the range ["+s.min+"-"+s.max+"]");return $(this)}C.text(E);q.slider("value",E);s.value=E}}})});$("<div style='clear: both;'/>").appendTo(v)});var p=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var k=$("<input type='submit'>").attr("value","Run").appendTo(p);var c=this;k.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(q){c.mode_div.text(q);c.mode=q;c.track_config.values.mode=q;c.tile_cache.clear();c.draw()};var a={};for(var f=0,h=c.display_modes.length;f<h;f++){var g=c.display_modes[f];a[g]=function(q){return function(){d(q)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide Tool":"Show Tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},draw:function(a,d){var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),m=this.view.resolution;var e=$("<div style='position: relative;'></div>"),f=l/j;if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}if(d){var k=this;var q=setInterval(function(){if(obj_length(c)===0){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var x=$(v[w]);if(u){x.remove()}else{if(x.children().length!==0){u=true}}}clearInterval(q)}},50)}for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,g,l,c,e,k,m,f){var d=this;var h=function(u,n,p,o,s,t,q){returned_tile=d.draw_tile(n,p,o,s,t,q);var r=$("<div class='track-tile'>").prepend(returned_tile);tile_element=r;d.tile_cache.set(j,tile_element);d.show_tile(tile_element,s,g,t);delete f[u]};var a=setTimeout(function(){if(g<=d.view.high&&l>=d.view.low){var n=(b?undefined:d.tile_cache.get(j));if(n){d.show_tile(n,k,g,m);delete f[a]}else{$.when(d.data_cache.get_data(view.chrom,g,l,d.mode,e,d.data_url_extra_params)).then(function(){var o=d.data_cache.get_data(view.chrom,g,l,d.mode,e,d.data_url_extra_params);if(view.reference_track&&m>CHAR_WIDTH_PX){$.when(view.reference_track.data_cache.get_data(view.chrom,g,l,d.mode,e,view.reference_track.data_url_extra_params)).then(function(){var p=view.reference_track.data_cache.get_data(view.chrom,g,l,d.mode,e,view.reference_track.data_url_extra_params);h(a,o,e,c,k,m,p)})}else{h(a,o,e,c,k,m)}})}}},50);f[a]=true},show_tile:function(h,j,e,k){var a=this;var c=this.view.high-this.view.low,b=(e-this.view.low)*k;if(this.left_offset){b-=this.left_offset}h.css({position:"absolute",top:0,left:b,height:""});j.append(h);a.max_height=Math.max(a.max_height,h.height());a.content_div.css("height",a.max_height+"px");j.children().css("height",a.max_height+"px");if(a.hidden){return}for(var g=0;g<a.filters.length;g++){a.filters[g].update_ui_elt()}var d=false;if(a.example_feature){for(var g=0;g<a.filters.length;g++){if(a.filters[g].applies_to(a.example_feature)){d=true;break}}}if(a.filters_available!==d){a.filters_available=d;if(!a.filters_available){a.filters_div.hide()}a.make_name_popup_menu()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:a.dbkey};this.data_cache=new DataManager(CACHED_DATA,this,false);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{draw_tile:function(m,g,b,j,n){var f=this,d=DENSITY*g;if(n>CHAR_WIDTH_PX){if(m===null){f.content_div.css("height","0px");return}var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var l=e.get(0).getContext("2d");e.get(0).width=Math.ceil(d*n+f.left_offset);e.get(0).height=f.height_px;l.font=DEFAULT_FONT;l.textAlign="center";for(var h=0,k=m.length;h<k;h++){var a=Math.round(h*n);l.fillText(m[h],a+f.left_offset,10)}return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataManager(CACHED_DATA,this);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var k=false;var j=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){k=true;h.show()},function(){k=false;if(!j){h.hide()}});h.hide().bind("dragstart",function(l,m){j=true;m.original_height=$(g.content_div).height()}).bind("drag",function(m,n){var l=Math.min(Math.max(n.original_height+n.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",l);g.height_px=l;g.draw(true)}).bind("dragend",function(l,m){g.tile_cache.clear();j=false;if(!k){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(j,q,t,c,e){if(this.vertical_range===undefined){return}var o=this,u=t*DENSITY*q,a=DENSITY*q,B=q+"_"+t,v={hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution};var b=document.createElement("canvas"),z=j.data;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);b.get(0).width=Math.ceil(a*e);b.get(0).height=o.height_px;var p=b.get(0).getContext("2d"),k=false,l=o.prefs.min_value,g=o.prefs.max_value,n=o.vertical_range,w=o.total_frequency,d=o.height_px,m=o.mode;var A=Math.round(d+l/n*d);p.beginPath();p.moveTo(0,A);p.lineTo(a*e,A);p.fillStyle="#aaa";p.stroke();p.beginPath();p.fillStyle=o.prefs.color;var x,h,f;if(z.length>1){f=Math.ceil((z[1][0]-z[0][0])*e)}else{f=10}for(var r=0,s=z.length;r<s;r++){x=Math.round((z[r][0]-u)*e);h=z[r][1];if(h===null){if(k&&m==="Filled"){p.lineTo(x,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(h/n*d);p.fillRect(x,A,f,-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);p.fillStyle="rgb("+h+","+h+","+h+")";p.fillRect(x,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){p.lineTo(x,h)}else{k=true;if(m==="Filled"){p.moveTo(x,d);p.lineTo(x,h)}else{p.moveTo(x,h)}}}}}if(m==="Filled"){if(k){p.lineTo(x,A);p.lineTo(0,A)}p.fill()}else{p.stroke()}return b}});var FeatureTrack=function(a,f,e,j,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=j;this.original_dataset_id=j;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataManager(20,this);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j+1},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<div />").addClass("yaxislabel");h.text(l);h.css({position:"absolute",top:"22px",left:"10px"});h.prependTo(this.container_div);var q=b.get(0).getContext("2d");for(var d=0,g=o.length;d<g;d++){var m=Math.floor((o[d][0]-f)*r);var k=o[d][1];if(!k){continue}var p=k/l*j;q.fillStyle="black";q.fillRect(m+e,c-p,delta_x_px,p);var a=4;if(this.prefs.show_counts&&(q.measureText(k).width+a)<delta_x_px){q.fillStyle="#666";q.textAlign="center";q.fillText(k,m+e+(delta_x_px/2),10)}}},draw_element:function(p,f,g,x,j,r,I,M,N,a,A){var u=x[0],K=x[1],C=x[2]-1,s=x[3],D=Math.floor(Math.max(0,(K-r)*M)),q=Math.ceil(Math.min(a,Math.max(0,(C-r)*M))),B=ERROR_PADDING+(g==="Dense"?0:(0+j))*N,o,G,t=null,O=null,d=this.prefs.block_color,F=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(D+A,B,q-D,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(D+A,B+5,q-D,DENSE_FEATURE_HEIGHT)}else{var n=x[5],z=x[6],E=x[7],e=x[8];if(z&&E){t=Math.floor(Math.max(0,(z-r)*M));O=Math.ceil(Math.min(a,Math.max(0,(E-r)*M)))}var L,v;if(g==="Squish"){L=1;v=SQUISH_FEATURE_HEIGHT}else{L=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(D+A,B,q-D,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=B+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=B;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(D+A,m,q-D,w);for(var J=0,c=e.length;J<c;J++){var h=e[J],b=Math.floor(Math.max(0,(h[0]-r)*M)),y=Math.ceil(Math.min(a,Math.max((h[1]-1-r)*M)));if(b>y){continue}p.fillStyle=d;p.fillRect(b+A,B+(v-L)/2+1,y-b,L);if(t!==undefined&&!(b>O||y<t)){var H=Math.max(b,t),l=Math.min(y,O);p.fillRect(H+A,B+1,l-H,v)}}}if(g==="Pack"&&K>r){p.fillStyle=F;if(f===0&&D-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+A+LABEL_SPACING,B+8)}else{p.textAlign="right";p.fillText(s,D+A-LABEL_SPACING,B+8)}p.fillStyle=d}}}},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(o,x,C,k,m,d){var t=this;var E=C*DENSITY*x,a=(C+1)*DENSITY*x,q=a-E,F={hda_ldda:t.hda_ldda,dataset_id:t.dataset_id,resolution:this.view.resolution,mode:this.mode};var v=Math.ceil(q*m),s=this.mode,H=25,g=this.left_offset,p,h;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(s==="Auto"){if(o.dataset_type==="summary_tree"){s=o.dataset_type}else{if(o.extra_info==="no_detail"){s="no_detail"}else{var G=o.data;if((G.length&&G.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){s="Squish"}else{s="Pack"}}}}var y=this.get_y_scale(s);if(s==="summary_tree"){h=this.summary_draw_height}if(s==="Dense"){h=H}else{if(s==="no_detail"||s==="Squish"||s==="Pack"){h=this.incremental_slots(m,o.data,s)*y+H;p=this.inc_slots[m]}}c.get(0).width=v+g;c.get(0).height=h;if(o.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}k.parent().css("height",Math.max(this.height_px,h)+"px");var w=c.get(0).getContext("2d");w.fillStyle=this.prefs.block_color;w.font=this.default_font;w.textAlign="right";this.container_div.find(".yaxislabel").remove();if(s==="summary_tree"){this.draw_summary_tree(c,o.data,o.delta,o.max,m,h,E,g);return c}if(o.message){c.css({"border-top":"1px solid red"});w.fillStyle="red";w.textAlign="left";var r=w.textBaseline;w.textBaseline="top";w.fillText(o.message,g,0);w.textBaseline=r;if(!o.data){return c}}this.example_feature=(o.data.length?o.data[0]:undefined);var G=o.data;for(var z=0,B=G.length;z<B;z++){var j=G[z],l=j[0],u=j[1],b=j[2],e=(p&&p[l]!==undefined?p[l]:null);var A=false;var n;for(var D=0;D<this.filters.length;D++){n=this.filters[D];n.update_attrs(j);if(!n.keep(j)){A=true;break}}if(A){continue}if(is_overlap([u,b],[E,a])&&(s=="Dense"||e!==null)){this.draw_element(w,C,s,j,e,E,a,m,y,v,g,d)}}return c}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=ERROR_PADDING+(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:c,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.track_config.values.show_insertions){a*=2}}}return a},draw_read:function(m,d,J,n,D,G,e,o,y,a){m.textAlign="center";var l=this,u=[n,D],C=0,z=0,f=0;var r=[];if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){f=Math.round(J/2)}if(!e){e=[[0,o.length]]}for(var h=0,k=e.length;h<k;h++){var b=e[h],g="MIDNSHP=X"[b[0]],v=b[1];if(g==="H"||g==="S"){C-=v}var x=G+C,B=Math.floor(Math.max(0,(x-n)*J)),E=Math.floor(Math.max(0,(x+v-n)*J));switch(g){case"H":break;case"S":case"M":case"=":var p=compute_overlap([x,x+v],u);if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(f>0){m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset-f,y+1,E-B,9);m.fillStyle=CONNECTOR_COLOR;for(var I=0,j=q.length;I<j;I++){if(this.track_config.values.show_differences&&a){var s=a[x-n+I];if(!s||s.toLowerCase()===q[I].toLowerCase()){continue}}if(x+I>=n&&x+I<=D){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset,y+9)}}}else{m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset,y+(this.mode!=="Dense"?4:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}z+=v;C+=v;break;case"N":m.fillStyle=CONNECTOR_COLOR;m.fillRect(B+this.left_offset-f,y+5,E-B,1);C+=v;break;case"D":m.fillStyle="red";m.fillRect(B+this.left_offset-f,y+4,E-B,3);C+=v;break;case"P":break;case"I":var p=compute_overlap([x,x+v],u),K=this.left_offset+B-f;if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(this.track_config.values.show_insertions){var w=this.left_offset+B-(E-B)/2;if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){m.fillStyle="yellow";m.fillRect(w-f,y-9,E-B,9);r[r.length]={type:"triangle",data:[K,y+4,5]};m.fillStyle=CONNECTOR_COLOR;switch(p){case (OVERLAP_START):q=q.slice(n-x);break;case (OVERLAP_END):q=q.slice(0,x-D);break;case (CONTAINED_BY):break;case (CONTAINS):q=q.slice(n-x,x-D);break}for(var I=0,j=q.length;I<j;I++){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset-(E-B)/2,y)}}else{m.fillStyle="yellow";m.fillRect(w,y+(this.mode!=="Dense"?2:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){r[r.length]={type:"text",data:[q.length,K,y+9]}}else{}}}z+=v;break;case"X":z+=v;break}}m.fillStyle="yellow";var t,L,H;for(var F=0;F<r.length;F++){t=r[F];L=t.type;H=t.data;if(L==="text"){m.font="bold "+DEFAULT_FONT;m.fillText(H[0],H[1],H[2]);m.font=DEFAULT_FONT}else{if(L=="triangle"){m.drawDownwardEquilateralTriangle(H[0],H[1],H[2])}}}},draw_element:function(w,y,r,k,e,A,b,n,x,u,f,c){var m=k[0],v=k[1],d=k[2],o=k[3],h=Math.floor(Math.max(0,(v-A)*n)),j=Math.ceil(Math.min(u,Math.max(0,(d-A)*n))),g=(r==="Dense"?1:(1+e))*x,z=this.prefs.block_color,l=this.prefs.label_color;t=0;w.fillStyle=z;if(k[5] instanceof Array){var s=Math.floor(Math.max(0,(k[4][0]-A)*n)),q=Math.ceil(Math.min(u,Math.max(0,(k[4][1]-A)*n))),p=Math.floor(Math.max(0,(k[5][0]-A)*n)),a=Math.ceil(Math.min(u,Math.max(0,(k[5][1]-A)*n)));if(k[4][1]>=A&&k[4][0]<=b&&k[4][2]){this.draw_read(w,r,n,A,b,k[4][0],k[4][2],k[4][3],g,c)}if(k[5][1]>=A&&k[5][0]<=b&&k[5][2]){this.draw_read(w,r,n,A,b,k[5][0],k[5][2],k[5][3],g,c)}if(p>q){w.fillStyle=CONNECTOR_COLOR;w.dashedLine(q+f,g+5,f+p,g+5)}}else{w.fillStyle=z;this.draw_read(w,r,n,A,b,v,k[4],k[5],g,c)}if(r==="Pack"&&v>A){w.fillStyle=this.prefs.label_color;if((r==="Pack"||this.mode==="Auto")&&n>CHAR_WIDTH_PX){var t=Math.round(n/2)}if(y===0&&h-w.measureText(o).width<0){w.textAlign="left";w.fillText(o,j+f+LABEL_SPACING-t,g+8)}else{w.textAlign="right";w.fillText(o,h+f-LABEL_SPACING-t,g+8)}w.fillStyle=z}}});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}}); \ No newline at end of file --- a/static/scripts/trackster.js Thu Mar 24 15:05:28 2011 -0400 +++ b/static/scripts/trackster.js Thu Mar 24 17:12:16 2011 -0400 @@ -245,9 +245,10 @@ /** * Data manager for a track. */ -var DataManager = function(num_elements, track) { +var DataManager = function(num_elements, track, subset) { Cache.call(this, num_elements); this.track = track; + this.subset = (subset !== undefined ? subset : true); }; $.extend(DataManager.prototype, Cache.prototype, { /** @@ -283,30 +284,33 @@ } // + // If data supports subsetting: // Look in cache for data that can be used. Data can be reused if it // has the requested data and is not summary tree and has details. // TODO: this logic could be improved if the visualization knew whether // the data was "index" or "data." Also could slice the data so that // only data points in request are returned. // - var key, split_key, entry_low, entry_high, mode, entry; - for (var i = 0; i < this.key_ary.length; i++) { - key = this.key_ary[i]; - split_key = this.split_key(key); - entry_low = split_key[0]; - entry_high = split_key[1]; + if (this.subset) { + var key, split_key, entry_low, entry_high, mode, entry; + for (var i = 0; i < this.key_ary.length; i++) { + key = this.key_ary[i]; + split_key = this.split_key(key); + entry_low = split_key[0]; + entry_high = split_key[1]; - if (low >= entry_low && high <= entry_high) { - // This track has the range of data needed; check other attributes. - entry = this.obj_cache[key]; - if (entry.dataset_type !== "summary_tree" && entry.extra_info !== "no_detail") { - // Data is usable. - this.move_key_to_end(key, i); - return entry; + if (low >= entry_low && high <= entry_high) { + // This track has the range of data needed; check other attributes. + entry = this.obj_cache[key]; + if (entry.dataset_type !== "summary_tree" && entry.extra_info !== "no_detail") { + // Data is usable. + this.move_key_to_end(key, i); + return entry; + } } } } - + // // Load data from server. // @@ -1477,20 +1481,7 @@ track.make_name_popup_menu(); }; } - - // - // For ReadTracks: show/hide insertions. - // - if (track.track_type == "ReadTrack") { - // Show/hide insertions. - var text = (track.show_insertions ? "Hide Insertions" : "Show Insertions"); - track_dropdown[text] = function() { - track.show_insertions = !track.show_insertions; - track.draw(true); - track.make_name_popup_menu(); - }; - } - + // // List chrom/contigs with data option. // @@ -1526,7 +1517,6 @@ * tiles after drawing new tiles. */ draw: function(force, clear_after) { - console.log(this.name, force, clear_after); var low = this.view.low, high = this.view.high, range = high - low, @@ -1643,16 +1633,16 @@ $.when(track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, resolution, track.data_url_extra_params)).then(function() { // Data available for track. - result = track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, - resolution, track.data_url_extra_params); + var result = track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, + resolution, track.data_url_extra_params); // If sequence data needed, get that and draw. Otherwise draw. if (view.reference_track && w_scale > CHAR_WIDTH_PX) { $.when(view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, resolution, view.reference_track.data_url_extra_params)).then(function() { - seq_data = view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high, - track.mode, resolution, - view.reference_track.data_url_extra_params); + var seq_data = view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high, + track.mode, resolution, + view.reference_track.data_url_extra_params); draw_and_show_tile(id, result, resolution, tile_index, parent_element, w_scale, seq_data); }); } @@ -1871,7 +1861,7 @@ this.content_div.css("border", "none"); this.data_url = reference_url; this.data_url_extra_params = {dbkey: view.dbkey}; - this.data_cache = new DataManager(CACHED_DATA, this); + this.data_cache = new DataManager(CACHED_DATA, this, false); this.tile_cache = new Cache(CACHED_TILES_LINE); }; $.extend(ReferenceTrack.prototype, TiledTrack.prototype, { @@ -2517,9 +2507,7 @@ * Draw FeatureTrack tile. */ draw_tile: function(result, resolution, tile_index, parent_element, w_scale, ref_seq) { - // Fetch reference sequence data if it exists and we are displaying var track = this; - var tile_low = tile_index * DENSITY * resolution, tile_high = ( tile_index + 1 ) * DENSITY * resolution, tile_span = tile_high - tile_low, @@ -2736,9 +2724,26 @@ var ReadTrack = function (name, view, hda_ldda, dataset_id, prefs, filters) { FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters); + + this.track_config = new TrackConfig( { + track: this, + params: [ + { key: 'block_color', label: 'Block color', type: 'color', default_value: '#444' }, + { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' }, + { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false }, + { key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true }, + { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true }, + { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, + ], + saved_values: prefs, + onchange: function() { + this.track.tile_cache.clear(); + this.track.draw(); + } + }); + this.prefs = this.track_config.values; + this.track_type = "ReadTrack"; - this.difference_mode = true; - this.show_insertions = false; this.make_name_popup_menu(); }; $.extend(ReadTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { @@ -2758,7 +2763,7 @@ } else { // mode === "Pack" y_scale = PACK_TRACK_HEIGHT; - if (this.show_insertions) { + if (this.track_config.values.show_insertions) { y_scale *= 2; } } @@ -2781,7 +2786,7 @@ // Gap is needed so that read is offset and hence first base can be drawn on read. // TODO-FIX: using this gap offsets reads so that their start is not visually in sync with other tracks. if ((mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) { - gap = Math.ceil(CHAR_WIDTH_PX/2 + 1); + gap = Math.round(w_scale/2); } if (!cigar) { // If no cigar string, then assume all matches @@ -2819,7 +2824,7 @@ // TODO: this can be made much more efficient by computing the complete sequence // to draw and then drawing it. for (var c = 0, str_len = seq.length; c < str_len; c++) { - if (this.difference_mode && ref_seq) { + if (this.track_config.values.show_differences && ref_seq) { var ref_char = ref_seq[seq_start - tile_low + c]; if (!ref_char || ref_char.toLowerCase() === seq[c].toLowerCase()) { continue; @@ -2869,7 +2874,7 @@ var seq = orig_seq.slice(seq_offset, seq_offset + cig_len); // Insertion point is between the sequence start and the previous base: (-gap) moves // back from sequence start to insertion point. - if (this.show_insertions) { + if (this.track_config.values.show_insertions) { // // Show inserted sequence above, centered on insertion point. // @@ -2955,7 +2960,6 @@ * Draw a complete read. */ draw_element: function(ctx, tile_index, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width, left_offset, ref_seq) { - // All features need a start, end, and vertical center. var feature_uid = feature[0], @@ -3029,7 +3033,7 @@ this.dataset_check_url = dataset_state_url; }; -$.extend( ToolDataFeatureTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { +$.extend(ToolDataFeatureTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { /** * For this track type, the predraw init sets up postdraw init. */ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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