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commit/galaxy-central: 2 new changesets
by Bitbucket 03 Mar '11

03 Mar '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6f881204cc20/ changeset: r5167:6f881204cc20 user: natefoo date: 2011-03-03 18:21:22 summary: Cause lines_diff on pdf test outputs to only count the lines of a pdf which are not already ignored. affected #: 1 file (346 bytes) --- a/test/base/twilltestcase.py Thu Mar 03 12:03:41 2011 -0500 +++ b/test/base/twilltestcase.py Thu Mar 03 12:21:22 2011 -0500 @@ -64,7 +64,6 @@ allowed_diff_count = int(attributes.get( 'lines_diff', 0 )) diff = list( difflib.unified_diff( local_file, history_data, "local_file", "history_data" ) ) diff_lines = get_lines_diff( diff ) - log.debug('## files diff on %s and %s lines_diff=%d, found diff = %d' % (file1,file2,allowed_diff_count,diff_lines)) if diff_lines > allowed_diff_count: diff_slice = diff[0:40] #FIXME: This pdf stuff is rather special cased and has not been updated to consider lines_diff @@ -78,6 +77,7 @@ # not differ we're ok. valid_diff_strs = [ 'description', 'createdate', 'creationdate', 'moddate', 'id', 'producer', 'creator', 'extgstate', 'ais' ] valid_diff = False + invalid_diff_lines = 0 for line in diff_slice: # Make sure to lower case strings before checking. line = line.lower() @@ -91,10 +91,14 @@ # Stop checking as soon as we know we have a valid difference break if not valid_diff: - # Print out diff_slice so we can see what failed - print "###### diff_slice ######" - raise AssertionError( "".join( diff_slice ) ) + invalid_diff_lines += 1 + log.info('## files diff on %s and %s lines_diff=%d, found diff = %d, found pdf invalid diff = %d' % (file1,file2,allowed_diff_count,diff_lines,invalid_diff_lines)) + if invalid_diff_lines > allowed_diff_count: + # Print out diff_slice so we can see what failed + print "###### diff_slice ######" + raise AssertionError( "".join( diff_slice ) ) else: + log.info('## files diff on %s and %s lines_diff=%d, found diff = %d' % (file1,file2,allowed_diff_count,diff_lines)) for line in diff_slice: for char in line: if ord( char ) > 128: http://bitbucket.org/galaxy/galaxy-central/changeset/a184ad71d151/ changeset: r5168:a184ad71d151 user: natefoo date: 2011-03-03 18:21:44 summary: Use lines_diff on the pdf outputs of various R-based tools. affected #: 5 files (105 bytes) --- a/tools/multivariate_stats/cca.xml Thu Mar 03 12:21:22 2011 -0500 +++ b/tools/multivariate_stats/cca.xml Thu Mar 03 12:21:44 2011 -0500 @@ -52,7 +52,7 @@ <param name="y_scale" value="scale"/><param name="std_scores" value="yes"/><output name="out_file1" file="cca_out1.tabular"/> - <output name="out_file2" file="cca_out2.pdf"/> + <output name="out_file2" file="cca_out2.pdf" lines_diff="6"/></test></tests><help> --- a/tools/multivariate_stats/kpca.xml Thu Mar 03 12:21:22 2011 -0500 +++ b/tools/multivariate_stats/kpca.xml Thu Mar 03 12:21:44 2011 -0500 @@ -108,7 +108,7 @@ <param name="scale" value="1"/><param name="degree" value="2"/><output name="out_file1" file="kpca_out1.tabular"/> - <output name="out_file2" file="kpca_out2.pdf"/> + <output name="out_file2" file="kpca_out2.pdf" lines_diff="6"/></test></tests><help> --- a/tools/multivariate_stats/pca.xml Thu Mar 03 12:21:22 2011 -0500 +++ b/tools/multivariate_stats/pca.xml Thu Mar 03 12:21:44 2011 -0500 @@ -47,14 +47,14 @@ <param name="var_cols" value="1,2,3,4"/><param name="method" value="cor"/><output name="out_file1" file="pca_out1.tabular"/> - <output name="out_file2" file="pca_out2.pdf"/> + <output name="out_file2" file="pca_out2.pdf" lines_diff="6"/></test><test><param name="input1" value="iris.tabular"/><param name="var_cols" value="1,2,3,4"/><param name="method" value="cov"/><output name="out_file1" file="pca_out3.tabular"/> - <output name="out_file2" file="pca_out4.pdf"/> + <output name="out_file2" file="pca_out4.pdf" lines_diff="6"/></test><test><param name="input1" value="iris.tabular"/> @@ -62,7 +62,7 @@ <param name="method" value="svd"/><param name="scale" value="both"/><output name="out_file1" file="pca_out5.tabular"/> - <output name="out_file2" file="pca_out6.pdf"/> + <output name="out_file2" file="pca_out6.pdf" lines_diff="6"/></test></tests><help> --- a/tools/plotting/histogram2.xml Thu Mar 03 12:21:22 2011 -0500 +++ b/tools/plotting/histogram2.xml Thu Mar 03 12:21:44 2011 -0500 @@ -22,7 +22,7 @@ <param name="xlab" value="V1"/><param name="density" value="true"/><param name="frequency" value="false"/> - <output name="out_file1" file="histogram_out1.pdf" /> + <output name="out_file1" file="histogram_out1.pdf" lines_diff="6" /></test></tests><requirements> --- a/tools/regVariation/linear_regression.xml Thu Mar 03 12:21:22 2011 -0500 +++ b/tools/regVariation/linear_regression.xml Thu Mar 03 12:21:44 2011 -0500 @@ -29,7 +29,7 @@ <param name="response_col" value="3"/><param name="predictor_cols" value="1,2"/><output name="out_file1" file="regr_out.tabular"/> - <output name="out_file2" file="regr_out.pdf"/> + <output name="out_file2" file="regr_out.pdf" lines_diff="6"/></test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kellyv: Updated first test output file for SRMA wrapper to get it passing
by Bitbucket 03 Mar '11

03 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b42ad6209632/ changeset: r5166:b42ad6209632 user: kellyv date: 2011-03-03 18:03:41 summary: Updated first test output file for SRMA wrapper to get it passing affected #: 1 file (22 bytes) Binary file test-data/srma_out1.bam has changed 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 bug fixes for drawing feature tracks in squish and dense mode.
by Bitbucket 03 Mar '11

03 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/637aab626ea7/ changeset: r5165:637aab626ea7 user: jgoecks date: 2011-03-03 17:47:10 summary: Trackster bug fixes for drawing feature tracks in squish and dense mode. affected #: 1 file (48 bytes) --- a/static/scripts/trackster.js Thu Mar 03 08:29:15 2011 -0500 +++ b/static/scripts/trackster.js Thu Mar 03 11:47:10 2011 -0500 @@ -1,5 +1,5 @@ /* Trackster - 2010, James Taylor, Kanwei Li, Jeremy Goecks + 2010-2011: James Taylor, Kanwei Li, Jeremy Goecks */ /** @@ -2336,7 +2336,7 @@ // Dense mode displays the same for all data. if (mode === "Dense") { ctx.fillStyle = block_color; - ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, DENSE_FEATURE_HEIGHT); + ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, DENSE_FEATURE_HEIGHT); } else if (mode === "no_detail") { // No details for feature, so only one way to display. @@ -2345,7 +2345,7 @@ ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, DENSE_FEATURE_HEIGHT); } else { // Mode is either Squish or Pack: - // Feature has details. + // Feature details. var feature_strand = feature[5], feature_ts = feature[6], feature_te = feature[7], @@ -2378,10 +2378,9 @@ } } else { // No strand. - ctx.fillStyle = CONNECTOR_COLOR; + ctx.fillStyle = block_color; } - ctx.fillRect(f_start + left_offset, y_center + (thick_height-thin_height)/2 + 1, - f_end - f_start, thick_height); + ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, thick_height); } else { // There are feature blocks and mode is either Squish or Pack. @@ -2642,8 +2641,8 @@ continue; } - // Draw feature. - if (is_overlap([feature_start, feature_end], [tile_low, tile_high]) && slot !== null) { + // 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)) { this.draw_element(ctx, tile_index, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width, left_offset, ref_seq); } 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: New test data output for histogram tool.
by Bitbucket 03 Mar '11

03 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/cea1443d9f75/ changeset: r5164:cea1443d9f75 user: natefoo date: 2011-03-03 14:29:15 summary: New test data output for histogram tool. affected #: 1 file (84 bytes) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: trackster: reorganize drawing so that it's callback based. Now it will only draw read tracks after reference sequence is downloaded, if applicable.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/819b32d5a336/ changeset: r5163:819b32d5a336 user: kanwei date: 2011-03-03 00:03:51 summary: trackster: reorganize drawing so that it's callback based. Now it will only draw read tracks after reference sequence is downloaded, if applicable. affected #: 2 files (1.2 KB) --- a/static/scripts/packed/trackster.js Wed Mar 02 17:31:09 2011 -0500 +++ b/static/scripts/packed/trackster.js Wed Mar 02 18:03:51 2011 -0500 @@ -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;for(var 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=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(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)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!=NO_OVERLAP)}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. 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"+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.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;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<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)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.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=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.name_div.data("menu_options")["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+a.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.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(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.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.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(u){u.stopPropagation()}).bind("dblclick",function(u){u.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(x,A){var w=$("<tr>").appendTo(t);var z=$("<th class='filter-info'>").appendTo(w);var v=$("<span class='name'>").appendTo(z);v.text(A.name+" ");var u=$("<span class='values'>").appendTo(z);var y=$("<td>").appendTo(w);A.control_element=$("<div id='"+A.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(y);A.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(C,D){var B=D.values;u.text("["+B[0]+"-"+B[1]+"]");A.low=B[0];A.high=B[1];o.draw(true)},change:function(B,C){A.control_element.slider("option","slide").call(A.control_element,B,C)}});A.slider=A.control_element;A.slider_label=u});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(u){u.stopPropagation()}).bind("click",function(u){u.stopPropagation()}).bind("dblclick",function(u){u.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(B,w){var z=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var y=$("<div>").addClass("slider-label").appendTo(z);var D=$("<span class='param-name'>").text(w.label+" ").appendTo(y);var x=$("<span/>").text(w.value);var A=$("<span class='param-value'>").appendTo(y).append("[").append(x).append("]");var C=$("<div/>").addClass("slider").appendTo(z);var u=$("<div id='"+w.name+"-param-control'>").appendTo(C);var v=(w.max<=1?0.01:(w.max<=1000?1:5));u.slider({min:w.min,max:w.max,step:v,value:w.value,slide:function(E,G){var F=G.value;w.value=F;if(0<F&&F<1){F=parseFloat(F).toFixed(2)}x.text(F)},change:function(E,F){w.value=F.value}});A.click(function(){var G=x,F=G.text(),E=(w.max<=1?4:w.max.length);G.text("");$("<input type='text'/>").attr("size",E).attr("maxlength",E).attr("value",F).appendTo(G).focus().select().click(function(H){H.stopPropagation()}).blur(function(){$(this).remove();G.text(F)}).keyup(function(J){if(J.keyCode===27){$(this).trigger("blur")}else{if(J.keyCode===13){var H=$(this),I=parseFloat(H.val());if(isNaN(I)||I>w.max||I<w.min){alert("Parameter value must be in the range ["+w.min+"-"+w.max+"]");return $(this)}G.text(I);u.slider("value",I);w.value=I}}})});$("<div style='clear: both;'/>").appendTo(z)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=(o.track_config&&o.track_config.values.mode?o.track_config.values.mode:o.display_modes[0]);o.mode=m;o.mode_div.text(m);var a=function(u){o.mode_div.text(u);o.mode=u;o.track_config.values.mode=u;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(u){return function(){a(u)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var w=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},v=function(x){if((x.keyCode||x.which)===27){w()}else{if((x.keyCode||x.which)===13){u()}}};$(window).bind("keypress.check_enter_esc",v);show_modal("Configure Track",o.track_config.build_form(),{Cancel:w,OK:u})};if(o.filters.length>0){h["Show filters"]=function(){var u;if(!o.filtering_div.is(":visible")){u="Hide filters";o.filters_visible=true}else{u="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var u;if(!o.dynamic_tool_div.is(":visible")){u="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{u="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,j=g-m,c=this.view.container.width(),f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),r=c/j;this.content_div.append(p);this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=0;while((a*DENSITY*f)<g){var n=c+"_"+r+"_"+a;var e=this.tile_cache.get(n);var k=a*DENSITY*this.view.resolution;var q=k+DENSITY*this.view.resolution;if(!b&&e){this.show_tile(e,p,k,r)}else{this.delayed_draw(b,n,k,q,a,f,p,r)}a+=1}var d=this;var o=setInterval(function(){if(l===0){var u=d.content_div.children();var t=false;for(var v=u.length-1,s=0;v>=s;v--){var x=$(u[v]);if(t){x.remove()}else{if(x.children().length!==0){t=true}}}for(var w=0;w<d.filters.length;w++){d.filters[w].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(b)}},delayed_draw:function(b,g,f,j,c,e,h,k){var d=this;var a=setTimeout(function(){if(f<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(g)}if(!l){l=d.draw_tile(e,c,h,k);if(l){var m=$("<div class='track-tile'>").prepend(l);if(l.hasClass(FILTERABLE_CLASS)){m.addClass(FILTERABLE_CLASS)}l=m}}if(l){d.tile_cache.set(g,l);d.show_tile(l,h,f,k)}}},50)},show_tile:function(a,f,d,g){var b=this;var c=this.view.high-this.view.low,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},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};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.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($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,l,p){var g=b*DENSITY*f,d=DENSITY*f,k=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var o=e.get(0).getContext("2d");if(p>CHAR_WIDTH_PX){if(this.data_cache.get(k)===undefined){this.get_data(f,b);return}var n=this.data_cache.get(k);if(n===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*p+this.left_offset);e.get(0).height=this.height_px;for(var h=0,m=n.length;h<m;h++){var a=Math.round(h*p),j=Math.round(p/2);o.fillText(n[h],a+this.left_offset+j,10)}l.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(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 DataCache(CACHED_DATA);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=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.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.data_queue={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<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],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=(g==="Dense"?1:(1+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+5,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=CONNECTOR_COLOR}p.fillRect(D+A,B+(v-L)/2+1,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]-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-1);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}}}},draw_tile:function(u,z,j,l){var B=z*DENSITY*u,a=(z+1)*DENSITY*u,p=a-B;var n=this.data_cache.get_data(B,a,this.mode);if(n===undefined||n==="pending"||(this.mode!=="Auto"&&n.dataset_type==="summary_tree")){this.data_queue[[B,a]]=true;this.get_data(B,a);return}var s=Math.ceil(p*l),q=this.mode,D=25,e=this.left_offset,o,g,v;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(q==="Auto"){if(n.dataset_type==="summary_tree"){q=n.dataset_type}else{if(n.extra_info==="no_detail"){q="no_detail"}else{var C=n.data;if((C.length&&C.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){q="Squish"}else{q="Pack"}}}}if(q==="summary_tree"){g=this.summary_draw_height}if(q==="Dense"){g=D;v=DENSE_TRACK_HEIGHT}else{if(q==="no_detail"){v=NO_DETAIL_TRACK_HEIGHT}else{if(q==="Squish"){v=SQUISH_TRACK_HEIGHT}else{v=PACK_TRACK_HEIGHT}}}if(q==="no_detail"||q==="Squish"||q==="Pack"){g=this.incremental_slots(l,n.data,q)*v+D;o=this.inc_slots[l]}c.get(0).width=s+e;c.get(0).height=g;if(n.dataset_type=="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}j.parent().css("height",Math.max(this.height_px,g)+"px");var t=c.get(0).getContext("2d");t.fillStyle=this.prefs.block_color;t.font=this.default_font;t.textAlign="right";this.container_div.find(".yaxislabel").remove();if(q==="summary_tree"){this.draw_summary_tree(c,n.data,n.delta,n.max,l,g,B,e);return c}if(n.message){c.css({"border-color":"red"});t.fillStyle="red";t.textAlign="left";t.fillText(n.message,100+e,v);if(!n.data){return c}}for(var A=0;A<this.filters.length;A++){if(n.data.length&&this.filters[A].applies_to(n.data[0])){c.addClass(FILTERABLE_CLASS);break}}var C=n.data;for(var w=0,y=C.length;w<y;w++){var h=C[w],k=h[0],r=h[1],b=h[2],d=(o&&o[k]!==undefined?o[k]:null);var x=false;var m;for(var A=0;A<this.filters.length;A++){m=this.filters[A];m.update_attrs(h);if(!m.keep(h)){x=true;break}}if(x){continue}if(is_overlap([r,b],[B,a])&&d!==null){this.draw_element(t,z,q,h,d,B,a,l,v,s,e)}}return c}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.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=(p==="Dense"?1:(1+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"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_read:function(w,s,n,A,d,v,l,h,g){w.textAlign="center";var b=[A,d],q=0,x=0,u=Math.round(n/2);var F=[];for(var o=0,z=l.length;o<z;o++){var m=l[o],e="MIDNSHP=X"[m[0]],p=m[1];if(e==="H"||e==="S"){q-=p}var j=v+q,E=Math.floor(Math.max(0,(j-A)*n)),k=Math.floor(Math.max(0,(j+p-A)*n));switch(e){case"H":break;case"S":case"M":case"=":var r=compute_overlap([j,j+p],b);if(r!=NO_OVERLAP){var t=h.slice(x,x+p);if((s==="Pack"||this.mode==="Auto")&&h!==undefined&&n>CHAR_WIDTH_PX){w.fillStyle=this.prefs.block_color;w.fillRect(E+this.left_offset,g+1,k-E,9);w.fillStyle=CONNECTOR_COLOR;for(var C=0,a=t.length;C<a;C++){if(j+C>=A&&j+C<=d){var D=Math.floor(Math.max(0,(j+C-A)*n));w.fillText(t[C],D+this.left_offset+u,g+9)}}}else{w.fillStyle=this.prefs.block_color;w.fillRect(E+this.left_offset,g+(this.mode!="Dense"?4:5),k-E,(s!="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}x+=p;q+=p;break;case"N":w.fillStyle=CONNECTOR_COLOR;w.fillRect(E+this.left_offset,g+5,k-E,1);q+=p;break;case"D":w.fillStyle="red";w.fillRect(E+this.left_offset,g+4,k-E,3);q+=p;break;case"P":break;case"I":var r=compute_overlap([j,j+p],b);if(r!=NO_OVERLAP){var t=h.slice(x,x+p);var f=this.left_offset+E-(k-E)/2;if((s==="Pack"||this.mode==="Auto")&&h!==undefined&&n>CHAR_WIDTH_PX){w.fillStyle="yellow";w.fillRect(f,g-9,k-E,9);F[F.length]=[f+(k-E)/2,g+4,5];w.fillStyle=CONNECTOR_COLOR;switch(r){case (OVERLAP_START):t=t.slice(A-j);break;case (OVERLAP_END):t=t.slice(0,j-d);break;case (CONTAINED_BY):break;case (CONTAINS):t=t.slice(A-j,j-d);break}for(var C=0,a=t.length;C<a;C++){var D=Math.floor(Math.max(0,(j+C-A)*n));w.fillText(t[C],D+this.left_offset+u-(k-E)/2,g)}}else{w.fillStyle="yellow";w.fillRect(f,g+(this.mode!="Dense"?2:5),k-E,(s!="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}x+=p;break;case"X":x+=p;break}}var B;for(var y=0;y<F.length;y++){B=F[y];w.fillStyle="yellow";w.drawDownwardEquilateralTriangle(B[0],B[1],B[2])}},draw_element:function(u,w,q,h,d,y,b,m,v,s,e){var l=h[0],t=h[1],c=h[2],n=h[3],g=Math.floor(Math.max(0,(t-y)*m)),j=Math.ceil(Math.min(s,Math.max(0,(c-y)*m))),f=(q==="Dense"?1:(1+d))*v,x=this.prefs.block_color,k=this.prefs.label_color;u.fillStyle=x;if(h[5] instanceof Array){var r=Math.floor(Math.max(0,(h[4][0]-y)*m)),p=Math.ceil(Math.min(s,Math.max(0,(h[4][1]-y)*m))),o=Math.floor(Math.max(0,(h[5][0]-y)*m)),a=Math.ceil(Math.min(s,Math.max(0,(h[5][1]-y)*m)));if(h[4][1]>=y&&h[4][0]<=b&&h[4][2]){this.draw_read(u,q,m,y,b,h[4][0],h[4][2],h[4][3],f)}if(h[5][1]>=y&&h[5][0]<=b&&h[5][2]){this.draw_read(u,q,m,y,b,h[5][0],h[5][2],h[5][3],f)}if(o>p){u.fillStyle=CONNECTOR_COLOR;u.dashedLine(p+e,f+5,e+o,f+5)}}else{u.fillStyle=x;this.draw_read(u,q,m,y,b,t,h[4],h[5],f)}if(q==="Pack"&&t>y){u.fillStyle=this.prefs.label_color;if(w===0&&g-u.measureText(n).width<0){u.textAlign="left";u.fillText(n,j+e+LABEL_SPACING,f+8)}else{u.textAlign="right";u.fillText(n,g+e-LABEL_SPACING,f+8)}u.fillStyle=x}}});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;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}}); \ No newline at end of file +CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(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,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",FILTERABLE_CLASS="filterable",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()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!==-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},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=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);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;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e==="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e==="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.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;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<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)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!==null){$.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=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.name_div.data("menu_options")["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+a.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.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(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.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.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(u){u.stopPropagation()}).bind("dblclick",function(u){u.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(x,A){var w=$("<tr>").appendTo(t);var z=$("<th class='filter-info'>").appendTo(w);var v=$("<span class='name'>").appendTo(z);v.text(A.name+" ");var u=$("<span class='values'>").appendTo(z);var y=$("<td>").appendTo(w);A.control_element=$("<div id='"+A.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(y);A.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(C,D){var B=D.values;u.text("["+B[0]+"-"+B[1]+"]");A.low=B[0];A.high=B[1];o.draw(true)},change:function(B,C){A.control_element.slider("option","slide").call(A.control_element,B,C)}});A.slider=A.control_element;A.slider_label=u});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(u){u.stopPropagation()}).bind("click",function(u){u.stopPropagation()}).bind("dblclick",function(u){u.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(B,w){var z=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var y=$("<div>").addClass("slider-label").appendTo(z);var D=$("<span class='param-name'>").text(w.label+" ").appendTo(y);var x=$("<span/>").text(w.value);var A=$("<span class='param-value'>").appendTo(y).append("[").append(x).append("]");var C=$("<div/>").addClass("slider").appendTo(z);var u=$("<div id='"+w.name+"-param-control'>").appendTo(C);var v=(w.max<=1?0.01:(w.max<=1000?1:5));u.slider({min:w.min,max:w.max,step:v,value:w.value,slide:function(E,G){var F=G.value;w.value=F;if(0<F&&F<1){F=parseFloat(F).toFixed(2)}x.text(F)},change:function(E,F){w.value=F.value}});A.click(function(){var G=x,F=G.text(),E=(w.max<=1?4:w.max.length);G.text("");$("<input type='text'/>").attr("size",E).attr("maxlength",E).attr("value",F).appendTo(G).focus().select().click(function(H){H.stopPropagation()}).blur(function(){$(this).remove();G.text(F)}).keyup(function(J){if(J.keyCode===27){$(this).trigger("blur")}else{if(J.keyCode===13){var H=$(this),I=parseFloat(H.val());if(isNaN(I)||I>w.max||I<w.min){alert("Parameter value must be in the range ["+w.min+"-"+w.max+"]");return $(this)}G.text(I);u.slider("value",I);w.value=I}}})});$("<div style='clear: both;'/>").appendTo(z)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=(o.track_config&&o.track_config.values.mode?o.track_config.values.mode:o.display_modes[0]);o.mode=m;o.mode_div.text(m);var a=function(u){o.mode_div.text(u);o.mode=u;o.track_config.values.mode=u;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(u){return function(){a(u)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var w=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},v=function(x){if((x.keyCode||x.which)===27){w()}else{if((x.keyCode||x.which)===13){u()}}};$(window).bind("keypress.check_enter_esc",v);show_modal("Configure Track",o.track_config.build_form(),{Cancel:w,OK:u})};if(o.filters.length>0){h["Show filters"]=function(){var u;if(!o.filtering_div.is(":visible")){u="Hide filters";o.filters_visible=true}else{u="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var u;if(!o.dynamic_tool_div.is(":visible")){u="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{u="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,j=g-m,c=this.view.container.width(),f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),r=c/j;this.content_div.append(p);this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=0;while((a*DENSITY*f)<g){var n=c+"_"+r+"_"+a;var e=this.tile_cache.get(n);var k=a*DENSITY*this.view.resolution;var q=k+DENSITY*this.view.resolution;if(!b&&e){this.show_tile(e,p,k,r)}else{this.delayed_draw(b,n,k,q,a,f,p,r)}a+=1}var d=this;var o=setInterval(function(){if(l===0){var u=d.content_div.children();var t=false;for(var v=u.length-1,s=0;v>=s;v--){var x=$(u[v]);if(t){x.remove()}else{if(x.children().length!==0){t=true}}}for(var w=0;w<d.filters.length;w++){d.filters[w].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(b)}},delayed_draw:function(b,h,g,k,c,e,j,l){var d=this;var f=function(m){d.tile_cache.set(h,m);d.show_tile(m,j,g,l)};var a=setTimeout(function(){if(g<=d.view.high&&k>=d.view.low){var m;if(!b){m=d.tile_cache.get(h)}if(!m){d.draw_tile(e,c,j,l,function(o){if(o){var n=$("<div class='track-tile'>").prepend(o);if(o.hasClass(FILTERABLE_CLASS)){n.addClass(FILTERABLE_CLASS)}m=n}f(m)})}if(m){f(m)}}},50)},show_tile:function(a,f,d,g){var b=this;var c=this.view.high-this.view.low,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},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($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{fetch_data:function(a,e,c,f){var b=this,d=b.data_cache.get(c);if(d){f(d)}else{$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:e,dbkey:this.view.dbkey},success:function(g){b.data_cache.set(c,g);f(g)},error:function(h,g,j){console.log(h,g,j)}})}},tile_data:function(c,b,f){var a=b*DENSITY*c,e=(b+1)*DENSITY*c,d=a+"_"+e;this.fetch_data(a,e,d,function(g){f(g)})},draw_tile:function(e,a,j,l,h){var d=this,f=a*DENSITY*e,c=DENSITY*e,g=e+"_"+a;if(l>CHAR_WIDTH_PX){var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);var k=b.get(0).getContext("2d");d.tile_data(e,a,function(m){if(m===null){d.content_div.css("height","0px");return}b.get(0).width=Math.ceil(c*l+d.left_offset);b.get(0).height=d.height_px;k.font=DEFAULT_FONT;k.textAlign="center";for(var p=0,n=m.length;p<n;p++){var o=Math.round(p*l);k.fillText(m[p],o+d.left_offset,10)}h(b)})}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 DataCache(CACHED_DATA);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=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,s,d,f,c){if(this.vertical_range===undefined){return}var t=s*DENSITY*p,a=DENSITY*p,z=p+"_"+s;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(z)===undefined){this.get_data(p,s);return}var w=this.data_cache.get(z);if(!w){return}b.get(0).width=Math.ceil(a*f);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,h=this.prefs.max_value,n=this.vertical_range,u=this.total_frequency,e=this.height_px,m=this.mode;var x=Math.round(e+l/n*e);o.beginPath();o.moveTo(0,x);o.lineTo(a*f,x);o.fillStyle="#aaa";o.stroke();o.beginPath();o.fillStyle=this.prefs.color;var v,j,g;if(w.length>1){g=Math.ceil((w[1][0]-w[0][0])*f)}else{g=10}for(var q=0,r=w.length;q<r;q++){v=Math.round((w[q][0]-t)*f);j=w[q][1];if(j===null){if(k&&m==="Filled"){o.lineTo(v,e)}k=false;continue}if(j<l){j=l}else{if(j>h){j=h}}if(m==="Histogram"){j=Math.round(j/n*e);o.fillRect(v,x,g,-j)}else{if(m==="Intensity"){j=255-Math.floor((j-l)/n*255);o.fillStyle="rgb("+j+","+j+","+j+")";o.fillRect(v,0,g,e)}else{j=Math.round(e-(j-l)/n*e);if(k){o.lineTo(v,j)}else{k=true;if(m==="Filled"){o.moveTo(v,e);o.lineTo(v,j)}else{o.moveTo(v,j)}}}}}if(m==="Filled"){if(k){o.lineTo(v,x);o.lineTo(0,x)}o.fill()}else{o.stroke()}c(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.data_queue={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<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],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=(g==="Dense"?1:(1+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+5,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=CONNECTOR_COLOR}p.fillRect(D+A,B+(v-L)/2+1,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]-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-1);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}}}},draw_tile:function(x,C,l,n,h,d){var t=this;if(t.view.reference_track&&n>CHAR_WIDTH_PX&&d===undefined){return t.view.reference_track.tile_data(x,C,function(f){t.draw_tile(x,C,l,n,h,f)})}var E=C*DENSITY*x,a=(C+1)*DENSITY*x,r=a-E;var p=this.data_cache.get_data(E,a,this.mode);if(p===undefined||p==="pending"||(this.mode!=="Auto"&&p.dataset_type==="summary_tree")){this.data_queue[[E,a]]=true;this.get_data(E,a);return}var v=Math.ceil(r*n),s=this.mode,G=25,g=this.left_offset,q,j,y;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(s==="Auto"){if(p.dataset_type==="summary_tree"){s=p.dataset_type}else{if(p.extra_info==="no_detail"){s="no_detail"}else{var F=p.data;if((F.length&&F.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){s="Squish"}else{s="Pack"}}}}if(s==="summary_tree"){j=this.summary_draw_height}if(s==="Dense"){j=G;y=DENSE_TRACK_HEIGHT}else{if(s==="no_detail"){y=NO_DETAIL_TRACK_HEIGHT}else{if(s==="Squish"){y=SQUISH_TRACK_HEIGHT}else{y=PACK_TRACK_HEIGHT}}}if(s==="no_detail"||s==="Squish"||s==="Pack"){j=this.incremental_slots(n,p.data,s)*y+G;q=this.inc_slots[n]}c.get(0).width=v+g;c.get(0).height=j;if(p.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}l.parent().css("height",Math.max(this.height_px,j)+"px");var w=c.get(0).getContext("2d");w.fillStyle=this.prefs.block_color;w.font=this.default_font;w.textAlign="right";this.container_div.find(".yaxislabel").remove();if(s==="summary_tree"){this.draw_summary_tree(c,p.data,p.delta,p.max,n,j,E,g);return c}if(p.message){c.css({"border-color":"red"});w.fillStyle="red";w.textAlign="left";w.fillText(p.message,100+g,y);if(!p.data){return c}}for(var D=0;D<this.filters.length;D++){if(p.data.length&&this.filters[D].applies_to(p.data[0])){c.addClass(FILTERABLE_CLASS);break}}var F=p.data;for(var z=0,B=F.length;z<B;z++){var k=F[z],m=k[0],u=k[1],b=k[2],e=(q&&q[m]!==undefined?q[m]:null);var A=false;var o;for(var D=0;D<this.filters.length;D++){o=this.filters[D];o.update_attrs(k);if(!o.keep(k)){A=true;break}}if(A){continue}if(is_overlap([u,b],[E,a])&&e!==null){this.draw_element(w,C,s,k,e,E,a,n,y,v,g,d)}}h(c)}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.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=(p==="Dense"?1:(1+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};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_read:function(z,u,p,D,d,y,m,j,h,f){z.textAlign="center";var x=this,b=[D,d],s=0,A=0,w=0;var I=[];if((u==="Pack"||this.mode==="Auto")&&j!==undefined&&p>CHAR_WIDTH_PX){w=Math.round(p/2)}for(var q=0,C=m.length;q<C;q++){var n=m[q],e="MIDNSHP=X"[n[0]],r=n[1];if(e==="H"||e==="S"){s-=r}var k=y+s,H=Math.floor(Math.max(0,(k-D)*p)),l=Math.floor(Math.max(0,(k+r-D)*p));switch(e){case"H":break;case"S":case"M":case"=":var t=compute_overlap([k,k+r],b);if(t!==NO_OVERLAP){var v=j.slice(A,A+r);if(w>0){z.fillStyle=this.prefs.block_color;z.fillRect(H+this.left_offset-w,h+1,l-H,9);z.fillStyle=CONNECTOR_COLOR;for(var F=0,a=v.length;F<a;F++){if(this.difference_mode&&f){var o=f[k-D+F];if(!o||o.toLowerCase()===v[F].toLowerCase()){continue}}if(k+F>=D&&k+F<=d){var G=Math.floor(Math.max(0,(k+F-D)*p));z.fillText(v[F],G+this.left_offset,h+9)}}}else{z.fillStyle=this.prefs.block_color;z.fillRect(H+this.left_offset,h+(this.mode!=="Dense"?4:5),l-H,(u!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}A+=r;s+=r;break;case"N":z.fillStyle=CONNECTOR_COLOR;z.fillRect(H+this.left_offset-w,h+5,l-H,1);s+=r;break;case"D":z.fillStyle="red";z.fillRect(H+this.left_offset-w,h+4,l-H,3);s+=r;break;case"P":break;case"I":var t=compute_overlap([k,k+r],b);if(t!==NO_OVERLAP){var v=j.slice(A,A+r);var g=this.left_offset+H-(l-H)/2;if((u==="Pack"||this.mode==="Auto")&&j!==undefined&&p>CHAR_WIDTH_PX){z.fillStyle="yellow";z.fillRect(g-w,h-9,l-H,9);I[I.length]=[g+(l-H)/2,h+4,5];z.fillStyle=CONNECTOR_COLOR;switch(t){case (OVERLAP_START):v=v.slice(D-k);break;case (OVERLAP_END):v=v.slice(0,k-d);break;case (CONTAINED_BY):break;case (CONTAINS):v=v.slice(D-k,k-d);break}for(var F=0,a=v.length;F<a;F++){var G=Math.floor(Math.max(0,(k+F-D)*p));z.fillText(v[F],G+this.left_offset-(l-H)/2-w,h)}}else{z.fillStyle="yellow";z.fillRect(g,h+(this.mode!=="Dense"?2:5),l-H,(u!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}A+=r;break;case"X":A+=r;break}}var E;for(var B=0;B<I.length;B++){E=I[B];z.fillStyle="yellow";z.drawDownwardEquilateralTriangle(E[0],E[1],E[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 Wed Mar 02 17:31:09 2011 -0500 +++ b/static/scripts/trackster.js Wed Mar 02 18:03:51 2011 -0500 @@ -373,7 +373,7 @@ return false; } }; - this.nav_input = $("<input/>").addClass("nav-input").hide().bind("keypress focusout", submit_nav).appendTo(this.chrom_form); + this.nav_input = $("<input/>").addClass("nav-input").hide().bind("keyup focusout", submit_nav).appendTo(this.chrom_form); this.location_span = $("<span/>").addClass("location").appendTo(this.chrom_form); this.location_span.bind("click", function() { view.location_span.hide(); @@ -1533,6 +1533,10 @@ delayed_draw: function(force, key, tile_low, tile_high, tile_index, resolution, parent_element, w_scale) { var track = this; // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data + var draw_tile = function(tile_element) { + track.tile_cache.set(key, tile_element); + track.show_tile(tile_element, parent_element, tile_low, w_scale); + }; var id = setTimeout(function() { if (tile_low <= track.view.high && tile_high >= track.view.low) { // Show/draw tile: check cache for tile; if tile not in cache, draw it. @@ -1541,16 +1545,18 @@ tile_element = track.tile_cache.get(key); } if (!tile_element) { - tile_element = track.draw_tile(resolution, tile_index, parent_element, w_scale); - if ( tile_element ) { - // Wrap element in div for background - var wrapper_element = $("<div class='track-tile'>").prepend( tile_element ); - // HACK: filtering - if ( tile_element.hasClass( FILTERABLE_CLASS ) ) { - wrapper_element.addClass( FILTERABLE_CLASS ); + track.draw_tile(resolution, tile_index, parent_element, w_scale, function(returned_tile) { + if ( returned_tile ) { + // Wrap element in div for background + var wrapper_element = $("<div class='track-tile'>").prepend( returned_tile ); + // HACK: filtering + if ( returned_tile.hasClass( FILTERABLE_CLASS ) ) { + wrapper_element.addClass( FILTERABLE_CLASS ); + } + tile_element = wrapper_element; } - tile_element = wrapper_element; - } + draw_tile(tile_element); + }); } if (tile_element) { // Store initial canvas in case we need to use it for overview @@ -1565,9 +1571,7 @@ track.set_overview(); } */ - // Add tile to cache and show tile. - track.tile_cache.set(key, tile_element); - track.show_tile(tile_element, parent_element, tile_low, w_scale); + draw_tile(tile_element); } } }, 50); @@ -1631,24 +1635,24 @@ // // Create track for tool's output immediately to provide user feedback. // - var - current_track = this, + var + current_track = this, // Set name of track to include tool name, parameters, and region used. - track_name = url_params.tool_id + - current_track.tool_region_and_parameters_str(url_params.chrom, url_params.low, url_params.high), - new_track; - - // TODO: add support for other kinds of tool data tracks. - if (current_track.track_type === 'FeatureTrack') { - new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); - } - - this.add_track(new_track); - new_track.content_div.text("Starting job."); - view.has_changes = true; - - // Run tool. - var json_run_tool = function() { + track_name = url_params.tool_id + + current_track.tool_region_and_parameters_str(url_params.chrom, url_params.low, url_params.high), + new_track; + + // TODO: add support for other kinds of tool data tracks. + if (current_track.track_type === 'FeatureTrack') { + new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); + } + + this.add_track(new_track); + new_track.content_div.text("Starting job."); + view.has_changes = true; + + // Run tool. + var json_run_tool = function() { $.getJSON(run_tool_url, url_params, function(track_data) { if (track_data === "no converter") { // No converter available for input datasets, so cannot run tool. @@ -1673,8 +1677,8 @@ new_track.init(); } }); - }; - json_run_tool(); + }; + json_run_tool(); }, /** * Utility function that creates a label string describing the region and parameters of a track's tool. @@ -1755,68 +1759,62 @@ this.tile_cache = new Cache(CACHED_TILES_LINE); }; $.extend( ReferenceTrack.prototype, TiledTrack.prototype, { - get_data: function(resolution, tile_index, key) { + fetch_data: function(low, high, key, callback) { var track = this, - low = tile_index * DENSITY * resolution, - high = ( tile_index + 1 ) * DENSITY * resolution, - internal_key = low + "_" + high; - - if (key === undefined) { key = internal_key; } - if (!track.data_queue[internal_key]) { - track.data_queue[internal_key] = true; + cached = track.data_cache.get(key); + + if (cached) { + callback(cached); + } else { $.ajax({ 'url': reference_url, 'dataType': 'json', 'data': { "chrom": this.view.chrom, "low": low, "high": high, "dbkey": this.view.dbkey }, success: function (seq) { track.data_cache.set(key, seq); - track.data_cache.set(internal_key, seq); - delete track.data_queue[internal_key]; - track.draw(); + callback(seq); }, error: function(r, t, e) { console.log(r, t, e); } }); } }, - range_data: function(low, high) { - var key = low + "_" + high; + tile_data: function(resolution, tile_index, callback) { + var low = tile_index * DENSITY * resolution, + high = ( tile_index + 1 ) * DENSITY * resolution, + key = low + "_" + high; - var data = this.data_cache.get(key); - return data; + this.fetch_data(low, high, key, function (seq) { + callback(seq); + }); }, - draw_tile: function( resolution, tile_index, parent_element, w_scale ) { - var tile_low = tile_index * DENSITY * resolution, + draw_tile: function( resolution, tile_index, parent_element, w_scale, callback ) { + var track = this, + tile_low = tile_index * DENSITY * resolution, tile_length = DENSITY * resolution, key = resolution + "_" + tile_index; - var canvas = document.createElement("canvas"); - if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } // EXCANVAS HACK - canvas = $(canvas); - - var ctx = canvas.get(0).getContext("2d"); - if (w_scale > CHAR_WIDTH_PX) { - if (this.data_cache.get(key) === undefined) { - this.get_data(resolution, tile_index, key); - return; - } + var canvas = document.createElement("canvas"); + if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } // EXCANVAS HACK + canvas = $(canvas); - var seq = this.data_cache.get(key); - if (seq === null) { - this.content_div.css("height", "0px"); - return; - } + var ctx = canvas.get(0).getContext("2d"); - canvas.get(0).width = Math.ceil( tile_length * w_scale + this.left_offset); - canvas.get(0).height = this.height_px; - ctx.font = DEFAULT_FONT; - ctx.textAlign = "center"; - for (var c = 0, str_len = seq.length; c < str_len; c++) { - var c_start = Math.round(c * w_scale); - - ctx.fillText(seq[c], c_start + this.left_offset, 10); - } - parent_element.append(canvas); - return canvas; + track.tile_data(resolution, tile_index, function(seq) { + if (seq === null) { + track.content_div.css("height", "0px"); + return; + } + canvas.get(0).width = Math.ceil( tile_length * w_scale + track.left_offset); + canvas.get(0).height = track.height_px; + ctx.font = DEFAULT_FONT; + ctx.textAlign = "center"; + for (var c = 0, str_len = seq.length; c < str_len; c++) { + var c_start = Math.round(c * w_scale); + ctx.fillText(seq[c], c_start + track.left_offset, 10); + } + // parent_element.append(canvas); + callback(canvas); + }); } this.content_div.css("height", "0px"); } @@ -1959,7 +1957,7 @@ }); } }, - draw_tile: function( resolution, tile_index, parent_element, w_scale ) { + draw_tile: function( resolution, tile_index, parent_element, w_scale, callback ) { if (this.vertical_range === undefined) { return; } @@ -2060,7 +2058,7 @@ } else { ctx.stroke(); } - return canvas; + callback(canvas); } }); @@ -2459,12 +2457,19 @@ /** * Draw FeatureTrack tile. */ - draw_tile: function(resolution, tile_index, parent_element, w_scale) { + draw_tile: function(resolution, tile_index, parent_element, w_scale, callback, ref_seq) { + // Fetch reference sequence data if it exists and we are displaying + var track = this; + if (track.view.reference_track && w_scale > CHAR_WIDTH_PX && ref_seq === undefined) { + return track.view.reference_track.tile_data(resolution, tile_index, function(ret_ref_seq) { + track.draw_tile(resolution, tile_index, parent_element, w_scale, callback, ret_ref_seq); + }); + } var tile_low = tile_index * DENSITY * resolution, tile_high = ( tile_index + 1 ) * DENSITY * resolution, tile_span = tile_high - tile_low; //console.log("drawing " + tile_low + " to " + tile_high); - + /*for (var k in this.data_cache.obj_cache) { var k_split = k.split("_"), k_low = k_split[0], k_high = k_split[1]; if (k_low <= tile_low && k_high >= tile_high) { @@ -2640,10 +2645,10 @@ // Draw feature. if (is_overlap([feature_start, feature_end], [tile_low, tile_high]) && slot !== null) { this.draw_element(ctx, tile_index, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, - width, left_offset); + width, left_offset, ref_seq); } } - return canvas; + callback(canvas); } }); @@ -2717,21 +2722,19 @@ /** * Draw a single read. */ - draw_read: function(ctx, mode, w_scale, tile_low, tile_high, feature_start, cigar, orig_seq, y_center) { + draw_read: function(ctx, mode, w_scale, tile_low, tile_high, feature_start, cigar, orig_seq, y_center, ref_seq) { ctx.textAlign = "center"; - var tile_region = [tile_low, tile_high], + var track = this, + tile_region = [tile_low, tile_high], base_offset = 0, seq_offset = 0, - gap = 0, - seq_data; + gap = 0; // Keep list of triangles that need to be drawn on top of initial drawing layer. // TODO: Eventually, we'll probably want to keep an ordered list of items to draw and then draw all // items at once. var draw_last = []; - if (view.reference_track) { - seq_data = view.reference_track.range_data(tile_low, tile_high); - } + if ((mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) { gap = Math.round(w_scale/2); } @@ -2767,8 +2770,11 @@ // 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 && seq_data && seq_data[seq_start - tile_low + c] === seq[c]) { - continue; + if (this.difference_mode && ref_seq) { + var ref_char = ref_seq[seq_start - tile_low + c]; + if (!ref_char || ref_char.toLowerCase() === seq[c].toLowerCase()) { + continue; + } } if (seq_start + c >= tile_low && seq_start + c <= tile_high) { var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); @@ -2872,7 +2878,8 @@ /** * Draw a complete read. */ - draw_element: function(ctx, tile_index, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width, left_offset) { + 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], @@ -2897,11 +2904,11 @@ // Draw left/forward read. if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) { - this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], y_center); + this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], y_center, ref_seq); } // Draw right/reverse read. if (feature[5][1] >= tile_low && feature[5][0] <= tile_high && feature[5][2]) { - this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], y_center); + this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], y_center, ref_seq); } // Draw connector. if (b2_start > b1_end) { @@ -2912,7 +2919,7 @@ } else { // Read is single. ctx.fillStyle = block_color; - this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature_start, feature[4], feature[5], y_center); + this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature_start, feature[4], feature[5], y_center, ref_seq); } if (mode === "Pack" && feature_start > tile_low) { // Draw label. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Set message type to error when history deletion fails due to sharing. Fixes #477
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/70a9d3998da6/ changeset: r5162:70a9d3998da6 user: jgoecks date: 2011-03-02 23:31:09 summary: Set message type to error when history deletion fails due to sharing. Fixes #477 affected #: 1 file (31 bytes) --- a/lib/galaxy/web/controllers/history.py Wed Mar 02 17:15:08 2011 -0500 +++ b/lib/galaxy/web/controllers/history.py Wed Mar 02 17:31:09 2011 -0500 @@ -250,9 +250,11 @@ n_deleted = 0 deleted_current = False message_parts = [] + status = SUCCESS for history in histories: if history.users_shared_with: message_parts.append( "History (%s) has been shared with others, unshare it before deleting it. " % history.name ) + status = ERROR elif not history.deleted: # We'll not eliminate any DefaultHistoryPermissions in case we undelete the history later history.deleted = True @@ -262,7 +264,6 @@ trans.new_history() trans.log_event( "History (%s) marked as deleted" % history.name ) n_deleted += 1 - status = SUCCESS if n_deleted: message_parts.append( "Deleted %d %s. " % ( n_deleted, iff( n_deleted != 1, "histories", "history" ) ) ) if deleted_current: 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: make visual analytics code compatible with HDA/LDDA changes.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2728b804c2ed/ changeset: r5161:2728b804c2ed user: jgoecks date: 2011-03-02 23:15:08 summary: Trackster: make visual analytics code compatible with HDA/LDDA changes. affected #: 1 file (46 bytes) --- a/static/scripts/trackster.js Wed Mar 02 16:21:36 2011 -0500 +++ b/static/scripts/trackster.js Wed Mar 02 17:15:08 2011 -0500 @@ -1640,7 +1640,7 @@ // TODO: add support for other kinds of tool data tracks. if (current_track.track_type === 'FeatureTrack') { - new_track = new ToolDataFeatureTrack(track_name, view, undefined, {}, {}, current_track); + new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); } this.add_track(new_track); @@ -2964,7 +2964,7 @@ 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 }, function(track_data) {}); + $.getJSON(track.dataset_state_url, { dataset_id : track.dataset_id, hda_ldda: track.hda_ldda }, function(track_data) {}); } }; post_init(); 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: Generalize setup of chrom length files for buildbot.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/defc14c13e9f/ changeset: r5160:defc14c13e9f user: natefoo date: 2011-03-02 22:21:36 summary: Generalize setup of chrom length files for buildbot. affected #: 4 files (73 bytes) --- a/buildbot_setup.sh Wed Mar 02 16:20:16 2011 -0500 +++ b/buildbot_setup.sh Wed Mar 02 16:21:36 2011 -0500 @@ -112,10 +112,13 @@ done # for wig_to_bigWig and bed_to_bigBed -if [ ! -f "tool-data/shared/ucsc/chrom/hg17.len" -a -f "test-data/wig_to_bigwig_hg17.len" ]; then - mkdir -p tool-data/shared/ucsc/chrom - cp test-data/wig_to_bigwig_hg17.len tool-data/shared/ucsc/chrom/hg17.len -fi +for build in hg17 hg18; do + if [ -f "test-data/chrom/$build.len" ]; then + echo "Copying test-data/chrom/$build.len to tool-data/shared/ucsc/chrom/" + mkdir -p tool-data/shared/ucsc/chrom + cp test-data/chrom/$build.len tool-data/shared/ucsc/chrom/$build.len + fi +done if [ -d "test-data-repo" ]; then echo "Updating test data repository" --- a/test-data/wig_to_bigwig_hg17.len Wed Mar 02 16:20:16 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -chr10 135413628 -chr10_random 113275 -chr11 134452384 -chr12 132449811 -chr12_random 466818 -chr13 114142980 -chr13_random 186858 -chr14 106368585 -chr15 100338915 -chr15_random 784346 -chr16 88827254 -chr16_random 105485 -chr17 78774742 -chr17_random 2618010 -chr18 76117153 -chr18_random 4262 -chr19 63811651 -chr19_random 301858 -chr1 245522847 -chr1_random 3897131 -chr20 62435964 -chr21 46944323 -chr22 49554710 -chr22_random 257318 -chr2 243018229 -chr2_random 418158 -chr3 199505740 -chr3_random 970716 -chr4 191411218 -chr4_random 1030282 -chr5 180857866 -chr5_random 143687 -chr6 170975699 -chr6_random 1875562 -chr6_hla_hap1 139182 -chr6_hla_hap2 150447 -chr7 158628139 -chr7_random 778964 -chr8 146274826 -chr8_random 943810 -chr9 138429268 -chr9_random 1312665 -chrM 16571 -chrX 154824264 -chrX_random 1719168 -chrY 57701691 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: Fix symlink to microbial_data.loc in buildbot setup.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e5c0e7205ae2/ changeset: r5159:e5c0e7205ae2 user: natefoo date: 2011-03-02 22:20:16 summary: Fix symlink to microbial_data.loc in buildbot setup. affected #: 1 file (9 bytes) --- a/buildbot_setup.sh Wed Mar 02 13:46:07 2011 -0500 +++ b/buildbot_setup.sh Wed Mar 02 16:20:16 2011 -0500 @@ -48,7 +48,7 @@ /galaxy/data/location/liftOver.loc /galaxy/data/location/maf_index.loc /galaxy/data/location/maf_pairwise.loc -/galaxy/data/location/microbes/microbial_data.loc +/galaxy/data/location/microbial_data.loc /galaxy/data/location/mosaik_index.loc /galaxy/data/location/perm_base_index.loc /galaxy/data/location/perm_color_index.loc Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Fix the qual_stats_boxplot and quality_score_distribution tests again, hopefully
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/db8c44cdd4d9/ changeset: r5158:db8c44cdd4d9 user: natefoo date: 2011-03-02 19:46:07 summary: Fix the qual_stats_boxplot and quality_score_distribution tests again, hopefully affected #: 3 files (1.2 KB) Binary file test-data/454Score.png has changed Binary file test-data/boxplot_summary_statistics_out.png has changed Binary file test-data/solexaScore.png has changed Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Enhance Bowtie wrapper to accept non-sanger variant FASTQ files.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7a9476924daf/ changeset: r5157:7a9476924daf user: dan date: 2011-03-02 17:40:58 summary: Enhance Bowtie wrapper to accept non-sanger variant FASTQ files. affected #: 10 files (7.5 KB) --- a/tools/sr_mapping/bowtie_color_wrapper.xml Wed Mar 02 11:34:36 2011 -0500 +++ b/tools/sr_mapping/bowtie_color_wrapper.xml Wed Mar 02 11:40:58 2011 -0500 @@ -7,7 +7,7 @@ --threads="4" ## Outputs --output=$output - #if $singlePaired == "single" + #if str( $singlePaired.sPaired ) == "single" #if $output_unmapped_reads_l --output_unmapped_reads=$output_unmapped_reads_l #end if --- a/tools/sr_mapping/bowtie_wrapper.py Wed Mar 02 11:34:36 2011 -0500 +++ b/tools/sr_mapping/bowtie_wrapper.py Wed Mar 02 11:40:58 2011 -0500 @@ -67,6 +67,11 @@ import optparse, os, shutil, subprocess, sys, tempfile +#Allow more than Sanger encoded variants +DEFAULT_ASCII_ENCODING = '--phred33-quals' +GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = { 'fastqsanger':'--phred33-quals', 'fastqillumina':'--phred64-quals', 'fastqsolexa':'--solexa-quals' } +#FIXME: Integer quality scores are supported only when the '--integer-quals' argument is specified to bowtie; this is not currently able to be set in the tool/wrapper/config + def stop_err( msg ): sys.stderr.write( '%s\n' % msg ) sys.exit() @@ -131,6 +136,7 @@ parser.add_option( '-c', '--icutoff', dest='icutoff', help='Number of first bases of the reference sequence to index' ) parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' ) parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) + parser.add_option( '--galaxy_input_format', dest='galaxy_input_format', default="fastqsanger", help='galaxy input format' ) parser.add_option( '--do_not_build_index', dest='do_not_build_index', action="store_true", default=False, help='Flag to specify that provided file is already indexed, use as is' ) (options, args) = parser.parse_args() stdout = '' @@ -255,9 +261,10 @@ mateOrient = '--%s' % options.mateOrient else: mateOrient = '' + quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING ) if options.params == 'preSet': - aligning_cmds = '-q %s %s -p %s -S %s %s ' % \ - ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace ) + aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \ + ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding ) else: try: if options.skip and int( options.skip ) > 0: @@ -386,14 +393,15 @@ else: keepends = '' aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \ - '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s' % \ + '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \ ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, skip, alignLimit, trimH, trimL, maqSoapAlign, mismatchSeed, mismatchQual, seedLen, rounding, minInsert, maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks, tryHard, valAlign, allValAligns, suppressAlign, best, strata, offrate, seed, snpphred, snpfrac, keepends, - output_unmapped_reads, output_suppressed_reads ) + output_unmapped_reads, output_suppressed_reads, + quality_score_encoding ) except ValueError, e: # clean up temp dir if os.path.exists( tmp_index_dir ): --- a/tools/sr_mapping/bowtie_wrapper.xml Wed Mar 02 11:34:36 2011 -0500 +++ b/tools/sr_mapping/bowtie_wrapper.xml Wed Mar 02 11:40:58 2011 -0500 @@ -8,13 +8,14 @@ --threads="4" ## Outputs --output=$output - #if $singlePaired == "single" + #if str( $singlePaired.sPaired ) == "single" #if $output_unmapped_reads_l --output_unmapped_reads=$output_unmapped_reads_l #end if #if $output_suppressed_reads_l --output_suppressed_reads=$output_suppressed_reads_l #end if + --galaxy_input_format="${singlePaired.sInput1.ext}" #else #if $output_unmapped_reads_l and $output_unmapped_reads_r --output_unmapped_reads_l=$output_unmapped_reads_l @@ -24,9 +25,10 @@ --output_suppressed_reads_l=$output_suppressed_reads_l --output_suppressed_reads_r=$output_suppressed_reads_r #end if + --galaxy_input_format="${singlePaired.pInput1.ext}" #end if ## Inputs - --dataType="solexa" + --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper --suppressHeader=$suppressHeader --genomeSource=$refGenomeSource.genomeSource #if $refGenomeSource.genomeSource == "history": @@ -59,7 +61,8 @@ #end if #else ##use pre-built index - --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" + ##--ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" + --ref="${ refGenomeSource.index.fields.path }" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": @@ -191,7 +194,7 @@ <option value="paired">Paired-end</option></param><when value="single"> - <param name="sInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/><conditional name="sParams"><param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"><option value="preSet">Commonly used</option> @@ -245,8 +248,14 @@ </conditional></when><when value="paired"> - <param name="pInput1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> - <param name="pInput2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> + <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"> + <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">> + <column name="name" index="0"/> + <column name="value" index="0"/> + <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/> + </options> + </param><param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" /><param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)"><option value="fr">FR (for Illumina)</option> @@ -333,7 +342,7 @@ </conditional></actions></data> - <data format="fastqsanger" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"> + <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"><filter>(( singlePaired['sPaired'] == "single" and singlePaired['sParams']['sSettingsType'] == "full" and @@ -344,13 +353,41 @@ singlePaired['pParams']['pMaxFile'] is True )) </filter> + <actions> + <conditional name="singlePaired.sPaired"> + <when value="single"> + <action type="format"> + <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions></data> - <data format="fastqsanger" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)"> + <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)"><filter>singlePaired['sPaired'] == "paired"</filter><filter>singlePaired['pParams']['pSettingsType'] == "full"</filter><filter>singlePaired['pParams']['pMaxFile'] is True</filter> + <actions> + <conditional name="singlePaired.sPaired"> + <when value="single"> + <action type="format"> + <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions></data> - <data format="fastqsanger" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)"> + <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)"><filter> (( singlePaired['sPaired'] == "single" and @@ -362,11 +399,39 @@ singlePaired['pParams']['pUnmappedFile'] is True )) </filter> + <actions> + <conditional name="singlePaired.sPaired"> + <when value="single"> + <action type="format"> + <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions></data> - <data format="fastqsanger" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> + <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"><filter>singlePaired['sPaired'] == "paired"</filter><filter>singlePaired['pParams']['pSettingsType'] == "full"</filter><filter>singlePaired['pParams']['pUnmappedFile'] is True</filter> + <actions> + <conditional name="singlePaired.sPaired"> + <when value="single"> + <action type="format"> + <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions></data></outputs><tests> @@ -379,6 +444,7 @@ chrM_base needs to be the base location/name of the index files. --><param name="genomeSource" value="indexed" /> + <param name="index" value="equCab2chrM" /><param name="sPaired" value="single" /><param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> @@ -437,6 +503,86 @@ <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" /><output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" /></test> +  + <test> + <param name="genomeSource" value="history" /> + <param name="ownFile" value="phiX.fasta" /> + <param name="indexSettings" value="indexPreSet" /> + <param name="sPaired" value="paired" /> + <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" /> + <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" /> + <param name="pMaxInsert" value="1000" /> + <param name="pMateOrient" value="ff" /> + <param name="pSettingsType" value="full" /> + <param name="pSkip" value="0" /> + <param name="pAlignLimit" value="-1" /> + <param name="pTrimH" value="0" /> + <param name="pTrimL" value="0" /> + <param name="pMismatchSeed" value="2" /> + <param name="pMismatchQual" value="70" /> + <param name="pSeedLen" value="28" /> + <param name="pRounding" value="round" /> + <param name="pMaqSoapAlign" value="-1" /> + <param name="pMinInsert" value="0" /> + <param name="pMaxAlignAttempt" value="100" /> + <param name="pForwardAlign" value="forward" /> + <param name="pReverseAlign" value="reverse" /> + <param name="pTryHard" value="noTryHard" /> + <param name="pValAlign" value="1" /> + <param name="pAllValAligns" value="noAllValAligns" /> + <param name="pSuppressAlign" value="-1" /> + <param name="pUnmappedFile" value="true" /> + <param name="pMaxFile" value="false" /> + <param name="pBest" value="doBest" /> + <param name="pdMaxBacktracks" value="800" /> + <param name="pdStrata" value="noStrata" /> + <param name="pOffrate" value="-1" /> + <param name="pSeed" value="-1" /> + <param name="suppressHeader" value="true" /> + <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> + <output name="output_unmapped_reads_l" ftype="fastqillumna" file="bowtie_out8_1.fastqillumina.sorted" sort="True" /> + <output name="output_unmapped_reads_r" ftype="fastqillumna" file="bowtie_out8_2.fastqillumina.sorted" sort="True" /> + </test> + <test> + <param name="genomeSource" value="history" /> + <param name="ownFile" value="phiX.fasta" /> + <param name="indexSettings" value="indexPreSet" /> + <param name="sPaired" value="paired" /> + <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" /> + <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" /> + <param name="pMaxInsert" value="1000" /> + <param name="pMateOrient" value="ff" /> + <param name="pSettingsType" value="full" /> + <param name="pSkip" value="0" /> + <param name="pAlignLimit" value="-1" /> + <param name="pTrimH" value="0" /> + <param name="pTrimL" value="0" /> + <param name="pMismatchSeed" value="2" /> + <param name="pMismatchQual" value="70" /> + <param name="pSeedLen" value="28" /> + <param name="pRounding" value="round" /> + <param name="pMaqSoapAlign" value="-1" /> + <param name="pMinInsert" value="0" /> + <param name="pMaxAlignAttempt" value="100" /> + <param name="pForwardAlign" value="forward" /> + <param name="pReverseAlign" value="reverse" /> + <param name="pTryHard" value="noTryHard" /> + <param name="pValAlign" value="1" /> + <param name="pAllValAligns" value="noAllValAligns" /> + <param name="pSuppressAlign" value="-1" /> + <param name="pUnmappedFile" value="true" /> + <param name="pMaxFile" value="false" /> + <param name="pBest" value="doBest" /> + <param name="pdMaxBacktracks" value="800" /> + <param name="pdStrata" value="noStrata" /> + <param name="pOffrate" value="-1" /> + <param name="pSeed" value="-1" /> + <param name="suppressHeader" value="true" /> + <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> + <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" /> + <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" /> + </test> + <test><!-- Bowtie command: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Allow FromParamToolOutputActionOption and ParamValueToolOutputActionOptionFilter to access attributes of parameter values.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/be70b8497349/ changeset: r5156:be70b8497349 user: dan date: 2011-03-02 17:34:36 summary: Allow FromParamToolOutputActionOption and ParamValueToolOutputActionOptionFilter to access attributes of parameter values. affected #: 1 file (532 bytes) --- a/lib/galaxy/tools/parameters/output.py Wed Mar 02 11:34:03 2011 -0500 +++ b/lib/galaxy/tools/parameters/output.py Wed Mar 02 11:34:36 2011 -0500 @@ -179,11 +179,16 @@ self.column = int( self.column ) self.offset = elem.get( 'offset', -1 ) self.offset = int( self.offset ) + self.param_attribute = elem.get( 'param_attribute', [] ) + if self.param_attribute: + self.param_attribute = self.param_attribute.split( '.' ) def get_value( self, other_values ): value = other_values for ref_name in self.name: assert ref_name in value, "Required dependency '%s' not found in incoming values" % ref_name value = value.get( ref_name ) + for attr_name in self.param_attribute: + value = getattr( value, attr_name ) options = [ [ str( value ) ] ] for filter in self.filters: options = filter.filter_options( options, other_values ) @@ -276,6 +281,9 @@ self.keep = util.string_as_bool( elem.get( "keep", 'True' ) ) self.compare = parse_compare_type( elem.get( 'compare', None ) ) self.cast = parse_cast_attribute( elem.get( "cast", None ) ) + self.param_attribute = elem.get( 'param_attribute', [] ) + if self.param_attribute: + self.param_attribute = self.param_attribute.split( '.' ) def filter_options( self, options, other_values ): if self.ref: #find ref value @@ -283,6 +291,8 @@ for ref_name in self.ref: assert ref_name in value, "Required dependency '%s' not found in incoming values" % ref_name value = value.get( ref_name ) + for attr_name in self.param_attribute: + value = getattr( value, attr_name ) value = str( value ) else: value = self.value Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Allow DataToolParameter to be filtered on attributes other than dbkey.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f1495dd691c2/ changeset: r5155:f1495dd691c2 user: dan date: 2011-03-02 17:34:03 summary: Allow DataToolParameter to be filtered on attributes other than dbkey. affected #: 1 file (1.3 KB) --- a/lib/galaxy/tools/parameters/basic.py Wed Mar 02 09:59:24 2011 -0500 +++ b/lib/galaxy/tools/parameters/basic.py Wed Mar 02 11:34:03 2011 -0500 @@ -1256,8 +1256,14 @@ options = elem.find( 'options' ) if options is None: self.options = None + self.options_filter_attribute = None else: self.options = dynamic_options.DynamicOptions( options, self ) + + #HACK to get around current hardcoded limitation of when a set of dynamic options is defined for a DataToolParameter + #it always causes available datasets to be filtered by dbkey + #this behavior needs to be entirely reworked (in a backwards compatible manner) + self.options_filter_attribute = options.get( 'options_filter_attribute', None ) self.is_dynamic = self.options is not None # Load conversions required for the dataset input self.conversions = [] @@ -1302,7 +1308,7 @@ # associated with the dataset that restrict it's access from "public". if self.tool and self.tool.tool_type == 'data_destination' and not trans.app.security_agent.dataset_is_public( hda.dataset ): continue - if self.options and hda.get_dbkey() != filter_value: + if self.options and self._options_filter_attribute( hda ) != filter_value: continue if isinstance( hda.datatype, self.formats): selected = ( value and ( hda in value ) ) @@ -1363,7 +1369,7 @@ return False for i, data in enumerate( datasets ): if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): - if self.options and data.get_dbkey() != filter_value: + if self.options and self._options_filter_attribute( data ) != filter_value: continue most_recent_dataset[0] = data # Also collect children via association object @@ -1437,6 +1443,25 @@ self.tool.visit_inputs( other_values, visitor ) return False not in converter_safe + def _options_filter_attribute( self, value ): + #HACK to get around current hardcoded limitation of when a set of dynamic options is defined for a DataToolParameter + #it always causes available datasets to be filtered by dbkey + #this behavior needs to be entirely reworked (in a backwards compatible manner) + options_filter_attribute = self.options_filter_attribute + if options_filter_attribute is None: + return value.get_dbkey() + if options_filter_attribute.endswith( "()" ): + call_attribute = True + options_filter_attribute = options_filter_attribute[:-2] + else: + call_attribute = False + ref = value + for attribute in options_filter_attribute.split( '.' ): + ref = getattr( ref, attribute ) + if call_attribute: + ref = ref() + return ref + # class RawToolParameter( ToolParameter ): # """ # Completely nondescript parameter, HTML representation is provided as text Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Clarify what's being searched in the tool shed.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a5cfff74d467/ changeset: r5154:a5cfff74d467 user: greg date: 2011-03-02 15:59:24 summary: Clarify what's being searched in the tool shed. affected #: 1 file (24 bytes) --- a/lib/galaxy/webapps/community/controllers/common.py Wed Mar 02 09:40:10 2011 -0500 +++ b/lib/galaxy/webapps/community/controllers/common.py Wed Mar 02 09:59:24 2011 -0500 @@ -30,6 +30,7 @@ # User has previously rated item; update rating. item_rating.rating = rating item_rating.comment = comment + trans.sa_session.add( item_rating ) trans.sa_session.flush() return item_rating @@ -85,12 +86,10 @@ NameColumn( "Name", key="Tool.name", link=( lambda item: dict( operation="view_tool", id=item.id, webapp="community" ) ), - attach_popup=False - ), + attach_popup=False ), DescriptionColumn( "Description", key="description", - attach_popup=False - ), + attach_popup=False ), VersionColumn( "Version", key="version", attach_popup=False, @@ -119,7 +118,7 @@ key="Category.name", visible=False ) ] - columns.append( grids.MulticolFilterColumn( "Search", + columns.append( grids.MulticolFilterColumn( "Search tool name, description, version", cols_to_filter=[ columns[0], columns[1], columns[2] ], key="free-text-search", visible=False, @@ -165,13 +164,11 @@ key="name", link=( lambda item: dict( operation="tools_by_category", id=item.id, webapp="community" ) ), attach_popup=False, - filterable="advanced" - ), + filterable="advanced" ), DescriptionColumn( "Description", key="description", attach_popup=False, - filterable="advanced" - ), + filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", @@ -181,7 +178,7 @@ model_class=model.Tool, attach_popup=False ) ] - columns.append( grids.MulticolFilterColumn( "Search", + columns.append( grids.MulticolFilterColumn( "Search category name, description", cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, 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: rc: Fix for vcf_extract tool test
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/69552e72d144/ changeset: r5153:69552e72d144 user: rc date: 2011-03-02 15:40:10 summary: Fix for vcf_extract tool test affected #: 1 file (15 bytes) --- a/tools/vcf_tools/extract.xml Wed Mar 02 08:38:19 2011 -0500 +++ b/tools/vcf_tools/extract.xml Wed Mar 02 09:40:10 2011 -0500 @@ -40,7 +40,7 @@ <param name="keep_info" value='' /><param name="discard_info" value='' /><param name="pass_filter" value='true' /> - <output name="output" file="test_extract_pass_filter_quality_9_DP_2000_lt.vcf" ftype="vcf" /> + <output name="output" file="test_extract_pass_filter_quality_9_DP_2000_lt.vcf" lines_diff="6" ftype="vcf" /></test><test><param name="input1" value="test.small.vcf" ftype="vcf" /> 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: dannon: Remove ftype from mosaik/freebayes test outputs.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c44bf3bfdec5/ changeset: r5152:c44bf3bfdec5 user: dannon date: 2011-03-02 14:38:19 summary: Remove ftype from mosaik/freebayes test outputs. affected #: 2 files (24 bytes) --- a/tools/human_genome_variation/freebayes.xml Wed Mar 02 08:28:30 2011 -0500 +++ b/tools/human_genome_variation/freebayes.xml Wed Mar 02 08:38:19 2011 -0500 @@ -115,7 +115,7 @@ <param name="reference" ftype="fasta" value="mosaik_test_ref.fasta"/><param name="bamfile" ftype="bam" value="freebayes_in.bam"/><param name="source_select" value="pre_set"/> - <output name="output" ftype="vcf" file="freebayes_out.vcf" lines_diff="4"/> + <output name="output" file="freebayes_out.vcf" lines_diff="4"/></test></tests><help> --- a/tools/sr_mapping/mosaik.xml Wed Mar 02 08:28:30 2011 -0500 +++ b/tools/sr_mapping/mosaik.xml Wed Mar 02 08:38:19 2011 -0500 @@ -94,7 +94,7 @@ <param name="act" value="35"/><param name="bw" value="19"/><param name="mhp" value="100"/> - <output name="output" ftype="sam" file="mosaik_test_out.sam" compare="sim_size" delta="0"/> + <output name="output" file="mosaik_test_out.sam" compare="sim_size" delta="0"/></test></tests><help> 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: Drop the ftype attribute from tophat test outputs
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0d30654210e9/ changeset: r5151:0d30654210e9 user: natefoo date: 2011-03-02 14:28:30 summary: Drop the ftype attribute from tophat test outputs affected #: 1 file (118 bytes) --- a/tools/ngs_rna/tophat_wrapper.xml Tue Mar 01 16:39:46 2011 -0500 +++ b/tools/ngs_rna/tophat_wrapper.xml Wed Mar 02 08:28:30 2011 -0500 @@ -412,8 +412,8 @@ <param name="sPaired" value="single" /><param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" /><param name="sSettingsType" value="preSet" /> - <output name="junctions" file="tophat_out1j.bed" ftype="bed" /> - <output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" ftype="bam" /> + <output name="junctions" file="tophat_out1j.bed" /> + <output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" /></test><test> @@ -428,8 +428,8 @@ <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" /><param name="mate_inner_distance" value="20" /><param name="pSettingsType" value="preSet" /> - <output name="junctions" file="tophat_out2j.bed" ftype="bed" /> - <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" ftype="bam" /> + <output name="junctions" file="tophat_out2j.bed" /> + <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" /></test><test> @@ -469,10 +469,10 @@ <param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" /><param name="microexon_search" value="Yes" /> - <output name="insertions" file="tophat_out3i.bed" ftype="bed"/> - <output name="deletions" file="tophat_out3d.bed" ftype="bed"/> - <output name="junctions" file="tophat_out3j.bed" ftype="bed" /> - <output name="accepted_hits" file="tophat_out3h.bam" compare="sim_size" ftype="bam" /> + <output name="insertions" file="tophat_out3i.bed" /> + <output name="deletions" file="tophat_out3d.bed" /> + <output name="junctions" file="tophat_out3j.bed" /> + <output name="accepted_hits" file="tophat_out3h.bam" compare="sim_size" /></test><test> @@ -512,8 +512,8 @@ <param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" /><param name="microexon_search" value="Yes" /> - <output name="junctions" file="tophat_out4j.bed" ftype="bed" /> - <output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" ftype="bam" /> + <output name="junctions" file="tophat_out4j.bed" /> + <output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" /></test></tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: trackster: Difference view setting for ReadTracks: only see sequence on reads if they don't match reference. Align sequence with positional ticks.
by Bitbucket 01 Mar '11

01 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/24028b35c1cc/ changeset: r5150:24028b35c1cc user: kanwei date: 2011-03-01 22:39:46 summary: trackster: Difference view setting for ReadTracks: only see sequence on reads if they don't match reference. Align sequence with positional ticks. affected #: 1 file (1.1 KB) --- a/static/scripts/trackster.js Tue Mar 01 15:46:35 2011 -0500 +++ b/static/scripts/trackster.js Tue Mar 01 16:39:46 2011 -0500 @@ -9,15 +9,16 @@ * rectangles instead. */ CanvasRenderingContext2D.prototype.dashedLine = function(x1, y1, x2, y2, dashLen) { - if (dashLen == undefined) { dashLen = 4; } + if (dashLen === undefined) { dashLen = 4; } var dX = x2 - x1; var dY = y2 - y1; var dashes = Math.floor(Math.sqrt(dX * dX + dY * dY) / dashLen); var dashX = dX / dashes; var dashY = dY / dashes; + var q; - for (var q= 0; q < dashes; q++, x1 += dashX, y1 += dashY) { - if (q % 2 != 0) { + for (q = 0; q < dashes; q++, x1 += dashX, y1 += dashY) { + if (q % 2 !== 0) { continue; } this.fillRect(x1, y1, dashLen, 1); @@ -45,7 +46,7 @@ this.fill(); this.stroke(); this.closePath(); -} +}; /** * Make `element` sortable in parent by dragging `handle` (a selector) @@ -54,8 +55,9 @@ element.bind( "drag", { handle: handle, relative: true }, function ( e, d ) { var parent = $(this).parent(); var children = parent.children(); + var i; // Determine new position - for ( var i = 0; i < children.length; i++ ) { + for ( i = 0; i < children.length; i++ ) { if ( d.offsetY < $(children.get(i)).position().top ) { break; } @@ -63,12 +65,12 @@ // If not already in the right place, move. Need // to handle the end specially since we don't have // insert at index - if ( i == children.length ) { - if ( this != children.get( i - 1 ) ) { + if ( i === children.length ) { + if ( this !== children.get( i - 1 ) ) { parent.append( this ); } } - else if ( this != children.get( i ) ) { + else if ( this !== children.get( i ) ) { $(this).insertBefore( children.get( i ) ); } }); @@ -115,7 +117,7 @@ * Returns true if there is any overlap between regions. */ function is_overlap(first_region, second_region) { - return (compute_overlap(first_region, second_region) != NO_OVERLAP); + return (compute_overlap(first_region, second_region) !== NO_OVERLAP); } /** @@ -129,7 +131,8 @@ NO_DETAIL_TRACK_HEIGHT = 3, SQUISH_TRACK_HEIGHT = 5, PACK_TRACK_HEIGHT = 10, - NO_DETAIL_FEATURE_HEIGHT = DENSE_FEATURE_HEIGHT = 1, + NO_DETAIL_FEATURE_HEIGHT = 1, + DENSE_FEATURE_HEIGHT = 1, SQUISH_FEATURE_HEIGHT = 3, PACK_FEATURE_HEIGHT = 9, LABEL_SPACING = 2, @@ -206,7 +209,7 @@ $.extend(Cache.prototype, { get: function(key) { var index = this.key_ary.indexOf(key); - if (index != -1) { + if (index !== -1) { this.move_key_to_end(key, index); } return this.obj_cache[key]; @@ -558,11 +561,11 @@ // // If user is navigating to previous/next set of chroms, load new chrom set and return. // - if (chrom == "previous") { + if (chrom === "previous") { view.load_chroms({low: this.chrom_start_index - MAX_CHROMS_SELECTABLE}); return; } - if (chrom == "next") { + if (chrom === "next") { view.load_chroms({low: this.chrom_start_index + MAX_CHROMS_SELECTABLE}); return; } @@ -797,7 +800,7 @@ // Uses a dictionary to construct a tool object. var get_tool_from_dict = function(tool_dict) { - if (obj_length(tool_dict) == 0) { + if (obj_length(tool_dict) === 0) { return undefined; } @@ -901,7 +904,7 @@ for (var i = 0; i < filters_dict.length; i++) { var filter_dict = filters_dict[i]; var name = filter_dict.name, type = filter_dict.type, index = filter_dict.index; - if (type == 'int' || type == 'float') { + if (type === 'int' || type === 'float') { filters[i] = new NumberFilter(name, index); } else { filters[i] = new Filter(name, index, type); @@ -938,9 +941,9 @@ var id = 'param_' + index; var row = $("<div class='form-row' />").appendTo( container ); row.append( $('<label />').attr("for", id ).text( param.label + ":" ) ); - if ( param.type == 'bool' ) { + if ( param.type === 'bool' ) { row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', track_config.values[ param.key ] ) ); - } else if ( param.type == 'color' ) { + } else if ( param.type === 'color' ) { var value = track_config.values[ param.key ]; var input = $('<input />').attr("id", id ).attr("name", id ).val( value ); // Color picker in tool tip style float @@ -978,11 +981,11 @@ // Parse value from form element var id = 'param_' + index; var value = container.find( '#' + id ).val(); - if ( param.type == 'float' ) { + if ( param.type === 'float' ) { value = parseFloat( value ); - } else if ( param.type == 'int' ) { + } else if ( param.type === 'int' ) { value = parseInt( value ); - } else if ( param.type == 'bool' ) { + } else if ( param.type === 'bool' ) { value = container.find( '#' + id ).is( ':checked' ); } // Save value only if changed @@ -1066,7 +1069,7 @@ return; } - if ( track.view.chrom != null ) { + if ( track.view.chrom !== null ) { // Get dataset state; if state is fine, enable and draw track. Otherwise, show message // about track status. $.getJSON(converted_datasets_state_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, chrom: track.view.chrom}, @@ -1636,7 +1639,7 @@ new_track; // TODO: add support for other kinds of tool data tracks. - if (current_track.track_type == 'FeatureTrack') { + if (current_track.track_type === 'FeatureTrack') { new_track = new ToolDataFeatureTrack(track_name, view, undefined, {}, {}, current_track); } @@ -1647,7 +1650,7 @@ // Run tool. var json_run_tool = function() { $.getJSON(run_tool_url, url_params, function(track_data) { - if (track_data == "no converter") { + if (track_data === "no converter") { // No converter available for input datasets, so cannot run tool. new_track.container_div.addClass("error"); new_track.content_div.text(DATA_NOCONVERTER); @@ -1657,7 +1660,7 @@ new_track.container_div.addClass("error"); new_track.content_div.text(DATA_CANNOT_RUN_TOOL + track_data.message); } - else if (track_data == "pending") { + else if (track_data === "pending") { // Converting/indexing input datasets; show message and try again. new_track.container_div.addClass("pending"); new_track.content_div.text("Converting input data so that it can be easily reused."); @@ -1739,8 +1742,10 @@ Track.call( this, null, view, view.top_labeltrack ); TiledTrack.call( this ); + view.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"); @@ -1750,19 +1755,21 @@ this.tile_cache = new Cache(CACHED_TILES_LINE); }; $.extend( ReferenceTrack.prototype, TiledTrack.prototype, { - get_data: function(resolution, position) { + get_data: function(resolution, tile_index, key) { var track = this, - low = position * DENSITY * resolution, - high = ( position + 1 ) * DENSITY * resolution, - key = resolution + "_" + position; - - if (!track.data_queue[key]) { - track.data_queue[key] = true; + low = tile_index * DENSITY * resolution, + high = ( tile_index + 1 ) * DENSITY * resolution, + internal_key = low + "_" + high; + + if (key === undefined) { key = internal_key; } + if (!track.data_queue[internal_key]) { + track.data_queue[internal_key] = true; $.ajax({ 'url': reference_url, 'dataType': 'json', 'data': { "chrom": this.view.chrom, "low": low, "high": high, "dbkey": this.view.dbkey }, success: function (seq) { track.data_cache.set(key, seq); - delete track.data_queue[key]; + track.data_cache.set(internal_key, seq); + delete track.data_queue[internal_key]; track.draw(); }, error: function(r, t, e) { console.log(r, t, e); @@ -1770,6 +1777,12 @@ }); } }, + range_data: function(low, high) { + var key = low + "_" + high; + + var data = this.data_cache.get(key); + return data; + }, draw_tile: function( resolution, tile_index, parent_element, w_scale ) { var tile_low = tile_index * DENSITY * resolution, tile_length = DENSITY * resolution, @@ -1783,7 +1796,7 @@ if (w_scale > CHAR_WIDTH_PX) { if (this.data_cache.get(key) === undefined) { - this.get_data( resolution, tile_index ); + this.get_data(resolution, tile_index, key); return; } @@ -1795,11 +1808,12 @@ canvas.get(0).width = Math.ceil( tile_length * w_scale + this.left_offset); canvas.get(0).height = this.height_px; - + ctx.font = DEFAULT_FONT; + ctx.textAlign = "center"; for (var c = 0, str_len = seq.length; c < str_len; c++) { - var c_start = Math.round(c * w_scale), - gap = Math.round(w_scale / 2); - ctx.fillText(seq[c], c_start + this.left_offset + gap, 10); + var c_start = Math.round(c * w_scale); + + ctx.fillText(seq[c], c_start + this.left_offset, 10); } parent_element.append(canvas); return canvas; @@ -2225,7 +2239,7 @@ // if slot can be found. // TODO: are there any checks we need to do to ensure that text // will fit on tile? - if (text_align == "left") { + if (text_align === "left") { f_start -= text_len; f_end -= text_len; text_align = "right"; @@ -2346,11 +2360,11 @@ // Set vars that depend on mode. var thin_height, thick_height; - if (mode == "Squish") { + if (mode === "Squish") { thin_height = 1; thick_height = SQUISH_FEATURE_HEIGHT; } - else { // mode == "Pack" + else { // mode === "Pack" thin_height = 5; thick_height = PACK_FEATURE_HEIGHT; } @@ -2359,9 +2373,9 @@ if (!feature_blocks) { // If there are no blocks, treat the feature as one big exon. if ( feature.strand ) { - if (feature.strand == "+") { + if (feature.strand === "+") { ctx.fillStyle = RIGHT_STRAND_INV; - } else if (feature.strand == "-") { + } else if (feature.strand === "-") { ctx.fillStyle = LEFT_STRAND_INV; } } @@ -2381,18 +2395,18 @@ // Draw whole feature as connector/intron. var cur_y_center, cur_height; - if (mode == "Squish") { + if (mode === "Squish") { ctx.fillStyle = CONNECTOR_COLOR; cur_y_center = y_center + Math.floor(SQUISH_FEATURE_HEIGHT/2) + 1; cur_height = 1; } - else { // mode == "Pack" + else { // mode === "Pack" if (feature_strand) { var cur_y_center = y_center; var cur_height = thick_height; - if (feature_strand == "+") { + if (feature_strand === "+") { ctx.fillStyle = RIGHT_STRAND; - } else if (feature_strand == "-") { + } else if (feature_strand === "-") { ctx.fillStyle = LEFT_STRAND; } } @@ -2546,7 +2560,7 @@ // canvas.get(0).width = width + left_offset; canvas.get(0).height = required_height; - if (result.dataset_type == "summary_tree") { + if (result.dataset_type === "summary_tree") { // Increase canvas height in order to display max label. canvas.get(0).height += LABEL_SPACING + CHAR_HEIGHT_PX; } @@ -2697,6 +2711,7 @@ var ReadTrack = function (name, view, hda_ldda, dataset_id, prefs, filters) { FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters); this.track_type = "ReadTrack"; + this.difference_mode = true; }; $.extend(ReadTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { /** @@ -2704,17 +2719,22 @@ */ draw_read: function(ctx, mode, w_scale, tile_low, tile_high, feature_start, cigar, orig_seq, y_center) { ctx.textAlign = "center"; - var - tile_region = [tile_low, tile_high], - base_offset = 0, + var tile_region = [tile_low, tile_high], + base_offset = 0, seq_offset = 0, - gap = Math.round(w_scale / 2); + gap = 0, + seq_data; // Keep list of triangles that need to be drawn on top of initial drawing layer. // TODO: Eventually, we'll probably want to keep an ordered list of items to draw and then draw all // items at once. var draw_last = []; - + if (view.reference_track) { + seq_data = view.reference_track.range_data(tile_low, tile_high); + } + if ((mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) { + gap = Math.round(w_scale/2); + } for (var cig_id = 0, len = cigar.length; cig_id < len; cig_id++) { var cig = cigar[cig_id], cig_op = "MIDNSHP=X"[cig[0]], @@ -2737,28 +2757,31 @@ case "M": // Match. case "=": // Equals. var seq_tile_overlap = compute_overlap([seq_start, seq_start + cig_len], tile_region); - if (seq_tile_overlap != NO_OVERLAP) { + if (seq_tile_overlap !== NO_OVERLAP) { // Draw. var seq = orig_seq.slice(seq_offset, seq_offset + cig_len); - if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) { + if (gap > 0) { ctx.fillStyle = this.prefs.block_color; - ctx.fillRect(s_start + this.left_offset, y_center + 1, s_end - s_start, 9); + ctx.fillRect(s_start + this.left_offset - gap, y_center + 1, s_end - s_start, 9); ctx.fillStyle = CONNECTOR_COLOR; // 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 && seq_data && seq_data[seq_start - tile_low + c] === seq[c]) { + continue; + } if (seq_start + c >= tile_low && seq_start + c <= tile_high) { var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); - ctx.fillText(seq[c], c_start + this.left_offset + gap, y_center + 9); + ctx.fillText(seq[c], c_start + this.left_offset, y_center + 9); } } } else { ctx.fillStyle = this.prefs.block_color; // TODO: This is a pretty hack-ish way to fill rectangle based on mode. ctx.fillRect(s_start + this.left_offset, - y_center + (this.mode != "Dense" ? 4 : 5), + y_center + (this.mode !== "Dense" ? 4 : 5), s_end - s_start, - (mode != "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT) ); + (mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT) ); } } seq_offset += cig_len; @@ -2766,14 +2789,14 @@ break; case "N": // Skipped bases. ctx.fillStyle = CONNECTOR_COLOR; - ctx.fillRect(s_start + this.left_offset, y_center + 5, s_end - s_start, 1); + ctx.fillRect(s_start + this.left_offset - gap, y_center + 5, s_end - s_start, 1); //ctx.dashedLine(s_start + this.left_offset, y_center + 5, this.left_offset + s_end, y_center + 5); // No change in seq_offset because sequence not used when skipping. base_offset += cig_len; break; case "D": // Deletion. ctx.fillStyle = "red"; - ctx.fillRect(s_start + this.left_offset, y_center + 4, s_end - s_start, 3); + ctx.fillRect(s_start + this.left_offset - gap, y_center + 4, s_end - s_start, 3); // TODO: is this true? No change in seq_offset because sequence not used when skipping. base_offset += cig_len; break; @@ -2788,7 +2811,7 @@ // Check to see if sequence should be drawn at all by looking at the overlap between // the sequence region and the tile region. var seq_tile_overlap = compute_overlap([seq_start, seq_start + cig_len], tile_region); - if (seq_tile_overlap != NO_OVERLAP) { + if (seq_tile_overlap !== NO_OVERLAP) { // Draw sequence. var seq = orig_seq.slice(seq_offset, seq_offset + cig_len); // X center is offset + start - <half_sequence_length> @@ -2796,7 +2819,7 @@ if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) { // Draw sequence container. ctx.fillStyle = "yellow"; - ctx.fillRect(x_center, y_center - 9, s_end - s_start, 9); + ctx.fillRect(x_center - gap, y_center - 9, s_end - s_start, 9); draw_last[draw_last.length] = [x_center + (s_end - s_start)/2, y_center + 4, 5]; ctx.fillStyle = CONNECTOR_COLOR; // Based on overlap b/t sequence and tile, get sequence to be drawn. @@ -2817,15 +2840,15 @@ // Draw sequence. for (var c = 0, str_len = seq.length; c < str_len; c++) { var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); - ctx.fillText(seq[c], c_start + this.left_offset + gap - (s_end - s_start)/2, y_center); + ctx.fillText(seq[c], c_start + this.left_offset - (s_end - s_start)/2 - gap, y_center); } } else { // Draw block. ctx.fillStyle = "yellow"; // TODO: This is a pretty hack-ish way to fill rectangle based on mode. - ctx.fillRect(x_center, y_center + (this.mode != "Dense" ? 2 : 5), - s_end - s_start, (mode != "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT)); + ctx.fillRect(x_center, y_center + (this.mode !== "Dense" ? 2 : 5), + s_end - s_start, (mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT)); } } seq_offset += cig_len; @@ -2861,6 +2884,7 @@ 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 // Draw read. ctx.fillStyle = block_color; @@ -2893,12 +2917,15 @@ 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, y_center + 8); + ctx.fillText(feature_name, f_end + left_offset + LABEL_SPACING - gap, y_center + 8); } else { ctx.textAlign = "right"; - ctx.fillText(feature_name, f_start + left_offset - LABEL_SPACING, y_center + 8); + ctx.fillText(feature_name, f_start + left_offset - LABEL_SPACING - gap, y_center + 8); } ctx.fillStyle = block_color; } @@ -2927,7 +2954,7 @@ // Postdraw init: once data has been fetched, reset data url, wait time and start indexing. var track = this; var post_init = function() { - if (track.data_cache.size() == 0) { + if (track.data_cache.size() === 0) { // Track still drawing initial data, so do nothing. setTimeout(post_init, 300); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Enable the ftype attribute for test outputs, fixes the sam-to-bam test.
by Bitbucket 01 Mar '11

01 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9e717f1746c8/ changeset: r5149:9e717f1746c8 user: natefoo date: 2011-03-01 21:46:35 summary: Enable the ftype attribute for test outputs, fixes the sam-to-bam test. affected #: 2 files (116 bytes) --- a/lib/galaxy/tools/__init__.py Tue Mar 01 15:21:25 2011 -0500 +++ b/lib/galaxy/tools/__init__.py Tue Mar 01 15:46:35 2011 -0500 @@ -642,6 +642,8 @@ attributes['delta'] = int( attrib.pop( 'delta', '10000' ) ) attributes['sort'] = util.string_as_bool( attrib.pop( 'sort', False ) ) attributes['extra_files'] = [] + if 'ftype' in attrib: + attributes['ftype'] = attrib['ftype'] for extra in output_elem.findall( 'extra_files' ): # File or directory, when directory, compare basename # by basename --- a/tools/samtools/sam_to_bam.xml Tue Mar 01 15:21:25 2011 -0500 +++ b/tools/samtools/sam_to_bam.xml Tue Mar 01 15:46:35 2011 -0500 @@ -60,7 +60,7 @@ --><param name="index_source" value="cached" /><param name="input1" value="3.sam" ftype="sam" dbkey="equCab2" /> - <output name="output1" file="sam_to_bam_out2.bam" /> + <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" /></test></tests><help> 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: Update bwa_color_wrapper cached indices name to match the key used in the test data repository
by Bitbucket 01 Mar '11

01 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dd69759ef4a6/ changeset: r5148:dd69759ef4a6 user: natefoo date: 2011-03-01 21:21:25 summary: Update bwa_color_wrapper cached indices name to match the key used in the test data repository affected #: 1 file (6 bytes) --- a/tools/sr_mapping/bwa_color_wrapper.xml Tue Mar 01 13:00:27 2011 -0500 +++ b/tools/sr_mapping/bwa_color_wrapper.xml Tue Mar 01 15:21:25 2011 -0500 @@ -168,7 +168,7 @@ python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out5.u.sam bwa_wrapper_out5.sam --><param name="refGenomeSource" value="indexed" /> - <param name="indices" value="equCab2chrM_cs" /> + <param name="indices" value="equCab2chrM" /><param name="sPaired" value="paired" /><param name="input1" value="bwa_wrapper_in5.fastqcssanger" ftype="fastqcssanger" /><param name="input2" value="bwa_wrapper_in6.fastqcssanger" ftype="fastqcssanger" /> @@ -188,7 +188,7 @@ python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out6.u.sam bwa_wrapper_out6.sam --><param name="refGenomeSource" value="indexed" /> - <param name="indices" value="hg19chrX_midpart_cs" /> + <param name="indices" value="hg19chrX_midpart" /><param name="sPaired" value="single" /><param name="input1" value="bwa_wrapper_in4.fastqcssanger" ftype="fastqcssanger" /><param name="source_select" value="full" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Have YeastMine datasource tool point to the production server location and add configuration to tool_conf.xml.main.
by Bitbucket 01 Mar '11

01 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7a28ce53e034/ changeset: r5147:7a28ce53e034 user: dan date: 2011-03-01 19:00:27 summary: Have YeastMine datasource tool point to the production server location and add configuration to tool_conf.xml.main. affected #: 2 files (55 bytes) --- a/tool_conf.xml.main Mon Feb 28 15:17:35 2011 -0500 +++ b/tool_conf.xml.main Tue Mar 01 13:00:27 2011 -0500 @@ -11,6 +11,7 @@ <tool file="data_source/fly_modencode.xml" /><tool file="data_source/modmine.xml" /><tool file="data_source/ratmine.xml" /> + <tool file="data_source/yeastmine.xml" /><tool file="data_source/worm_modencode.xml" /><tool file="data_source/wormbase.xml" /><tool file="data_source/eupathdb.xml" /> --- a/tools/data_source/yeastmine.xml Mon Feb 28 15:17:35 2011 -0500 +++ b/tools/data_source/yeastmine.xml Tue Mar 01 13:00:27 2011 -0500 @@ -2,7 +2,7 @@ <tool name="YeastMine" id="yeastmine" tool_type="data_source"><description>server</description><command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://yeastmine-test.yeastgenome.org/yeastmine-dev/begin.do" check_values="false" method="get" target="_top"> + <inputs action="http://yeastmine.yeastgenome.org/yeastmine/begin.do" check_values="false" method="get" target="_top"><display>go to yeastMine server $GALAXY_URL</display></inputs><uihints minwidth="800"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Remove unused parameters from TopHat and Cufflinks tool tests.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/25a02a5c286f/ changeset: r5146:25a02a5c286f user: dan date: 2011-02-28 21:17:35 summary: Remove unused parameters from TopHat and Cufflinks tool tests. affected #: 2 files (171 bytes) --- a/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 15:03:45 2011 -0500 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 15:17:35 2011 -0500 @@ -105,7 +105,6 @@ <test><param name="sPaired" value="No"/><param name="input" value="cufflinks_in.sam"/> - <param name="mean_inner_distance" value="20"/><param name="max_intron_len" value="300000"/><param name="min_isoform_fraction" value="0.05"/><param name="pre_mrna_fraction" value="0.05"/> --- a/tools/ngs_rna/tophat_wrapper.xml Mon Feb 28 15:03:45 2011 -0500 +++ b/tools/ngs_rna/tophat_wrapper.xml Mon Feb 28 15:17:35 2011 -0500 @@ -448,7 +448,6 @@ <param name="splice_mismatches" value="0"/><param name="min_intron_length" value="70"/><param name="max_intron_length" value="500000"/> - <param name="quals_scale" value="default"/><param name="junction_filter" value="0.15"/><param name="max_multihits" value="40"/><param name="min_segment_intron" value="50" /> @@ -494,7 +493,6 @@ <param name="splice_mismatches" value="0"/><param name="min_intron_length" value="70"/><param name="max_intron_length" value="500000"/> - <param name="quals_scale" value="default"/><param name="junction_filter" value="0.15"/><param name="max_multihits" value="40"/><param name="min_segment_intron" value="50" /> 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: rc: Adding tests for vcf extract and filter tools
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/162fb94f7621/ changeset: r5145:162fb94f7621 user: rc date: 2011-02-28 21:03:45 summary: Adding tests for vcf extract and filter tools affected #: 11 files (3.1 KB) Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: mosaik: Test case uses sim_size instead of diff now, to get around the changing RG tag.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/05b089557d0d/ changeset: r5144:05b089557d0d user: dannon date: 2011-02-28 20:32:36 summary: mosaik: Test case uses sim_size instead of diff now, to get around the changing RG tag. affected #: 1 file (18 bytes) --- a/tools/sr_mapping/mosaik.xml Mon Feb 28 14:04:53 2011 -0500 +++ b/tools/sr_mapping/mosaik.xml Mon Feb 28 14:32:36 2011 -0500 @@ -13,8 +13,7 @@ #end if MosaikBuild -fr #if $genomeSource.refGenomeSource == 'indexed': - ##$genomeSource.indexReference - ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] } + ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] } #else: $genomeSource.historyReference #end if @@ -95,7 +94,7 @@ <param name="act" value="35"/><param name="bw" value="19"/><param name="mhp" value="100"/> - <output name="output" ftype="sam" file="mosaik_test_out.sam" sort="True"/> + <output name="output" ftype="sam" file="mosaik_test_out.sam" compare="sim_size" delta="0"/></test></tests><help> 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: guru: Fixed functional test for 'compute q values' tool - q-value is rounded to 6 significant digits, which shouldn't differ between different runs of the tool.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3dce98e473f1/ changeset: r5143:3dce98e473f1 user: guru date: 2011-02-28 20:04:53 summary: Fixed functional test for 'compute q values' tool - q-value is rounded to 6 significant digits, which shouldn't differ between different runs of the tool. Also, fixed a bug in microsatellite birth/death tool - cases where microsatellite boundaries aren't defined are skipped. affected #: 4 files (317 bytes) --- a/test-data/q_values.tabular Mon Feb 28 12:16:28 2011 -0500 +++ b/test-data/q_values.tabular Mon Feb 28 14:04:53 2011 -0500 @@ -1,4 +1,4 @@ -pi0: 0.243863648325601 +pi0: 0.243864 FDR level: 0.05 --- a/tools/regVariation/compute_q_values.pl Mon Feb 28 12:16:28 2011 -0500 +++ b/tools/regVariation/compute_q_values.pl Mon Feb 28 14:04:53 2011 -0500 @@ -11,6 +11,8 @@ use strict; use warnings; use IO::Handle; +use File::Temp qw/ tempfile tempdir /; +my $tdir = tempdir( CLEANUP => 0 ); # check to make sure having correct input and output files my $usage = "usage: compute_q_values.pl [TABULAR.in] [lambda] [pi0_method] [fdr_level] [robust] [TABULAR.out] [PDF.out] \n"; @@ -44,7 +46,8 @@ my $r_script; # R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values -# construct an R script file and save it in the same directory where the perl file is located +# construct an R script file and save it in a temp directory +chdir $tdir; $r_script = "q_values_computation.r"; open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; @@ -76,6 +79,7 @@ dev.off(); #save the q-values in the output file $q_valuesOutputFile + qobj\$pi0 <- signif(qobj\$pi0,digits=6) qwrite(qobj, filename=\"$q_valuesOutputFile\"); #options(show.error.messages = TRUE); --- a/tools/regVariation/compute_q_values.xml Mon Feb 28 12:16:28 2011 -0500 +++ b/tools/regVariation/compute_q_values.xml Mon Feb 28 14:04:53 2011 -0500 @@ -1,4 +1,4 @@ -<tool id="compute_q_values" name="Compute q-values" version="1.0.0"> +<tool id="compute_q_values" name="Compute q-values" version="1.0.1"><description>based on multiple simultaneous tests p-values</description><command interpreter="perl"> --- a/tools/regVariation/microsatellite_birthdeath.pl Mon Feb 28 12:16:28 2011 -0500 +++ b/tools/regVariation/microsatellite_birthdeath.pl Mon Feb 28 14:04:53 2011 -0500 @@ -643,7 +643,11 @@ my %microsatstarts=(); #1 WITHIN EACH ALIGNMENT, IF THERE EXISTS A MICROSATELLITE #2 THIS HASH CONTAINS THE START SITE OF THE MICROSATELLITE #3 WIHIN THE ALIGNMENT - + next if !defined $extreme_start; + next if !defined $extreme_end; + next if $extreme_start > length($sequences{$tags[0]}); + next if $extreme_start < 0; + next if $extreme_end > length($sequences{$tags[0]}); for my $i (0 ... $#tags){ #1 NOW THAT WE HAVE GATHERED INFORMATION REGARDING #2 SEQUENCE ALIGNMENT AND MICROSATELLITE COORDINATES @@ -3977,3 +3981,4 @@ foreach my $line (@_) {print "$line\n";} print "::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<\n"; } + 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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