galaxy-dist commit 7084aafd2e1a: Enable bedgraph files to be displayed in UCSC genome browser.
by commits-noreply＠bitbucket.org 16 Jul '10
by commits-noreply＠bitbucket.org 16 Jul '10
16 Jul '10
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User jeremy goecks <jeremy.goecks(a)emory.edu>
# Date 1278981206 14400
# Node ID 7084aafd2e1a77200935a15b64774b0f65ca06f5
# Parent 67392693199489978700ecd35ec463d1901ffe1e
Enable bedgraph files to be displayed in UCSC genome browser.
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -332,6 +332,56 @@ class BedGraph( Interval ):
def get_track_type( self ):
return "LineTrack", {"data": "array_tree"}
+
+ def as_ucsc_display_file( self, dataset, **kwd ):
+ """
+ Returns file contents as is with no modifications.
+ TODO: this is a functional stub and will need to be enhanced moving forward to provide additional support for bedgraph.
+ """
+ return open( dataset.file_name )
+
+ def get_estimated_display_viewport( self, dataset ):
+ """
+ Set viewport based on dataset's first 100 lines.
+ """
+ if dataset.has_data() and dataset.state == dataset.states.OK:
+ try:
+ # Set seqid, start, stop.
+ seqid = None
+ start = 2147483647 # Maximum value of a signed 32 bit integer ( 2**31 - 1 )
+ stop = 0
+ for i, line in enumerate( file( dataset.file_name ) ):
+ line = line.rstrip( '\r\n' )
+ if not line:
+ continue
+ elts = line.split('\t')
+ if len( elts ) == 4:
+ # Update seq id, start, end.
+ if not seqid:
+ # We can only set the viewport for a single chromosome
+ seqid = elems[0]
+ if seqid == elems[0]:
+ # Make sure we have not spanned chromosomes
+ start = min( start, int( elems[1] ) )
+ stop = max( stop, int( elems[2] ) )
+ else:
+ # We've spanned a chromosome
+ break
+ else:
+ continue
+ # Only look through 100 lines.
+ if i > 100:
+ break
+
+ # Set valid values for start, stop if necessary.
+ if start == 2147483647:
+ start = 0
+ if stop == 0:
+ stop = 1
+ return ( seqid, str( start ), str( stop ) )
+ except:
+ return( '', '', '' )
+ return( '', '', '' )
class Bed( Interval ):
"""Tab delimited data in BED format"""
1
0
galaxy-dist commit 673926931994: Fixed creation of new tracks, missing template-generated css for trackster, add .DS_Store, *.rej and *.orig to hgignore
by commits-noreply＠bitbucket.org 16 Jul '10
by commits-noreply＠bitbucket.org 16 Jul '10
16 Jul '10
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User Kanwei Li <kanwei(a)gmail.com>
# Date 1278961151 14400
# Node ID 67392693199489978700ecd35ec463d1901ffe1e
# Parent 3a6391d4f46980fd8b86c9f9b15fd5684357552b
Fixed creation of new tracks, missing template-generated css for trackster, add .DS_Store, *.rej and *.orig to hgignore
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -85,8 +85,8 @@
%endfor
init();
%else:
- continue_fn = function() {
- view = new View( undefined, $("#new-title").val(), undefined, $("#new-dbkey").val() );
+ var continue_fn = function() {
+ view = new View( $("#center"), undefined, $("#new-title").val(), undefined, $("#new-dbkey").val() );
init();
hide_modal();
};
@@ -105,18 +105,20 @@
});
%endif
- $(document).bind( "redraw", function( e ) {
+ $(document).bind( "redraw", function() {
view.redraw();
});
// To adjust the size of the viewport to fit the fixed-height footer
- var refresh = function( e ) {
- view.viewport_container.height( $(window).height() - 100 );
- view.nav_container.width( $("#center").width() );
- view.redraw();
+ var refresh = function() {
+ if (view !== undefined) {
+ view.viewport_container.height( $(window).height() - 100 );
+ view.nav_container.width( $("#center").width() );
+ view.redraw();
+ }
};
- $(window).bind( "resize", function(e) { refresh(e); } );
- $("#right-border").bind( "click dragend", function(e) { refresh(e); } );
+ $(window).bind( "resize", function() { refresh(); } );
+ $("#right-border").bind( "click dragend", function() { refresh(); } );
$(window).trigger( "resize" );
// Execute initializer for EDITOR specific javascript
@@ -154,9 +156,10 @@
error: function() {},
success: function(track_data) {
var td = track_data,
- track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack };
-
- view.add_track(new track_types[track_data.track_type]( track_data.name, view, track_data.dataset_id, track_data.prefs) );
+ track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack },
+ new_track = new track_types[track_data.track_type]( track_data.name, view, track_data.dataset_id, track_data.prefs);
+
+ view.add_track(new_track);
view.has_changes = true;
sidebar_box(new_track);
}
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -110,15 +110,15 @@ var View = function( container, chrom, t
this.low_input = $("<input/>").addClass("low").css("width", "10em").appendTo(this.chrom_form);
$("<span/>").text(" - ").appendTo(this.chrom_form);
this.high_input = $("<input/>").addClass("high").css("width", "10em").appendTo(this.chrom_form);
- this.hidden_input = $("<input/>").attr("type", "hidden").val(this.vis_id).appendTo(this.chrom_form);
+ if (this.vis_id !== undefined) {
+ this.hidden_input = $("<input/>").attr("type", "hidden").val(this.vis_id).appendTo(this.chrom_form);
+ }
this.zi_link = $("<a/>").click(function() { view.zoom_in(); view.redraw() }).html('<img src="../images/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);
this.zo_link = $("<a/>").click(function() { view.zoom_out(); view.redraw() }).html('<img src="../images/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);;
- var data_d = (this.vis_id !== undefined ? { vis_id: this.vis_id } : { dbkey: this.dbkey });
-
$.ajax({
url: chrom_url,
- data: data_d,
+ data: (this.vis_id !== undefined ? { vis_id: this.vis_id } : { dbkey: this.dbkey }),
dataType: "json",
success: function ( result ) {
if (result['reference']) {
--- a/.hgignore
+++ b/.hgignore
@@ -38,3 +38,9 @@ run_functional_tests.html
# Chrom len files
*.len
+
+# Misc
+*.orig
+.DS_Store
+*.rej
+
--- a/static/june_2007_style/blue/trackster.css
+++ b/static/june_2007_style/blue/trackster.css
@@ -1,125 +1,23 @@
-.viewport-container {
- overflow-x: hidden;
- overflow-y: auto;
-}
-
-/*canvas{
- border-left: 1px solid green;
- border-right: 1px solid red; } /* debugging */
-.nav {
- padding: 0 0;
- color:#333;font-weight:bold;
-}
-
-.nav-controls {
- text-align: center;
- background:#cccccc;
- background-image:url(style/panel_header_bg.png);
- background-position:top center;
- background-repeat:repeat-x;
- padding: 2px 0;
-}
-.nav-controls input {
- margin: 0 5px;
-}
-.nav-controls a {
- padding: 0 0.4em;
-}
-
-.overview {
- width: 100%;
- margin: 0px;
- color: white;
- margin-top: -6px;
- margin-bottom: -4px;
-}
-
-.overview-viewport {
- position: relative;
- height: 14px;
-/* border-top: solid #666 1px;*/
-/* border-bottom: solid #aaa 1px;*/
- background: white;
- border-top: solid gray 1px;
- border-bottom: solid gray 1px;
- margin: 5px 0;
-}
-.overview-box {
- position: absolute;
- margin-top: 0px;
- height: 14px;
- background: #ddd url(images/visualization/draggable_horizontal.png) center center no-repeat;
- /*border-style: outset;*/
-}
-
-.viewport {
-/* overflow-x: hidden;*/
- background-color: #fff;
-/* overflow: scroll;*/
-/* border-bottom: 2px solid black;*/
-}
-
-.viewport-canvas {
- width: 100%;
- height: 100px;
-}
-
-.yaxislabel {
- color: #777;
-}
-/* Line track needs borders to show range */
-.line-track .track-content {
- border-top: 1px solid #ddd;
- border-bottom: 1px solid #ddd;
-}
-
-.track {
- /* border-top: solid #DDDDDD 1px; */
- /* border-bottom: solid #DDDDDD 1px; */
- background: white;
-}
-
-.track-header {
- text-align: center;
- padding: 4px;
- color: #666;
-}
-
-.track-content {
- overflow: hidden;
- text-align: center;
-}
-
-.track.error {
- background-color: #ECB4AF;
-}
-.track.nodata {
- background-color: #ddd;
-}
-
-.loading {
- min-height: 100px;
-}
-
-.label-track {
- /* font-weight: bold; */
- /* font-size: 10px; */
-}
-.label-track .label {
- border-left: solid #999 1px;
- padding: 1px;
- display: inline-block;
-}
-.right-float {
- float: right;
- margin-left: 5px;
-}
-
-.top-labeltrack {
- border-bottom: solid #999 1px;
-}
-
-.nav-labeltrack {
- border-top: solid #999 1px;
- border-bottom: solid #999 1px;
-}
+.viewport-container{overflow-x:hidden;overflow-y:auto;}
+.nav{padding:0 0;color:#333;font-weight:bold;}
+.nav-controls{text-align:center;background:#cccccc;background-image:url(panel_header_bg.png);background-position:top center;background-repeat:repeat-x;padding:2px 0;}
+.nav-controls input{margin:0 5px;}
+.nav-controls a{padding:0 0.4em;}
+.overview{width:100%;margin:0px;color:white;margin-top:-6px;margin-bottom:-4px;}
+.overview-viewport{position:relative;height:14px;background:white;border-top:solid gray 1px;border-bottom:solid gray 1px;margin:5px 0;}
+.overview-box{position:absolute;margin-top:0px;height:14px;background:#ddd url(../images/visualization/draggable_horizontal.png) center center no-repeat;}
+.viewport{background-color:#fff;}
+.viewport-canvas{width:100%;height:100px;}
+.yaxislabel{color:#777;}
+.line-track .track-content{border-top:1px solid #ddd;border-bottom:1px solid #ddd;}
+.track{background:white;}
+.track-header{text-align:center;padding:4px;color:#666;}
+.track-content{overflow:hidden;text-align:center;}
+.track.error{background-color:#ECB4AF;}
+.track.nodata{background-color:#ddd;}
+.loading{min-height:100px;}
+.label-track{}
+.label-track .label{border-left:solid #999 1px;padding:1px;display:inline-block;}
+.right-float{float:right;margin-left:5px;}
+.top-labeltrack{border-bottom:solid #999 1px;}
+.nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #999 1px;}
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1,1 +1,1 @@
-var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/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="/static/images/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="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.p
rototype,{init:function(){var c=this.container,a=this;this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.content_div);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.viewport=$("<div/>").addClass("viewport").appendTo(this.viewport_container);this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form
=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);this.low_input=$("<input/>").addClass("low").css("width","10em").appendTo(this.chrom_form);$("<span/>").text(" - ").appendTo(this.chrom_form);this.high_input=$("<input/>").addClass("high").css("width","10em").appendTo(this.chrom_form);this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="../images/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="../images/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);var b=(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey});$.ajax({url:chrom_url,data:b,dataT
ype:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.chrom_select.bind("change",function(){a.chrom=a.chrom_select.val();var h=$.grep(a.chrom_data,function(k,l){return k.chrom===a.chrom})[0];a.max_high=h.len;a.reset();a.redraw(true);for(var j in a.tracks){var g=a.tracks[j];if(g.init){g.init()}}a.redraw()})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("mousewheel",function(d,f){if(Math.abs(f)<0.5){return}if(f>0){a.zoom_in(d.pageX,this.viewport_container)}else{a.zoom_out()}d.preventDefault()});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-
this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.high-a.low));a.move_delta(-2*f)});this.viewport_container.bind("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX}).bind("drag",function(g){var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);if(f<d.get(0).scrollHeight-d.height()){d.scrollTop(f)}this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height(),top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x),d=Math.max(j.c
lientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width();a.low_input.val(commatize(Math.round(f/g*h)+a.low));a.high_input.val(commatize(Math.round(d/g*h)+a.low));this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.
track_id_counter+=1},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(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)]},update_options:function(){this.has_changes=true;var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];this.viewport.append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(f){var d=this.high-this.low,b=this.low,e=this.high;if(b<this.max_low){b=this.max_low}if(e>this.max_high){e=this.max_high}if(d<this.min_separation){e=b+this.min_separation}this.low=Math.floor(b);this.high=Math.ceil(e);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEAT
URE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));this.overview_box.css({left:(this.low/(this.max_high-this.max_low))*this.overview_viewport.width(),width:Math.max(12,(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())}).show();this.low_input.val(commatize(this.low));this.high_input.val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor
)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div />").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error")
;$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){this.left_offset=200};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove()
;this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a,b){Track.call(this,null,a,b);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(1
0,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";Track.call(this,null,a,a.nav_labeltrack);TiledTrack.call(this);this.hidden=true;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:
a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),n=e.get(0).getContext("2d"),j=f+"_"+b;if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o+this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o);n.fillText(m[h],a+this.left_offset,10)}k.append(e);return e}}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,
mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}if(c.mode!==undefined){this.prefs.mode=c.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div />").add
Class("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=M
ath.ceil(a*e+this.left_offset);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(o){var a=$("<div />").addClass("form-row");var h="track_"+o+"_minval",m=$("<label></label>"
).attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),n=$("<input></input>").attr("id",h).val(b),l="track_"+o+"_maxval",g=$("<label></label>").attr("for",l).text("Max value:"),k=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",l).val(k),e="track_"+o+"_mode",d=$("<label></label>").attr("for",e).text("Display mode:"),j=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+j).attr("selected","selected");return a.append(m).append(n).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this
.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.
label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;a.mode="Auto";if(a.mode_div){a.mode_div.remove()}this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(d){a.mode_div=$("<div class='right-float menubutton popup' />").text("Display Mode");a.header_div.append(a.mode_div);a.mode="Auto";var c=function(e){a.mode_div.text(e);a.mode=e;a.tile_cache.clear();a.draw()};make_popupmenu(a.mode_div,{Auto:function(){c("Auto")},Dense:function(){c("Dense")},Squish:function(){c("Squish")},Pack:function(){c("Pack")}});a.data_cache.set(b,d);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,res
olution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_
by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(X,h,n,ak){var E=h*DENSITY*X,ad=(h+1)*DENSITY*X,D=DENSITY*X;var ae=E+"_"+ad;var z=this.data_cache.get(ae);if(z===undefined){this.data_queue[[E,ad]]=true;this.get_data(E,ad);return}var a=Math.ceil(D*ak),L=$("<canvas class='tile'></canvas>"),Z=this.prefs.label_color,f=this.pr
efs.block_color,m=this.mode,V=(m==="Squish")||(m==="Dense")&&(m!=="Pack")||(m==="Auto"&&(z.extra_info==="no_detail")),P=this.left_offset,aj,s,al;if(z.dataset_type==="summary_tree"){s=30}else{if(m==="Dense"){s=15;al=10}else{al=(V?this.vertical_nodetail_px:this.vertical_detail_px);s=this.incremental_slots(this.view.zoom_res,z.data,V,m)*al+15;aj=this.inc_slots[this.view.zoom_res]}}L.css({position:"absolute",top:0,left:(E-this.view.low)*ak-P});L.get(0).width=a+P;L.get(0).height=s;n.parent().css("height",Math.max(this.height_px,s)+"px");var A=L.get(0).getContext("2d");A.fillStyle=f;A.font=this.default_font;A.textAlign="right";if(z.dataset_type=="summary_tree"){var K,H=55,ac=255-H,g=ac*2/3,R=z.data,C=z.max,l=z.avg;if(R.length>2){var b=Math.ceil((R[1][0]-R[0][0])*ak)}else{var b=50}for(var ag=0,w=R.length;ag<w;ag++){var T=Math.ceil((R[ag][0]-E)*ak);var S=R[ag][1];if(!S){continue}K=Math.floor(ac-(S/C)*ac);A.fillStyle="rgb("+K+","+K+","+K+")";A.fillRect(T+P,0,b,20);if(this.prefs.show_
counts){if(K>g){A.fillStyle="black"}else{A.fillStyle="#ddd"}A.textAlign="center";A.fillText(R[ag][1],T+P+(b/2),12)}}n.append(L);return L}var ai=z.data;var af=0;for(var ag=0,w=ai.length;ag<w;ag++){var M=ai[ag],J=M[0],ah=M[1],U=M[2],F=M[3];if(ah<=ad&&U>=E){var W=Math.floor(Math.max(0,(ah-E)*ak)),B=Math.ceil(Math.min(a,Math.max(0,(U-E)*ak))),Q=(m==="Dense"?0:aj[J]*al);if(z.dataset_type==="bai"){A.fillStyle=f;if(M[4] instanceof Array){var t=Math.floor(Math.max(0,(M[4][0]-E)*ak)),I=Math.ceil(Math.min(a,Math.max(0,(M[4][1]-E)*ak))),r=Math.floor(Math.max(0,(M[5][0]-E)*ak)),p=Math.ceil(Math.min(a,Math.max(0,(M[5][1]-E)*ak)));if(M[4][1]>=E&&M[4][0]<=ad){this.rect_or_text(A,ak,E,ad,M[4][0],M[4][2],t+P,I-t,Q)}if(M[5][1]>=E&&M[5][0]<=ad){this.rect_or_text(A,ak,E,ad,M[5][0],M[5][2],r+P,p-r,Q)}if(r>I){A.fillStyle="#999";A.fillRect(I+P,Q+5,r-I,1)}}else{A.fillStyle=f;this.rect_or_text(A,ak,E,ad,ah,F,W+P,B-W,Q)}if(m!=="Dense"&&!V&&ah>E){A.fillStyle=this.prefs.label_color;if(h===0&&W-A.measur
eText(F).width<0){A.textAlign="left";A.fillText(J,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(J,W-2+P,Q+8)}A.fillStyle=f}}else{if(z.dataset_type==="interval_index"){if(V){A.fillRect(W+P,Q+5,B-W,1)}else{var v=M[4],O=M[5],Y=M[6],e=M[7];var u,aa,G=null,am=null;if(O&&Y){G=Math.floor(Math.max(0,(O-E)*ak));am=Math.ceil(Math.min(a,Math.max(0,(Y-E)*ak)))}if(m!=="Dense"&&F!==undefined&&ah>E){A.fillStyle=Z;if(h===0&&W-A.measureText(F).width<0){A.textAlign="left";A.fillText(F,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(F,W-2+P,Q+8)}A.fillStyle=f}if(e){if(v){if(v=="+"){A.fillStyle=RIGHT_STRAND}else{if(v=="-"){A.fillStyle=LEFT_STRAND}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=f}for(var ae=0,d=e.length;ae<d;ae++){var o=e[ae],c=Math.floor(Math.max(0,(o[0]-E)*ak)),N=Math.ceil(Math.min(a,Math.max((o[1]-E)*ak)));if(c>N){continue}u=5;aa=3;A.fillRect(c+P,Q+aa,N-c,u);if(G!==undefined&&!(c>am||N<G)){u=9;aa=1;var ab=Math.max(c,G),q=Math.min(N,am);A.fillRect(ab+P,Q+aa,q-ab,u)}}}else{u=9;aa=1;A.fil
lRect(W+P,Q+aa,B-W,u);if(M.strand){if(M.strand=="+"){A.fillStyle=RIGHT_STRAND_INV}else{if(M.strand=="-"){A.fillStyle=LEFT_STRAND_INV}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=prefs.block_color}}}}}af++}}n.append(L);return L},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_l
abel_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});
+var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND
_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.p
rototype,{init:function(){var b=this.container,a=this;this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(b);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.content_div);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.viewport=$("<div/>").addClass("viewport").appendTo(this.viewport_container);this.nav_container=$("<div/>").addClass("nav-container").appendTo(b);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form
=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);this.low_input=$("<input/>").addClass("low").css("width","10em").appendTo(this.chrom_form);$("<span/>").text(" - ").appendTo(this.chrom_form);this.high_input=$("<input/>").addClass("high").css("width","10em").appendTo(this.chrom_form);if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="../images/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="../images/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbke
y:this.dbkey}),dataType:"json",success:function(c){if(c.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=c.chrom_info;var e='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var d=a.chrom_data[i]["chrom"];e+='<option value="'+d+'">'+d+"</option>"}a.chrom_select.html(e);a.chrom_select.bind("change",function(){a.chrom=a.chrom_select.val();var g=$.grep(a.chrom_data,function(j,k){return j.chrom===a.chrom})[0];a.max_high=g.len;a.reset();a.redraw(true);for(var h in a.tracks){var f=a.tracks[h];if(f.init){f.init()}}a.redraw()})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("mousewheel",function(c,d){if(Math.abs(d)<0.5){return}if(d>0){a.zoom_in(c.pageX,this.viewport_container)}else{a.zoom_out()}c.preventDefault()});this.content_div.bind("dblclick",function(c){a.zoom_in(c.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(c){this.current_x=c.offsetX}).bind("drag",function
(c){var f=c.offsetX-this.current_x;this.current_x=c.offsetX;var d=Math.round(f/a.viewport_container.width()*(a.high-a.low));a.move_delta(-2*d)});this.viewport_container.bind("dragstart",function(c){this.original_low=a.low;this.current_height=c.clientY;this.current_x=c.offsetX}).bind("drag",function(f){var c=$(this);var h=f.offsetX-this.current_x;var d=c.scrollTop()-(f.clientY-this.current_height);if(d<c.get(0).scrollHeight-c.height()){c.scrollTop(d)}this.current_height=f.clientY;this.current_x=f.offsetX;var g=Math.round(h/a.viewport_container.width()*(a.high-a.low));a.move_delta(g)});this.top_labeltrack.bind("dragstart",function(c){this.drag_origin_x=c.clientX;this.drag_origin_pos=c.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height(),top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5}).appendTo($(this))}).bind("drag",function(h){var d=Math.min(h.clientX,this.drag_orig
in_x),c=Math.max(h.clientX,this.drag_origin_x),g=(a.high-a.low),f=a.viewport_container.width();a.low_input.val(commatize(Math.round(d/f*g)+a.low));a.high_input.val(commatize(Math.round(c/f*g)+a.low));this.drag_div.css({left:d+"px",width:(c-d)+"px"})}).bind("dragend",function(j){var d=Math.min(j.clientX,this.drag_origin_x),c=Math.max(j.clientX,this.drag_origin_x),g=(a.high-a.low),f=a.viewport_container.width(),h=a.low;a.low=Math.round(d/f*g)+h;a.high=Math.round(c/f*g)+h;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track
_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)]},update_options:function(){this.has_changes=true;var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];this.viewport.append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(f){var d=this.high-this.low,b=this.low,e=this.high;if(b<this.max_low){b=this.max_low}if(e>this.max_high){e=this.max_high}if(d<this.min_separation){e=b+this.min_separation}this.low=Math.floor(b);this.high=Math.ceil(e);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zo
om_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));this.overview_box.css({left:(this.low/(this.max_high-this.max_low))*this.overview_viewport.width(),width:Math.max(12,(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())}).show();this.low_input.val(commatize(this.low));this.high_input.val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;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()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div />").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("C
lick to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){this.left_offset=200};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.childre
n(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a,b){Track.call(this,null,a,b);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=M
ath.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";Track.call(this,null,a,a.nav_labeltrack);TiledTrack.call(this);this.hidden=true;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:
this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),n=e.get(0).getContext("2d"),j=f+"_"+b;if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o+this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o);n.fillText(m[h],a+this.left_offset,10)}k.append(e);return e}}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,
max_value:undefined,mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}if(c.mode!==undefined){this.prefs.mode=c.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);va
r d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*
e});b.get(0).width=Math.ceil(a*e+this.left_offset);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(o){var a=$("<div />").addClass("form-row");var h="track_"+o+"_minval",m
=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),n=$("<input></input>").attr("id",h).val(b),l="track_"+o+"_maxval",g=$("<label></label>").attr("for",l).text("Max value:"),k=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",l).val(k),e="track_"+o+"_mode",d=$("<label></label>").attr("for",e).text("Display mode:"),j=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+j).attr("selected","selected");return a.append(m).append(n).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs
.max_value||b!==this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(c.block_color!==undefined){this.prefs.block_color
=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;a.mode="Auto";if(a.mode_div){a.mode_div.remove()}this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(d){a.mode_div=$("<div class='right-float menubutton popup' />").text("Display Mode");a.header_div.append(a.mode_div);a.mode="Auto";var c=function(e){a.mode_div.text(e);a.mode=e;a.tile_cache.clear();a.draw()};make_popupmenu(a.mode_div,{Auto:function(){c("Auto")},Dense:function(){c("Dense")},Squish:function(){c("Squish")},Pack:function(){c("Pack")}});a.data_cache.set(b,d);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset
_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for
(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(X,h,n,ak){var E=h*DENSITY*X,ad=(h+1)*DENSITY*X,D=DENSITY*X;var ae=E+"_"+ad;var z=this.data_cache.get(ae);if(z===undefined){this.data_queue[[E,ad]]=true;this.get_data(E,ad);return}var a=Math.ceil(D*ak),L=$("<canvas class='tile'></canvas>"),Z=this.prefs.l
abel_color,f=this.prefs.block_color,m=this.mode,V=(m==="Squish")||(m==="Dense")&&(m!=="Pack")||(m==="Auto"&&(z.extra_info==="no_detail")),P=this.left_offset,aj,s,al;if(z.dataset_type==="summary_tree"){s=30}else{if(m==="Dense"){s=15;al=10}else{al=(V?this.vertical_nodetail_px:this.vertical_detail_px);s=this.incremental_slots(this.view.zoom_res,z.data,V,m)*al+15;aj=this.inc_slots[this.view.zoom_res]}}L.css({position:"absolute",top:0,left:(E-this.view.low)*ak-P});L.get(0).width=a+P;L.get(0).height=s;n.parent().css("height",Math.max(this.height_px,s)+"px");var A=L.get(0).getContext("2d");A.fillStyle=f;A.font=this.default_font;A.textAlign="right";if(z.dataset_type=="summary_tree"){var K,H=55,ac=255-H,g=ac*2/3,R=z.data,C=z.max,l=z.avg;if(R.length>2){var b=Math.ceil((R[1][0]-R[0][0])*ak)}else{var b=50}for(var ag=0,w=R.length;ag<w;ag++){var T=Math.ceil((R[ag][0]-E)*ak);var S=R[ag][1];if(!S){continue}K=Math.floor(ac-(S/C)*ac);A.fillStyle="rgb("+K+","+K+","+K+")";A.fillRect(T+P,0,b,20)
;if(this.prefs.show_counts){if(K>g){A.fillStyle="black"}else{A.fillStyle="#ddd"}A.textAlign="center";A.fillText(R[ag][1],T+P+(b/2),12)}}n.append(L);return L}var ai=z.data;var af=0;for(var ag=0,w=ai.length;ag<w;ag++){var M=ai[ag],J=M[0],ah=M[1],U=M[2],F=M[3];if(ah<=ad&&U>=E){var W=Math.floor(Math.max(0,(ah-E)*ak)),B=Math.ceil(Math.min(a,Math.max(0,(U-E)*ak))),Q=(m==="Dense"?0:aj[J]*al);if(z.dataset_type==="bai"){A.fillStyle=f;if(M[4] instanceof Array){var t=Math.floor(Math.max(0,(M[4][0]-E)*ak)),I=Math.ceil(Math.min(a,Math.max(0,(M[4][1]-E)*ak))),r=Math.floor(Math.max(0,(M[5][0]-E)*ak)),p=Math.ceil(Math.min(a,Math.max(0,(M[5][1]-E)*ak)));if(M[4][1]>=E&&M[4][0]<=ad){this.rect_or_text(A,ak,E,ad,M[4][0],M[4][2],t+P,I-t,Q)}if(M[5][1]>=E&&M[5][0]<=ad){this.rect_or_text(A,ak,E,ad,M[5][0],M[5][2],r+P,p-r,Q)}if(r>I){A.fillStyle="#999";A.fillRect(I+P,Q+5,r-I,1)}}else{A.fillStyle=f;this.rect_or_text(A,ak,E,ad,ah,F,W+P,B-W,Q)}if(m!=="Dense"&&!V&&ah>E){A.fillStyle=this.prefs.label_color;
if(h===0&&W-A.measureText(F).width<0){A.textAlign="left";A.fillText(J,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(J,W-2+P,Q+8)}A.fillStyle=f}}else{if(z.dataset_type==="interval_index"){if(V){A.fillRect(W+P,Q+5,B-W,1)}else{var v=M[4],O=M[5],Y=M[6],e=M[7];var u,aa,G=null,am=null;if(O&&Y){G=Math.floor(Math.max(0,(O-E)*ak));am=Math.ceil(Math.min(a,Math.max(0,(Y-E)*ak)))}if(m!=="Dense"&&F!==undefined&&ah>E){A.fillStyle=Z;if(h===0&&W-A.measureText(F).width<0){A.textAlign="left";A.fillText(F,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(F,W-2+P,Q+8)}A.fillStyle=f}if(e){if(v){if(v=="+"){A.fillStyle=RIGHT_STRAND}else{if(v=="-"){A.fillStyle=LEFT_STRAND}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=f}for(var ae=0,d=e.length;ae<d;ae++){var o=e[ae],c=Math.floor(Math.max(0,(o[0]-E)*ak)),N=Math.ceil(Math.min(a,Math.max((o[1]-E)*ak)));if(c>N){continue}u=5;aa=3;A.fillRect(c+P,Q+aa,N-c,u);if(G!==undefined&&!(c>am||N<G)){u=9;aa=1;var ab=Math.max(c,G),q=Math.min(N,am);A.fillRect(ab+P,Q+aa,q-ab,u)}}
}else{u=9;aa=1;A.fillRect(W+P,Q+aa,B-W,u);if(M.strand){if(M.strand=="+"){A.fillStyle=RIGHT_STRAND_INV}else{if(M.strand=="-"){A.fillStyle=LEFT_STRAND_INV}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=prefs.block_color}}}}}af++}}n.append(L);return L},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val()
,d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});
1
0
galaxy-dist commit e785da8dfaa2: Move trackster.css to current stylesheets folder.
by commits-noreply＠bitbucket.org 16 Jul '10
by commits-noreply＠bitbucket.org 16 Jul '10
16 Jul '10
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User jeremy goecks <jeremy.goecks(a)emory.edu>
# Date 1278944456 14400
# Node ID e785da8dfaa235cebbd6d932e3943f15ac091d04
# Parent e65936a1fa4923925a7a5c3848c9ced7c1ad883f
Move trackster.css to current stylesheets folder.
--- a/static/june_2007_style/trackster.css
+++ /dev/null
@@ -1,125 +0,0 @@
-.viewport-container {
- overflow-x: hidden;
- overflow-y: auto;
-}
-
-/*canvas{
- border-left: 1px solid green;
- border-right: 1px solid red; } /* debugging */
-.nav {
- padding: 0 0;
- color:#333;font-weight:bold;
-}
-
-.nav-controls {
- text-align: center;
- background:#cccccc;
- background-image:url(style/panel_header_bg.png);
- background-position:top center;
- background-repeat:repeat-x;
- padding: 2px 0;
-}
-.nav-controls input {
- margin: 0 5px;
-}
-.nav-controls a {
- padding: 0 0.4em;
-}
-
-.overview {
- width: 100%;
- margin: 0px;
- color: white;
- margin-top: -6px;
- margin-bottom: -4px;
-}
-
-.overview-viewport {
- position: relative;
- height: 14px;
-/* border-top: solid #666 1px;*/
-/* border-bottom: solid #aaa 1px;*/
- background: white;
- border-top: solid gray 1px;
- border-bottom: solid gray 1px;
- margin: 5px 0;
-}
-.overview-box {
- position: absolute;
- margin-top: 0px;
- height: 14px;
- background: #ddd url(images/visualization/draggable_horizontal.png) center center no-repeat;
- /*border-style: outset;*/
-}
-
-.viewport {
-/* overflow-x: hidden;*/
- background-color: #fff;
-/* overflow: scroll;*/
-/* border-bottom: 2px solid black;*/
-}
-
-.viewport-canvas {
- width: 100%;
- height: 100px;
-}
-
-.yaxislabel {
- color: #777;
-}
-/* Line track needs borders to show range */
-.line-track .track-content {
- border-top: 1px solid #ddd;
- border-bottom: 1px solid #ddd;
-}
-
-.track {
- /* border-top: solid #DDDDDD 1px; */
- /* border-bottom: solid #DDDDDD 1px; */
- background: white;
-}
-
-.track-header {
- text-align: center;
- padding: 4px;
- color: #666;
-}
-
-.track-content {
- overflow: hidden;
- text-align: center;
-}
-
-.track.error {
- background-color: #ECB4AF;
-}
-.track.nodata {
- background-color: #ddd;
-}
-
-.loading {
- min-height: 100px;
-}
-
-.label-track {
- /* font-weight: bold; */
- /* font-size: 10px; */
-}
-.label-track .label {
- border-left: solid #999 1px;
- padding: 1px;
- display: inline-block;
-}
-.right-float {
- float: right;
- margin-left: 5px;
-}
-
-.top-labeltrack {
- border-bottom: solid #999 1px;
-}
-
-.nav-labeltrack {
- border-top: solid #999 1px;
- border-bottom: solid #999 1px;
-}
--- /dev/null
+++ b/static/june_2007_style/blue/trackster.css
@@ -0,0 +1,125 @@
+.viewport-container {
+ overflow-x: hidden;
+ overflow-y: auto;
+}
+
+/*canvas{
+ border-left: 1px solid green;
+ border-right: 1px solid red; } /* debugging */
+.nav {
+ padding: 0 0;
+ color:#333;font-weight:bold;
+}
+
+.nav-controls {
+ text-align: center;
+ background:#cccccc;
+ background-image:url(style/panel_header_bg.png);
+ background-position:top center;
+ background-repeat:repeat-x;
+ padding: 2px 0;
+}
+.nav-controls input {
+ margin: 0 5px;
+}
+.nav-controls a {
+ padding: 0 0.4em;
+}
+
+.overview {
+ width: 100%;
+ margin: 0px;
+ color: white;
+ margin-top: -6px;
+ margin-bottom: -4px;
+}
+
+.overview-viewport {
+ position: relative;
+ height: 14px;
+/* border-top: solid #666 1px;*/
+/* border-bottom: solid #aaa 1px;*/
+ background: white;
+ border-top: solid gray 1px;
+ border-bottom: solid gray 1px;
+ margin: 5px 0;
+}
+.overview-box {
+ position: absolute;
+ margin-top: 0px;
+ height: 14px;
+ background: #ddd url(images/visualization/draggable_horizontal.png) center center no-repeat;
+ /*border-style: outset;*/
+}
+
+.viewport {
+/* overflow-x: hidden;*/
+ background-color: #fff;
+/* overflow: scroll;*/
+/* border-bottom: 2px solid black;*/
+}
+
+.viewport-canvas {
+ width: 100%;
+ height: 100px;
+}
+
+.yaxislabel {
+ color: #777;
+}
+/* Line track needs borders to show range */
+.line-track .track-content {
+ border-top: 1px solid #ddd;
+ border-bottom: 1px solid #ddd;
+}
+
+.track {
+ /* border-top: solid #DDDDDD 1px; */
+ /* border-bottom: solid #DDDDDD 1px; */
+ background: white;
+}
+
+.track-header {
+ text-align: center;
+ padding: 4px;
+ color: #666;
+}
+
+.track-content {
+ overflow: hidden;
+ text-align: center;
+}
+
+.track.error {
+ background-color: #ECB4AF;
+}
+.track.nodata {
+ background-color: #ddd;
+}
+
+.loading {
+ min-height: 100px;
+}
+
+.label-track {
+ /* font-weight: bold; */
+ /* font-size: 10px; */
+}
+.label-track .label {
+ border-left: solid #999 1px;
+ padding: 1px;
+ display: inline-block;
+}
+.right-float {
+ float: right;
+ margin-left: 5px;
+}
+
+.top-labeltrack {
+ border-bottom: solid #999 1px;
+}
+
+.nav-labeltrack {
+ border-top: solid #999 1px;
+ border-bottom: solid #999 1px;
+}
1
0
galaxy-dist commit e683c6995fb5: Pack scripts and update JS version.
by commits-noreply＠bitbucket.org 16 Jul '10
by commits-noreply＠bitbucket.org 16 Jul '10
16 Jul '10
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User jeremy goecks <jeremy.goecks(a)emory.edu>
# Date 1278947449 14400
# Node ID e683c6995fb5d032660d1c28cff2e1bc578d1298
# Parent 399d6d2b7eee9a4e6e9670c44ca3b3a2848ea7a4
Pack scripts and update JS version.
--- a/lib/galaxy/web/framework/helpers/__init__.py
+++ b/lib/galaxy/web/framework/helpers/__init__.py
@@ -44,7 +44,7 @@ def js( *args ):
TODO: This has a hardcoded "?v=X" to defeat caching. This should be done
in a better way.
"""
- return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=5" ) for name in args ] )
+ return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=6" ) for name in args ] )
# Hashes
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1,1 +1,1 @@
-var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/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="/static/images/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="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.p
rototype,{init:function(){var c=this.container,a=this;this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.content_div);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.viewport=$("<div/>").addClass("viewport").appendTo(this.viewport_container);this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form
=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);this.low_input=$("<input/>").addClass("low").css("width","10em").appendTo(this.chrom_form);$("<span/>").text(" - ").appendTo(this.chrom_form);this.high_input=$("<input/>").addClass("high").css("width","10em").appendTo(this.chrom_form);this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="/images/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="/images/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);var b=(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey});$.ajax({url:chrom_url,data:b,dataType:
"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.chrom_select.bind("change",function(){a.chrom=a.chrom_select.val();var h=$.grep(a.chrom_data,function(k,l){return k.chrom===a.chrom})[0];a.max_high=h.len;a.reset();a.redraw(true);for(var j in a.tracks){var g=a.tracks[j];if(g.init){g.init()}}a.redraw()})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("mousewheel",function(d,f){if(Math.abs(f)<0.5){return}if(f>0){a.zoom_in(d.pageX,this.viewport_container)}else{a.zoom_out()}d.preventDefault()});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this
.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.high-a.low));a.move_delta(-2*f)});this.viewport_container.bind("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX}).bind("drag",function(g){var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);if(f<d.get(0).scrollHeight-d.height()){d.scrollTop(f)}this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height(),top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x),d=Math.max(j.clien
tX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width();a.low_input.val(commatize(Math.round(f/g*h)+a.low));a.high_input.val(commatize(Math.round(d/g*h)+a.low));this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.trac
k_id_counter+=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(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)]},update_options:function(){this.has_changes=true;var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];this.viewport.append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(f){var d=this.high-this.low,b=this.low,e=this.high;if(b<this.max_low){b=this.max_low}if(e>this.max_high){e=this.max_high}if(d<this.min_separation){e=b+this.min_separation}this.low=Math.floor(b);this.high=Math.ceil(e);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_
LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));this.overview_box.css({left:(this.low/(this.max_high-this.max_low))*this.overview_viewport.width(),width:Math.max(12,(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())}).show();this.low_input.val(commatize(this.low));this.high_input.val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;
this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div />").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("
#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){this.left_offset=200};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();thi
s.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a,b){Track.call(this,null,a,b);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Ma
th.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";Track.call(this,null,a,a.nav_labeltrack);TiledTrack.call(this);this.hidden=true;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,hi
gh: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,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),n=e.get(0).getContext("2d"),j=f+"_"+b;if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o+this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o);n.fillText(m[h],a+this.left_offset,10)}k.append(e);return e}}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode
:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}if(c.mode!==undefined){this.prefs.mode=c.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div />").addClas
s("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.
ceil(a*e+this.left_offset);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(o){var a=$("<div />").addClass("form-row");var h="track_"+o+"_minval",m=$("<label></label>").at
tr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),n=$("<input></input>").attr("id",h).val(b),l="track_"+o+"_maxval",g=$("<label></label>").attr("for",l).text("Max value:"),k=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",l).val(k),e="track_"+o+"_mode",d=$("<label></label>").attr("for",e).text("Display mode:"),j=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+j).attr("selected","selected");return a.append(m).append(n).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.pre
fs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.labe
l_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;a.mode="Auto";if(a.mode_div){a.mode_div.remove()}this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(d){a.mode_div=$("<div class='right-float menubutton popup' />").text("Display Mode");a.header_div.append(a.mode_div);a.mode="Auto";var c=function(e){a.mode_div.text(e);a.mode=e;a.tile_cache.clear();a.draw()};make_popupmenu(a.mode_div,{Auto:function(){c("Auto")},Dense:function(){c("Dense")},Squish:function(){c("Squish")},Pack:function(){c("Pack")}});a.data_cache.set(b,d);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolut
ion:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_t
ile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(X,h,n,ak){var E=h*DENSITY*X,ad=(h+1)*DENSITY*X,D=DENSITY*X;var ae=E+"_"+ad;var z=this.data_cache.get(ae);if(z===undefined){this.data_queue[[E,ad]]=true;this.get_data(E,ad);return}var a=Math.ceil(D*ak),L=$("<canvas class='tile'></canvas>"),Z=this.prefs.label_color,f=this.prefs.
block_color,m=this.mode,V=(m==="Squish")||(m==="Dense")&&(m!=="Pack")||(m==="Auto"&&(z.extra_info==="no_detail")),P=this.left_offset,aj,s,al;if(z.dataset_type==="summary_tree"){s=30}else{if(m==="Dense"){s=15;al=10}else{al=(V?this.vertical_nodetail_px:this.vertical_detail_px);s=this.incremental_slots(this.view.zoom_res,z.data,V,m)*al+15;aj=this.inc_slots[this.view.zoom_res]}}L.css({position:"absolute",top:0,left:(E-this.view.low)*ak-P});L.get(0).width=a+P;L.get(0).height=s;n.parent().css("height",Math.max(this.height_px,s)+"px");var A=L.get(0).getContext("2d");A.fillStyle=f;A.font=this.default_font;A.textAlign="right";if(z.dataset_type=="summary_tree"){var K,H=55,ac=255-H,g=ac*2/3,R=z.data,C=z.max,l=z.avg;if(R.length>2){var b=Math.ceil((R[1][0]-R[0][0])*ak)}else{var b=50}for(var ag=0,w=R.length;ag<w;ag++){var T=Math.ceil((R[ag][0]-E)*ak);var S=R[ag][1];if(!S){continue}K=Math.floor(ac-(S/C)*ac);A.fillStyle="rgb("+K+","+K+","+K+")";A.fillRect(T+P,0,b,20);if(this.prefs.show_coun
ts){if(K>g){A.fillStyle="black"}else{A.fillStyle="#ddd"}A.textAlign="center";A.fillText(R[ag][1],T+P+(b/2),12)}}n.append(L);return L}var ai=z.data;var af=0;for(var ag=0,w=ai.length;ag<w;ag++){var M=ai[ag],J=M[0],ah=M[1],U=M[2],F=M[3];if(ah<=ad&&U>=E){var W=Math.floor(Math.max(0,(ah-E)*ak)),B=Math.ceil(Math.min(a,Math.max(0,(U-E)*ak))),Q=(m==="Dense"?0:aj[J]*al);if(z.dataset_type==="bai"){A.fillStyle=f;if(M[4] instanceof Array){var t=Math.floor(Math.max(0,(M[4][0]-E)*ak)),I=Math.ceil(Math.min(a,Math.max(0,(M[4][1]-E)*ak))),r=Math.floor(Math.max(0,(M[5][0]-E)*ak)),p=Math.ceil(Math.min(a,Math.max(0,(M[5][1]-E)*ak)));if(M[4][1]>=E&&M[4][0]<=ad){this.rect_or_text(A,ak,E,ad,M[4][0],M[4][2],t+P,I-t,Q)}if(M[5][1]>=E&&M[5][0]<=ad){this.rect_or_text(A,ak,E,ad,M[5][0],M[5][2],r+P,p-r,Q)}if(r>I){A.fillStyle="#999";A.fillRect(I+P,Q+5,r-I,1)}}else{A.fillStyle=f;this.rect_or_text(A,ak,E,ad,ah,F,W+P,B-W,Q)}if(m!=="Dense"&&!V&&ah>E){A.fillStyle=this.prefs.label_color;if(h===0&&W-A.measureTex
t(F).width<0){A.textAlign="left";A.fillText(J,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(J,W-2+P,Q+8)}A.fillStyle=f}}else{if(z.dataset_type==="interval_index"){if(V){A.fillRect(W+P,Q+5,B-W,1)}else{var v=M[4],O=M[5],Y=M[6],e=M[7];var u,aa,G=null,am=null;if(O&&Y){G=Math.floor(Math.max(0,(O-E)*ak));am=Math.ceil(Math.min(a,Math.max(0,(Y-E)*ak)))}if(m!=="Dense"&&F!==undefined&&ah>E){A.fillStyle=Z;if(h===0&&W-A.measureText(F).width<0){A.textAlign="left";A.fillText(F,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(F,W-2+P,Q+8)}A.fillStyle=f}if(e){if(v){if(v=="+"){A.fillStyle=RIGHT_STRAND}else{if(v=="-"){A.fillStyle=LEFT_STRAND}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=f}for(var ae=0,d=e.length;ae<d;ae++){var o=e[ae],c=Math.floor(Math.max(0,(o[0]-E)*ak)),N=Math.ceil(Math.min(a,Math.max((o[1]-E)*ak)));if(c>N){continue}u=5;aa=3;A.fillRect(c+P,Q+aa,N-c,u);if(G!==undefined&&!(c>am||N<G)){u=9;aa=1;var ab=Math.max(c,G),q=Math.min(N,am);A.fillRect(ab+P,Q+aa,q-ab,u)}}}else{u=9;aa=1;A.fillRec
t(W+P,Q+aa,B-W,u);if(M.strand){if(M.strand=="+"){A.fillStyle=RIGHT_STRAND_INV}else{if(M.strand=="-"){A.fillStyle=LEFT_STRAND_INV}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=prefs.block_color}}}}}af++}}n.append(L);return L},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label
_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});
+var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND
_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.p
rototype,{init:function(){var c=this.container,a=this;this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.content_div);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.viewport=$("<div/>").addClass("viewport").appendTo(this.viewport_container);this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form
=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);this.low_input=$("<input/>").addClass("low").css("width","10em").appendTo(this.chrom_form);$("<span/>").text(" - ").appendTo(this.chrom_form);this.high_input=$("<input/>").addClass("high").css("width","10em").appendTo(this.chrom_form);this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="../images/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="../images/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);var b=(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey});$.ajax({url:chrom_url,data:b,dataT
ype:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.chrom_select.bind("change",function(){a.chrom=a.chrom_select.val();var h=$.grep(a.chrom_data,function(k,l){return k.chrom===a.chrom})[0];a.max_high=h.len;a.reset();a.redraw(true);for(var j in a.tracks){var g=a.tracks[j];if(g.init){g.init()}}a.redraw()})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("mousewheel",function(d,f){if(Math.abs(f)<0.5){return}if(f>0){a.zoom_in(d.pageX,this.viewport_container)}else{a.zoom_out()}d.preventDefault()});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-
this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.high-a.low));a.move_delta(-2*f)});this.viewport_container.bind("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX}).bind("drag",function(g){var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);if(f<d.get(0).scrollHeight-d.height()){d.scrollTop(f)}this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height(),top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x),d=Math.max(j.c
lientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width();a.low_input.val(commatize(Math.round(f/g*h)+a.low));a.high_input.val(commatize(Math.round(d/g*h)+a.low));this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.
track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)]},update_options:function(){this.has_changes=true;var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];this.viewport.append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(f){var d=this.high-this.low,b=this.low,e=this.high;if(b<this.max_low){b=this.max_low}if(e>this.max_high){e=this.max_high}if(d<this.min_separation){e=b+this.min_separation}this.low=Math.floor(b);this.high=Math.ceil(e);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEAT
URE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));this.overview_box.css({left:(this.low/(this.max_high-this.max_low))*this.overview_viewport.width(),width:Math.max(12,(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())}).show();this.low_input.val(commatize(this.low));this.high_input.val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;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()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div />").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error")
;$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){this.left_offset=200};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove()
;this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a,b){Track.call(this,null,a,b);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(1
0,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";Track.call(this,null,a,a.nav_labeltrack);TiledTrack.call(this);this.hidden=true;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:
a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),n=e.get(0).getContext("2d"),j=f+"_"+b;if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o+this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o);n.fillText(m[h],a+this.left_offset,10)}k.append(e);return e}}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,
mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}if(c.mode!==undefined){this.prefs.mode=c.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div />").add
Class("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=M
ath.ceil(a*e+this.left_offset);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(o){var a=$("<div />").addClass("form-row");var h="track_"+o+"_minval",m=$("<label></label>"
).attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),n=$("<input></input>").attr("id",h).val(b),l="track_"+o+"_maxval",g=$("<label></label>").attr("for",l).text("Max value:"),k=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",l).val(k),e="track_"+o+"_mode",d=$("<label></label>").attr("for",e).text("Display mode:"),j=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+j).attr("selected","selected");return a.append(m).append(n).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this
.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.
label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;a.mode="Auto";if(a.mode_div){a.mode_div.remove()}this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(d){a.mode_div=$("<div class='right-float menubutton popup' />").text("Display Mode");a.header_div.append(a.mode_div);a.mode="Auto";var c=function(e){a.mode_div.text(e);a.mode=e;a.tile_cache.clear();a.draw()};make_popupmenu(a.mode_div,{Auto:function(){c("Auto")},Dense:function(){c("Dense")},Squish:function(){c("Squish")},Pack:function(){c("Pack")}});a.data_cache.set(b,d);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,res
olution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_
by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(X,h,n,ak){var E=h*DENSITY*X,ad=(h+1)*DENSITY*X,D=DENSITY*X;var ae=E+"_"+ad;var z=this.data_cache.get(ae);if(z===undefined){this.data_queue[[E,ad]]=true;this.get_data(E,ad);return}var a=Math.ceil(D*ak),L=$("<canvas class='tile'></canvas>"),Z=this.prefs.label_color,f=this.pr
efs.block_color,m=this.mode,V=(m==="Squish")||(m==="Dense")&&(m!=="Pack")||(m==="Auto"&&(z.extra_info==="no_detail")),P=this.left_offset,aj,s,al;if(z.dataset_type==="summary_tree"){s=30}else{if(m==="Dense"){s=15;al=10}else{al=(V?this.vertical_nodetail_px:this.vertical_detail_px);s=this.incremental_slots(this.view.zoom_res,z.data,V,m)*al+15;aj=this.inc_slots[this.view.zoom_res]}}L.css({position:"absolute",top:0,left:(E-this.view.low)*ak-P});L.get(0).width=a+P;L.get(0).height=s;n.parent().css("height",Math.max(this.height_px,s)+"px");var A=L.get(0).getContext("2d");A.fillStyle=f;A.font=this.default_font;A.textAlign="right";if(z.dataset_type=="summary_tree"){var K,H=55,ac=255-H,g=ac*2/3,R=z.data,C=z.max,l=z.avg;if(R.length>2){var b=Math.ceil((R[1][0]-R[0][0])*ak)}else{var b=50}for(var ag=0,w=R.length;ag<w;ag++){var T=Math.ceil((R[ag][0]-E)*ak);var S=R[ag][1];if(!S){continue}K=Math.floor(ac-(S/C)*ac);A.fillStyle="rgb("+K+","+K+","+K+")";A.fillRect(T+P,0,b,20);if(this.prefs.show_
counts){if(K>g){A.fillStyle="black"}else{A.fillStyle="#ddd"}A.textAlign="center";A.fillText(R[ag][1],T+P+(b/2),12)}}n.append(L);return L}var ai=z.data;var af=0;for(var ag=0,w=ai.length;ag<w;ag++){var M=ai[ag],J=M[0],ah=M[1],U=M[2],F=M[3];if(ah<=ad&&U>=E){var W=Math.floor(Math.max(0,(ah-E)*ak)),B=Math.ceil(Math.min(a,Math.max(0,(U-E)*ak))),Q=(m==="Dense"?0:aj[J]*al);if(z.dataset_type==="bai"){A.fillStyle=f;if(M[4] instanceof Array){var t=Math.floor(Math.max(0,(M[4][0]-E)*ak)),I=Math.ceil(Math.min(a,Math.max(0,(M[4][1]-E)*ak))),r=Math.floor(Math.max(0,(M[5][0]-E)*ak)),p=Math.ceil(Math.min(a,Math.max(0,(M[5][1]-E)*ak)));if(M[4][1]>=E&&M[4][0]<=ad){this.rect_or_text(A,ak,E,ad,M[4][0],M[4][2],t+P,I-t,Q)}if(M[5][1]>=E&&M[5][0]<=ad){this.rect_or_text(A,ak,E,ad,M[5][0],M[5][2],r+P,p-r,Q)}if(r>I){A.fillStyle="#999";A.fillRect(I+P,Q+5,r-I,1)}}else{A.fillStyle=f;this.rect_or_text(A,ak,E,ad,ah,F,W+P,B-W,Q)}if(m!=="Dense"&&!V&&ah>E){A.fillStyle=this.prefs.label_color;if(h===0&&W-A.measur
eText(F).width<0){A.textAlign="left";A.fillText(J,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(J,W-2+P,Q+8)}A.fillStyle=f}}else{if(z.dataset_type==="interval_index"){if(V){A.fillRect(W+P,Q+5,B-W,1)}else{var v=M[4],O=M[5],Y=M[6],e=M[7];var u,aa,G=null,am=null;if(O&&Y){G=Math.floor(Math.max(0,(O-E)*ak));am=Math.ceil(Math.min(a,Math.max(0,(Y-E)*ak)))}if(m!=="Dense"&&F!==undefined&&ah>E){A.fillStyle=Z;if(h===0&&W-A.measureText(F).width<0){A.textAlign="left";A.fillText(F,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(F,W-2+P,Q+8)}A.fillStyle=f}if(e){if(v){if(v=="+"){A.fillStyle=RIGHT_STRAND}else{if(v=="-"){A.fillStyle=LEFT_STRAND}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=f}for(var ae=0,d=e.length;ae<d;ae++){var o=e[ae],c=Math.floor(Math.max(0,(o[0]-E)*ak)),N=Math.ceil(Math.min(a,Math.max((o[1]-E)*ak)));if(c>N){continue}u=5;aa=3;A.fillRect(c+P,Q+aa,N-c,u);if(G!==undefined&&!(c>am||N<G)){u=9;aa=1;var ab=Math.max(c,G),q=Math.min(N,am);A.fillRect(ab+P,Q+aa,q-ab,u)}}}else{u=9;aa=1;A.fil
lRect(W+P,Q+aa,B-W,u);if(M.strand){if(M.strand=="+"){A.fillStyle=RIGHT_STRAND_INV}else{if(M.strand=="-"){A.fillStyle=LEFT_STRAND_INV}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=prefs.block_color}}}}}af++}}n.append(L);return L},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_l
abel_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});
1
0
galaxy-dist commit 3a6391d4f469: Fix bug so that page editor's 'insert link to page' option works.
by commits-noreply＠bitbucket.org 16 Jul '10
by commits-noreply＠bitbucket.org 16 Jul '10
16 Jul '10
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User jeremy goecks <jeremy.goecks(a)emory.edu>
# Date 1278956233 14400
# Node ID 3a6391d4f46980fd8b86c9f9b15fd5684357552b
# Parent e683c6995fb5d032660d1c28cff2e1bc578d1298
Fix bug so that page editor's 'insert link to page' option works.
--- a/templates/page/editor.mako
+++ b/templates/page/editor.mako
@@ -104,12 +104,13 @@
item_plural = "Pages";
item_controller = "page";
item_class = "Page";
+ break;
case( Galaxy.ITEM_VISUALIZATION ):
item_singular = "Visualization";
item_plural = "Visualizations";
item_controller = "visualization";
item_class = "Visualization";
- break;
+ break;
}
// Build ajax URL that lists items for selection.
1
0
galaxy-dist commit 399d6d2b7eee: Make URLs for viz zoom in/out images relative.
by commits-noreply＠bitbucket.org 16 Jul '10
by commits-noreply＠bitbucket.org 16 Jul '10
16 Jul '10
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User jeremy goecks <jeremy.goecks(a)emory.edu>
# Date 1278947222 14400
# Node ID 399d6d2b7eee9a4e6e9670c44ca3b3a2848ea7a4
# Parent e785da8dfaa235cebbd6d932e3943f15ac091d04
Make URLs for viz zoom in/out images relative.
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -111,8 +111,8 @@ var View = function( container, chrom, t
$("<span/>").text(" - ").appendTo(this.chrom_form);
this.high_input = $("<input/>").addClass("high").css("width", "10em").appendTo(this.chrom_form);
this.hidden_input = $("<input/>").attr("type", "hidden").val(this.vis_id).appendTo(this.chrom_form);
- this.zi_link = $("<a/>").click(function() { view.zoom_in(); view.redraw() }).html('<img src="/images/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);
- this.zo_link = $("<a/>").click(function() { view.zoom_out(); view.redraw() }).html('<img src="/images/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);;
+ this.zi_link = $("<a/>").click(function() { view.zoom_in(); view.redraw() }).html('<img src="../images/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);
+ this.zo_link = $("<a/>").click(function() { view.zoom_out(); view.redraw() }).html('<img src="../images/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);;
var data_d = (this.vis_id !== undefined ? { vis_id: this.vis_id } : { dbkey: this.dbkey });
1
0
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User Dannon Baker <dannon.baker(a)emory.edu>
# Date 1278796427 14400
# Node ID e65936a1fa4923925a7a5c3848c9ced7c1ad883f
# Parent 19e07ef6eb25ea4bd1531ba42c2187f3f5d384d6
# Parent 2d046444998edb1c4a5126897990bddd25de69f5
Merge
--- a/templates/admin/requests/show_request.mako
+++ /dev/null
@@ -1,528 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/requests/sample_state.mako" import="render_sample_state" />
-<%namespace file="/requests/sample_datasets.mako" import="render_sample_datasets" />
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
- $( "select[refresh_on_change='true']").change( function() {
- var refresh = false;
- var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
- if ( refresh_on_change_values ) {
- refresh_on_change_values = refresh_on_change_values.value.split( ',' );
- var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
- for( i= 0; i < refresh_on_change_values.length; i++ ) {
- if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
- refresh = true;
- break;
- }
- }
- }
- else {
- refresh = true;
- }
- if ( refresh ){
- $( "#show_request" ).submit();
- }
- });
-});
-</script>
-
-
-<script type="text/javascript">
-$(document).ready(function(){
- //hide the all of the element with class msg_body
- $(".msg_body").hide();
- //toggle the componenet with class msg_body
- $(".msg_head").click(function(){
- $(this).next(".msg_body").slideToggle(450);
- });
-});
-</script>
-
-<script type="text/javascript">
- // Looks for changes in sample states using an async request. Keeps
- // calling itself (via setTimeout) until all samples are in a terminal
- // state.
- var updater = function ( sample_states ) {
- // Check if there are any items left to track
- var empty = true;
- for ( i in sample_states ) {
- empty = false;
- break;
- }
- if ( ! empty ) {
- setTimeout( function() { updater_callback( sample_states ) }, 1000 );
- }
- };
- var updater_callback = function ( sample_states ) {
- // Build request data
- var ids = []
- var states = []
- $.each( sample_states, function ( id, state ) {
- ids.push( id );
- states.push( state );
- });
- // Make ajax call
- $.ajax( {
- type: "POST",
- url: "${h.url_for( controller='requests_admin', action='sample_state_updates' )}",
- dataType: "json",
- data: { ids: ids.join( "," ), states: states.join( "," ) },
- success : function ( data ) {
- $.each( data, function( id, val ) {
- // Replace HTML
- var cell1 = $("#sampleState-" + id);
- cell1.html( val.html_state );
- var cell2 = $("#sampleDatasets-" + id);
- cell2.html( val.html_datasets );
- sample_states[ parseInt(id) ] = val.state;
- });
- updater( sample_states );
- },
- error: function() {
- // Just retry, like the old method, should try to be smarter
- updater( sample_states );
- }
- });
- };
-</script>
-
-<style type="text/css">
-.msg_head {
- padding: 0px 0px;
- cursor: pointer;
-}
-</style>
-
-<script type="text/javascript">
- function stopRKey(evt) {
- var evt = (evt) ? evt : ((event) ? event : null);
- var node = (evt.target) ? evt.target : ((evt.srcElement) ? evt.srcElement : null);
- if ((evt.keyCode == 13) && (node.type=="text")) {return false;}
- }
- document.onkeypress = stopRKey
-</script>
-
-%if request.submitted():
- <% samples_not_ready = request.sequence_run_ready() %>
- %if samples_not_ready:
- ${render_msg( "Select a target library and folder for all the samples before starting the sequence run", "warning" )}
- %endif
-%endif
-
-%if request.rejected():
- ${render_msg( "Reason for rejection: "+request.last_comment(), "warning" )}
-%endif
-
-<div class="grid-header">
- <h2>Sequencing Request "${request.name}"</h2>
-</div>
-
-<ul class="manage-table-actions">
-
- %if request.unsubmitted() and request.samples:
- <li>
- <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_admin', action='list', operation='Submit', id=trans.security.encode_id(request.id) )}">
- <span>Submit request</span></a>
- </li>
- %endif
- %if request.submitted():
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='Reject', id=trans.security.encode_id(request.id))}">
- <span>Reject request</span></a>
- </li>
- %endif
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">
- <span>History</span></a>
- </li>
-
-
-</ul>
-
-<%def name="show_basic_info_form( sample_index, sample, info )">
- <td>
- <input type="text" name=sample_${sample_index}_name value="${info['name']}" size="10"/>
- <div class="toolParamHelp" style="clear: both;">
- <i>${' (required)' }</i>
- </div>
- </td>
- %if sample:
- %if sample.request.unsubmitted():
- <td></td>
- %else:
- <td><input type="text" name=sample_${sample_index}_barcode value="${info['barcode']}" size="10"/></td>
- %endif
- %else:
- <td></td>
- %endif
- %if sample:
- %if sample.request.unsubmitted():
- <td>Unsubmitted</td>
- %else:
- <td><a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a></td>
- %endif
- %else:
- <td></td>
- %endif
- <td>${info['lib_widget'].get_html()}</td>
- <td>${info['folder_widget'].get_html()}</td>
- %if request.submitted() or request.complete():
- %if sample:
- <td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a></td>
- %else:
- <td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">Add</a></td>
- %endif
- %endif
-</%def>
-
-## This function displays the "Basic Information" grid
-<%def name="render_basic_info_grid()">
- <h4>Sample Information</h4>
- <table class="grid">
- <thead>
- <tr>
- <th>Name</th>
- <th>Barcode</th>
- <th>State</th>
- <th>Data Library</th>
- <th>Folder</th>
- %if request.submitted() or request.complete():
- <th>Dataset(s) Transferred</th>
- %endif
- <th></th>
- </tr>
- <thead>
- <tbody>
- <%
- trans.sa_session.refresh( request )
- %>
- %for sample_index, info in enumerate(current_samples):
- <%
- if sample_index in range(len(request.samples)):
- sample = request.samples[sample_index]
- else:
- sample = None
- %>
- %if edit_mode == 'True':
- <tr>
- ${show_basic_info_form( sample_index, sample, info )}
- </tr>
- %else:
- <tr>
- %if sample_index in range(len(request.samples)):
- <td>${info['name']}</td>
- <td>${info['barcode']}</td>
- %if sample.request.unsubmitted():
- <td>Unsubmitted</td>
- %else:
- <td id="sampleState-${sample.id}">${render_sample_state( sample )}</td>
- %endif
-
-## <td>
-## %if sample:
-## %if sample.request.unsubmitted():
-## Unsubmitted
-## %else:
-## <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
-## %endif
-## %endif
-## </td>
- %if info['library']:
- <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td>
- %else:
- <td></td>
- %endif
- %if info['folder']:
- <td>${info['folder'].name}</td>
- %else:
- <td></td>
- %endif
- %if request.submitted() or request.complete():
- <td id="sampleDatasets-${sample.id}">
- ${render_sample_datasets( sample )}
-## <a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a>
- </td>
- %endif
-
-
- %else:
- ${show_basic_info_form( sample_index, sample, info )}
- %endif
- %if request.unsubmitted() or request.rejected():
- <td>
- %if sample:
- %if sample.request.unsubmitted():
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index )}">
- <img src="${h.url_for('/static/images/delete_icon.png')}" />
- <span></span></a>
- %endif
- %endif
- </td>
- %endif
- </tr>
- %endif
- %endfor
- </tbody>
- </table>
-</%def>
-
-<%def name="render_sample_form( index, sample_name, sample_values, fields_dict )">
- <td>
- ${sample_name}
- </td>
- %for field_index, field in fields_dict.items():
- <td>
- %if field['type'] == 'TextField':
- <input type="text" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/>
- %elif field['type'] == 'SelectField':
- <select name="sample_${index}_field_${field_index}" last_selected_value="2">
- %for option_index, option in enumerate(field['selectlist']):
- %if option == sample_values[field_index]:
- <option value="${option}" selected>${option}</option>
- %else:
- <option value="${option}">${option}</option>
- %endif
- %endfor
- </select>
- %elif field['type'] == 'WorkflowField':
- <select name="sample_${index}_field_${field_index}">
- %if str(sample_values[field_index]) == 'none':
- <option value="none" selected>Select one</option>
- %else:
- <option value="none">Select one</option>
- %endif
- %for option_index, option in enumerate(request.user.stored_workflows):
- %if not option.deleted:
- %if str(option.id) == str(sample_values[field_index]):
- <option value="${option.id}" selected>${option.name}</option>
- %else:
- <option value="${option.id}">${option.name}</option>
- %endif
- %endif
- %endfor
- </select>
- %elif field['type'] == 'CheckboxField':
- <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/>
- %endif
- <div class="toolParamHelp" style="clear: both;">
- <i>${'('+field['required']+')' }</i>
- </div>
- </td>
- %endfor
-</%def>
-
-<%def name="render_sample( index, sample_name, sample_values, fields_dict )">
- <td>
- ${sample_name}
- </td>
- %for field_index, field in fields_dict.items():
- <td>
- %if sample_values[field_index]:
- %if field['type'] == 'WorkflowField':
- %if str(sample_values[field_index]) != 'none':
- <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %>
- <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a>
- %endif
- %else:
- ${sample_values[field_index]}
- %endif
- %else:
- <i>None</i>
- %endif
- </td>
- %endfor
-</%def>
-
-<div class="toolForm">
- <div class="form-row">
- <div class="msg_list">
- <h4 class="msg_head"><u>Request Information</u></h4>
- <div class="msg_body">
- %for index, rd in enumerate(request_details):
- <div class="form-row">
- <label>${rd['label']}</label>
- %if not rd['value']:
- <i>None</i>
- %else:
- %if rd['label'] == 'State':
- <a href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">${rd['value']}</a>
- %else:
- ${rd['value']}
- %endif
- %endif
- </div>
- <div style="clear: both"></div>
- %endfor
- <div class="form-row">
- <ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='Edit', id=trans.security.encode_id(request.id))}">
- <span>Edit request details</span></a>
- </li>
- </ul>
- </div>
- </div>
- </div>
- </div>
-</div>
-
-<br/>
-
-
-<%def name="render_grid( grid_index, grid_name, fields_dict )">
- <br/>
- <div class="msg_list">
- %if grid_name:
- <h4 class="msg_head"><u>${grid_name}</u></h4>
- %else:
- <h4>Grid ${grid_index}</h4>
- %endif
- %if edit_mode == 'False' or len(current_samples) <= len(request.samples):
- <div class="msg_body">
- %else:
- <div class="msg_body2">
- %endif
- <table class="grid">
- <thead>
- <tr>
- <th>Name</th>
- %for index, field in fields_dict.items():
- <th>
- ${field['label']}
- <div class="toolParamHelp" style="clear: both;">
- <i>${field['helptext']}</i>
- </div>
- </th>
- %endfor
- <th></th>
- </tr>
- <thead>
- <tbody>
- <%
- trans.sa_session.refresh( request )
- %>
- %for sample_index, sample in enumerate(current_samples):
- %if edit_mode == 'True':
- <tr>
- ${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
- </tr>
- %else:
- <tr>
- %if sample_index in range(len(request.samples)):
- ${render_sample( sample_index, sample['name'], sample['field_values'], fields_dict )}
- %else:
- ${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
- %endif
- </tr>
- %endif
- %endfor
- </tbody>
- </table>
- </div>
- </div>
-</%def>
-
-<div class="toolForm">
- ##<div class="toolFormTitle">Samples (${len(request.samples)})</div>
- <form id="show_request" name="show_request" action="${h.url_for( controller='requests_admin', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
- <div class="form-row">
- %if current_samples:
- ## first render the basic info grid
- ${render_basic_info_grid()}
- ## then render the other grid(s)
- <% trans.sa_session.refresh( request.type.sample_form ) %>
- %for grid_index, grid_name in enumerate(request.type.sample_form.layout):
- ${render_grid( grid_index, grid_name, request.type.sample_form.fields_of_grid( grid_index ) )}
- <br/>
- %endfor
- %else:
- <label>There are no samples.</label>
- %endif
- </div>
- %if request.samples and request.submitted():
- <script type="text/javascript">
- // Updater
- updater({${ ",".join( [ '"%s" : "%s"' % ( s.id, s.current_state().name ) for s in request.samples ] ) }});
- </script>
- %endif
-
- %if edit_mode == 'False':
- <table class="grid">
- <tbody>
- <tr>
- <div class="form-row">
-
- %if request.unsubmitted():
- <td>
- %if current_samples:
- <label>Copy </label>
- <input type="integer" name="num_sample_to_copy" value="1" size="3"/>
- <label>sample(s) from sample</label>
- ${sample_copy.get_html()}
- %endif
- <input type="submit" name="add_sample_button" value="Add New"/>
- </td>
- %endif
- <td>
- %if len(current_samples) and len(current_samples) <= len(request.samples):
- <input type="submit" name="edit_samples_button" value="Edit samples"/>
- %endif
- </td>
- </div>
- </tr>
- </tbody>
- </table>
- %endif
- %if request.samples or current_samples:
- <div class="form-row">
- <div style="float: left; width: 250px; margin-right: 10px;">
- <input type="hidden" name="refresh" value="true" size="40"/>
- </div>
- <div style="clear: both"></div>
- </div>
- %if edit_mode == 'True':
- <div class="form-row">
- <input type="submit" name="save_samples_button" value="Save"/>
- <input type="submit" name="cancel_changes_button" value="Cancel"/>
- </div>
- %elif request.unsubmitted():
- <div class="form-row">
- <input type="submit" name="save_samples_button" value="Save"/>
- </div>
- %endif
-
- %endif
- <input type="hidden" name="request_id" value="${request.id}" />
- </form>
-</div>
-
-<br/>
-
-%if request.unsubmitted():
-<div class="toolForm">
- <form id="show_request" name="show_request" action="${h.url_for( controller='requests_admin', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
- <div class="form-row">
- <div class="msg_list">
- <h4 class="msg_head"><u>Import samples from csv file</u></h4>
- <div class="msg_body">
- <input type="file" name="file_data" />
- <input type="submit" name="import_samples_button" value="Import samples"/>
- <br/>
- <div class="toolParamHelp" style="clear: both;">
- The csv file must be in the following format:<br/>
- SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...
- </div>
- </div>
- </div>
- </div>
- <input type="hidden" name="request_id" value="${request.id}" />
- </form>
-</div>
-%endif
-
--- a/templates/admin/samples/events.mako
+++ /dev/null
@@ -1,63 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<%def name="title()">Events for Sample ${sample.name}</%def>
-
-<h2>Events for Sample "${sample.name}"</h2>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(sample.request.id) )}">
- <span>Browse this request</span></a>
- </li>
-</ul>
-<h3>User: ${sample.request.user.email}</h3>
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
- <table class="grid">
- <thead>
- <tr>
- <th>State</th>
- <th>Description</th>
- <th>Last Update</th>
- <th>Comments</th>
- </tr>
- </thead>
- <tbody>
- %for state, desc, updated, comments in events_list:
- <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
- <td><b><a>${state}</a></b></td>
- <td><a>${desc}</a></td>
- <td><a>${updated}</a></td>
- <td><a>${comments}</a></td>
- </tr>
- %endfor
- </tbody>
- </table>
-</div>
-<div class="toolForm">
- <div class="toolFormTitle">Change current state</div>
- <div class="toolFormBody">
- <form name="event" action="${h.url_for( controller='requests_admin', action='save_state', new=True, sample_id=sample.id)}" method="post" >
- %for w in widgets:
- <div class="form-row">
- <label>
- ${w[0]}
- </label>
- ${w[1].get_html()}
- %if w[0] == 'Comments':
- <div class="toolParamHelp" style="clear: both;">
- Optional
- </div>
- %endif
- </div>
- %endfor
- <div class="form-row">
- <input type="submit" name="add_event_button" value="Save"/>
- </div>
- </form>
- </div>
-</div>
--- a/tool-data/shared/bx/bx_build_sites.txt
+++ /dev/null
@@ -1,1 +0,0 @@
-main http://main.genome-browser.bx.psu.edu/cgi-bin/hgTracks? hg18,hg19,mm8,mm9 bx-main
--- a/static/trackster.css
+++ /dev/null
@@ -1,132 +0,0 @@
-#content {
- width: 100%;
-}
-
-#center {
- overflow: auto;
-}
-
-#nav-container {
- position: fixed;
- left: 0;
- bottom: 0;
-}
-
-/*canvas{
- border-left: 1px solid green;
- border-right: 1px solid red; } /* debugging */
-#nav {
- padding: 0 0;
- color:#333;font-weight:bold;
-}
-
-#nav-controls {
- text-align: center;
- background:#cccccc;
- background-image:url(style/panel_header_bg.png);
- background-position:top center;
- background-repeat:repeat-x;
- padding-bottom: 5px;
-}
-
-#nav-controls a {
- padding: 5px 0.4em;
-}
-
-#overview {
- width: 100%;
- margin: 0px;
- color: white;
- margin-top: -6px;
- margin-bottom: -4px;
-}
-
-#overview-viewport {
- position: relative;
- height: 14px;
-/* border-top: solid #666 1px;*/
-/* border-bottom: solid #aaa 1px;*/
- background: white;
- border-top: solid gray 1px;
- border-bottom: solid gray 1px;
- margin: 5px 0;
-}
-#overview-box {
- position: absolute;
- margin-top: 0px;
- height: 14px;
- background: #ddd url(images/visualization/draggable_horizontal.png) center center no-repeat;
- /*border-style: outset;*/
-}
-
-#viewport {
-/* overflow-x: hidden;*/
- background-color: #fff;
-/* overflow: scroll;*/
-/* border-bottom: 2px solid black;*/
-}
-
-#viewport-canvas {
- width: 100%;
- height: 100px;
-}
-
-.yaxislabel {
- color: #777;
-}
-/* Line track needs borders to show range */
-.line-track .track-content {
- border-top: 1px solid #ddd;
- border-bottom: 1px solid #ddd;
-}
-
-.track {
- /* border-top: solid #DDDDDD 1px; */
- /* border-bottom: solid #DDDDDD 1px; */
- background: white;
-}
-
-.track-header {
- text-align: center;
- padding: 4px;
- color: #666;
-}
-
-.track-content {
- overflow: hidden;
- text-align: center;
-}
-
-.track.error {
- background-color: #ECB4AF;
-}
-.track.nodata {
- background-color: #ddd;
-}
-
-.loading {
- min-height: 100px;
-}
-
-.label-track {
- /* font-weight: bold; */
- /* font-size: 10px; */
-}
-.label-track .label {
- border-left: solid #999 1px;
- padding: 1px;
- display: inline-block;
-}
-.right-float {
- float: right;
- margin-left: 5px;
-}
-
-#top-labeltrack {
- border-bottom: solid #999 1px;
-}
-
-#nav-labeltrack {
- border-top: solid #999 1px;
- border-bottom: solid #999 1px;
-}
--- a/templates/requests/sample_state.mako
+++ /dev/null
@@ -1,5 +0,0 @@
-<%def name="render_sample_state( sample )">
- <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
-</%def>
-
-${render_sample_state( sample )}
--- a/templates/admin/samples/bar_codes.mako
+++ /dev/null
@@ -1,46 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-
-<h2>Bar codes for Samples of Request "${request.name}"</h2>
-<h3>User: ${user.email}</h3>
-
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
- <span>Browse this request</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- <form name="bar_codes" action="${h.url_for( controller='requests_admin', action='save_bar_codes', request_id=request.id)}" method="post" >
- <table class="grid">
- <thead>
- <tr>
- <th>Name</th>
- <th>Description</th>
- <th>Bar code</th>
- </tr>
- </thead>
- <tbody>
- %for index, sample in enumerate(samples_list):
- <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
- <td><b><a>${sample.name}</a></b></td>
- <td><a>${sample.desc}</a></td>
- <td>
- ${widgets[index].get_html()}
- </td>
- </tr>
- %endfor
- </tbody>
- </table>
- <div class="form-row">
- <input type="submit" name="save_bar_codes" value="Save"/>
- </div>
- </form>
-</div>
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -1251,7 +1251,9 @@ class Admin( object ):
# sort filter instead of this class's.
kwargs[ 'user_id' ] = kwargs[ 'id' ]
kwargs[ 'sort' ] = 'name'
- return self.browse_tools( trans, **kwargs )
+ return trans.response.send_redirect( web.url_for( controller='admin',
+ action='browse_tools',
+ **kwargs ) )
# Render the list view
return self.user_list_grid( trans, **kwargs )
@web.expose
--- a/templates/requests/edit_request.mako
+++ /dev/null
@@ -1,84 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
- $( "select[refresh_on_change='true']").change( function() {
- var refresh = false;
- var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
- if ( refresh_on_change_values ) {
- refresh_on_change_values = refresh_on_change_values.value.split( ',' );
- var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
- for( i= 0; i < refresh_on_change_values.length; i++ ) {
- if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
- refresh = true;
- break;
- }
- }
- }
- else {
- refresh = true;
- }
- if ( refresh ){
- $( "#edit_request" ).submit();
- }
- });
-});
-</script>
-
-<br/>
-<br/>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests', action='list')}">
- <span>Browse requests</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- <div class="toolFormTitle">Edit request "${request.name}"</div>
- %if len(select_request_type.options) == 1:
- There are no request types created for a new request.
- %else:
- <div class="toolFormBody">
- <form name="edit_request" id="edit_request" action="${h.url_for( controller='requests', action='edit', request_id=request.id)}" method="post" >
- <div class="form-row">
- <label>
- Select Request Type:
- </label>
- ${select_request_type.get_html()}
- </div>
-
- %if select_request_type.get_selected() != ('Select one', 'none'):
- %for i, field in enumerate(widgets):
- <div class="form-row">
- <label>${field['label']}</label>
- ${field['widget'].get_html()}
- %if field['label'] == 'Data library' and new_library:
- ${new_library.get_html()}
- %endif
- <div class="toolParamHelp" style="clear: both;">
- ${field['helptext']}
- </div>
- <div style="clear: both"></div>
- </div>
- %endfor
- <div class="form-row">
- <div style="float: left; width: 250px; margin-right: 10px;">
- <input type="hidden" name="refresh" value="true" size="40"/>
- </div>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit" name="save_changes_request_button" value="Save changes"/>
- ##<input type="submit" name="edit_samples_button" value="Edit samples"/>
- </div>
- %endif
- </form>
- </div>
-</div>
-%endif
--- a/templates/root/index.mako
+++ b/templates/root/index.mako
@@ -43,9 +43,9 @@
"Show structure": function() {
galaxy_main.location = "${h.url_for( controller='history', action='display_structured' )}";
},
- "Export to File": function() {
- galaxy_main.location = "${h.url_for( controller='history', action='export_archive' )}";
- },
+ ##"Export to File": function() {
+ ## galaxy_main.location = "${h.url_for( controller='history', action='export_archive' )}";
+ ##},
"Delete": function()
{
if ( confirm( "Really delete the current history?" ) )
@@ -53,10 +53,10 @@
galaxy_main.location = "${h.url_for( controller='history', action='delete_current' )}";
}
},
- "Other Actions": null,
- "Import from File": function() {
- galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}";
- }
+ ##"Other Actions": null,
+ ##"Import from File": function() {
+ ## galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}";
+ ##}
});
// Init tool options.
--- a/templates/requests/new_request.mako
+++ /dev/null
@@ -1,94 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
- $( "select[refresh_on_change='true']").change( function() {
- var refresh = false;
- var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
- if ( refresh_on_change_values ) {
- refresh_on_change_values = refresh_on_change_values.value.split( ',' );
- var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
- for( i= 0; i < refresh_on_change_values.length; i++ ) {
- if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
- refresh = true;
- break;
- }
- }
- }
- else {
- refresh = true;
- }
- if ( refresh ){
- $( "#new_request" ).submit();
- }
- });
-});
-</script>
-
-<%def name="javascripts()">
- ${parent.javascripts()}
- ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
-</%def>
-
-<%def name="stylesheets()">
- ${parent.stylesheets()}
- ${h.css( "autocomplete_tagging" )}
-</%def>
-
-<br/>
-<br/>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests', action='list')}">
- <span>Browse requests</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- <div class="toolFormTitle">Add a new request</div>
- %if len(select_request_type.options) == 1:
- There are no request types created for a new request.
- %else:
- <div class="toolFormBody">
- <form name="new_request" id="new_request" action="${h.url_for( controller='requests', action='new', create=True )}" method="post" >
- <div class="form-row">
- <label>
- Select Request Type:
- </label>
- ${select_request_type.get_html()}
- </div>
-
- %if select_request_type.get_selected() != ('Select one', 'none'):
- %for i, field in enumerate(widgets):
- <div class="form-row">
- <label>${field['label']}</label>
- ${field['widget'].get_html()}
- ##%if field['label'] == 'Data library' and new_library:
- ## ${new_library.get_html()}
- ##%endif
- <div class="toolParamHelp" style="clear: both;">
- ${field['helptext']}
- </div>
- <div style="clear: both"></div>
- </div>
- %endfor
- <div class="form-row">
- <div style="float: left; width: 250px; margin-right: 10px;">
- <input type="hidden" name="refresh" value="true" size="40"/>
- </div>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit" name="create_request_button" value="Save"/>
- <input type="submit" name="create_request_samples_button" value="Add samples"/>
- </div>
- %endif
- </form>
- </div>
-</div>
-%endif
--- a/lib/galaxy/util/memory_usage.py
+++ /dev/null
@@ -1,44 +0,0 @@
-import os, platform, logging
-from galaxy.datatypes.data import nice_size
-
-log = logging.getLogger( __name__ )
-
-_proc_status = '/proc/%d/status' % os.getpid()
-
-_scale = { 'kB': 1024.0, 'mB': 1024.0*1024.0, 'KB': 1024.0, 'MB': 1024.0*1024.0 }
-
-def _VmB( VmKey ):
- '''Private.
- '''
- global _proc_status, _scale
- # get pseudo file /proc/<pid>/status
- try:
- t = open( _proc_status )
- v = t.read()
- t.close()
- except:
- log.debug("memory_usage is currently supported only on Linux, your platform is %s %s" % ( platform.system(), platform.release() ) )
- return 0.0 # non-Linux?
- # get VmKey line e.g. 'VmRSS: 9999 kB\n ...'
- i = v.index( VmKey )
- v = v[ i: ].split( None, 3 ) # whitespace
- if len( v ) < 3:
- return 0.0 # invalid format?
- # convert Vm value to bytes
- return float( v[ 1 ] ) * _scale[ v[ 2 ] ]
-def memory( since=0.0, pretty=False ):
- '''Return memory usage in bytes.
- '''
- size = _VmB( 'VmSize:' ) - since
- if pretty:
- return nice_size( size )
- else:
- return size
-def resident( since=0.0 ):
- '''Return resident memory usage in bytes.
- '''
- return _VmB( 'VmRSS:' ) - since
-def stacksize( since=0.0 ):
- '''Return stack size in bytes.
- '''
- return _VmB( 'VmStk:' ) - since
--- a/templates/sample/index.mako
+++ /dev/null
@@ -1,16 +0,0 @@
-<%inherit file="/webapps/galaxy/base_panels.mako"/>
-
-<%def name="init()">
-<%
- self.has_left_panel=False
- self.has_right_panel=False
- self.active_view="requests"
-
-%>
-</%def>
-
-<%def name="center_panel()">
-
- <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="sample", action="list", request_id=request_id )}"></iframe>
-
-</%def>
--- a/templates/requests/show_request.mako
+++ /dev/null
@@ -1,430 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
- $( "select[refresh_on_change='true']").change( function() {
- var refresh = false;
- var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
- if ( refresh_on_change_values ) {
- refresh_on_change_values = refresh_on_change_values.value.split( ',' );
- var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
- for( i= 0; i < refresh_on_change_values.length; i++ ) {
- if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
- refresh = true;
- break;
- }
- }
- }
- else {
- refresh = true;
- }
- if ( refresh ){
- $( "#show_request" ).submit();
- }
- });
-});
-</script>
-
-
-<script type="text/javascript">
-$(document).ready(function(){
- //hide the all of the element with class msg_body
- $(".msg_body").hide();
- //toggle the componenet with class msg_body
- $(".msg_head").click(function(){
- $(this).next(".msg_body").slideToggle(450);
- });
-});
-</script>
-<style type="text/css">
-.msg_head {
- padding: 0px 0px;
- cursor: pointer;
-}
-
-}
-</style>
-
-%if request.rejected():
- ${render_msg( "Reason for rejection: "+request.last_comment(), "warning" )}
-%endif
-
-<div class="grid-header">
- <h2>Sequencing Request "${request.name}"</h2>
-</div>
-
-<ul class="manage-table-actions">
- %if request.unsubmitted() and request.samples:
- <li>
- <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests', action='list', operation='Submit', id=trans.security.encode_id(request.id) )}">
- <span>Submit request</span></a>
- </li>
- %endif
- <li>
- <a class="action-button" href="${h.url_for( controller='requests', action='list', operation='events', id=trans.security.encode_id(request.id) )}">
- <span>History</span></a>
- </li>
- <li>
- <a class="action-button" href="${h.url_for( controller='requests', action='list')}">
- <span>Browse requests</span></a>
- </li>
-</ul>
-
-<%def name="show_basic_info_form( sample_index, sample, info )">
- <td>
- <input type="text" name=sample_${sample_index}_name value="${info['name']}" size="10"/>
- <div class="toolParamHelp" style="clear: both;">
- <i>${' (required)' }</i>
- </div>
- </td>
- %if sample:
- %if sample.request.unsubmitted():
- <td></td>
- %else:
- <td><input type="text" name=sample_${sample_index}_barcode value="${info['barcode']}" size="10"/></td>
- %endif
- %else:
- <td></td>
- %endif
- %if sample:
- %if not sample.current_state():
- <td>Unsubmitted</td>
- %else:
- <td><a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a></td>
- %endif
- %else:
- <td></td>
- %endif
- <td>${info['lib_widget'].get_html()}</td>
- <td>${info['folder_widget'].get_html()}</td>
- %if request.submitted() or request.complete():
- %if sample:
- <td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a></td>
- %else:
- <td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">Add</a></td>
- %endif
- %endif
-</%def>
-
-## This function displays the "Basic Information" grid
-<%def name="render_basic_info_grid()">
- <h4>Sample Information</h4>
- <table class="grid">
- <thead>
- <tr>
- <th>Name</th>
- <th>Barcode</th>
- <th>State</th>
- <th>Data Library</th>
- <th>Folder</th>
- %if request.submitted() or request.complete():
- <th>Dataset(s) Transferred</th>
- %endif
- <th></th>
- </tr>
- <thead>
- <tbody>
- <%
- trans.sa_session.refresh( request )
- %>
- %for sample_index, info in enumerate(current_samples):
- <%
- if sample_index in range(len(request.samples)):
- sample = request.samples[sample_index]
- else:
- sample = None
- %>
- %if edit_mode == 'True':
- <tr>
- ${show_basic_info_form( sample_index, sample, info )}
- </tr>
- %else:
- <tr>
- %if sample_index in range(len(request.samples)):
- <td>${info['name']}</td>
- <td>${info['barcode']}</td>
- <td>
- %if sample.current_state():
- <a href="${h.url_for( controller='requests', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
- %else:
- Unsubmitted
- %endif
- </td>
- %if info['library']:
- <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td>
- %else:
- <td></td>
- %endif
- %if info['folder']:
- <td>${info['folder'].name}</td>
- %else:
- <td></td>
- %endif
- %if request.submitted() or request.complete():
- <td>
- <a href="${h.url_for( controller='requests', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a>
- </td>
- %endif
-
-
- %else:
- ${show_basic_info_form( sample_index, sample, info )}
- %endif
- %if request.unsubmitted() or request.rejected():
- <td>
- %if sample:
- %if sample.request.unsubmitted():
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index )}">
- <img src="${h.url_for('/static/images/delete_icon.png')}" />
- <span></span></a>
- %endif
- %endif
- </td>
- %endif
- </tr>
- %endif
- %endfor
- </tbody>
- </table>
-</%def>
-
-<%def name="render_sample_form( index, sample_name, sample_values, fields_dict )">
- <td>
- ${sample_name}
- </td>
- %for field_index, field in fields_dict.items():
- <td>
- %if field['type'] == 'TextField':
- <input type="text" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/>
- %elif field['type'] == 'SelectField':
- <select name="sample_${index}_field_${field_index}" last_selected_value="2">
- %for option_index, option in enumerate(field['selectlist']):
- %if option == sample_values[field_index]:
- <option value="${option}" selected>${option}</option>
- %else:
- <option value="${option}">${option}</option>
- %endif
- %endfor
- </select>
- %elif field['type'] == 'WorkflowField':
- <select name="sample_${index}_field_${field_index}">
- %if str(sample_values[field_index]) == 'none':
- <option value="none" selected>Select one</option>
- %else:
- <option value="none">Select one</option>
- %endif
- %for option_index, option in enumerate(request.user.stored_workflows):
- %if not option.deleted:
- %if str(option.id) == str(sample_values[field_index]):
- <option value="${option.id}" selected>${option.name}</option>
- %else:
- <option value="${option.id}">${option.name}</option>
- %endif
- %endif
- %endfor
- </select>
- %elif field['type'] == 'CheckboxField':
- <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/>
- %endif
- <div class="toolParamHelp" style="clear: both;">
- <i>${'('+field['required']+')' }</i>
- </div>
- </td>
- %endfor
-</%def>
-
-<%def name="render_sample( index, sample_name, sample_values, fields_dict )">
- <td>
- ${sample_name}
- </td>
- %for field_index, field in fields_dict.items():
- <td>
- %if sample_values[field_index]:
- %if field['type'] == 'WorkflowField':
- %if str(sample_values[field_index]) != 'none':
- <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %>
- <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a>
- %endif
- %else:
- ${sample_values[field_index]}
- %endif
- %else:
- <i>None</i>
- %endif
-
- </td>
- %endfor
-</%def>
-
-<%def name="render_grid( grid_index, grid_name, fields_dict )">
- <br/>
- <div class="msg_list">
- %if grid_name:
- <h4 class="msg_head"><u>${grid_name}</u></h4>
- %else:
- <h4>Grid ${grid_index}</h4>
- %endif
- %if edit_mode == 'False' or len(current_samples) <= len(request.samples):
- <div class="msg_body">
- %else:
- <div class="msg_body2">
- %endif
- <table class="grid">
- <thead>
- <tr>
- <th>Name</th>
- %for index, field in fields_dict.items():
- <th>
- ${field['label']}
- <div class="toolParamHelp" style="clear: both;">
- <i>${field['helptext']}</i>
- </div>
- </th>
- %endfor
- <th></th>
- </tr>
- <thead>
- <tbody>
- <%
- trans.sa_session.refresh( request )
- %>
- %for sample_index, sample in enumerate(current_samples):
- %if edit_mode == 'True':
- <tr>
- ${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
- </tr>
- %else:
- <tr>
- %if sample_index in range(len(request.samples)):
- ${render_sample( sample_index, sample['name'], sample['field_values'], fields_dict )}
- %else:
- ${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
- %endif
- </tr>
- %endif
- %endfor
- </tbody>
- </table>
- </div>
- </div>
-</%def>
-
-<div class="toolForm">
- <form id="request_details" name="request_details" >
- <div class="form-row">
- <div class="msg_list">
- <h4 class="msg_head"><u>Request Information</u></h4>
- <div class="msg_body">
- %for index, rd in enumerate(request_details):
- <div class="form-row">
- <label>${rd['label']}</label>
- %if not rd['value']:
- <i>None</i>
- %else:
- %if rd['label'] == 'State':
- <a href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">${rd['value']}</a>
- %else:
- ${rd['value']}
- %endif
- %endif
- </div>
- <div style="clear: both"></div>
- %endfor
- <div class="form-row">
- <ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='Edit', id=trans.security.encode_id(request.id))}">
- <span>Edit request details</span></a>
- </li>
- </ul>
- </div>
- </div>
- </div>
- </div>
- </form>
- <form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
- <div class="form-row">
- %if current_samples:
- ## first render the basic info grid
- ${render_basic_info_grid()}
- ## then render the other grid(s)
- <% trans.sa_session.refresh( request.type.sample_form ) %>
- %for grid_index, grid_name in enumerate(request.type.sample_form.layout):
- ${render_grid( grid_index, grid_name, request.type.sample_form.fields_of_grid( grid_index ) )}
- <br/>
- %endfor
- %else:
- <label>There are no samples.</label>
- %endif
- </div>
- %if request.unsubmitted() and edit_mode == 'False':
- <table class="grid">
- <tbody>
- <tr>
- <div class="form-row">
- <td>
- %if current_samples:
- <label>Copy </label>
- <input type="integer" name="num_sample_to_copy" value="1" size="3"/>
- <label>sample(s) from sample</label>
- ${sample_copy.get_html()}
- %endif
- <input type="submit" name="add_sample_button" value="Add New"/>
- </td>
- <td>
- %if len(current_samples) and len(current_samples) <= len(request.samples):
- <input type="submit" name="edit_samples_button" value="Edit samples"/>
- %endif
- </td>
- </div>
- </tr>
- </tbody>
- </table>
- %endif
- %if request.unsubmitted() and (request.samples or current_samples):
- <div class="form-row">
- <div style="float: left; width: 250px; margin-right: 10px;">
- <input type="hidden" name="refresh" value="true" size="40"/>
- </div>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit" name="save_samples_button" value="Save"/>
- %if edit_mode == 'True':
- <input type="submit" name="cancel_changes_button" value="Cancel"/>
- %endif
- </div>
- %endif
- <input type="hidden" name="request_id" value="${request.id}" />
- </form>
-</div>
-
-
-<br/>
-%if request.unsubmitted():
-<div class="toolForm">
- <form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
- <div class="form-row">
- <div class="msg_list">
- <h4 class="msg_head"><u>Import samples from csv file</u></h4>
- <div class="msg_body">
- <input type="file" name="file_data" />
- <input type="submit" name="import_samples_button" value="Import samples"/>
- <br/>
- <div class="toolParamHelp" style="clear: both;">
- The csv file must be in the following format:<br/>
- SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...
- </div>
- </div>
- </div>
- </div>
- <input type="hidden" name="request_id" value="${request.id}" />
- </form>
-</div>
-%endif
--- a/templates/admin/requests/get_data.mako
+++ /dev/null
@@ -1,227 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$(document).ready(function(){
- //hide the all of the element with class msg_body
- $(".msg_body").hide();
- //toggle the componenet with class msg_body
- $(".msg_head").click(function(){
- $(this).next(".msg_body").slideToggle(450);
- });
-});
-
-
-
-
-</script>
-
-<script type="text/javascript">
- function display_file_details(sample_id, folder_path)
- {
- var w = document.get_data.files_list.selectedIndex;
- var selected_value = document.get_data.files_list.options[w].value;
- var cell = $("#file_details");
- if(selected_value.charAt(selected_value.length-1) != '/')
- {
- // Make ajax call
- $.ajax( {
- type: "POST",
- url: "${h.url_for( controller='requests_admin', action='get_file_details' )}",
- dataType: "json",
- data: { id: sample_id, folder_path: document.get_data.folder_path.value+selected_value },
- success : function ( data ) {
- cell.html( '<label>'+data+'</label>' )
- }
- });
- }
- else
- {
- cell.html( '' )
- }
-
-
- }
-</script>
-
-<script type="text/javascript">
- function open_folder1(sample_id, folder_path)
- {
- var w = document.get_data.files_list.selectedIndex;
- var selected_value = document.get_data.files_list.options[w].value;
- var cell = $("#file_details");
- if(selected_value.charAt(selected_value.length-1) == '/')
- {
- document.get_data.folder_path.value = document.get_data.folder_path.value+selected_value
- // Make ajax call
- $.ajax( {
- type: "POST",
- url: "${h.url_for( controller='requests_admin', action='open_folder' )}",
- dataType: "json",
- data: { id: sample_id, folder_path: document.get_data.folder_path.value },
- success : function ( data ) {
- document.get_data.files_list.options.length = 0
- for(i=0; i<data.length; i++)
- {
- var newOpt = new Option(data[i], data[i]);
- document.get_data.files_list.options[i] = newOpt;
- }
- //cell.html( '<label>'+data+'</label>' )
-
- }
- });
- }
- else
- {
- cell.html( '' )
- }
- }
-</script>
-
-
-<style type="text/css">
-.msg_head {
- padding: 0px 0px;
- cursor: pointer;
-}
-
-}
-</style>
-
-
-<h2>Data transfer from Sequencer</h2>
-<h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3>
-<br/>
-<br/>
-
-<ul class="manage-table-actions">
- %if sample.request.submitted() and sample.inprogress_dataset_files():
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">
- <span>Refresh this page</span></a>
- </li>
- %endif
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_request_types', operation='view', id=trans.security.encode_id(sample.request.type.id) )}">
- <span>Sequencer information</span></a>
- </li>
- <li>
- <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=trans.security.encode_id( sample.library.id ) )}">
- <span>${sample.library.name} Data Library</span></a>
- </li>
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(sample.request.id) )}">
- <span>Browse this request</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- %if len(dataset_files):
-## <form name="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
- <div class="form-row">
- <h4>Sample Dataset(s)</h4>
- %if sample.untransferred_dataset_files():
- <div class="form-row">
- <ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', start_transfer_button=True, sample_id=sample.id )}">
- <span>Start transfer</span></a>
- </li>
- </ul>
- </div>
- %endif
- <div class="form-row">
- <table class="grid">
- <thead>
- <tr>
- <th>Dataset File</th>
- <th>Transfer Status</th>
- <th></th>
- </tr>
- <thead>
- <tbody>
- %for dataset_index, dataset_file in enumerate(dataset_files):
- ${sample_dataset_files( dataset_index, dataset_file['name'], dataset_file['status'] )}
- %endfor
- </tbody>
- </table>
- </div>
- </div>
-
-## </form>
-##</div>
-
-
-<br/>
-<br/>
-%endif
-
-##<div class="toolForm">
- <form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
- <div class="form-row">
- ##<div class="toolFormTitle">Select files for transfer</div>
- <h4>Select files for transfer</h4>
- <div style="width: 60%;">
- <div class="form-row">
- <label>Folder path on the sequencer:</label>
- <input type="text" name="folder_path" value="${folder_path}" size="100"/>
- <input type="submit" name="browse_button" value="List contents"/>
- ##<input type="submit" name="open_folder" value="Open folder"/>
- <input type="submit" name="folder_up" value="Up"/>
- </div>
- <div class="form-row">
- <select name="files_list" id="files_list" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" ondblclick="open_folder1(${sample.id}, '${folder_path}')" onChange="display_file_details(${sample.id}, '${folder_path}')" multiple>
- %for index, f in enumerate(files):
- <option value="${f}">${f}</option>
- %endfor
- </select>
- <br/>
- <div id="file_details" class="toolParamHelp" style="clear: both;">
-
- </div>
- </div>
- <div class="form-row">
- <div class="toolParamHelp" style="clear: both;">
- After selecting dataset(s), be sure to click on the <b>Start transfer</b> button.
- Once the transfer is complete the dataset(s) will show up on this page.
- </div>
- <input type="submit" name="select_files_button" value="Select"/>
- </div>
- </div>
- </div>
- </form>
-</div>
-
-<%def name="sample_dataset_files( dataset_index, dataset_name, status )">
- <tr>
- <td>
- <label class="msg_head"><a href="${h.url_for( controller='requests_admin', action='dataset_details', sample_id=trans.security.encode_id(sample.id), dataset_index=dataset_index )}">${dataset_name}</a></label>
-## <div class="msg_head"><u>${dataset_file.split('/')[-1]}</u></div>
-## <div class="msg_body">
-## ${dataset_file}
-## </div>
- </td>
- <td>
- %if status not in [sample.transfer_status.NOT_STARTED, sample.transfer_status.COMPLETE]:
- <i>${status}</i>
- %else:
- ${status}
- %endif
- </td>
- ##<td></td>
- %if status == sample.transfer_status.NOT_STARTED:
- <td>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id, remove_dataset_button=True, dataset_index=dataset_index )}">
- <img src="${h.url_for('/static/images/delete_icon.png')}" />
- <span></span></a>
- </td>
- %else:
- <td></td>
- %endif
- </tr>
-</%def>
--- a/templates/admin/requests/add_states.mako
+++ /dev/null
@@ -1,26 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
- <div class="toolFormTitle">Create ${num_states} states for the '${request_type_name}' request type</div>
- <form name="new_form_fields" action="${h.url_for( controller='requests_admin', action='request_type', name=request_type_name, description=desc, num_states=num_states, request_form_id=request_form_id, sample_form_id=sample_form_id)}" method="post" >
- <div class="toolFormBody">
- %for element_count in range( num_states ):
- <div class="form-row">
- <label>${1+element_count}) State name:</label>
- <input type="text" name="state_name_${element_count}" value="" size="40"/>
- <label>State help text (optional):</label>
- <input type="text" name="state_desc_${element_count}" value="" size="40"/>
- </div>
- <div style="clear: both"></div>
- %endfor
- </div>
- <div class="form-row">
- <input type="submit" name="save_request_type" value="Save"/>
- </div>
- </form>
-</div>
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -115,6 +115,7 @@ class Job( object ):
self.job_runner_name = None
self.job_runner_external_id = None
self.post_job_actions = None
+ self.imported = False
def add_parameter( self, name, value ):
self.parameters.append( JobParameter( name, value ) )
@@ -964,16 +965,16 @@ class LibraryFolder( object ):
intermed.sort()
return map( operator.getitem, intermed, ( -1, ) * len( intermed ) )
# This needs to be a list
- active_library_datasets = [ ld for ld in self.datasets if not ld.library_dataset_dataset_association.deleted ]
+ active_library_datasets = [ ld for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.deleted ]
return sort_by_attr( [ ld for ld in active_library_datasets ], 'name' )
@property
def activatable_library_datasets( self ):
# This needs to be a list
- return [ ld for ld in self.datasets if not ld.library_dataset_dataset_association.dataset.deleted ]
+ return [ ld for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.dataset.deleted ]
@property
def active_datasets( self ):
# This needs to be a list
- return [ ld.library_dataset_dataset_association.dataset for ld in self.datasets if not ld.library_dataset_dataset_association.deleted ]
+ return [ ld.library_dataset_dataset_association.dataset for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.deleted ]
def get_display_name( self ):
# Library folder name can be either a string or a unicode object. If string,
# convert to unicode object assuming 'utf-8' format.
@@ -1558,6 +1559,7 @@ class RequestEvent( object ):
class RequestType( object ):
rename_dataset_options = Bunch( NO = 'Do not rename',
SAMPLE_NAME = 'Preprend sample name',
+ EXPERIMENT_NAME = 'Prepend experiment name',
EXPERIMENT_AND_SAMPLE_NAME = 'Prepend experiment and sample name')
permitted_actions = get_permitted_actions( filter='REQUEST_TYPE' )
def __init__(self, name=None, desc=None, request_form=None, sample_form=None,
--- a/templates/admin/requests/edit_request.mako
+++ /dev/null
@@ -1,88 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
- $( "select[refresh_on_change='true']").change( function() {
- var refresh = false;
- var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
- if ( refresh_on_change_values ) {
- refresh_on_change_values = refresh_on_change_values.value.split( ',' );
- var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
- for( i= 0; i < refresh_on_change_values.length; i++ ) {
- if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
- refresh = true;
- break;
- }
- }
- }
- else {
- refresh = true;
- }
- if ( refresh ){
- $( "#edit_request" ).submit();
- }
- });
-});
-</script>
-
-<br/>
-<br/>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
- <span>Browse this request</span></a>
- </li>
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='list')}">
- <span>Browse requests</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- <div class="toolFormTitle">Edit request "${request.name}" from ${request.user.email}</div>
- %if len(select_request_type.options) == 1:
- There are no request types created for a new request.
- %else:
- <div class="toolFormBody">
- <form name="edit_request" id="edit_request" action="${h.url_for( controller='requests_admin', action='edit', request_id=request.id)}" method="post" >
- <div class="form-row">
- <label>
- Select Request Type:
- </label>
- ${select_request_type.get_html()}
- </div>
-
- %if select_request_type.get_selected() != ('Select one', 'none'):
- %for i, field in enumerate(widgets):
- <div class="form-row">
- <label>${field['label']}</label>
- ${field['widget'].get_html()}
- %if field['label'] == 'Library' and new_library:
- ${new_library.get_html()}
- %endif
- <div class="toolParamHelp" style="clear: both;">
- ${field['helptext']}
- </div>
- <div style="clear: both"></div>
- </div>
- %endfor
- <div class="form-row">
- <div style="float: left; width: 250px; margin-right: 10px;">
- <input type="hidden" name="refresh" value="true" size="40"/>
- </div>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit" name="save_changes_request_button" value="Save changes"/>
- ##<input type="submit" name="edit_samples_button" value="Edit samples"/>
- </div>
- %endif
- </form>
- </div>
-</div>
-%endif
--- a/static/about.html
+++ /dev/null
@@ -1,78 +0,0 @@
-<?xml version="1.0" encoding="utf-8" ?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" />
-<title>ABOUT GALAXY</title>
-<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
-<link rel="stylesheet" href="/static/style/help.css" type="text/css" />
-</head>
-<body>
-<div class="document" id="about-galaxy">
-<h1 class="title">ABOUT GALAXY</h1>
-<div class="section" id="people">
-<h2><a name="people">People:</a></h2>
-<ul class="simple">
-<li>Istvan Albert - <em>Co-PI</em></li>
-<li>Daniel Blankenberg - <em>Graduate student</em></li>
-<li>Richard Burhans - <em>Sysadmin</em></li>
-<li>Laura Elnitski - <em>Co-PI</em></li>
-<li>Belinda Giardine - <em>Programmer</em></li>
-<li>Ross Hardison - <em>Co-PI</em></li>
-<li>Jim Kent - <em>Co-PI</em></li>
-<li>David King - <em>Graduate student</em></li>
-<li>Webb Miller - <em>Co-PI</em></li>
-<li>Anton Nekrutenko - <em>PI</em></li>
-<li>Cathy Riemer - <em>Programmer</em></li>
-<li>Prachi Shah - <em>Programmer</em></li>
-<li>Ian Schenck - <em>Undergraduate student</em></li>
-<li>James Taylor - <em>Graduate student</em></li>
-<li>Yi Zhang - <em>Programmer</em></li>
-</ul>
-</div>
-<hr class="docutils" />
-<div class="section" id="development">
-<h2><a name="development">Development:</a></h2>
-<p><strong>Galaxy core</strong> - <em>Istvan Albert</em> and <em>James Taylor</em></p>
-<p><strong>Interface</strong> - <em>James Taylor</em>, <em>Istvan Albert</em>, <em>Anton Nekrutenko</em></p>
-<p><strong>Tools</strong> -</p>
-<ul class="simple">
-<li>Data sources - <em>Istvan Albert</em></li>
-<li>EMBOSS, Phylip, mafs - <em>Daniel Blankenberg</em></li>
-<li>Text Tools, Sequence Extractors - <em>Richard Burhans</em>, <em>Anton Nekrutenko</em>, <em>Ian Schenck</em></li>
-<li>Operations - <em>James Taylor</em>, <em>Yi Zhang</em></li>
-<li>Statistics, Graphs - <em>Istvan Albert</em>, <em>David King</em></li>
-</ul>
-<p><strong>Project management</strong> - <em>Anton Nekrutenko</em></p>
-<p>Current version of Galaxy uses many ideas developed by <em>Laura Elnitski</em>, <em>Belinda Giardine</em>, and <em>Cathy Riemer</em> in Galaxy1 and GALA.</p>
-</div>
-<hr class="docutils" />
-<div class="section" id="special-thanks-to">
-<h2><a name="special-thanks-to">Special thanks to:</a></h2>
-<ul class="simple">
-<li>David Haussler</li>
-<li>Ewan Birney</li>
-<li>Hiram Clawson</li>
-<li>Angie Hinrichs</li>
-<li>Darin London</li>
-<li>Members of Hardison, Makova, Miller, and Nekrutenko Labs</li>
-</ul>
-</div>
-<hr class="docutils" />
-<div class="section" id="technology">
-<h2><a name="technology">Technology:</a></h2>
-<p>Galaxy core is written entirely in Python. It uses the following open source technologies:</p>
-<ul class="simple">
-<li>web-server <a class="reference" href="http://www.cherrypy.org/">CherryPy</a></li>
-<li>database <a class="reference" href="http://www.sleepycat.com/products/db.shtml">BerkelyDB</a></li>
-<li>XML library <a class="reference" href="http://effbot.org/zone/element-index.htm">ElementTree</a></li>
-<li>HTML templating library <a class="reference" href="http://www.cheetahtemplate.org/">Cheetah</a></li>
-</ul>
-<p>Galaxy API generated from source code can be found <a class="reference" href="http://www.bx.psu.edu/trac/local/docs/index.html">here</a></p>
-<hr class="docutils" />
-<p><a class="reference" href="http://www.bx.psu.edu">The Center for Comparative Genomics and Bioinformatics</a> at <a class="reference" href="http://www.psu.edu">Penn State</a> | 2005</p>
-</div>
-</div>
-</body>
-</html>
--- a/templates/requests/sample_datasets.mako
+++ /dev/null
@@ -1,7 +0,0 @@
-<%def name="render_sample_datasets( sample )">
- <a href="${h.url_for(controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id))}">${sample.transferred_dataset_files()}/${len(sample.dataset_files)}</a>
-</%def>
-
-
-
-${render_sample_datasets( sample )}
--- a/static/about.rst
+++ /dev/null
@@ -1,82 +0,0 @@
-ABOUT GALAXY
-============
-
-People:
--------
-
-* Istvan Albert - *Co-PI*
-* Daniel Blankenberg - *Graduate student*
-* Richard Burhans - *Sysadmin*
-* Laura Elnitski - *Co-PI*
-* Belinda Giardine - *Programmer*
-* Ross Hardison - *Co-PI*
-* Jim Kent - *Co-PI*
-* David King - *Graduate student*
-* Webb Miller - *Co-PI*
-* Anton Nekrutenko - *PI*
-* Cathy Riemer - *Programmer*
-* Prachi Shah - *Programmer*
-* Ian Schenck - *Undergraduate student*
-* James Taylor - *Graduate student*
-* Yi Zhang - *Programmer*
-
------
-
-Development:
-------------
-
-**Galaxy core** - *Istvan Albert* and *James Taylor*
-
-**Interface** - *James Taylor*, *Istvan Albert*, *Anton Nekrutenko*
-
-**Tools** -
-
-* Data sources - *Istvan Albert*
-* EMBOSS, Phylip, mafs - *Daniel Blankenberg*
-* Text Tools, Sequence Extractors - *Richard Burhans*, *Anton Nekrutenko*, *Ian Schenck*
-* Operations - *James Taylor*, *Yi Zhang*
-* Statistics, Graphs - *Istvan Albert*, *David King*
-
-**Project management** - *Anton Nekrutenko*
-
-Current version of Galaxy uses many ideas developed by *Laura Elnitski*, *Belinda Giardine*, and *Cathy Riemer* in Galaxy1 and GALA.
-
------
-
-Special thanks to:
-------------------
-
-* David Haussler
-* Ewan Birney
-* Hiram Clawson
-* Angie Hinrichs
-* Darin London
-* Members of Hardison, Makova, Miller, and Nekrutenko Labs
-
------
-
-Technology:
------------
-
-Galaxy core is written entirely in Python. It uses the following open source technologies:
-
-* web-server `CherryPy`__
-* database `BerkelyDB`__
-* XML library `ElementTree`__
-* HTML templating library `Cheetah`__
-
-Galaxy API generated from source code can be found `here`__
-
-.. __: http://www.cherrypy.org/
-.. __: http://www.sleepycat.com/products/db.shtml
-.. __: http://effbot.org/zone/element-index.htm
-.. __: http://www.cheetahtemplate.org/
-.. __: http://www.bx.psu.edu/trac/local/docs/index.html
-
------
-
-`The Center for Comparative Genomics and Bioinformatics`__ at `Penn State`__ | 2005
-
-.. __: http://www.bx.psu.edu
-.. __: http://www.psu.edu
-
--- a/templates/admin/requests/new_request.mako
+++ /dev/null
@@ -1,94 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
- $( "select[refresh_on_change='true']").change( function() {
- var refresh = false;
- var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
- if ( refresh_on_change_values ) {
- refresh_on_change_values = refresh_on_change_values.value.split( ',' );
- var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
- for( i= 0; i < refresh_on_change_values.length; i++ ) {
- if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
- refresh = true;
- break;
- }
- }
- }
- else {
- refresh = true;
- }
- if ( refresh ){
- $( "#new_request" ).submit();
- }
- });
-});
-</script>
-
-<%def name="javascripts()">
- ${parent.javascripts()}
- ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
-</%def>
-
-<%def name="stylesheets()">
- ${parent.stylesheets()}
- ${h.css( "autocomplete_tagging" )}
-</%def>
-
-<br/>
-<br/>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='list')}">
- <span>Browse requests</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- <div class="toolFormTitle">Add a new request</div>
- %if len(select_request_type.options) == 1:
- There are no request types created for a new request.
- %else:
- <div class="toolFormBody">
- <form name="new_request" id="new_request" action="${h.url_for( controller='requests_admin', action='new', create=True )}" method="post" >
- <div class="form-row">
- <label>
- Select Request Type
- </label>
- ${select_request_type.get_html()}
- </div>
-
- %if select_request_type.get_selected() != ('Select one', 'none'):
- %for i, field in enumerate(widgets):
- <div class="form-row">
- <label>${field['label']}</label>
- ${field['widget'].get_html()}
- %if field['label'] == 'Library' and new_library:
- ${new_library.get_html()}
- %endif
- <div class="toolParamHelp" style="clear: both;">
- ${field['helptext']}
- </div>
- <div style="clear: both"></div>
- </div>
- %endfor
- <div class="form-row">
- <div style="float: left; width: 250px; margin-right: 10px;">
- <input type="hidden" name="refresh" value="true" size="40"/>
- </div>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit" name="create_request_button" value="Save"/>
- <input type="submit" name="create_request_samples_button" value="Add samples"/>
- </div>
- %endif
- </form>
- </div>
-</div>
-%endif
--- a/templates/sample/sample_events.mako
+++ /dev/null
@@ -1,45 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<%def name="title()">Events for Sample ${sample_name}</%def>
-
-
-<h2>Events for Sample "${sample_name}"</h2>
-
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
- <span>Browse this request</span></a>
- </li>
- <li>
- <a class="action-button" href="${h.url_for( controller='requests', action='list')}">
- <span>Browse requests</span></a>
- </li>
-</ul>
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
- <table class="grid">
- <thead>
- <tr>
- <th>State</th>
- <th>Description</th>
- <th>Updated</th>
- <th>Comments</th>
- </tr>
- </thead>
- <tbody>
- %for state, desc, updated, comments in events_list:
- <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
- <td><b><a>${state}</a></b></td>
- <td><a>${desc}</a></td>
- <td><a>${updated}</a></td>
- <td><a>${comments}</a></td>
- </tr>
- %endfor
- </tbody>
- </table>
-</div>
Binary file test-data/1.scf.zip has changed
--- a/templates/requests/show_data.mako
+++ /dev/null
@@ -1,86 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$(document).ready(function(){
- //hide the all of the element with class msg_body
- $(".msg_body").hide();
- //toggle the componenet with class msg_body
- $(".msg_head").click(function(){
- $(this).next(".msg_body").slideToggle(450);
- });
-});
-</script>
-<style type="text/css">
-.msg_head {
- padding: 0px 0px;
- cursor: pointer;
-}
-
-}
-</style>
-
-
-<h2>Data transfer from Sequencer</h2>
-<h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3>
-
-<ul class="manage-table-actions">
- %if sample.request.submitted() and sample.inprogress_dataset_files():
- <li>
- <a class="action-button" href="${h.url_for( controller='requests', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">
- <span>Refresh this page</span></a>
- </li>
- %endif
- %if sample.library:
- <li>
- <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( sample.library.id ) )}">
- <span>${sample.library.name} Data Library</span></a>
- </li>
- %endif
- <li>
- <a class="action-button" href="${h.url_for( controller='requests', action='list', operation='show_request', id=trans.security.encode_id(sample.request.id) )}">
- <span>Browse this request</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- <form name="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
- <div class="form-row">
- %if len(dataset_files):
- <table class="grid">
- <thead>
- <tr>
- <th>Dataset File</th>
- <th>Transfer Status</th>
- </tr>
- <thead>
- <tbody>
- %for dataset_index, dataset_file in enumerate(dataset_files):
- ${sample_dataset_files( dataset_index, dataset_file[0], dataset_file[1] )}
- %endfor
- </tbody>
- </table>
- %else:
- There are no dataset files.
- %endif
- </div>
- </form>
-</div>
-
-<%def name="sample_dataset_files( dataset_index, dataset_file, status )">
- <tr>
- <td>${dataset_file.split('/')[-1]}</td>
- <td>
- %if status == sample.transfer_status.IN_PROGRESS:
- <i>${status}</i>
- %else:
- ${status}
- %endif
- </td>
- </tr>
-</%def>
--- a/templates/requests/events.mako
+++ /dev/null
@@ -1,39 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<h2>History of Sequencing Request "${request.name}"</h2>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
- <span>Browse this request</span></a>
- </li>
- <li>
- <a class="action-button" href="${h.url_for( controller='requests', action='list')}">
- <span>Browse all requests</span></a>
- </li>
-</ul>
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
- <table class="grid">
- <thead>
- <tr>
- <th>State</th>
- <th>Last Update</th>
- <th>Comments</th>
- </tr>
- </thead>
- <tbody>
- %for state, updated, comments in events_list:
- <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
- <td><b><a>${state}</a></b></td>
- <td><a>${updated}</a></td>
- <td><a>${comments}</a></td>
- </tr>
- %endfor
- </tbody>
- </table>
-</div>
--- a/templates/admin/requests/events.mako
+++ /dev/null
@@ -1,36 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<h2>History of Sequencing Request "${request.name}"</h2>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
- <span>Browse this request</span></a>
- </li>
-</ul>
-<h3>User: ${request.user.email}</h3>
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
- <table class="grid">
- <thead>
- <tr>
- <th>State</th>
- <th>Last Update</th>
- <th>Comments</th>
- </tr>
- </thead>
- <tbody>
- %for state, updated, comments in events_list:
- <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
- <td><b><a>${state}</a></b></td>
- <td><a>${updated}</a></td>
- <td><a>${comments}</a></td>
- </tr>
- %endfor
- </tbody>
- </table>
-</div>
1
0
galaxy-dist commit e5e9f6214433: Feature: Ability to view hidden datasets in the same fashion as you would deleted ones. Unhiding also works in the same fashion.
by commits-noreply＠bitbucket.org 16 Jul '10
by commits-noreply＠bitbucket.org 16 Jul '10
16 Jul '10
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User Dannon Baker <dannon.baker(a)emory.edu>
# Date 1278785782 14400
# Node ID e5e9f62144336658f80d7c3308e8f44110fdede8
# Parent 71b1a5920fc12514a9e151770eaf250d6fc6da46
Feature: Ability to view hidden datasets in the same fashion as you would deleted ones. Unhiding also works in the same fashion.
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -279,7 +279,7 @@ class UsesHistory( SharableItemSecurity
err+msg( "History not found" )
else:
return self.security_check( trans.get_user(), history, check_ownership, check_accessible )
- def get_history_datasets( self, trans, history, show_deleted=False ):
+ def get_history_datasets( self, trans, history, show_deleted=False, show_hidden=False):
""" Returns history's datasets. """
query = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) \
.filter( trans.model.HistoryDatasetAssociation.history == history ) \
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/lib/galaxy/web/controllers/dataset.py
@@ -631,6 +631,26 @@ class DatasetInterface( BaseController,
trans.log_event( "Dataset id %s has been undeleted" % str(id) )
return True
return False
+
+ def _unhide( self, trans, id ):
+ try:
+ id = int( id )
+ except ValueError, e:
+ return False
+ history = trans.get_history()
+ data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
+ if data:
+ # Walk up parent datasets to find the containing history
+ topmost_parent = data
+ while topmost_parent.parent:
+ topmost_parent = topmost_parent.parent
+ assert topmost_parent in history.datasets, "Data does not belong to current history"
+ # Mark undeleted
+ data.mark_unhidden()
+ trans.sa_session.flush()
+ trans.log_event( "Dataset id %s has been unhidden" % str(id) )
+ return True
+ return False
@web.expose
def undelete( self, trans, id ):
@@ -639,6 +659,13 @@ class DatasetInterface( BaseController,
raise "Error undeleting"
@web.expose
+ def unhide( self, trans, id ):
+ if self._unhide( trans, id ):
+ return trans.response.send_redirect( web.url_for( controller='root', action='history', show_hidden = True ) )
+ raise "Error unhiding"
+
+
+ @web.expose
def undelete_async( self, trans, id ):
if self._undelete( trans, id ):
return "OK"
--- a/templates/root/index.mako
+++ b/templates/root/index.mako
@@ -37,6 +37,9 @@
"Show Deleted Datasets": function() {
galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}";
},
+ "Show Hidden Datasets": function() {
+ galaxy_history.location = "${h.url_for( controller='root', action='history', show_hidden=True)}";
+ },
"Show structure": function() {
galaxy_main.location = "${h.url_for( controller='history', action='display_structured' )}";
},
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -685,6 +685,11 @@ class DatasetInstance( object ):
if include_children:
for child in self.children:
child.mark_undeleted()
+ def mark_unhidden( self, include_children=True ):
+ self.visible = True
+ if include_children:
+ for child in self.children:
+ child.mark_unhidden()
def undeletable( self ):
if self.purged:
return False
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -338,6 +338,12 @@ div.form-row {
</div>
%endif
+%if show_hidden:
+<div class="historyLinks">
+ <a href="${h.url_for('history', show_hidden=False)}">${_('hide hidden')}</a>
+</div>
+%endif
+
<div id="history-name-area" class="historyLinks">
%if trans.get_user():
@@ -385,7 +391,7 @@ div.form-row {
## Render requested datasets, ordered from newest to oldest
%for data in reversed( datasets ):
- %if data.visible:
+ %if data.visible or show_hidden:
<div class="historyItemContainer" id="historyItemContainer-${data.id}">
${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing = True )}
</div>
--- a/lib/galaxy/web/controllers/root.py
+++ b/lib/galaxy/web/controllers/root.py
@@ -76,7 +76,7 @@ class RootController( BaseController, Us
return trans.fill_template_mako( "/my_data.mako" )
@web.expose
- def history( self, trans, as_xml=False, show_deleted=False, hda_id=None ):
+ def history( self, trans, as_xml=False, show_deleted=False, show_hidden=False, hda_id=None ):
"""
Display the current history, creating a new history if necessary.
NOTE: No longer accepts "id" or "template" options for security reasons.
@@ -86,16 +86,21 @@ class RootController( BaseController, Us
history = trans.get_history( create=True )
if as_xml:
trans.response.set_content_type('text/xml')
- return trans.fill_template_mako( "root/history_as_xml.mako", history=history, show_deleted=util.string_as_bool( show_deleted ) )
+ return trans.fill_template_mako( "root/history_as_xml.mako",
+ history=history,
+ show_deleted=util.string_as_bool( show_deleted ),
+ show_hidden=util.string_as_bool( show_hidden ) )
else:
show_deleted = util.string_as_bool( show_deleted )
- datasets = self.get_history_datasets( trans, history, show_deleted )
+ show_hidden = util.string_as_bool( show_hidden )
+ datasets = self.get_history_datasets( trans, history, show_deleted, show_hidden )
return trans.stream_template_mako( "root/history.mako",
history = history,
annotation = self.get_item_annotation_str( trans, trans.user, history ),
datasets = datasets,
hda_id = hda_id,
- show_deleted = show_deleted )
+ show_deleted = show_deleted,
+ show_hidden=show_hidden )
@web.expose
def dataset_state ( self, trans, id=None, stamp=None ):
--- a/templates/root/history_common.mako
+++ b/templates/root/history_common.mako
@@ -21,6 +21,13 @@
</div>
%endif
+ %if data.visible is False:
+ <div class="warningmessagesmall">
+ <strong>This dataset has been hidden. Click <a href="${h.url_for( controller='dataset', action='unhide', id=data.id )}" class="historyItemUnhide" id="historyItemUnhider-${data.id}" target="galaxy_history">here</a> to unhide.</strong>
+ </div>
+ %endif
+
+
## Header row for history items (name, state, action buttons)
<div style="overflow: hidden;" class="historyItemTitleBar"><div class="historyItemButtons">
1
0
galaxy-dist commit 19e07ef6eb25: Tweaked wording for locking the job queue
by commits-noreply＠bitbucket.org 16 Jul '10
by commits-noreply＠bitbucket.org 16 Jul '10
16 Jul '10
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User Dannon Baker <dannon.baker(a)emory.edu>
# Date 1278788080 14400
# Node ID 19e07ef6eb25ea4bd1531ba42c2187f3f5d384d6
# Parent e5e9f62144336658f80d7c3308e8f44110fdede8
Tweaked wording for locking the job queue
--- a/templates/admin/jobs.mako
+++ b/templates/admin/jobs.mako
@@ -126,7 +126,7 @@
</div>
%else:
<div class="form-row">
- <p>To prevent new jobs from dispatching, you can lock down the job queue here.</p>
+ <p>To prevent new jobs from dispatching, you can lock the job queue here.</p><input type='hidden' name='job_lock' value='lock'/></div><div class="form-row">
1
0
galaxy-dist commit 2d046444998e: Enable 'extract genomic DNA' tool to accept and produce GFF files and added functional tests for this feature.
by commits-noreply＠bitbucket.org 16 Jul '10
by commits-noreply＠bitbucket.org 16 Jul '10
16 Jul '10
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User jeremy goecks <jeremy.goecks(a)emory.edu>
# Date 1278618202 14400
# Node ID 2d046444998edb1c4a5126897990bddd25de69f5
# Parent 41089d12cdd9eaaeb8e75e09157d412ccf935eae
Enable 'extract genomic DNA' tool to accept and produce GFF files and added functional tests for this feature.
--- a/tools/extract/extract_genomic_dna.xml
+++ b/tools/extract/extract_genomic_dna.xml
@@ -1,20 +1,27 @@
<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.1"><description>using coordinates from assembled/unassembled genomes</description>
- <command interpreter="python">extract_genomic_dna.py $input $out_file1 -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol} -d $dbkey -o $out_format -g ${GALAXY_DATA_INDEX_DIR}</command>
+ <command interpreter="python">
+ extract_genomic_dna.py $input $out_file1 -d $dbkey -o $out_format -g ${GALAXY_DATA_INDEX_DIR}
+ #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
+ -1 1,4,5,7 --gff
+ #else:
+ -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
+ #end if
+ </command><inputs>
- <param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query">
- <validator type="unspecified_build" />
- <validator type="dataset_metadata_in_file" filename="alignseq.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="seq" />
+ <param format="interval,gff" name="input" type="data" label="Fetch sequences corresponding to Query">
+ <validator type="unspecified_build" />
+ <validator type="dataset_metadata_in_file" filename="alignseq.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="seq" /></param><param name="out_format" type="select" label="Output data type">
- <option value="fasta">FASTA</option>
- <option value="interval">Interval</option>
+ <option value="fasta">FASTA</option>
+ <option value="interval">Interval</option></param></inputs><outputs>
- <data format="fasta" name="out_file1" metadata_source="input">
+ <data format="input" name="out_file1" metadata_source="input"><change_format>
- <when input="out_format" value="interval" format="interval" />
+ <when input="out_format" value="fasta" format="fasta" /></change_format></data></outputs>
@@ -34,6 +41,17 @@
<param name="out_format" value="interval"/><output name="out_file1" file="extract_genomic_dna_out3.interval" /></test>
+ <!-- Test GFF file support. -->
+ <test>
+ <param name="input" value="gff_filtering_out1.gff" dbkey="mm9" ftype="gff" />
+ <param name="out_format" value="interval"/>
+ <output name="out_file1" file="extract_genomic_dna_out4.gff" />
+ </test>
+ <test>
+ <param name="input" value="gff_filtering_out1.gff" dbkey="mm9" ftype="gff" />
+ <param name="out_format" value="fasta"/>
+ <output name="out_file1" file="extract_genomic_dna_out5.fasta" />
+ </test></tests><help>
@@ -90,7 +108,7 @@ Extracting sequences with **FASTA** outp
CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC
ACACG
-Extrracting sequences with **Interval** output data type returns::
+Extracting sequences with **Interval** output data type returns::
chr7 127475281 127475310 NM_000230 0 + GTAGGAATCGCAGCGCCAGCGGTTGCAAG
chr7 127485994 127486166 NM_000230 0 + GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
--- /dev/null
+++ b/test-data/extract_genomic_dna_out5.fasta
@@ -0,0 +1,258 @@
+>mm9_chr10_62044836_62045189_+
+AATTACAAGATCGACACACCAAGATAGGCAGATCCATGGTTGGTTTTACT
+TTGTAAATCTAAAAGTATGTTGGAAAACGATGCAATGAATTCTTATCCTT
+TTTCAAAATGAAGAATTTGTGATGGTTAGTGGACAGTTCAGAAGCCTCTC
+TGCAAGAAAGGGGGCGCTGAGAAGTGGTAAAAAAAGGAAGGAAGCACTCG
+GGCTTTGTCAGCAGGGTGGACCCTGGGGTCCACAGTGGGAACAGTCCCTT
+CTGGCCTCTACTCACTGACCAAACGCTTTACTAAAACTCCGCTTCTGGCC
+TCTGTTGCCACCTCCTGGTCGCTGTCCTCGGAAGTTTCTACTTCCTCCTC
+GCT
+>mm9_chr10_75372918_75373002_+
+GCGTCTCGCAGCTTCTGCCCGTCGATCTCCATGTCGAGCCGGATGGGCAC
+CAGCACCTCAGGCTGTGACGCATTCTCATGGATC
+>mm9_chr10_80362427_80363292_-
+ATGACGGACAAGTGTTTCCGGAAGTGCATCGGGAAGCCCGGGGGCTCCTT
+GGATAACTCGGAGCAGGTGAGACATCTCGGGAACCCGGGGTGGTGAGGGG
+CGCGGGGTCAGGAGCGTCTAGGAGGTTGAGAGATGTGCGCGTGCGCGGCC
+TCTAGCCTTAGCTACTGAGGAAGTTGTGCGCGTGCGCGGGGTGAGGACCC
+GGCTTCTGTGCCTAGATCGGTGCAGCCTTCATGGGTGATCCTCGGGTCGT
+GTGACCGTCAGTCAGGGATCCCCCTCCACGCTTTGCAGAAATGCATCGCC
+ATGTGCATGGACCGCTACATGGACGCCTGGAATACCGTGTCCCGCGCCTA
+CAACTCTCGACTGCAGCGGGAACGAGCCAACATGTGACCGGGACCTGTGC
+CTCGGGACACCGTGCTTATGGTCTGAACTGTTTTCCCTGCCAGTTAGGGT
+GTCTCCTCCTAGCCGCCCTGAAGTCTGGCAGCATGGAGGGCTTGGGGATC
+GAGGCCTCTCCCCTGGGTTGCTGCGTCCAGCTCAATCTCAGAAGAGAGTG
+AGGACCCGACAGAGCACAGGGATCTGGCTGGCCCCACTGACCTGTGACCT
+CAGGAGAGCAGGCCAATAAATCGCTGCTGGGGCAGTAAAGCAGGCGTGTC
+ACCTCACTGCTTCAGGTCCCTTCCCCTGAGTAGGCCCAGACCTCCCAGGG
+TATCTTTCCCCTTGGGGTCAGTGGGCTGCTGGCTCTCAGGGAATTCGGAG
+CATGATCTCAGGTGTTTGGTCATCCCGGGGAGACCAGCCGAGGTTAAGAA
+GCAAGGCTTCATGTagccttcacctatcatgcatgaggcccagggtgctg
+accttaactctgaat
+>mm9_chr11_7904564_7904642_+
+CATCTTCTATTTGAGCCTCCATCCAGGCACCTCTGAAACAAAGGTGCACT
+CACTGCATGTCCACTTGTCACAGGAGCC
+>mm9_chr11_78140155_78140259_+
+CTGCTTGCTAATTTTCTCTCTTGGGATCAGGGGGACGTGAACTCCAGCCC
+TGACTCGTGCTCCTTATGCTCTGAGTACATAGCAAATAAATGAGAGCAAA
+ACAC
+>mm9_chr11_105616461_105616737_+
+TAGGTGTAATAGTGGAAAACAATAGTTTTTAAACTTCAGAGTCCAGGGCT
+GTAACTCAGTAGTAACAGTGTTCTCTAAGTATGTTATTCTTCCTCTACAT
+GCTGAAATTTTTCATATTTGGAGCATTCACTGTTCCATGTATCAGTAAAT
+TATATTGTGAGCTGTCATCATATCTAAGCACCATATTGAATATTTTTCAT
+GATTAAAATTTGTTGAAACAACAATTCTATGACCGAAAAAAGCAAGGCTT
+TGTAAATAACATGTTTGTTACTAGTA
+>mm9_chr12_30701761_30702509_+
+TGTGGAGTGTACTTATATGATCCCTATGCTGATAGGATTACCTTCCTAGA
+CATAGCTAGACGCAAAGCCACATGTGTAAGGCTGCTGAGCAAAGACAGCA
+TCCCAGCATGGGTGTGTTCACGGTGGATTCACCACGTTGCATATGTAAAG
+TGGTCCCCTTGGCTTACCCTTCACTTTGCTCATGAGATTCAGAAGCTGGT
+GGTCCAGCAGGGGTGAGCATTTGTGAAATAGTAAGCTGAACTTAGTGGTG
+AGATTTCAGAACAGACTTCTGTGAAGTAAGAGATGTAACCATGCATCTAA
+AATCAGATGGCCGTGTAACTGCTCGGGCATAGAAATGGTGGGAGAACCTG
+TCCTGGGTACCTGGCATTTCACATGAGCCCAGGGATATGTCTTGTGCCAA
+GGCACACAAGTGTCCATGGACTTGGACAGGTGCCAAGGGTTTTTGTCTCT
+GTTCCTATGTGGGAGGCTGGCTGTGATTTACATTAATTTCTGTATTTCAA
+ACGAAGATGTCTGCAGATCTCCATTTTGATGTTACAGCCTCATTGCCCAG
+GCAGTGGGCAGTGCCCAGACACCCTTTCTGACTAGCCACTGCATTGGGCT
+TCTGTGATTCAAAGTAGTGTATATATTTATTTACTTCTCTGACTGTGGCC
+AACAGCCAAATGCCATTTTATGTTCCTTGTATTCAGTCCATTACCAAAGA
+GGTGTTTGCACTTTGTAATGATACCTTTCAGTTCAAATAAAAGGACCA
+>mm9_chr13_49159495_49159569_+
+ttttcttttggattacttgatttttttttatttgatcttatttatgatga
+ttttgagtacatttttgaacagtt
+>mm9_chr13_100200303_100200330_+
+TCTCATATGAATAGCCACCCTCTTCTG
+>mm9_chr14_31949102_31949152_+
+GGATGCTATCCGCGATGTGCATGTAAAGGGCCTCATGTACCAGTGGATCG
+>mm9_chr14_67604226_67604668_+
+TTCACCGTGAGAGTTTTCTCCATTTCACTCTTCACTGTGCTGTTCTCTGT
+GCCGCTTTCCTCTTGACTTATAAACATCTGAGCCAGTTTTCAATAAACTT
+AAAACGAAGCCTGCTTCTCATCCCAAATTGTAAACAGGAATAAAGCTTTT
+TAAACCTTATCTTAAATTTTAACTTTGTTGAATTCTGCTTTGTGATAGGA
+CAATCTGTTTCACCCAACAAGAATCTGTGTAGGAGGATGAACATCCCGCA
+TGTTGGAGCTGCAAATCAGCACTGTACAAGCTCACTGATGGACAGCTGTT
+CTGTGATGTATTCCATGATTTTACTAATACTTTCAAAAATGGCAAAACTA
+ACTTCAGTTTTAATGTTGAAAGAAAATCATAAATGTTCCCATAGTTCAAT
+GGCACTGTCGATGAAACTGCTACTGAATTTAGAGAGAAAACG
+>mm9_chr14_75165581_75165744_+
+ggccctgggatgataTAACAGAAGAGTCTAAAGGAGGCTTCTGAGATGTG
+CAGTAGGAAAGCCTGGCACATAATAGGTTATTATCTAAATCCCTTCACTA
+CTCTTCAAAGACAGCAGGATGCCTCTGCTCCCATGTTTTATCTCTACTTA
+TGTGGAATTTATG
+>mm9_chr16_57154026_57154067_+
+GTTGAGGTTTATTTAAGTAAAATGATTTTTTAAAAAAGCAA
+>mm9_chr16_74862301_74862560_+
+GCATTGGCAGCAGATATTGGTACCCAGTGGCACTGCAGAGTACTTACAAT
+CAGGACTCGCTACTGTGCTTCATTCTGCTTTTCTCTCTGCTTCTATTACA
+GTTAAAGTGTTGCTAATTATAGAAACTCTCTGTTTATTGAACCTCGGTGT
+TAAGAAAAACTTGTAATCTTCAGATATGATCCGAAAGATTCCCAAACAAA
+TGTAACAAGGTCCACTTTTGTAGCCCTTTCTACCAGAAcactggttatca
+acctgtggg
+>mm9_chr16_98168778_98168914_+
+CCTATTTATTTCACTAAACATCTGCCTGCTAGCTGAGATAAACATTCTCT
+AAAAAACTGTTTACTGCAAAAAGTGATTACTGTTTTTTATTAGTTTCTTA
+GCATTTGAAATAGTTACATGAATGGAAGGATAGAGT
+>mm9_chr17_8483211_8483268_+
+AGACTTGTCAACAGCTCACCCAATGATGGAACTGAGGCTGCCCCTCAAGT
+GGCCAGA
+>mm9_chr17_30355790_30355913_+
+atctcatacccataagctcagaactcggggtggtaacataggaggactgc
+catgagtgtgactaacctgggctataggaggaggatctaccttaagcaaa
+tgaCCAACAAAACTAACAAGCTC
+>mm9_chr18_39571717_39571880_+
+TATAACATTCCATAAATGTACAATAATCTATTTTTGAGAAGCTCATTTTG
+AAACTTAACACTGTCATTGATAATCTTCAAGTGGTATTTCTTAGGCACCA
+TAAATTTCACATCCAGCTGGGTTACAATTATTTTAAAGTACTTTGAGACC
+AATTTAAACCATT
+>mm9_chr19_17633087_17633203_+
+TGGGAAATGAACTGCATGGCAATGAACCCCAGGGAATTTGGTGGTTAATT
+GTCTAAGGATAAGGACATCAGTTTTGTCTTTTGCATCACTGTGACCTTTG
+CCTCTAATTGTATAGA
+>mm9_chr19_41997623_41997859_+
+gctacacaacgactcacatagagggaagcaggcacacatcagataaaaca
+cAAAAGGATGGGTTGGTGATGGGCATAGTTAATGAGGGCCACTAGGTAAA
+TACACCTGATCCAAAAGTCACGCTACTACTTAGATTCTTCTCTCTGCTAA
+AGACAACAGAAgacatgttagccatgcttgtaatccctgcattggggaga
+tggagtcagaaatatcactgcaagttcacccaatag
+>mm9_chr19_56516514_56516684_+
+TGTATTCATTCACTATTCACTGATTTGTCAGATCATCCATCCACACAGGT
+GCTGAAGAGTAACCCATTTCACTTTGTATACAAGATAATGTTTTTGTACT
+TCAAATACATCTGGAATTCTTTCAAATATTCCAAGATTTTTTTTTTTTCT
+GAATAATCTTTGGTTACCTC
+>mm9_chr2_4543773_4543977_+
+gagccatttctccagccccTTTATGTGGAATATTAACAAGAGAAGACAAC
+ATAAAATGACTTACCATGCTGTGTGGCCTAACAGTGGATGAAGAATGAGT
+GATTTGGGCATTTCTGATAGTATTTATAAAGAAGACTTTTATGACCAAAC
+CACATGTCACAGTAGGGATTTGCTGCACATCTTATGAGAGTTTCTTCTTT
+GTCA
+>mm9_chr2_30200330_30200938_+
+CGCACACAAAGGATTTATTTGCCAGAGAGCAAGCAGACAGGCAGAGGTCA
+GAATGTTAGTTAGAAACTGAAGGAATGACTGCTGTAGCCACTGTGCCCAG
+CCAGAGCCATGAGGGAAGTGGGAGGCAGCACTTGGTGCTGCTGCTCTGGC
+TGACCCTTCTGGTTTCCTGCCACACTCCTAGCCCTGCCTGTGTGCTGCTG
+TCCCCCTCAACCTTCCACAGCCAGAAGGCAGATGTTCTTTCATGCCAAGA
+GCATCCATCCCCAGCATATCCTGGGCCCATGGTGGTGTCAAATGTAGTGA
+CCCTTCTGCCTTAAGGGAGCTGGGAAGCCTGGGGTGTGCAGGGTTGCAGG
+TCAGAAGCAGGACTAGCAGAGGGGCCTGGGGCCATTCTGTCTTGTGGGCT
+CTTTAATAGCTGAATGACGGGCACAGCCAGAAAAGGGTTAGGTCCCTTAT
+CCTAAGCAGCTCTGTGGCCAGCAGACGACTCTAAGTGGCAGAGCCTGGGA
+AGGGGCTGCTTAGCTGAGAAGTTCCAGGTAGGTGACAGGAACCTTGCCCT
+TCTTGTTGCCTCTCTCACCAATGAGCCAGTCGGGATCCATGCCTGGCAGG
+CTGTAGAC
+>mm9_chr2_106644219_106644341_+
+attcttaaggtaaatacctaggagtgatgtaacccagtcatagggaagaa
+ctacttttaatttgttgagcaacccccaacctgattttgacacaggtttg
+agtagtttacacttctactaac
+>mm9_chr2_125388930_125389219_+
+AGAGCACACAGCACATCACTTAGGCCTCCAACATTAAGGCAGCGCAAGTG
+CCTCAAGTAACTGAGAATACTTTACTCAGATACAAGGGTATCAAAAACAT
+GAGAACTGGCAGGAAGACCTCACAATGGTTTGTTAGCATCAAGTATTACC
+ATCCAGTTTCCTGTTTAAATAGTAATTAATGACTATTCTGAAATAAGGCA
+AATAATTACTCAAGCGGGCTGTCAAAGCCACTATCCTGTTGGCTGGGCAT
+CGGAGCAGTTAACTTTATCAAAGGCTTCTGACACAATGA
+>mm9_chr3_130936638_130936898_+
+CGAGGCTGCAGGCTGCAAATGTTCCCAGGCAGGCAAGACCTCACGTCCTA
+CTGGCTGCTGCCCTTGGGTGCATCTGTAGGCCCCGTGGCTCCTGCCCCTG
+GGGTTCAACACCGATAAACATAGAATACTCATTTTCAGAAGACCTGAGGG
+AATGAGTCTAAGCAACGCTTTTTACAAAAAGTGGCAAGGTTCAGGAAAAA
+AAAAAAAAAAGATGTTGCTCCAAGGCACCAAGGGTGTAATTTTTTTTCAG
+AAAAAGTCAG
+>mm9_chr3_136592670_136592771_+
+TGTCAGCCCATCACATTTTAGTGACAACAGTCATAGCCTTTATTTTCAGA
+TGACTTTCCTCTAAAACCACTGTCTATGAGTTGCCCCCCAAAACTCAAAA
+A
+>mm9_chr3_152861373_152861508_+
+ATCAAAAGCGACATGCAAGCATCTTGCTCTCACCACAGATCACTGAGACA
+TTAAGAGTGACGTCTCTTGAACTGTTGGCACGCCTAAGTTATTTCAGCAT
+TTCTTGCTCAGCAGTTGTTCTCTTGGCTTCCTCTG
+>mm9_chr4_13715309_13715630_+
+AACACATGGCCACATCATGTGATATTTTCAAAACACTTACACATAGCTTT
+GAGAAGGTCCCTGCAGGAATGATCCATCCTCTCACAGTTGGCCCATTTTT
+TAACAGCATATCTGCATTTTCCATTTAGGAGAGCTATATATTATTAGCTT
+ACATTTTTGGGTAGTAAAACAGTGCATTGCTGATTGTAAAACATGGACTT
+TATTATCTGCTGAAAATTGATTTGGCATTTATAGCCACTGTGTATTAGAC
+TGTTTTTCTGTTTTTAACATCAATGCTTAAAAGCGATGATTTGTGTTTaa
+aaaaattaaaaaaataaaata
+>mm9_chr4_147515028_147515097_+
+GCTGACGTGCTCTCCGAGTTCCTGGAGGTGGCCGTGCACCTGATTCTCTA
+TGTGCGCGAGGTCTACCCG
+>mm9_chr5_3949521_3949685_+
+AGTCCCAACCACCCCCTTGTTTAATGTATAACTTTCTGAAATGGGAGCGT
+TAGAATGGATTAAAATGGTTGGTAGGTGGTTGGATCACCAACCAAGACCA
+GAAATAGAGGGGTAGGCTGCTCAGGAGAGTATTGGGAGGGTAGCTATTAT
+TTGCATTTTGTGCT
+>mm9_chr5_68089693_68089831_+
+CAATGATAGAGAAGACTAAAATAAAAGCAGGCATGCTGGCACAAGCGACA
+GAAGGAAAAAGCCTCACCCGGCCCTGTTTGAGGCCACTCCTGGTGGCTCC
+TTTTCCAAGGACCATGCGGTCAAGCCTCTGAGTTGTTC
+>mm9_chr5_122819525_122819619_+
+CTTTAGAAAAGATGCATCTGTCATTGATTTAGGGATATGAATTGTTTGGA
+TTTGAGTAGTTTTCCATAACTCCTGCAGTTTGGCAATGTGTGCG
+>mm9_chr5_145619547_145619710_+
+CGGCGTTCTGAAAACTGTGCTCCGGGATGAGATCATTGCTTGGCACAAAA
+AGACACAGGAGGACACTTCCTCTCCACTGTCGGCCGCAGGGCAGCCTGAG
+AACATGGACAGCCAGCAGCTGGTTTCCTTAGTTCAGAAAGCCGTCACTGC
+CATCATGACCCGC
+>mm9_chr6_83928983_83929105_+
+ACAGGAACCATTATTTACATTTAATTTGGATGAATTTGTTACTGTGGATG
+AAGTCATAGAAGAAGTAAATCCTTCTCAAGCCAAGCAGAATCCATTAAAA
+GGAAAAAGAAAGGAAGCCCTCA
+>mm9_chr6_118857948_118858148_+
+CCAGGCTTGCTAGTTGGTGCAGTTAGCTACATCTCAGGACAGAGACAAGG
+TACTCTGAGCTCCCCTTGAACTGCCACACAAGCTGTCTCCTGGATGCCAA
+GCAGAGAAACCTGGAGACAACAATCATCATACTCAAAACCAGGATCTCTT
+TCTTAAGACTTTTGTATTTTGTCCCAGCCCTAACCCTGAGTTCTGCTGAA
+>mm9_chr7_85554209_85554343_+
+GTGAAACATCATGCTTCTGCATCAAGTTATTAGTGGGAAACCTGTAAAAG
+TTGACATTGAATGCTGATAACAAATTACTTTCATCCTGTCTCATAATGAA
+TCCTACATCAAGACAAGGCAAGTGAGAAAGAGGG
+>mm9_chr7_104055490_104055589_+
+ACATTTCTCCTCTCTTGGGGGAGCGCATCTCCTTGGGTGTGTCCACATCC
+GCCCCTAGGTACCCAGTGTGATGTGAGACACGAGTGTCTGTGCTAACTT
+>mm9_chr8_9970397_9970545_+
+AGTCTTCACCAAAATTAAGTCTCAGCTAACTTAAAAGTTGCAAGGATTTT
+TTTCAATAAAATTAATATCTTAAGTGTTTGGTGTTTAGATGATTCTCTCT
+CAACTTCCCCCACATTATCAAAAAACATTTGATGAACCTTAAAAACTC
+>mm9_chr9_20449845_20449932_+
+CCAGCACCGATGACACCATCGGCGACTTGAAGAAACTGATAGCTGCTCAA
+ACTGGCACCCGCTGGAACAAGATCGTTCTTAAAAAGT
+>mm9_chr9_107445869_107445930_+
+CAAGCAGAAGCTGGTGCCCATCATGACCATCCTGCTGGAAGAGCTGAATG
+CCTCCGGCCGC
+>mm9_chr9_120860475_120860606_+
+CTGCCATTGTACGCACCATGCAGAATACAAATGATGTAGAGACAGCTCGT
+TGTACTGCTGGGACTCTGCACAACCTTTCTCACCACCGCGAGGGCTTGCT
+GGCCATCTTTAAGTCTGGTGGCATCCCAGCG
+>mm9_chrX_10274056_10274087_+
+ACTTCGCTGTCATCATTTGTACAAACTCTTT
+>mm9_chrX_39881430_39881678_+
+AGCTAAAAAGAGTCCTTTTCTGACAGAAAGGCTGGACTTCTCCTTTTCAC
+CGTTTCTCTTACTGATGCTTTTGCCAGAAGAACAGTAAAGATTTAGACAC
+TGTCATGATTCATACACGTAAAATATTTTTCAAGGACACAATCTGATATA
+CTAACATTTATTTAAGAGGTTAAAGTCCACCACTAAATCTAAGGAAAGAT
+TTTTAACTGCCAAACACATTTCCTTTGACAAATAATGTAAGATGACAA
+>mm9_chrX_148249671_148249713_+
+AATGCTAGTATGAACAGTGGGAGGAATGAGCAAAATGTTACA
+>mm9_chrX_148481504_148482455_+
+CGCCACAACCTGCTACAGGCCTGTAAGATGCAGGACATCAAACTGCCACT
+GTCAAAGGGCACCATGGATGATATTAGTCAGGAAGAAGTGAGTATTATGG
+TGGGTGGTAGGAGTCATCTATGAATATTTAACCAGTAATGGGAGATTACA
+GATGGCCAGGAAGGGCAGGCAACAGATAGGACCACATAGAGTTGTGAGGG
+GCATAAAGATGGATGCAGAAGAAATGTGGCAAGGTGGAAGTAGTGAAGTC
+AGGCTTTGGTATGAGAGAGACATTGATTTGAGAGGAGAGCTGCAAGCCAG
+TGAGTACTCAGAAAGACCAAGAATGGGTCATTAATCTTAAGGATTTGAGC
+TCTTAGCTGCAGCAGATACTGGGCATGGGTAGGAGTGAGAATTGAGGAGC
+AGAGGAAGATGGGAAACTGGAGAACCTAAGGAGACTGATAGCTTAGCTGC
+AGTAAGGGAGGTTGGCCAGAAGAGGGTTGGGTAGGGGACTCAGCAAGGCA
+GAACTAAGGAAGCTTAGGTGGAGGGGAAGGAACAACATCTGAGCAACTAA
+AGCACTCTATCAACTGGAAGTGCAAGATGGTAGTGAGGGGTGGACAGGTG
+TAACTGAGTAACTCTTTGTAGGTAGCCTTTCAGTTTAATTCAGTAAAATA
+TTTTGAACACTAGTATTCCAGATACTGGTAGGCCATGACTTAACCATTCC
+TAATGTTAATCTCAGCTGTGCTAGCTGAGCTTGTGTTCACATTAGACATG
+AAGAAACTTAGTAAAAGGTAGAGCCCAGTTTTCGGTTTGGACCTTCCTGT
+TGGCCTCTGCTTCCGTGCCATCTAGCAAAGGAGTTCCTAATCTCTAGAGG
+GATACAAATGACTAGTCTGCTCCATCTGCCTCTTCCAACATTGCAGGGTA
+GCTCCCAGGGAGAAGAGTCAGTGAGTGGTTCCCAGAGAACATCCAGTATC
+T
--- a/tools/new_operations/gops_intersect.py
+++ b/tools/new_operations/gops_intersect.py
@@ -70,7 +70,7 @@ def main():
for line in intersect( [g1,g2], pieces=pieces, mincols=mincols ):
if type( line ) == GenomicInterval:
if in1_gff_format:
- line = convert_to_gff_coordinates( line )
+ line = convert_bed_coords_to_gff( line )
out_file.write( "%s\n" % "\t".join( line.fields ) )
else:
out_file.write( "%s\n" % line )
--- a/tools/extract/extract_genomic_dna.py
+++ b/tools/extract/extract_genomic_dna.py
@@ -5,6 +5,7 @@ usage: %prog $input $out_file1
-d, --dbkey=N: Genome build of input file
-o, --output_format=N: the data type of the output file
-g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc
+ -G, --gff: input and output file, when it is interval, coordinates are treated as GFF format (1-based, half-open) rather than 'traditional' 0-based, closed format.
"""
from galaxy import eggs
import pkg_resources
@@ -14,6 +15,7 @@ from bx.cookbook import doc_optparse
import bx.seq.nib
import bx.seq.twobit
from galaxy.tools.util.galaxyops import *
+from galaxy.tools.util.gff_util import *
assert sys.version_info[:2] >= ( 2, 4 )
@@ -50,6 +52,7 @@ def __main__():
chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols )
dbkey = options.dbkey
output_format = options.output_format
+ gff_format = options.gff
GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR
input_filename, output_filename = args
except:
@@ -80,6 +83,8 @@ def __main__():
chrom = fields[chrom_col]
start = int( fields[start_col] )
end = int( fields[end_col] )
+ if gff_format:
+ start, end = convert_gff_coords_to_bed( [start, end] )
if includes_strand_col:
strand = fields[strand_col]
except:
@@ -162,7 +167,11 @@ def __main__():
c = b
else: # output_format == "interval"
meta_data = "\t".join( fields )
- fout.write( "%s\t%s\n" % ( meta_data, str( sequence ) ) )
+ if gff_format:
+ format_str = "%s seq \"%s\";\n"
+ else:
+ format_str = "%s\t%s\n"
+ fout.write( format_str % ( meta_data, str( sequence ) ) )
fout.close()
--- a/tools/new_operations/gops_subtract.py
+++ b/tools/new_operations/gops_subtract.py
@@ -71,7 +71,7 @@ def main():
for line in subtract( [g1,g2], pieces=pieces, mincols=mincols ):
if type( line ) is GenomicInterval:
if in1_gff_format:
- line = convert_to_gff_coordinates( line )
+ line = convert_bed_coords_to_gff( line )
out_file.write( "%s\n" % "\t".join( line.fields ) )
else:
out_file.write( "%s\n" % line )
--- /dev/null
+++ b/test-data/extract_genomic_dna_out4.gff
@@ -0,0 +1,46 @@
+chr10 Cufflinks transcript 62044837 62045189 1000 . . gene_id "CUFF.23531"; transcript_id "CUFF.23531.1"; FPKM "19.5178121606"; frac "1.000000"; conf_lo "9.264456"; conf_hi "29.771168"; cov "1.108611"; seq "AATTACAAGATCGACACACCAAGATAGGCAGATCCATGGTTGGTTTTACTTTGTAAATCTAAAAGTATGTTGGAAAACGATGCAATGAATTCTTATCCTTTTTCAAAATGAAGAATTTGTGATGGTTAGTGGACAGTTCAGAAGCCTCTCTGCAAGAAAGGGGGCGCTGAGAAGTGGTAAAAAAAGGAAGGAAGCACTCGGGCTTTGTCAGCAGGGTGGACCCTGGGGTCCACAGTGGGAACAGTCCCTTCTGGCCTCTACTCACTGACCAAACGCTTTACTAAAACTCCGCTTCTGGCCTCTGTTGCCACCTCCTGGTCGCTGTCCTCGGAAGTTTCTACTTCCTCCTCGCT";
+chr10 Cufflinks transcript 75372919 75373002 1000 . . gene_id "CUFF.24985"; transcript_id "CUFF.24985.1"; FPKM "124.4970510798"; frac "1.000000"; conf_lo "71.411330"; conf_hi "177.582772"; cov "7.071429"; seq "GCGTCTCGCAGCTTCTGCCCGTCGATCTCCATGTCGAGCCGGATGGGCACCAGCACCTCAGGCTGTGACGCATTCTCATGGATC";
+chr10 Cufflinks transcript 80362428 80363292 1000 - . gene_id "CUFF.26065"; transcript_id "CUFF.26065.1"; FPKM "43.6170921216"; frac "1.000000"; conf_lo "32.260169"; conf_hi "54.974016"; cov "2.477449"; seq "ATGACGGACAAGTGTTTCCGGAAGTGCATCGGGAAGCCCGGGGGCTCCTTGGATAACTCGGAGCAGGTGAGACATCTCGGGAACCCGGGGTGGTGAGGGGCGCGGGGTCAGGAGCGTCTAGGAGGTTGAGAGATGTGCGCGTGCGCGGCCTCTAGCCTTAGCTACTGAGGAAGTTGTGCGCGTGCGCGGGGTGAGGACCCGGCTTCTGTGCCTAGATCGGTGCAGCCTTCATGGGTGATCCTCGGGTCGTGTGACCGTCAGTCAGGGATCCCCCTCCACGCTTTGCAGAAATGCATCGCCATGTGCATGGACCGCTACATGGACGCCTGGAATACCGTGTCCCGCGCCTACAACTCTCGACTGCAGCGGGAACGAGCCAACATGTGACCGGGACCTGTGCCTCGGGACACCGTGCTTATGGTCTGAACTGTTTTCCCTGCCAGTTAGGGTGTCTCCTCCTAGCCGCCCTGAAGTCTGGCAGCATGGAGGGCTTGGGGATCGAGGCCTCTCCCCTGGGTTGCTGCGTCCAGCTCAATCTCAGAAGAGAGTGAGGACCCGACAGAGCACAGGGATCTGGCTGGCCCCACTGACCTGTGACCTCAGGAGAGCAGGCCAATAAATCGCTGCTGGGGCAGTAAAGCAGGCGTGTCACCTCACTGCTTCAGGTCCCTTCCCCTGAGTAGGCCCAGACCTCCCAGGGTATCTTTCCCCTTGGGGTCAGTGGGCTGCTGGCTCTCAGGGAATTCGGAGCATGATCTCAGGTGTTTGGTCATCCCGGGGA
GACCAGCCGAGGTTAAGAAGCAAGGCTTCATGTagccttcacctatcatgcatgaggcccagggtgctgaccttaactctgaat";
+chr11 Cufflinks transcript 7904565 7904642 1000 . . gene_id "CUFF.33508"; transcript_id "CUFF.33508.1"; FPKM "61.6484988869"; frac "1.000000"; conf_lo "22.882428"; conf_hi "100.414569"; cov "3.501633"; seq "CATCTTCTATTTGAGCCTCCATCCAGGCACCTCTGAAACAAAGGTGCACTCACTGCATGTCCACTTGTCACAGGAGCC";
+chr11 Cufflinks exon 78140156 78140259 1000 . . gene_id "CUFF.43148"; transcript_id "CUFF.43148.1"; exon_number "1"; FPKM "54.8483511750"; frac "1.000000"; conf_lo "23.181641"; conf_hi "86.515061"; cov "3.115385"; seq "CTGCTTGCTAATTTTCTCTCTTGGGATCAGGGGGACGTGAACTCCAGCCCTGACTCGTGCTCCTTATGCTCTGAGTACATAGCAAATAAATGAGAGCAAAACAC";
+chr11 Cufflinks exon 105616462 105616737 1000 . . gene_id "CUFF.48385"; transcript_id "CUFF.48385.1"; exon_number "1"; FPKM "18.9452034252"; frac "1.000000"; conf_lo "7.520816"; conf_hi "30.369591"; cov "1.076087"; seq "TAGGTGTAATAGTGGAAAACAATAGTTTTTAAACTTCAGAGTCCAGGGCTGTAACTCAGTAGTAACAGTGTTCTCTAAGTATGTTATTCTTCCTCTACATGCTGAAATTTTTCATATTTGGAGCATTCACTGTTCCATGTATCAGTAAATTATATTGTGAGCTGTCATCATATCTAAGCACCATATTGAATATTTTTCATGATTAAAATTTGTTGAAACAACAATTCTATGACCGAAAAAAGCAAGGCTTTGTAAATAACATGTTTGTTACTAGTA";
+chr12 Cufflinks exon 30701762 30702509 1000 . . gene_id "CUFF.53897"; transcript_id "CUFF.53897.1"; exon_number "1"; FPKM "48.9333329111"; frac "1.000000"; conf_lo "37.780391"; conf_hi "60.086275"; cov "2.779412"; seq "TGTGGAGTGTACTTATATGATCCCTATGCTGATAGGATTACCTTCCTAGACATAGCTAGACGCAAAGCCACATGTGTAAGGCTGCTGAGCAAAGACAGCATCCCAGCATGGGTGTGTTCACGGTGGATTCACCACGTTGCATATGTAAAGTGGTCCCCTTGGCTTACCCTTCACTTTGCTCATGAGATTCAGAAGCTGGTGGTCCAGCAGGGGTGAGCATTTGTGAAATAGTAAGCTGAACTTAGTGGTGAGATTTCAGAACAGACTTCTGTGAAGTAAGAGATGTAACCATGCATCTAAAATCAGATGGCCGTGTAACTGCTCGGGCATAGAAATGGTGGGAGAACCTGTCCTGGGTACCTGGCATTTCACATGAGCCCAGGGATATGTCTTGTGCCAAGGCACACAAGTGTCCATGGACTTGGACAGGTGCCAAGGGTTTTTGTCTCTGTTCCTATGTGGGAGGCTGGCTGTGATTTACATTAATTTCTGTATTTCAAACGAAGATGTCTGCAGATCTCCATTTTGATGTTACAGCCTCATTGCCCAGGCAGTGGGCAGTGCCCAGACACCCTTTCTGACTAGCCACTGCATTGGGCTTCTGTGATTCAAAGTAGTGTATATATTTATTTACTTCTCTGACTGTGGCCAACAGCCAAATGCCATTTTATGTTCCTTGTATTCAGTCCATTACCAAAGAGGTGTTTGCACTTTGTAATGATACCTTTCAGTTCAAATAAAAGGACCA";
+chr13 Cufflinks exon 49159496 49159569 1000 . . gene_id "CUFF.67788"; transcript_id "CUFF.67788.1"; exon_number "1"; FPKM "44.9657653777"; frac "1.000000"; conf_lo "10.974842"; conf_hi "78.956689"; cov "2.554054"; seq "ttttcttttggattacttgatttttttttatttgatcttatttatgatgattttgagtacatttttgaacagtt";
+chr13 Cufflinks transcript 100200304 100200330 1000 . . gene_id "CUFF.73108"; transcript_id "CUFF.73108.1"; FPKM "123.2395051093"; frac "1.000000"; conf_lo "30.079196"; conf_hi "216.399814"; cov "7.000000"; seq "TCTCATATGAATAGCCACCCTCTTCTG";
+chr14 Cufflinks transcript 31949103 31949152 1000 . . gene_id "CUFF.77316"; transcript_id "CUFF.77316.1"; FPKM "85.5634278330"; frac "1.000000"; conf_lo "28.521143"; conf_hi "142.605713"; cov "4.860000"; seq "GGATGCTATCCGCGATGTGCATGTAAAGGGCCTCATGTACCAGTGGATCG";
+chr14 Cufflinks exon 67604227 67604668 1000 . . gene_id "CUFF.81446"; transcript_id "CUFF.81446.1"; exon_number "1"; FPKM "123.6776546104"; frac "1.000000"; conf_lo "100.611653"; conf_hi "146.743656"; cov "7.024887"; seq "TTCACCGTGAGAGTTTTCTCCATTTCACTCTTCACTGTGCTGTTCTCTGTGCCGCTTTCCTCTTGACTTATAAACATCTGAGCCAGTTTTCAATAAACTTAAAACGAAGCCTGCTTCTCATCCCAAATTGTAAACAGGAATAAAGCTTTTTAAACCTTATCTTAAATTTTAACTTTGTTGAATTCTGCTTTGTGATAGGACAATCTGTTTCACCCAACAAGAATCTGTGTAGGAGGATGAACATCCCGCATGTTGGAGCTGCAAATCAGCACTGTACAAGCTCACTGATGGACAGCTGTTCTGTGATGTATTCCATGATTTTACTAATACTTTCAAAAATGGCAAAACTAACTTCAGTTTTAATGTTGAAAGAAAATCATAAATGTTCCCATAGTTCAATGGCACTGTCGATGAAACTGCTACTGAATTTAGAGAGAAAACG";
+chr14 Cufflinks exon 75165582 75165744 1000 . . gene_id "CUFF.82088"; transcript_id "CUFF.82088.1"; exon_number "1"; FPKM "20.4139057543"; frac "1.000000"; conf_lo "4.982443"; conf_hi "35.845368"; cov "1.159509"; seq "ggccctgggatgataTAACAGAAGAGTCTAAAGGAGGCTTCTGAGATGTGCAGTAGGAAAGCCTGGCACATAATAGGTTATTATCTAAATCCCTTCACTACTCTTCAAAGACAGCAGGATGCCTCTGCTCCCATGTTTTATCTCTACTTATGTGGAATTTATG";
+chr16 Cufflinks transcript 57154027 57154067 1000 . . gene_id "CUFF.103364"; transcript_id "CUFF.103364.1"; FPKM "162.3154457537"; frac "1.000000"; conf_lo "75.554191"; conf_hi "249.076701"; cov "9.219512"; seq "GTTGAGGTTTATTTAAGTAAAATGATTTTTTAAAAAAGCAA";
+chr16 Cufflinks exon 74862302 74862560 1000 . . gene_id "CUFF.105450"; transcript_id "CUFF.105450.1"; exon_number "1"; FPKM "11.0120241741"; frac "1.000000"; conf_lo "2.020744"; conf_hi "20.003304"; cov "0.625483"; seq "GCATTGGCAGCAGATATTGGTACCCAGTGGCACTGCAGAGTACTTACAATCAGGACTCGCTACTGTGCTTCATTCTGCTTTTCTCTCTGCTTCTATTACAGTTAAAGTGTTGCTAATTATAGAAACTCTCTGTTTATTGAACCTCGGTGTTAAGAAAAACTTGTAATCTTCAGATATGATCCGAAAGATTCCCAAACAAATGTAACAAGGTCCACTTTTGTAGCCCTTTCTACCAGAAcactggttatcaacctgtggg";
+chr16 Cufflinks transcript 98168779 98168914 1000 . . gene_id "CUFF.107834"; transcript_id "CUFF.107834.1"; FPKM "24.4666664555"; frac "1.000000"; conf_lo "5.971605"; conf_hi "42.961728"; cov "1.389706"; seq "CCTATTTATTTCACTAAACATCTGCCTGCTAGCTGAGATAAACATTCTCTAAAAAACTGTTTACTGCAAAAAGTGATTACTGTTTTTTATTAGTTTCTTAGCATTTGAAATAGTTACATGAATGGAAGGATAGAGT";
+chr17 Cufflinks exon 8483212 8483268 1000 . . gene_id "CUFF.108498"; transcript_id "CUFF.108498.1"; exon_number "1"; FPKM "50.0370923000"; frac "1.000000"; conf_lo "9.181978"; conf_hi "90.892207"; cov "2.842105"; seq "AGACTTGTCAACAGCTCACCCAATGATGGAACTGAGGCTGCCCCTCAAGTGGCCAGA";
+chr17 Cufflinks exon 30355791 30355913 1000 . . gene_id "CUFF.111759"; transcript_id "CUFF.111759.1"; exon_number "1"; FPKM "19.3232673516"; frac "1.000000"; conf_lo "2.040012"; conf_hi "36.606523"; cov "1.097561"; seq "atctcatacccataagctcagaactcggggtggtaacataggaggactgccatgagtgtgactaacctgggctataggaggaggatctaccttaagcaaatgaCCAACAAAACTAACAAGCTC";
+chr18 Cufflinks transcript 39571718 39571880 1000 . . gene_id "CUFF.123569"; transcript_id "CUFF.123569.1"; FPKM "20.4139057543"; frac "1.000000"; conf_lo "4.982443"; conf_hi "35.845368"; cov "1.159509"; seq "TATAACATTCCATAAATGTACAATAATCTATTTTTGAGAAGCTCATTTTGAAACTTAACACTGTCATTGATAATCTTCAAGTGGTATTTCTTAGGCACCATAAATTTCACATCCAGCTGGGTTACAATTATTTTAAAGTACTTTGAGACCAATTTAAACCATT";
+chr19 Cufflinks exon 17633088 17633203 1000 . . gene_id "CUFF.131333"; transcript_id "CUFF.131333.1"; exon_number "1"; FPKM "20.4893265884"; frac "1.000000"; conf_lo "2.163116"; conf_hi "38.815537"; cov "1.163793"; seq "TGGGAAATGAACTGCATGGCAATGAACCCCAGGGAATTTGGTGGTTAATTGTCTAAGGATAAGGACATCAGTTTTGTCTTTTGCATCACTGTGACCTTTGCCTCTAATTGTATAGA";
+chr19 Cufflinks transcript 41997624 41997859 1000 . . gene_id "CUFF.133569"; transcript_id "CUFF.133569.1"; FPKM "28.1988698132"; frac "1.000000"; conf_lo "13.125940"; conf_hi "43.271800"; cov "1.601695"; seq "gctacacaacgactcacatagagggaagcaggcacacatcagataaaacacAAAAGGATGGGTTGGTGATGGGCATAGTTAATGAGGGCCACTAGGTAAATACACCTGATCCAAAAGTCACGCTACTACTTAGATTCTTCTCTCTGCTAAAGACAACAGAAgacatgttagccatgcttgtaatccctgcattggggagatggagtcagaaatatcactgcaagttcacccaatag";
+chr19 Cufflinks exon 56516515 56516684 1000 . . gene_id "CUFF.135203"; transcript_id "CUFF.135203.1"; exon_number "1"; FPKM "33.5542854247"; frac "1.000000"; conf_lo "14.181710"; conf_hi "52.926861"; cov "1.905882"; seq "TGTATTCATTCACTATTCACTGATTTGTCAGATCATCCATCCACACAGGTGCTGAAGAGTAACCCATTTCACTTTGTATACAAGATAATGTTTTTGTACTTCAAATACATCTGGAATTCTTTCAAATATTCCAAGATTTTTTTTTTTTCTGAATAATCTTTGGTTACCTC";
+chr2 Cufflinks transcript 4543774 4543977 1000 . . gene_id "CUFF.136435"; transcript_id "CUFF.136435.1"; FPKM "37.2825393608"; frac "1.000000"; conf_lo "18.641270"; conf_hi "55.923809"; cov "2.117647"; seq "gagccatttctccagccccTTTATGTGGAATATTAACAAGAGAAGACAACATAAAATGACTTACCATGCTGTGTGGCCTAACAGTGGATGAAGAATGAGTGATTTGGGCATTTCTGATAGTATTTATAAAGAAGACTTTTATGACCAAACCACATGTCACAGTAGGGATTTGCTGCACATCTTATGAGAGTTTCTTCTTTGTCA";
+chr2 Cufflinks transcript 30200331 30200938 1000 . . gene_id "CUFF.140289"; transcript_id "CUFF.140289.1"; FPKM "100.0741846001"; frac "1.000000"; conf_lo "82.383401"; conf_hi "117.764968"; cov "5.684211"; seq "CGCACACAAAGGATTTATTTGCCAGAGAGCAAGCAGACAGGCAGAGGTCAGAATGTTAGTTAGAAACTGAAGGAATGACTGCTGTAGCCACTGTGCCCAGCCAGAGCCATGAGGGAAGTGGGAGGCAGCACTTGGTGCTGCTGCTCTGGCTGACCCTTCTGGTTTCCTGCCACACTCCTAGCCCTGCCTGTGTGCTGCTGTCCCCCTCAACCTTCCACAGCCAGAAGGCAGATGTTCTTTCATGCCAAGAGCATCCATCCCCAGCATATCCTGGGCCCATGGTGGTGTCAAATGTAGTGACCCTTCTGCCTTAAGGGAGCTGGGAAGCCTGGGGTGTGCAGGGTTGCAGGTCAGAAGCAGGACTAGCAGAGGGGCCTGGGGCCATTCTGTCTTGTGGGCTCTTTAATAGCTGAATGACGGGCACAGCCAGAAAAGGGTTAGGTCCCTTATCCTAAGCAGCTCTGTGGCCAGCAGACGACTCTAAGTGGCAGAGCCTGGGAAGGGGCTGCTTAGCTGAGAAGTTCCAGGTAGGTGACAGGAACCTTGCCCTTCTTGTTGCCTCTCTCACCAATGAGCCAGTCGGGATCCATGCCTGGCAGGCTGTAGAC";
+chr2 Cufflinks transcript 106644220 106644341 1000 . . gene_id "CUFF.148977"; transcript_id "CUFF.148977.1"; FPKM "27.2743167045"; frac "1.000000"; conf_lo "6.656871"; conf_hi "47.891762"; cov "1.549180"; seq "attcttaaggtaaatacctaggagtgatgtaacccagtcatagggaagaactacttttaatttgttgagcaacccccaacctgattttgacacaggtttgagtagtttacacttctactaac";
+chr2 Cufflinks exon 125388931 125389219 1000 . . gene_id "CUFF.151331"; transcript_id "CUFF.151331.1"; exon_number "1"; FPKM "23.0274507817"; frac "1.000000"; conf_lo "10.718761"; conf_hi "35.336141"; cov "1.307958"; seq "AGAGCACACAGCACATCACTTAGGCCTCCAACATTAAGGCAGCGCAAGTGCCTCAAGTAACTGAGAATACTTTACTCAGATACAAGGGTATCAAAAACATGAGAACTGGCAGGAAGACCTCACAATGGTTTGTTAGCATCAAGTATTACCATCCAGTTTCCTGTTTAAATAGTAATTAATGACTATTCTGAAATAAGGCAAATAATTACTCAAGCGGGCTGTCAAAGCCACTATCCTGTTGGCTGGGCATCGGAGCAGTTAACTTTATCAAAGGCTTCTGACACAATGA";
+chr3 Cufflinks transcript 130936639 130936898 1000 . . gene_id "CUFF.171349"; transcript_id "CUFF.171349.1"; FPKM "20.1110620975"; frac "1.000000"; conf_lo "7.983635"; conf_hi "32.238489"; cov "1.142308"; seq "CGAGGCTGCAGGCTGCAAATGTTCCCAGGCAGGCAAGACCTCACGTCCTACTGGCTGCTGCCCTTGGGTGCATCTGTAGGCCCCGTGGCTCCTGCCCCTGGGGTTCAACACCGATAAACATAGAATACTCATTTTCAGAAGACCTGAGGGAATGAGTCTAAGCAACGCTTTTTACAAAAAGTGGCAAGGTTCAGGAAAAAAAAAAAAAAAGATGTTGCTCCAAGGCACCAAGGGTGTAATTTTTTTTCAGAAAAAGTCAG";
+chr3 Cufflinks exon 136592671 136592771 1000 . . gene_id "CUFF.171861"; transcript_id "CUFF.171861.1"; exon_number "1"; FPKM "32.9452142371"; frac "1.000000"; conf_lo "8.040973"; conf_hi "57.849455"; cov "1.871287"; seq "TGTCAGCCCATCACATTTTAGTGACAACAGTCATAGCCTTTATTTTCAGATGACTTTCCTCTAAAACCACTGTCTATGAGTTGCCCCCCAAAACTCAAAAA";
+chr3 Cufflinks transcript 152861374 152861508 1000 . . gene_id "CUFF.173007"; transcript_id "CUFF.173007.1"; FPKM "24.6479010219"; frac "1.000000"; conf_lo "6.015839"; conf_hi "43.279963"; cov "1.400000"; seq "ATCAAAAGCGACATGCAAGCATCTTGCTCTCACCACAGATCACTGAGACATTAAGAGTGACGTCTCTTGAACTGTTGGCACGCCTAAGTTATTTCAGCATTTCTTGCTCAGCAGTTGTTCTCTTGGCTTCCTCTG";
+chr4 Cufflinks exon 13715310 13715630 1000 . . gene_id "CUFF.174817"; transcript_id "CUFF.174817.1"; exon_number "1"; FPKM "19.2510308382"; frac "1.000000"; conf_lo "8.572480"; conf_hi "29.929581"; cov "1.093458"; seq "AACACATGGCCACATCATGTGATATTTTCAAAACACTTACACATAGCTTTGAGAAGGTCCCTGCAGGAATGATCCATCCTCTCACAGTTGGCCCATTTTTTAACAGCATATCTGCATTTTCCATTTAGGAGAGCTATATATTATTAGCTTACATTTTTGGGTAGTAAAACAGTGCATTGCTGATTGTAAAACATGGACTTTATTATCTGCTGAAAATTGATTTGGCATTTATAGCCACTGTGTATTAGACTGTTTTTCTGTTTTTAACATCAATGCTTAAAAGCGATGATTTGTGTTTaaaaaaattaaaaaaataaaata";
+chr4 Cufflinks exon 147515029 147515097 1000 . . gene_id "CUFF.190627"; transcript_id "CUFF.190627.1"; exon_number "1"; FPKM "34.4458244094"; frac "1.000000"; conf_lo "3.636542"; conf_hi "65.255106"; cov "1.956522"; seq "GCTGACGTGCTCTCCGAGTTCCTGGAGGTGGCCGTGCACCTGATTCTCTATGTGCGCGAGGTCTACCCG";
+chr5 Cufflinks exon 3949522 3949685 1000 . . gene_id "CUFF.192485"; transcript_id "CUFF.192485.1"; exon_number "1"; FPKM "23.1879208220"; frac "1.000000"; conf_lo "6.791585"; conf_hi "39.584257"; cov "1.317073"; seq "AGTCCCAACCACCCCCTTGTTTAATGTATAACTTTCTGAAATGGGAGCGTTAGAATGGATTAAAATGGTTGGTAGGTGGTTGGATCACCAACCAAGACCAGAAATAGAGGGGTAGGCTGCTCAGGAGAGTATTGGGAGGGTAGCTATTATTTGCATTTTGTGCT";
+chr5 Cufflinks transcript 68089694 68089831 1000 . . gene_id "CUFF.199409"; transcript_id "CUFF.199409.1"; FPKM "17.2229122047"; frac "1.000000"; conf_lo "1.818271"; conf_hi "32.627553"; cov "0.978261"; seq "CAATGATAGAGAAGACTAAAATAAAAGCAGGCATGCTGGCACAAGCGACAGAAGGAAAAAGCCTCACCCGGCCCTGTTTGAGGCCACTCCTGGTGGCTCCTTTTCCAAGGACCATGCGGTCAAGCCTCTGAGTTGTTC";
+chr5 Cufflinks exon 122819526 122819619 1000 . . gene_id "CUFF.205487"; transcript_id "CUFF.205487.1"; exon_number "1"; FPKM "25.2486782797"; frac "1.000000"; conf_lo "2.649470"; conf_hi "47.847887"; cov "1.434124"; seq "CTTTAGAAAAGATGCATCTGTCATTGATTTAGGGATATGAATTGTTTGGATTTGAGTAGTTTTCCATAACTCCTGCAGTTTGGCAATGTGTGCG";
+chr5 Cufflinks transcript 145619548 145619710 1000 . . gene_id "CUFF.209965"; transcript_id "CUFF.209965.1"; FPKM "40.8278115086"; frac "1.000000"; conf_lo "19.004428"; conf_hi "62.651195"; cov "2.319018"; seq "CGGCGTTCTGAAAACTGTGCTCCGGGATGAGATCATTGCTTGGCACAAAAAGACACAGGAGGACACTTCCTCTCCACTGTCGGCCGCAGGGCAGCCTGAGAACATGGACAGCCAGCAGCTGGTTTCCTTAGTTCAGAAAGCCGTCACTGCCATCATGACCCGC";
+chr6 Cufflinks exon 83928984 83929105 1000 . . gene_id "CUFF.219317"; transcript_id "CUFF.219317.1"; exon_number "1"; FPKM "46.7559714935"; frac "1.000000"; conf_lo "19.761399"; conf_hi "73.750544"; cov "2.655738"; seq "ACAGGAACCATTATTTACATTTAATTTGGATGAATTTGTTACTGTGGATGAAGTCATAGAAGAAGTAAATCCTTCTCAAGCCAAGCAGAATCCATTAAAAGGAAAAAGAAAGGAAGCCCTCA";
+chr6 Cufflinks exon 118857949 118858148 1000 . . gene_id "CUFF.223543"; transcript_id "CUFF.223543.1"; exon_number "1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "5.569100"; conf_hi "32.459091"; cov "1.080000"; seq "CCAGGCTTGCTAGTTGGTGCAGTTAGCTACATCTCAGGACAGAGACAAGGTACTCTGAGCTCCCCTTGAACTGCCACACAAGCTGTCTCCTGGATGCCAAGCAGAGAAACCTGGAGACAACAATCATCATACTCAAAACCAGGATCTCTTTCTTAAGACTTTTGTATTTTGTCCCAGCCCTAACCCTGAGTTCTGCTGAA";
+chr7 Cufflinks transcript 85554210 85554343 1000 . . gene_id "CUFF.235778"; transcript_id "CUFF.235778.1"; FPKM "17.7370289869"; frac "1.000000"; conf_lo "1.872548"; conf_hi "33.601510"; cov "1.007463"; seq "GTGAAACATCATGCTTCTGCATCAAGTTATTAGTGGGAAACCTGTAAAAGTTGACATTGAATGCTGATAACAAATTACTTTCATCCTGTCTCATAATGAATCCTACATCAAGACAAGGCAAGTGAGAAAGAGGG";
+chr7 Cufflinks exon 104055491 104055589 1000 . . gene_id "CUFF.238474"; transcript_id "CUFF.238474.1"; exon_number "1"; FPKM "28.8092349606"; frac "1.000000"; conf_lo "5.286593"; conf_hi "52.331877"; cov "1.636364"; seq "ACATTTCTCCTCTCTTGGGGGAGCGCATCTCCTTGGGTGTGTCCACATCCGCCCCTAGGTACCCAGTGTGATGTGAGACACGAGTGTCTGTGCTAACTT";
+chr8 Cufflinks exon 9970398 9970545 1000 . . gene_id "CUFF.245320"; transcript_id "CUFF.245320.1"; exon_number "1"; FPKM "22.4828826889"; frac "1.000000"; conf_lo "5.487421"; conf_hi "39.478345"; cov "1.277027"; seq "AGTCTTCACCAAAATTAAGTCTCAGCTAACTTAAAAGTTGCAAGGATTTTTTTCAATAAAATTAATATCTTAAGTGTTTGGTGTTTAGATGATTCTCTCTCAACTTCCCCCACATTATCAAAAAACATTTGATGAACCTTAAAAACTC";
+chr9 Cufflinks transcript 20449846 20449932 1000 . . gene_id "CUFF.260747"; transcript_id "CUFF.260747.1"; FPKM "234.9313045507"; frac "1.000000"; conf_lo "163.275950"; conf_hi "306.586659"; cov "13.344091"; seq "CCAGCACCGATGACACCATCGGCGACTTGAAGAAACTGATAGCTGCTCAAACTGGCACCCGCTGGAACAAGATCGTTCTTAAAAAGT";
+chr9 Cufflinks exon 107445870 107445930 1000 . . gene_id "CUFF.272761"; transcript_id "CUFF.272761.1"; exon_number "1"; FPKM "38.9633095779"; frac "1.000000"; conf_lo "4.113466"; conf_hi "73.813153"; cov "2.213115"; seq "CAAGCAGAAGCTGGTGCCCATCATGACCATCCTGCTGGAAGAGCTGAATGCCTCCGGCCGC";
+chr9 Cufflinks transcript 120860476 120860606 1000 . . gene_id "CUFF.275115"; transcript_id "CUFF.275115.1"; FPKM "25.4005086867"; frac "1.000000"; conf_lo "6.199529"; conf_hi "44.601488"; cov "1.442748"; seq "CTGCCATTGTACGCACCATGCAGAATACAAATGATGTAGAGACAGCTCGTTGTACTGCTGGGACTCTGCACAACCTTTCTCACCACCGCGAGGGCTTGCTGGCCATCTTTAAGTCTGGTGGCATCCCAGCG";
+chrX Cufflinks exon 10274057 10274087 1000 . . gene_id "CUFF.276147"; transcript_id "CUFF.276147.1"; exon_number "1"; FPKM "99.5432248142"; frac "1.000000"; conf_lo "21.405127"; conf_hi "177.681323"; cov "5.654052"; seq "ACTTCGCTGTCATCATTTGTACAAACTCTTT";
+chrX Cufflinks transcript 39881431 39881678 1000 . . gene_id "CUFF.277419"; transcript_id "CUFF.277419.1"; FPKM "42.1683560109"; frac "1.000000"; conf_lo "24.187709"; conf_hi "60.149003"; cov "2.395161"; seq "AGCTAAAAAGAGTCCTTTTCTGACAGAAAGGCTGGACTTCTCCTTTTCACCGTTTCTCTTACTGATGCTTTTGCCAGAAGAACAGTAAAGATTTAGACACTGTCATGATTCATACACGTAAAATATTTTTCAAGGACACAATCTGATATACTAACATTTATTTAAGAGGTTAAAGTCCACCACTAAATCTAAGGAAAGATTTTTAACTGCCAAACACATTTCCTTTGACAAATAATGTAAGATGACAA";
+chrX Cufflinks transcript 148249672 148249713 1000 . . gene_id "CUFF.282847"; transcript_id "CUFF.282847.1"; FPKM "56.5895686726"; frac "1.000000"; conf_lo "5.974320"; conf_hi "107.204818"; cov "3.214286"; seq "AATGCTAGTATGAACAGTGGGAGGAATGAGCAAAATGTTACA";
+chrX Cufflinks transcript 148481505 148482455 1000 + . gene_id "CUFF.282965"; transcript_id "CUFF.282965.1"; FPKM "40.1706233958"; frac "1.000000"; conf_lo "16.978103"; conf_hi "63.363144"; cov "2.281690"; seq "CGCCACAACCTGCTACAGGCCTGTAAGATGCAGGACATCAAACTGCCACTGTCAAAGGGCACCATGGATGATATTAGTCAGGAAGAAGTGAGTATTATGGTGGGTGGTAGGAGTCATCTATGAATATTTAACCAGTAATGGGAGATTACAGATGGCCAGGAAGGGCAGGCAACAGATAGGACCACATAGAGTTGTGAGGGGCATAAAGATGGATGCAGAAGAAATGTGGCAAGGTGGAAGTAGTGAAGTCAGGCTTTGGTATGAGAGAGACATTGATTTGAGAGGAGAGCTGCAAGCCAGTGAGTACTCAGAAAGACCAAGAATGGGTCATTAATCTTAAGGATTTGAGCTCTTAGCTGCAGCAGATACTGGGCATGGGTAGGAGTGAGAATTGAGGAGCAGAGGAAGATGGGAAACTGGAGAACCTAAGGAGACTGATAGCTTAGCTGCAGTAAGGGAGGTTGGCCAGAAGAGGGTTGGGTAGGGGACTCAGCAAGGCAGAACTAAGGAAGCTTAGGTGGAGGGGAAGGAACAACATCTGAGCAACTAAAGCACTCTATCAACTGGAAGTGCAAGATGGTAGTGAGGGGTGGACAGGTGTAACTGAGTAACTCTTTGTAGGTAGCCTTTCAGTTTAATTCAGTAAAATATTTTGAACACTAGTATTCCAGATACTGGTAGGCCATGACTTAACCATTCCTAATGTTAATCTCAGCTGTGCTAGCTGAGCTTGTGTTCACATTAGACATGAAGAAACTTAGTAAAAGGTAGAGCCCAG
TTTTCGGTTTGGACCTTCCTGTTGGCCTCTGCTTCCGTGCCATCTAGCAAAGGAGTTCCTAATCTCTAGAGGGATACAAATGACTAGTCTGCTCCATCTGCCTCTTCCAACATTGCAGGGTAGCTCCCAGGGAGAAGAGTCAGTGAGTGGTTCCCAGAGAACATCCAGTATCT";
--- a/lib/galaxy/tools/util/gff_util.py
+++ b/lib/galaxy/tools/util/gff_util.py
@@ -6,23 +6,37 @@ from bx.intervals.io import NiceReaderWr
class GFFReaderWrapper( NiceReaderWrapper ):
"""
- Reader wrapper converts GFF format--starting and ending coordinates are 1-based, closed--to the 'traditional' interval format--0 based,
- half-open. This is useful when using GFF files as inputs to tools that expect traditional interval format.
+ Reader wrapper converts GFF format--starting and ending coordinates are 1-based, closed--to the
+ 'traditional'/BED interval format--0 based, half-open. This is useful when using GFF files as inputs
+ to tools that expect traditional interval format.
"""
def parse_row( self, line ):
- interval = GenomicInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, self.end_col, self.strand_col, self.default_strand, fix_strand=self.fix_strand )
- # Change from 1-based to 0-based format.
- interval.start -= 1
- # Add 1 to end to move from closed to open format for end coordinate.
- interval.end += 1
+ interval = GenomicInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, self.end_col, \
+ self.strand_col, self.default_strand, fix_strand=self.fix_strand )
+ interval = convert_gff_coords_to_bed( interval )
return interval
-def convert_to_gff_coordinates( interval ):
+def convert_bed_coords_to_gff( interval ):
"""
- Converts a GenomicInterval's coordinates to GFF format.
+ Converts an interval object's coordinates from BED format to GFF format. Accepted object types include
+ GenomicInterval and list (where the first element in the list is the interval's start, and the second
+ element is the interval's end).
"""
if type( interval ) is GenomicInterval:
interval.start += 1
- interval.end -= 1
- return interval
+ elif type ( interval ) is list:
+ interval[ 0 ] += 1
return interval
+
+def convert_gff_coords_to_bed( interval ):
+ """
+ Converts an interval object's coordinates from GFF format to BED format. Accepted object types include
+ GenomicInterval and list (where the first element in the list is the interval's start, and the second
+ element is the interval's end).
+ """
+ if type( interval ) is GenomicInterval:
+ interval.start -= 1
+ elif type ( interval ) is list:
+ interval[ 0 ] -= 1
+ return interval
+
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