[hg] galaxy 3617: Add BedGraph datatype (wiggle-like data for in...
15 Apr
2010
15 Apr
'10
7:18 p.m.
details: http://www.bx.psu.edu/hg/galaxy/rev/8fa4e8c12dfc
changeset: 3617:8fa4e8c12dfc
user: Kanwei Li <kanwei@gmail.com>
date: Tue Apr 06 19:00:39 2010 -0400
description:
Add BedGraph datatype (wiggle-like data for intervals)
trackster:
- Fix various UI issues
- BedGraph -> array_tree converter
diffstat:
datatypes_conf.xml.sample | 3 +
lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py | 55 ++++++++++
lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml | 14 ++
lib/galaxy/datatypes/interval.py | 9 +-
lib/galaxy/visualization/tracks/data/array_tree.py | 2 +-
lib/galaxy/web/controllers/tracks.py | 6 +-
static/scripts/packed/trackster.js | 2 +-
static/scripts/trackster.js | 34 +++---
templates/tracks/browser.mako | 19 +--
9 files changed, 110 insertions(+), 34 deletions(-)
diffs (334 lines):
diff -r 2d415fb320b4 -r 8fa4e8c12dfc datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample Tue Apr 06 15:29:23 2010 -0400
+++ b/datatypes_conf.xml.sample Tue Apr 06 19:00:39 2010 -0400
@@ -16,6 +16,9 @@
<!-- <display file="ucsc/interval_as_bed.xml" /> -->
<display file="genetrack.xml" />
</datatype>
+ <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true">
+ <converter file="bedgraph_to_array_tree_converter.xml" target_datatype="array_tree"/>
+ </datatype>
<datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" />
<datatype extension="bed6" type="galaxy.datatypes.interval:Bed6">
<converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/>
diff -r 2d415fb320b4 -r 8fa4e8c12dfc lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py Tue Apr 06 19:00:39 2010 -0400
@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+
+from __future__ import division
+
+import sys
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.arrays.array_tree import *
+# from bx.arrays.wiggle import BedReader
+
+BLOCK_SIZE = 100
+
+class BedGraphReader:
+ def __init__( self, f ):
+ self.f = f
+
+ def __iter__( self ):
+ return self
+
+ def next( self ):
+ while True:
+ line = self.f.readline()
+ if not line:
+ raise StopIteration()
+ if line.isspace():
+ continue
+ if line[0] == "#":
+ continue
+ if line[0].isalpha():
+ if line.startswith( "track" ) or line.startswith( "browser" ):
+ continue
+
+ feature = line.strip().split()
+ chrom = feature[0]
+ chrom_start = int(feature[1])
+ chrom_end = int(feature[2])
+ score = int(feature[3])
+ return chrom, chrom_start, chrom_end, None, score
+def main():
+
+ input_fname = sys.argv[1]
+ out_fname = sys.argv[2]
+
+ reader = BedGraphReader( open( input_fname ) )
+
+ # Fill array from reader
+ d = array_tree_dict_from_reader( reader, {}, block_size = BLOCK_SIZE )
+
+ for array_tree in d.itervalues():
+ array_tree.root.build_summary()
+
+ FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) )
+
+if __name__ == "__main__":
+ main()
\ No newline at end of file
diff -r 2d415fb320b4 -r 8fa4e8c12dfc lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml Tue Apr 06 19:00:39 2010 -0400
@@ -0,0 +1,14 @@
+<tool id="CONVERTER_BedGraph_0" name="Index BedGraph for Track Viewer">
+ <!-- Used internally to generate track indexes -->
+ <command interpreter="python">bedgraph_to_array_tree_converter.py $input $output</command>
+ <inputs>
+ <page>
+ <param format="bedgraph" name="input" type="data" label="Choose BedGraph"/>
+ </page>
+ </inputs>
+ <outputs>
+ <data format="array_tree" name="output"/>
+ </outputs>
+ <help>
+ </help>
+</tool>
\ No newline at end of file
diff -r 2d415fb320b4 -r 8fa4e8c12dfc lib/galaxy/datatypes/interval.py
--- a/lib/galaxy/datatypes/interval.py Tue Apr 06 15:29:23 2010 -0400
+++ b/lib/galaxy/datatypes/interval.py Tue Apr 06 19:00:39 2010 -0400
@@ -345,7 +345,14 @@
def get_track_resolution( self, dataset, start, end):
return None
-
+class BedGraph( Interval ):
+ """Tab delimited chrom/start/end/datavalue dataset"""
+
+ file_ext = "bedgraph"
+
+ def get_track_type( self ):
+ return "LineTrack", {"data": "array_tree"}
+
class Bed( Interval ):
"""Tab delimited data in BED format"""
file_ext = "bed"
diff -r 2d415fb320b4 -r 8fa4e8c12dfc lib/galaxy/visualization/tracks/data/array_tree.py
--- a/lib/galaxy/visualization/tracks/data/array_tree.py Tue Apr 06 15:29:23 2010 -0400
+++ b/lib/galaxy/visualization/tracks/data/array_tree.py Tue Apr 06 19:00:39 2010 -0400
@@ -19,7 +19,7 @@
chrom_array_tree = d[chrom]
except KeyError:
f.close()
- return "no data"
+ return None
root_summary = chrom_array_tree.get_summary( 0, chrom_array_tree.levels )
diff -r 2d415fb320b4 -r 8fa4e8c12dfc lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py Tue Apr 06 15:29:23 2010 -0400
+++ b/lib/galaxy/web/controllers/tracks.py Tue Apr 06 19:00:39 2010 -0400
@@ -209,11 +209,13 @@
return messages.NO_CONVERTER
# Need to check states again for the converted version
+ if converted_dataset and converted_dataset.state == model.Dataset.states.ERROR:
+ return messages.ERROR
+
if not converted_dataset or converted_dataset.state != model.Dataset.states.OK:
return messages.PENDING
- if converted_dataset.state == model.Dataset.states.ERROR:
- return messages.ERROR
+
extra_info = None
if 'index' in data_sources:
diff -r 2d415fb320b4 -r 8fa4e8c12dfc static/scripts/packed/trackster.js
--- a/static/scripts/packed/trackster.js Tue Apr 06 15:29:23 2010 -0400
+++ b/static/scripts/packed/trackster.js Tue Apr 06 19:00:39 2010 -0400
@@ -1,1 +1,1 @@
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t){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Mat
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end(b)}});var LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("line-track");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(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.max_value!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.pre!
fs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.t
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ck_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for
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l_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(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:true};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.pre!
fs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTr
ack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;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(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,u=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,w=[];for(var r=0,s=g.length;r<s;r++){var e=g[r],l=e[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);w.push(this.inc_slots[a][l])}else{u.push(r)}}for(var r=0,s=u.length;r<s;r++){var e=g[u[r]];!
l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);if(!c){d-=b.measureText(feature_name).width}f=Math.ceil((feature_end-n)*m);var q=0;while(true){var o=true;if(this.s_e_by_tile[a][q]!==undefined){for(var p=0,v=this.s_e_by_tile[a][q].length;p<v;p++){var t=this.s_e_by_tile[a][q][p];if(f>t[0]&&d<t[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][q]===undefined){this.s_e_by_tile[a][q]=[]}this.s_e_by_tile[a][q].push([d,f]);this.inc_slots[a][l]=q;h=Math.max(h,q);break}q++}}return h},draw_tile:function(R,h,m,ae){var z=h*DENSITY*R,X=(h+1)*DENSITY*R,w=DENSITY*R;var ac,ad,p;var Y=z+"_"+X;var ac=this.data_cache.get(Y);if(!ac){this.data_queue[[z,X]]=true;this.get_data(z,X);return}if(ac.dataset_type=="array_tree"){p=30}else{var P=(ac.extra_info==="no_detail");var af=(P?this.vertical_nodetail_px:this.vertical_detail_px);p=this.incremental_slots(this.view.zoom_res,ac.data,P)*af+15;m.parent().css("height",Math.max(this.height_px,p)+"px");ad=this.!
inc_slots[this.view.zoom_res]}var a=Math.ceil(w*ae),F=$("<canvas class
='tile'></canvas>"),T=this.prefs.label_color,f=this.prefs.block_color,J=this.left_offset;F.css({position:"absolute",top:0,left:(z-this.view.low)*ae-J});F.get(0).width=a+J;F.get(0).height=p;var t=F.get(0).getContext("2d");t.fillStyle=this.prefs.block_color;t.font=this.default_font;t.textAlign="right";var C=55,W=255-C,g=W*2/3;if(ac.dataset_type=="summary_tree"){var L=ac.data;var v=ac.max;var l=ac.avg;if(ac.data.length>2){var b=Math.ceil((L[1][0]-L[0][0])*ae)}else{var b=50}for(var aa=0,s=L.length;aa<s;aa++){var N=Math.ceil((L[aa][0]-z)*ae);var M=L[aa][1];if(!M){continue}var E=Math.floor(W-(M/v)*W);t.fillStyle="rgb("+E+","+E+","+E+")";t.fillRect(N+J,0,b,20);if(this.prefs.show_counts){if(E>g){t.fillStyle="black"}else{t.fillStyle="#ddd"}t.textAlign="center";t.fillText(L[aa][1],N+J+(b/2),12)}}m.append(F);return F}var ac=ac.data;var Z=0;for(var aa=0,s=ac.length;aa<s;aa++){var G=ac[aa],D=G[0],ab=G[1],O=G[2],A=G[3];if(ab<=X&&O>=z){var Q=Math.floor(Math.max(0,(ab-z)*ae)),u=Math.ceil(Ma!
th.min(a,(O-z)*ae)),K=ad[D]*af;if(P){t.fillRect(Q+J,K+5,u-Q,1)}else{var r=G[4],I=G[5],S=G[6],e=G[7];var q,U,B=null,ag=null;if(I&&S){B=Math.floor(Math.max(0,(I-z)*ae));ag=Math.ceil(Math.min(a,(S-z)*ae))}if(ab>z){t.fillStyle=T;t.fillText(A,Q-1+J,K+8);t.fillStyle=f}if(e){if(r){if(r=="+"){t.fillStyle=RIGHT_STRAND}else{if(r=="-"){t.fillStyle=LEFT_STRAND}}t.fillRect(Q+J,K,u-Q,10);t.fillStyle=f}for(var Y=0,d=e.length;Y<d;Y++){var n=e[Y],c=Math.floor(Math.max(0,(n[0]-z)*ae)),H=Math.ceil(Math.min(a,(n[1]-z)*ae));if(c>H){continue}q=5;U=3;t.fillRect(c+J,K+U,H-c,q);if(B!==undefined&&!(c>ag||H<B)){q=9;U=1;var V=Math.max(c,B),o=Math.min(H,ag);t.fillRect(V+J,K+U,o-V,q)}}}else{q=9;U=1;t.fillRect(Q+J,K+U,u-Q,q);if(G.strand){if(G.strand=="+"){t.fillStyle=RIGHT_STRAND_INV}else{if(G.strand=="-"){t.fillStyle=LEFT_STRAND_INV}}t.fillRect(Q+J,K,u-Q,10);t.fillStyle=prefs.block_color}}}Z++}}m.append(F);return F},gen_options:function(h){var a=$("<div></div>").addClass("form-row");var d="track_"+h+"_b!
lock_color",j=$("<label></label>").attr("for",d).text("Block color:"),
k=$("<input></input>").attr("id",d).attr("name",d).val(this.prefs.block_color),i="track_"+h+"_label_color",f=$("<label></label>").attr("for",i).text("Text color:"),g=$("<input></input>").attr("id",i).attr("name",i).val(this.prefs.label_color),e="track_"+h+"_show_count",c=$("<label></label>").attr("for",e).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",e).attr("name",e).attr("checked",this.prefs.show_counts);return a.append(j).append(k).append(f).append(g).append(b).append(c)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack"};$.extend(ReadT!
rack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});
\ No newline at end of file
+var DEBUG=false;var DENSITY=1000,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=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../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="../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="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.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 Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_!
high=0;this.center=(this.max_high-this.max_low)/2;this.zoom_factor=3;t
his.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{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){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[a]},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");var d=[];var c=$("#viewport > div").sort(function(g,f){return b.indexOf($(g).attr("id"))>b.indexOf($(f).attr("id"))});$("#viewport > div").remove();$("#viewport").html(c);for(var e in view.tracks){var a=view.tracks[e];if(a.update_options){a.update_options(e)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.sp!
an/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);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))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/b.width()*(this.!
high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:fun
ction(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.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=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");a.content_div.text(DATA_LOADING);a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.dat!
a&&d.data.length===0||d.data===null){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(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(k);var l=this.content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset)!
{b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.
max(this.max_height,c.height())}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,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.appen!
d(b)}});var LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.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){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_fr
equency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px"});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;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,q,c,e){if(this.vertical_range===undefined){return}var r=q*DENSITY*o,a=DENSITY*o,b=$("<canvas class='tile'!
></canvas>"),u=o+"_"+q;if(this.data_cache.get(u)===undefined){this.get_data(o,q);return}var t=this.data_cache.get(u);if(t===null){return}b.css({position:"absolute",top:0,left:(r-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,s=this.total_frequency,d=this.height_px;n.beginPath();if(t.length>1){var f=Math.ceil((t[1][0]-t[0][0])*e)}else{var f=10}for(var p=0;p<t.length;p++){var j=t[p][0]-r;var h=t[p][1];if(this.prefs.mode=="Intensity"){if(h===null){continue}j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(j,0,f,this.height_px)}else{if(h===null){k=false;continue}else{j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/m*d);if(k){n.lineTo(j,h)}else{n.moveTo(j,h);k=true}}}}n.stroke();c.append(b);return b},gen_options:function(n){var a=$("<div></div>").addClass("form-row!
");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mo
de",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#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=parseF!
loat(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(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;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.left_offset=200;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(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color!
}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};
$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,u=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,w=[];for(var r=0,s=g.length;r<s;r++){var e=g[r],l=e[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);w.push(this.inc_slots[a][l])}else{u.push(r)}}for(var!
r=0,s=u.length;r<s;r++){var e=g[u[r]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);if(!c){d-=b.measureText(feature_name).width}f=Math.ceil((feature_end-n)*m);var q=0;while(true){var o=true;if(this.s_e_by_tile[a][q]!==undefined){for(var p=0,v=this.s_e_by_tile[a][q].length;p<v;p++){var t=this.s_e_by_tile[a][q][p];if(f>t[0]&&d<t[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][q]===undefined){this.s_e_by_tile[a][q]=[]}this.s_e_by_tile[a][q].push([d,f]);this.inc_slots[a][l]=q;h=Math.max(h,q);break}q++}}return h},draw_tile:function(R,h,m,ae){var z=h*DENSITY*R,X=(h+1)*DENSITY*R,w=DENSITY*R;var ac,ad,p;var Y=z+"_"+X;var ac=this.data_cache.get(Y);if(ac===undefined){this.data_queue[[z,X]]=true;this.get_data(z,X);return}if(ac.dataset_type=="array_tree"){p=30}else{var P=(ac.extra_info==="no_detail");var af=(P?this.vertical_nodetail_px:this.vertical_detail_px);p=this.incremental_slots(this.view.zoom_res,ac.data,P)*af+15;m.parent().css(!
"height",Math.max(this.height_px,p)+"px");ad=this.inc_slots[this.view.
zoom_res]}var a=Math.ceil(w*ae),F=$("<canvas class='tile'></canvas>"),T=this.prefs.label_color,f=this.prefs.block_color,J=this.left_offset;F.css({position:"absolute",top:0,left:(z-this.view.low)*ae-J});F.get(0).width=a+J;F.get(0).height=p;var t=F.get(0).getContext("2d");t.fillStyle=this.prefs.block_color;t.font=this.default_font;t.textAlign="right";var C=55,W=255-C,g=W*2/3;if(ac.dataset_type=="summary_tree"){var L=ac.data;var v=ac.max;var l=ac.avg;if(ac.data.length>2){var b=Math.ceil((L[1][0]-L[0][0])*ae)}else{var b=50}for(var aa=0,s=L.length;aa<s;aa++){var N=Math.ceil((L[aa][0]-z)*ae);var M=L[aa][1];if(!M){continue}var E=Math.floor(W-(M/v)*W);t.fillStyle="rgb("+E+","+E+","+E+")";t.fillRect(N+J,0,b,20);if(this.prefs.show_counts){if(E>g){t.fillStyle="black"}else{t.fillStyle="#ddd"}t.textAlign="center";t.fillText(L[aa][1],N+J+(b/2),12)}}m.append(F);return F}var ac=ac.data;var Z=0;for(var aa=0,s=ac.length;aa<s;aa++){var G=ac[aa],D=G[0],ab=G[1],O=G[2],A=G[3];if(ab<=X&&O>=z){var !
Q=Math.floor(Math.max(0,(ab-z)*ae)),u=Math.ceil(Math.min(a,(O-z)*ae)),K=ad[D]*af;if(P){t.fillRect(Q+J,K+5,u-Q,1)}else{var r=G[4],I=G[5],S=G[6],e=G[7];var q,U,B=null,ag=null;if(I&&S){B=Math.floor(Math.max(0,(I-z)*ae));ag=Math.ceil(Math.min(a,(S-z)*ae))}if(ab>z){t.fillStyle=T;t.fillText(A,Q-1+J,K+8);t.fillStyle=f}if(e){if(r){if(r=="+"){t.fillStyle=RIGHT_STRAND}else{if(r=="-"){t.fillStyle=LEFT_STRAND}}t.fillRect(Q+J,K,u-Q,10);t.fillStyle=f}for(var Y=0,d=e.length;Y<d;Y++){var n=e[Y],c=Math.floor(Math.max(0,(n[0]-z)*ae)),H=Math.ceil(Math.min(a,(n[1]-z)*ae));if(c>H){continue}q=5;U=3;t.fillRect(c+J,K+U,H-c,q);if(B!==undefined&&!(c>ag||H<B)){q=9;U=1;var V=Math.max(c,B),o=Math.min(H,ag);t.fillRect(V+J,K+U,o-V,q)}}}else{q=9;U=1;t.fillRect(Q+J,K+U,u-Q,q);if(G.strand){if(G.strand=="+"){t.fillStyle=RIGHT_STRAND_INV}else{if(G.strand=="-"){t.fillStyle=LEFT_STRAND_INV}}t.fillRect(Q+J,K,u-Q,10);t.fillStyle=prefs.block_color}}}Z++}}m.append(F);return F},gen_options:function(i){var a=$("<div>!
</div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<la
bel></label>").attr("for",e).text("Block color:"),l=$("<input></input>").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></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></div>").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c!
,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});
\ No newline at end of file
diff -r 2d415fb320b4 -r 8fa4e8c12dfc static/scripts/trackster.js
--- a/static/scripts/trackster.js Tue Apr 06 15:29:23 2010 -0400
+++ b/static/scripts/trackster.js Tue Apr 06 19:00:39 2010 -0400
@@ -238,7 +238,7 @@
} else if (result === "no converter") {
track.container_div.addClass("error");
track.content_div.text(DATA_NOCONVERTER);
- } else if ( (result.data && result.data.length === 0) || result === "no data") {
+ } else if (result.data && result.data.length === 0 || result.data === null) {
track.container_div.addClass("nodata");
track.content_div.text(DATA_NONE);
} else if (result === "pending") {
@@ -354,10 +354,10 @@
this.dataset_id = dataset_id;
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' };
+ this.prefs = { 'min_value': undefined, 'max_value': undefined, 'mode': 'Line' };
if (prefs.min_value !== undefined) { this.prefs.min_value = prefs.min_value; }
if (prefs.max_value !== undefined) { this.prefs.max_value = prefs.max_value; }
- if (prefs.max_value !== undefined) { this.prefs.mode = prefs.mode; }
+ if (prefs.mode !== undefined) { this.prefs.mode = prefs.mode; }
};
$.extend( LineTrack.prototype, TiledTrack.prototype, {
init: function() {
@@ -431,12 +431,13 @@
canvas = $("<canvas class='tile'></canvas>"),
key = resolution + "_" + tile_index;
- if (!this.data_cache.get(key)) {
+ if (this.data_cache.get(key) === undefined) {
this.get_data( resolution, tile_index );
return;
}
var data = this.data_cache.get(key);
+ if (data === null) { return; }
canvas.css( {
position: "absolute",
@@ -467,7 +468,7 @@
var x = data[i][0] - tile_low;
var y = data[i][1];
- if ( this.prefs.mode == "intensity" ) {
+ if ( this.prefs.mode == "Intensity" ) {
// DRAW INTENSITY
if (y === null) {
continue;
@@ -480,7 +481,7 @@
}
y = 255 - Math.floor( (y - min_value) / vertical_range * 255 );
ctx.fillStyle = "rgb(" +y+ "," +y+ "," +y+ ")";
- ctx.fillRect(x, 0, delta_x_px, 30);
+ ctx.fillRect(x, 0, delta_x_px, this.height_px);
}
else {
// Missing data causes us to stop drawing
@@ -523,10 +524,11 @@
max_val = (this.prefs.max_value === undefined ? "" : this.prefs.max_value),
max_input = $('<input></input>').attr("id", maxval).val(max_val),
mode_label = $('<label></label>').attr("for", mode).text("Display mode:"),
- mode_val = (this.prefs.mode === undefined ? "line" : this.prefs.mode),
- mode_input = $('<select id="' +mode+ '"><option value="line" id="mode_line">Line</option><option value="intensity" id="mode_intensity">Intensity</option></select>');
- $("#" + mode + " #mode_"+mode_val).attr('selected', 'selected');
-
+ mode_val = (this.prefs.mode === undefined ? "Line" : this.prefs.mode),
+ mode_input = $('<select id="' +mode+ '"><option value="Line" id="mode_Line">Line</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');
+
+ mode_input.children("#mode_"+mode_val).attr('selected', 'selected');
+
return container.append(min_label).append(min_input).append(max_label).append(max_input).append(mode_label).append(mode_input);
}, update_options: function(track_id) {
var min_value = $('#track_' + track_id + '_minval').val(),
@@ -567,7 +569,7 @@
this.tile_cache = new Cache(CACHED_TILES_FEATURE);
this.data_cache = new Cache(20);
- this.prefs = { 'block_color': 'black', 'label_color': 'black', 'show_counts': true };
+ this.prefs = { 'block_color': 'black', 'label_color': 'black', 'show_counts': false };
if (prefs.block_color !== undefined) { this.prefs.block_color = prefs.block_color; }
if (prefs.label_color !== undefined) { this.prefs.label_color = prefs.label_color; }
if (prefs.show_counts !== undefined) { this.prefs.show_counts = prefs.show_counts; }
@@ -581,9 +583,6 @@
high: track.view.max_high, dataset_id: track.dataset_id,
chrom: track.view.chrom, resolution: this.view.resolution }, function (result) {
track.data_cache.set(key, result);
- // track.values = result;
- // track.calc_slots();
- // track.slots = track.zo_slots;
track.draw();
});
},
@@ -691,7 +690,7 @@
var k = tile_low + '_' + tile_high;
var data = this.data_cache.get(k);
- if (!data) {
+ if (data === undefined) {
this.data_queue[ [tile_low, tile_high] ] = true;
this.get_data(tile_low, tile_high);
return;
@@ -866,9 +865,10 @@
label_color_input = $('<input></input>').attr("id", label_color).attr("name", label_color).val(this.prefs.label_color),
show_count = 'track_' + track_id + '_show_count',
show_count_label = $('<label></label>').attr("for", show_count).text("Show summary counts"),
- show_count_input = $('<input type="checkbox" style="float:left;"></input>').attr("id", show_count).attr("name", show_count).attr("checked", this.prefs.show_counts);
+ show_count_input = $('<input type="checkbox" style="float:left;"></input>').attr("id", show_count).attr("name", show_count).attr("checked", this.prefs.show_counts),
+ show_count_div = $('<div></div>').append(show_count_input).append(show_count_label);
- return container.append(block_color_label).append(block_color_input).append(label_color_label).append(label_color_input).append(show_count_input).append(show_count_label);
+ return container.append(block_color_label).append(block_color_input).append(label_color_label).append(label_color_input).append(show_count_div);
}, update_options: function(track_id) {
var block_color = $('#track_' + track_id + '_block_color').val(),
label_color = $('#track_' + track_id + '_label_color').val(),
diff -r 2d415fb320b4 -r 8fa4e8c12dfc templates/tracks/browser.mako
--- a/templates/tracks/browser.mako Tue Apr 06 15:29:23 2010 -0400
+++ b/templates/tracks/browser.mako Tue Apr 06 19:00:39 2010 -0400
@@ -45,7 +45,7 @@
</div>
</div>
<div id="nav-controls">
- <form name="chr" id="chr" method="get">
+ <form action="#">
<select id="chrom" name="chrom" style="width: 15em;">
<option value="">Loading</option>
</select>
@@ -68,14 +68,14 @@
<div class="unified-panel-header" unselectable="on">
<div class="unified-panel-header-inner">Configuration</div>
</div>
- <form action="${h.url_for( action='update_config' )}">
+ <form action="#" onsubmit="view.update_options();return false;">
## <input name="title" id="title" value="${config.title}" />
<div id="show-hide-move">
<ul id="sortable-ul"></ul>
</div>
- <input type="button" id="refresh-button" value="Refresh" />
+ <input type="submit" id="refresh-button" value="Refresh" />
<input type="button" id="save-button" value="Save" />
- <input id="add-track" type="button" value="Add Track" />
+ <input id="add-track" type="button" value="Add Tracks" />
</form>
</%def>
@@ -189,10 +189,6 @@
view.redraw();
});
- $("#refresh-button").bind( "click", function(e) {
- view.update_options();
- });
-
// Use a popup grid to add more tracks
$("#add-track").bind( "click", function(e) {
$.ajax({
@@ -311,16 +307,15 @@
del_icon = $('<a href="#" class="icon-button delete" />'),
edit_icon = $('<a href="#" class="icon-button edit" />'),
body = $('<div class="historyItemBody"></div>'),
- li = $('<li class="sortable"></li>').attr("id", "track_" + track_id),
+ li = $('<li class="sortable"></li>').attr("id", "track_" + track_id + "_li"),
div = $('<div class="historyItemContainer historyItem"></div>'),
editable = $('<div style="display:none"></div>').attr("id", "track_" + track_id + "_editable");
edit_icon.bind("click", function() {
$("#track_" + track_id + "_editable").toggle();
});
-
del_icon.bind("click", function() {
- li.fadeOut('slow', function() { $(this).remove(); });
+ $("#track_" + track_id + "_li").fadeOut('slow', function() { $("#track_" + track_id).remove(); });
view.remove_track(track);
view.update_options();
});
@@ -329,7 +324,7 @@
if (track.gen_options) {
editable.append(track.gen_options(track_id)).appendTo(body);
}
- div.append(title).append(body).appendTo(li)
+ div.append(title).append(body).appendTo(li);
$("ul#sortable-ul").append(li);
}
};
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-
Greg Von Kuster