[galaxy-dev] [hg] galaxy 3216: trackster: support BAM visualization with samt...

12 Jan 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/7d3667e8e415
changeset: 3216:7d3667e8e415
user:      Kanwei Li kanwei@gmail.com
date:      Thu Jan 07 15:45:15 2010 -0500
description:
trackster: support BAM visualization with samtools, automatically enable tracks for any datatype with "get_track_type" defined
diffstat:
datatypes_conf.xml.sample              |   4 +-
 eggs.ini                               |   2 +
 lib/galaxy/datatypes/binary.py         |   4 +-
 lib/galaxy/datatypes/coverage.py       |   2 -
 lib/galaxy/datatypes/interval.py       |   7 +-
 lib/galaxy/datatypes/registry.py       |   8 ++-
 lib/galaxy/web/controllers/tracks.py   |  38 ++++++--------
 static/scripts/packed/galaxy.panels.js |   2 +-
 static/scripts/packed/trackster.js     |   2 +-
 static/scripts/trackster.js            |  88 +++++++++++++++++++++++++++++----
 templates/tracks/browser.mako          |   2 +-
 templates/tracks/new_browser.mako      |   4 +-
 12 files changed, 117 insertions(+), 46 deletions(-)
diffs (439 lines):
diff -r 427d93bf3d39 -r 7d3667e8e415 datatypes_conf.xml.sample

--- a/datatypes_conf.xml.sample	Thu Jan 07 14:52:51 2010 -0500
+++ b/datatypes_conf.xml.sample	Thu Jan 07 15:45:15 2010 -0500
@@ -3,7 +3,9 @@
     <registration converters_path="lib/galaxy/datatypes/converters">
         <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/>
         <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/>
-        <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"/>
+        <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true">
+            <converter file="bam_to_bai.xml" target_datatype="bai"/>
+        </datatype>
         <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">
             <converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
             <converter file="interval_to_coverage.xml" target_datatype="coverage"/>
diff -r 427d93bf3d39 -r 7d3667e8e415 eggs.ini
--- a/eggs.ini	Thu Jan 07 14:52:51 2010 -0500
+++ b/eggs.ini	Thu Jan 07 15:45:15 2010 -0500
@@ -19,6 +19,7 @@
 pbs_python = 2.9.4
 psycopg2 = 2.0.6
 pycrypto = 2.0.1
+pysam = 0.1.1
 pysqlite = 2.5.6
 python_lzo = 1.08
 threadframe = 0.2
@@ -74,6 +75,7 @@
 pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz
 psycopg2 = http://initd.org/pub/software/psycopg/PSYCOPG-2-0/psycopg2-2.0.6.tar.gz ftp://ftp-archives.postgresql.org/pub/source/v8.2.6/postgresql-8.2.6.tar.bz2
 pycrypto = http://www.amk.ca/files/python/crypto/pycrypto-2.0.1.tar.gz
+pysam = http://bitbucket.org/kanwei/kanwei-pysam/get/e3c601a062fd.gz
 pysqlite = http://pypi.python.org/packages/source/p/pysqlite/pysqlite-2.5.6.tar.gz
 python_lzo = http://www.oberhumer.com/opensource/lzo/download/LZO-v1/python-lzo-1.08.tar.... http://www.oberhumer.com/opensource/lzo/download/LZO-v1/lzo-1.08.tar.gz
 threadframe = http://www.majid.info/python/threadframe/threadframe-0.2.tar.gz
diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/datatypes/binary.py
--- a/lib/galaxy/datatypes/binary.py	Thu Jan 07 14:52:51 2010 -0500
+++ b/lib/galaxy/datatypes/binary.py	Thu Jan 07 15:45:15 2010 -0500
@@ -132,7 +132,9 @@
             return dataset.peek
         except:
             return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) )
-
+    def get_track_type( self ):
+        return "ReadTrack", "bai"
+    
 class Binseq( Binary ):
     """Class describing a zip archive of binary sequence files"""
     file_ext = "binseq.zip"
diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/datatypes/coverage.py
--- a/lib/galaxy/datatypes/coverage.py	Thu Jan 07 14:52:51 2010 -0500
+++ b/lib/galaxy/datatypes/coverage.py	Thu Jan 07 15:45:15 2010 -0500
@@ -63,6 +63,4 @@
         resolution = max( resolution, 1 )
         return resolution
-    def get_track_type( self ):
-        return "LineTrack"
diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/datatypes/interval.py
--- a/lib/galaxy/datatypes/interval.py	Thu Jan 07 14:52:51 2010 -0500
+++ b/lib/galaxy/datatypes/interval.py	Thu Jan 07 15:45:15 2010 -0500
@@ -325,8 +325,6 @@
     def get_track_resolution( self, dataset, start, end):
         return None
-    def get_track_type( self ):
-        return "FeatureTrack"
class Bed( Interval ):
     """Tab delimited data in BED format"""
@@ -484,6 +482,9 @@
                 else: return False
             return True
         except: return False
+    
+    def get_track_type( self ):
+        return "FeatureTrack", "interval_index"
class _RemoteCallMixin:
     def _get_remote_call_url( self, redirect_url, site_name, dataset, type, app, base_url ):
@@ -904,7 +905,7 @@
         resolution = max( resolution, 1 )
         return resolution
     def get_track_type( self ):
-        return "LineTrack"
+        return "LineTrack", "array_tree"
class CustomTrack ( Tabular ):
     """UCSC CustomTrack"""
diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py	Thu Jan 07 14:52:51 2010 -0500
+++ b/lib/galaxy/datatypes/registry.py	Thu Jan 07 15:45:15 2010 -0500
@@ -18,6 +18,7 @@
         self.datatype_converters = odict()
         self.datatype_indexers = odict()
         self.converters = []
+        self.available_tracks = []
         self.set_external_metadata_tool = None
         self.indexers = []
         self.sniff_order = []
@@ -54,6 +55,8 @@
                             # Use default mime type as per datatype spec
                             mimetype = self.datatypes_by_extension[extension].get_mime()
                         self.mimetypes_by_extension[extension] = mimetype
+                        if hasattr( getattr( module, datatype_class ), "get_track_type" ):
+                            self.available_tracks.append( extension )
                         if display_in_upload:
                             self.upload_file_formats.append( extension )
                         for converter in elem.findall( 'converter' ):
@@ -206,7 +209,10 @@
                 if not included:
                     self.sniff_order.append(datatype)
         append_to_sniff_order()
-
+    
+    def get_available_tracks(self):
+        return self.available_tracks
+        
     def get_mimetype_by_extension(self, ext ):
         """Returns a mimetype based on an extension"""
         try:
diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py	Thu Jan 07 14:52:51 2010 -0500
+++ b/lib/galaxy/web/controllers/tracks.py	Thu Jan 07 15:45:15 2010 -0500
@@ -23,35 +23,26 @@
from galaxy.visualization.tracks.data.array_tree import ArrayTreeDataProvider
 from galaxy.visualization.tracks.data.interval_index import IntervalIndexDataProvider
+from galaxy.visualization.tracks.data.bam import BamDataProvider
# Message strings returned to browser
 messages = Bunch(
     PENDING = "pending",
     NO_DATA = "no data",
     NO_CHROMOSOME = "no chromosome",
+    NO_CONVERTER = "no converter",
     DATA = "data",
     ERROR = "error"
 )
-# Dataset type required for each track type. This needs to be more flexible,
-# there might be multiple types of indexes that suffice for a given track type.
-track_type_to_dataset_type = {
-    "line": "array_tree",
-    "feature": "interval_index"
-}
-
 # Mapping from dataset type to a class that can fetch data from a file of that
 # type. This also needs to be more flexible.
 dataset_type_to_data_provider = {
     "array_tree": ArrayTreeDataProvider,
-    "interval_index": IntervalIndexDataProvider
+    "interval_index": IntervalIndexDataProvider,
+    "bai": BamDataProvider
 }
-# FIXME: hardcoding this for now, but it should be derived from the available
-#        converters
-browsable_types = ( "wig", "bed" )
-
-
 class TracksController( BaseController ):
     """
     Controller for track browser interface. Handles building a new browser from
@@ -107,11 +98,12 @@
             # Find all datasets in the current history that are of that dbkey
             # and can be displayed
             datasets = {}
+            available_tracks = trans.app.datatypes_registry.get_available_tracks()
             for dataset in session.query( model.HistoryDatasetAssociation ).filter_by( deleted=False, history_id=trans.history.id ):
-                if dataset.metadata.dbkey == dbkey and dataset.extension in browsable_types:
+                if dataset.metadata.dbkey == dbkey and dataset.extension in available_tracks:
                     datasets[dataset.id] = (dataset.extension, dataset.name)
             # Render the template
-            return trans.fill_template( "tracks/new_browser.mako", converters=browsable_types, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets )
+            return trans.fill_template( "tracks/new_browser.mako", available_tracks=available_tracks, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets )
@web.expose
     def browser(self, trans, id, chrom=""):
@@ -127,8 +119,10 @@
         for t in vis.latest_revision.config['tracks']:
             dataset_id = t['dataset_id']
             dataset = hda_query.get( dataset_id )
+            track_type, indexer = dataset.datatype.get_track_type()
             tracks.append( {
-                "type": dataset.datatype.get_track_type(),
+                "type": track_type,
+                "indexer": indexer,
                 "name": dataset.name,
                 "dataset_id": dataset.id
             } )
@@ -184,14 +178,14 @@
         return manifest
@web.json
-    def data( self, trans, dataset_id, track_type, chrom, low, high, **kwargs ):
+    def data( self, trans, dataset_id, indexer, chrom, low, high, **kwargs ):
         """
         Called by the browser to request a block of data
         """
         # Load the requested dataset
         dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id )
         # No dataset for that id
-        if not dataset:
+        if not dataset or not chrom:
             return messages.NO_DATA
         # Dataset is in error state, can't display
         if dataset.state == trans.app.model.Job.states.ERROR:
@@ -200,12 +194,11 @@
         if dataset.state != trans.app.model.Job.states.OK:
             return messages.PENDING
         # Determine what to return based on the type of track being drawn.
-        converted_dataset_type = track_type_to_dataset_type[track_type]
+        converted_dataset_type = indexer
         converted_dataset = self.__dataset_as_type( trans, dataset, converted_dataset_type )
-        # If at this point we still don't have an `array_tree_dataset`, there
-        # is no way we can display this data as an array tree
         if not converted_dataset:
-            return messages.ERROR
+            # No converter
+            return messages.NO_CONVERTER
         # Need to check states again for the converted version
         if converted_dataset.state == model.Dataset.states.ERROR:
             return messages.ERROR
@@ -228,6 +221,7 @@
         converted dataset (possibly new) is returned, if it cannot be converted,
         None is returned.
         """
+        log.debug("Inside dataset as type")
         # Already of correct type
         if dataset.extension == type:
             return dataset
diff -r 427d93bf3d39 -r 7d3667e8e415 static/scripts/packed/galaxy.panels.js
--- a/static/scripts/packed/galaxy.panels.js	Thu Jan 07 14:52:51 2010 -0500
+++ b/static/scripts/packed/galaxy.panels.js	Thu Jan 07 15:45:15 2010 -0500
@@ -1,1 +1,1 @@
-function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(i){$("#DD-helper").show()}).bind("dragend
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 ;var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=true}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(k){$("#DD-helper").show()}).bind("dragend",function(k){$("#DD-helper").hide()}).bind("drag",function(k){x=k.offsetX;w=$(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(k){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").fadeOut(function(){$("#overlay").hide();$(".dialog-box").find(".body").children().remove()})}function show_modal(f,c,e,d){if(f){$(".dialog-box").find(".title").html(f);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dia
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 .children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}};
\ No newline at end of file
+function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(i){$("#DD-helper").show()}).bind("dragend
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 ;var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=true}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(k){$("#DD-helper").show()}).bind("dragend",function(k){$("#DD-helper").hide()}).bind("drag",function(k){x=k.offsetX;w=$(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(k){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").fadeOut(function(){$("#overlay").hide();$(".dialog-box").find(".body").children().remove()})}function show_modal(f,c,e,d){if(f){$(".dialog-box").find(".title").html(f);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dia
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 rolling='"+a+"' frameborder='0'></iframe></div>"));$("#close_button").bind("click",function(){hide_modal()})}$(function(){$(".tab").each(function(){var a=$(this).children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}};
\ No newline at end of file
diff -r 427d93bf3d39 -r 7d3667e8e415 static/scripts/packed/trackster.js
--- a/static/scripts/packed/trackster.js	Thu Jan 07 14:52:51 2010 -0500
+++ b/static/scripts/packed/trackster.js	Thu Jan 07 15:45:15 2010 -0500
@@ -1,1 +1,1 @@
-var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=100,DATA_ERROR="There was an error in indexing this dataset.",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,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.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}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=thi
 s.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.max(1,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS)));$("#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));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;thi
 s.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var l=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(l);var m=this.content_div.width()/f;var i=20;var h;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_off
 set){b-=this.left_offset}c.css({left:b});l.append(c);i=Math.max(i,c.height())}else{h=this.draw_tile(d,a,l,m);if(h){this.tile_cache.set(k,h);i=Math.max(i,h.height())}}this.content_div.css("height",i);a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass
 ("line-track");this.dataset_id=b;this.data_queue={};this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="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.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",t
 op:a.height_px+32+"px"});d.prependTo(a.container_div);a.draw()}}}})},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;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache.get(l)){this.get_data(d,a);return}var g=this.cache.get(l);c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke(
 );m.append(c);return c}});var FeatureTrack=function(c,b,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143";this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.data_cache=new Cache(20)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==
 "pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{track_type:b.track_type,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),a=this.view.max_high,e=this.view.max_low;for(var f=0,g=this.values.length;f<g;f++){var h,k,l=this.values[f];h=Math.floor((l.start-e)*b);k=Math.ceil((l.end-e)*b);var d=0;while(true){if(c[d]===undefined||c[d]<h){c[d]=k;this.zo_slots[l.uid]=d;break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:functi
 on(a,b){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=DENSITY/Math.pow(FEATURE_LEVELS,a+1)}var k=this.inc_slots[a];var d=[],l=[],c=0,m=$("<canvas></canvas>").get(0).getContext("2d"),f=this.view.max_low;for(var g=0,h=b.length;g<h;g++){var n=b[g];if(k[n.uid]){c=Math.max(c,k[n.uid]);d[k[n.uid]]=Math.ceil((n.end-f)*k.w_scale)}else{l.push(n)}}for(var g=0,h=l.length;g<h;g++){var n=l[g];f_start=Math.floor((n.start-f)*k.w_scale);f_start-=m.measureText(n.name).width;f_end=Math.ceil((n.end-f)*k.w_scale);var e=0;while(true){if(d[e]===undefined||d[e]<f_start){d[e]=f_end;k[n.uid]=e;c=Math.max(c,e);break}e++}}return c},draw_tile:function(A,F,n,r){if(!this.values){return}var G=F*DENSITY*A,c=(F+1)*DENSITY*A,v=DENSITY*A;var K,u,h;if(r>this.show_labels_scale){if(!this.showing_labels){this.showing_labels=true}for(var B in this.data_cache.obj_cache){var p=B.split("_"),e=p[0],d=p[1];if(e<=G&&d>=c){K=this.data_cache.get(B);break}}if(!K){this.data_queue[[G,c]]=true;this.get
 _data(G,c);return}h=this.incremental_slots(this.view.zoom_res,K)*this.vertical_gap+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_labels){this.showing_labels=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("<canvas class='tile'></canvas>");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D<E;D++){var m=K[D];if(m.start<=c&&m.end>=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*this.vertical_gap;var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_labels){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left_offset,f+8)}va
 r I=m.blocks;if(I){if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;B<J;B++){var q=I[B],o=Math.floor(Math.max(0,(q[0]-G)*r)),H=Math.ceil(Math.min(y,(q[1]-G)*r));if(o>H){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b&&(o<s||H>b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}});
\ No newline at end of file
+var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=100,DATA_ERROR="There was an error in indexing this dataset.",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,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.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}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=3;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=thi
 s.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.max(1,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS)));$("#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));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;thi
 s.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var l=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(l);var m=this.content_div.width()/f;var i=20;var h;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_off
 set){b-=this.left_offset}c.css({left:b});l.append(c);i=Math.max(i,c.height())}else{h=this.draw_tile(d,a,l,m);if(h){this.tile_cache.set(k,h);i=Math.max(i,h.height())}}this.content_div.css("height",i);a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.container_div.addClass("line
 -track");this.dataset_id=b;this.data_queue={};this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="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.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_
 px+32+"px"});d.prependTo(a.container_div);a.draw()}}}})},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;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache.get(l)){this.get_data(d,a);return}var g=this.cache.get(l);c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);retu
 rn c}});var FeatureTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143";this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.data_cache=new Cache(20)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addCla
 ss("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),a=this.view.max_high,e=this.view.max_low;for(var f=0,g=this.values.length;f<g;f++){var h,k,l=this.values[f];h=Math.floor((l.start-e)*b);k=Math.ceil((l.end-e)*b);var d=0;while(true){if(c[d]===undefined||c[d]<h){c[d]=k;this.zo_slots[l.uid]=d;break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,b){if(!this.inc_slots[a]){this.inc
 _slots[a]={};this.inc_slots[a].w_scale=DENSITY/Math.pow(FEATURE_LEVELS,a+1)}var k=this.inc_slots[a];var d=[],l=[],c=0,m=$("<canvas></canvas>").get(0).getContext("2d"),f=this.view.max_low;for(var g=0,h=b.length;g<h;g++){var n=b[g];if(k[n.uid]){c=Math.max(c,k[n.uid]);d[k[n.uid]]=Math.ceil((n.end-f)*k.w_scale)}else{l.push(n)}}for(var g=0,h=l.length;g<h;g++){var n=l[g];f_start=Math.floor((n.start-f)*k.w_scale);f_start-=m.measureText(n.name).width;f_end=Math.ceil((n.end-f)*k.w_scale);var e=0;while(true){if(d[e]===undefined||d[e]<f_start){d[e]=f_end;k[n.uid]=e;c=Math.max(c,e);break}e++}}return c},draw_tile:function(A,F,n,r){if(!this.values){return}var G=F*DENSITY*A,c=(F+1)*DENSITY*A,v=DENSITY*A;var K,u,h;if(r>this.show_labels_scale){if(!this.showing_labels){this.showing_labels=true}for(var B in this.data_cache.obj_cache){var p=B.split("_"),e=p[0],d=p[1];if(e<=G&&d>=c){K=this.data_cache.get(B);break}}if(!K){this.data_queue[[G,c]]=true;this.get_data(G,c);return}h=this.incremental_sl
 ots(this.view.zoom_res,K)*this.vertical_gap+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_labels){this.showing_labels=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("<canvas class='tile'></canvas>");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D<E;D++){var m=K[D];if(m.start<=c&&m.end>=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*this.vertical_gap;var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_labels){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left_offset,f+8)}var I=m.blocks;if(I){if(m.strand){if(m.st
 rand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;B<J;B++){var q=I[B],o=Math.floor(Math.max(0,(q[0]-G)*r)),H=Math.ceil(Math.min(y,(q[1]-G)*r));if(o>H){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b&&(o<s||H>b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}});var ReadTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,b,d,a);this.default_font="9px Monaco, Lucida Console, monospace"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureT
 rack.prototype,{draw_tile:function(w,A,n,o){if(!this.values){return}var B=A*DENSITY*w,f=(A+1)*DENSITY*w,r=DENSITY*w;var E,q,k;k=this.height_px;q=this.zo_slots;E=this.values;var u=Math.ceil(r*o),s=$("<canvas class='tile'></canvas>");var b=$("<canvas></canvas>").get(0).getContext("2d");s.css({position:"absolute",top:0,left:(B-this.view.low)*o-this.left_offset});s.get(0).width=u+this.left_offset;s.get(0).height=k;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font=this.default_font;v.textAlign="right";var t=v.measureText("A").width;var x=0;for(var y=0,z=E.length;y<z;y++){var m=E[y];if(m.start<=f&&m.end>=B){var h=Math.floor(Math.max(0,(m.start-B)*o)),l=Math.ceil(Math.min(u,(m.end-B)*o)),g=q[m.uid]*this.vertical_gap;var a,F,e=null,p=null;if(o>t){for(var C=0,d=m.name.length;C<d;C++){var D=Math.floor(Math.max(0,(m.start+C-B)*o));v.fillText(m.name[C],D+this.left_offset,g+8)}}else{v.fillRect(h+this.left_offset,g+4,l-h,3)}}}n.append(s);return s}});
\ No newline at end of file
diff -r 427d93bf3d39 -r 7d3667e8e415 static/scripts/trackster.js
--- a/static/scripts/trackster.js	Thu Jan 07 14:52:51 2010 -0500
+++ b/static/scripts/trackster.js	Thu Jan 07 15:45:15 2010 -0500
@@ -81,7 +81,7 @@
     this.max_high = max_high;
     this.center = (this.max_high - this.max_low) / 2;
     this.span = this.max_high - this.max_low;
-    this.zoom_factor = 2;
+    this.zoom_factor = 3;
     this.zoom_level = 0;
 };
 $.extend( View.prototype, {
@@ -241,12 +241,12 @@
     }
 });
-var LineTrack = function ( name, dataset_id, height ) {
+var LineTrack = function ( name, dataset_id, indexer, height ) {
     this.tile_cache = new Cache(CACHED_TILES_LINE);
     Track.call( this, name, $("#viewport") );
     TiledTrack.call( this );
-    this.track_type = "line";
+    this.indexer = indexer;
     this.height_px = (height ? height : 100);
     this.container_div.addClass( "line-track" );
     this.dataset_id = dataset_id;
@@ -258,7 +258,7 @@
     init: function() {
         var track = this;
         track.content_div.text(DATA_LOADING);
-        $.getJSON( data_url, {  stats: true, track_type: track.track_type,
+        $.getJSON( data_url, {  stats: true, indexer: track.indexer,
                                 chrom: track.view.chrom, low: null, high: null,
                                 dataset_id: track.dataset_id }, function ( data ) {
             if (!data || data == "error") {
@@ -300,7 +300,7 @@
if (!track.data_queue[key]) {
             track.data_queue[key] = true;
-            $.getJSON( data_url, {  track_type: this.track_type, chrom: this.view.chrom, 
+            $.getJSON( data_url, {  indexer: this.indexer, chrom: this.view.chrom, 
                                     low: low, high: high, dataset_id: this.dataset_id,
                                     resolution: this.view.resolution }, function ( data ) {
                 track.cache.set(key, data);
@@ -360,12 +360,12 @@
     }
 });
-var FeatureTrack = function ( name, dataset_id, height ) {
+var FeatureTrack = function ( name, dataset_id, indexer, height ) {
     this.tile_cache = new Cache(CACHED_TILES_FEATURE);
     Track.call( this, name, $("#viewport") );
     TiledTrack.call( this );
-    this.track_type = "feature";
+    this.indexer = indexer;
     this.height_px = (height ? height : 100);
     this.container_div.addClass( "feature-track" );
     this.dataset_id = dataset_id;
@@ -384,7 +384,7 @@
     init: function() {
         var track = this;
         track.content_div.text(DATA_LOADING);
-        $.getJSON( data_url, {  track_type: track.track_type, low: track.view.max_low, 
+        $.getJSON( data_url, {  indexer: track.indexer, low: track.view.max_low, 
                                 high: track.view.max_high, dataset_id: track.dataset_id,
                                 chrom: track.view.chrom }, function ( data ) {
             if (data == "error") {
@@ -414,7 +414,7 @@
if (!track.data_queue[key]) {
             track.data_queue[key] = true;
-            $.getJSON( data_url, {  track_type: track.track_type, chrom: track.view.chrom, 
+            $.getJSON( data_url, {  indexer: track.indexer, chrom: track.view.chrom, 
                                     low: low, high: high, dataset_id: track.dataset_id,
                                     include_blocks: true }, function ( data ) {
                 track.data_cache.set(key, data);
@@ -454,8 +454,6 @@
         if (!this.inc_slots[level]) {
             this.inc_slots[level] = {};
             this.inc_slots[level].w_scale = DENSITY / Math.pow(FEATURE_LEVELS, level+1);
-            // this.inc_slots[level].w_scale = 1000 / (this.view.high - this.view.low);
-            
         }
         var slots = this.inc_slots[level];
         // console.log(level, slots.w_scale, slots);
@@ -629,3 +627,71 @@
         return new_canvas;
     }
 });
+
+var ReadTrack = function ( name, dataset_id, indexer, height ) {
+    this.tile_cache = new Cache(CACHED_TILES_FEATURE);
+    Track.call( this, name, $("#viewport") );
+    TiledTrack.call( this );
+    FeatureTrack.call( this, name, dataset_id, indexer, height );
+    this.default_font = "9px Monaco, Lucida Console, monospace";
+    
+};
+$.extend( ReadTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, {
+    draw_tile: function( resolution, tile_index, parent_element, w_scale ) {
+        if (!this.values) {
+            return;
+        }
+        var tile_low = tile_index * DENSITY * resolution,
+            tile_high = ( tile_index + 1 ) * DENSITY * resolution,
+            tile_span = DENSITY * resolution;
+        // console.log("drawing " + tile_index);
+        // Once we zoom in enough, show name labels
+        var data, slots, required_height;
+            required_height = this.height_px;
+            slots = this.zo_slots;
+            data = this.values;
+        
+        // console.log(tile_low, tile_high, tile_length, w_scale);
+        var width = Math.ceil( tile_span * w_scale ),
+            new_canvas = $("<canvas class='tile'></canvas>");
+        
+        var dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d");
+        
+        new_canvas.css({
+            position: "absolute",
+            top: 0,
+            left: ( tile_low - this.view.low ) * w_scale - this.left_offset
+        });
+        new_canvas.get(0).width = width + this.left_offset;
+        new_canvas.get(0).height = required_height;
+        // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale);
+        var ctx = new_canvas.get(0).getContext("2d");
+        ctx.fillStyle = this.base_color;
+        ctx.font = this.default_font;
+        ctx.textAlign = "right";
+        var px_per_char = ctx.measureText("A").width;
+        
+        var j = 0;
+        for (var i = 0, len = data.length; i < len; i++) {
+            var feature = data[i];
+            if (feature.start <= tile_high && feature.end >= tile_low) {
+                var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ),
+                    f_end   = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ),
+                    y_center = slots[feature.uid] * this.vertical_gap;
+                
+                var thickness, y_start, thick_start = null, thick_end = null;
+                if (w_scale > px_per_char) {
+                    for (var c = 0, str_len = feature.name.length; c < str_len; c++) {
+                        var c_start = Math.floor( Math.max(0, (feature.start + c - tile_low) * w_scale) );
+                        ctx.fillText(feature.name[c], c_start + this.left_offset, y_center + 8);
+                    }
+                } else {
+                    ctx.fillRect(f_start + this.left_offset, y_center + 4, f_end - f_start, 3);
+                }
+            }
+        }        
+
+        parent_element.append( new_canvas );
+        return new_canvas;
+    }
+});
diff -r 427d93bf3d39 -r 7d3667e8e415 templates/tracks/browser.mako
--- a/templates/tracks/browser.mako	Thu Jan 07 14:52:51 2010 -0500
+++ b/templates/tracks/browser.mako	Thu Jan 07 15:45:15 2010 -0500
@@ -20,7 +20,7 @@
         view.add_track( new LabelTrack( $("#nav-labeltrack" ) ) );
%for track in tracks:
-            view.add_track( new ${track["type"]}( "${track['name']}", ${track['dataset_id']} ) );
+            view.add_track( new ${track["type"]}( "${track['name']}", ${track['dataset_id']}, "${track['indexer']}" ) );
         %endfor
$(document).bind( "redraw", function( e ) {
diff -r 427d93bf3d39 -r 7d3667e8e415 templates/tracks/new_browser.mako
--- a/templates/tracks/new_browser.mako	Thu Jan 07 14:52:51 2010 -0500
+++ b/templates/tracks/new_browser.mako	Thu Jan 07 15:45:15 2010 -0500
@@ -11,7 +11,7 @@
 </script>
 </%def>
-% if not converters:
+% if not available_tracks:
     <div class="errormessagelarge">
         There are no available converters needed for visualization. Please verify that your tool_conf.xml file contains
         converters for datatypes (see tool_conf.xml.sample) for examples.
@@ -46,7 +46,7 @@
                     <div style="clear: both;"></div>
                 </div>
                 <div class="form-row">
-                    <label for="dataset_ids">Datasets to include: </label>
+                    <label for="dataset_ids">Datasets to visualize: (${", ".join(available_tracks)} files are supported)</label>
                     %for dataset_id, (dataset_ext, dataset_name) in datasets.iteritems():
                     <div>
                         <input type="checkbox" id="${dataset_id}" name="dataset_ids" value="${dataset_id}" />

    

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[galaxy-dev] [hg] galaxy 3216: trackster: support BAM visualization with samt...