diff --git a/lib/galaxy/visualization/tracks/data/bam.py b/lib/galaxy/visualization/tracks/data/bam.py index 881fe00aed4..cda94766dc9 100644 --- a/lib/galaxy/visualization/tracks/data/bam.py +++ b/lib/galaxy/visualization/tracks/data/bam.py @@ -7,13 +7,14 @@ import pkg_resources; pkg_resources.require( "pysam" ) from pysam import csamtools from math import floor, ceil, log import logging +# log = logging.getLogger(__name__) class BamDataProvider( object ): """ Provides access to intervals from a sorted indexed BAM file. """ def __init__( self, index, original_dataset ): - # self.log = logging.getLogger(__name__) + self.index = index self.original_dataset = original_dataset @@ -27,8 +28,7 @@ class BamDataProvider( object ): try: data = bamfile.fetch(start=start, end=end, reference=chrom) except ValueError, e: - # Some BAM files do not prefix chromosome names with chr, try - # without + # Some BAM files do not prefix chromosome names with chr, try without if chrom.startswith( 'chr' ): data = bamfile.fetch( start=start, end=end, reference=chrom[3:] ) else: diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py index dafe2dd3a99..9bbcab43b33 100644 --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -19,6 +19,7 @@ log = logging.getLogger(__name__) from galaxy.util.json import to_json_string from galaxy.web.base.controller import * from galaxy.web.framework import simplejson +from galaxy.web.framework.helpers import time_ago, grids from galaxy.util.bunch import Bunch from galaxy.visualization.tracks.data.array_tree import ArrayTreeDataProvider @@ -43,12 +44,40 @@ dataset_type_to_data_provider = { "bai": BamDataProvider } +class DatasetSelectionGrid( grids.Grid ): + # Grid definition. + available_tracks = None + title = "Add Tracks" + template = "/tracks/add_tracks.mako" + async_template = "/page/select_histories_grid_async.mako" + model_class = model.HistoryDatasetAssociation + default_filter = { "deleted" : "False" , "shared" : "All" } + default_sort_key = "name" + use_async = True + use_paging = False + columns = [ + grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation ), + # grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), + grids.GridColumn( "Filetype", key="extension" ), + # Columns that are valid for filtering but are not visible. + # SharingColumn( "Shared", key="shared", visible=False, filterable="advanced" ) + ] + def apply_default_filter( self, trans, query, **kwargs ): + if self.available_tracks is None: + self.available_tracks = trans.app.datatypes_registry.get_available_tracks() + return query.select_from( model.HistoryDatasetAssociation.table \ + .join( model.History.table ) ) \ + .filter( model.History.user == trans.user ) \ + .filter( model.HistoryDatasetAssociation.extension.in_(self.available_tracks) ) + class TracksController( BaseController ): """ Controller for track browser interface. Handles building a new browser from datasets in the current history, and display of the resulting browser. """ - + + available_tracks = None + @web.expose def index( self, trans ): return trans.fill_template( "tracks/index.mako" ) @@ -98,12 +127,13 @@ class TracksController( BaseController ): # 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() + if self.available_tracks is None: + self.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 available_tracks: + if dataset.metadata.dbkey == dbkey and dataset.extension in self.available_tracks: datasets[dataset.id] = (dataset.extension, dataset.name) # Render the template - return trans.fill_template( "tracks/new_browser.mako", available_tracks=available_tracks, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) + return trans.fill_template( "tracks/new_browser.mako", available_tracks=self.available_tracks, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) @web.expose def browser(self, trans, id, chrom=""): @@ -118,13 +148,18 @@ class TracksController( BaseController ): hda_query = session.query( model.HistoryDatasetAssociation ) for t in vis.latest_revision.config['tracks']: dataset_id = t['dataset_id'] + try: + prefs = t['prefs'] + except KeyError: + prefs = {} dataset = hda_query.get( dataset_id ) track_type, indexer = dataset.datatype.get_track_type() tracks.append( { - "type": track_type, + "track_type": track_type, "indexer": indexer, "name": dataset.name, - "dataset_id": dataset.id + "dataset_id": dataset.id, + "prefs": simplejson.dumps(prefs), } ) dbkey = dataset.dbkey chrom_lengths = self._chroms( trans, dbkey ) @@ -252,7 +287,40 @@ class TracksController( BaseController ): return new_dataset @web.json - def update_config( self, trans, **kwargs ): - raise RuntimeError + def save( self, trans, **kwargs ): + decoded_id = trans.security.decode_id( kwargs['id'] ) + session = trans.sa_session + vis = session.query( model.Visualization ).get( decoded_id ) + + decoded_payload = simplejson.loads( kwargs['payload'] ) + vis_rev = model.VisualizationRevision() + vis_rev.visualization = vis + vis_rev.title = vis.title + tracks = [] + for track in decoded_payload: + tracks.append( { "dataset_id": str(track['dataset_id']), + "name": track['name'], + "indexer": track['indexer'], + "track_type": track['track_type'], + "prefs": track['prefs'] + } ) + vis_rev.config = { "tracks": tracks } + vis.latest_revision = vis_rev + session.add( vis_rev ) + session.flush() + + data_grid = DatasetSelectionGrid() + + @web.expose + @web.require_login( "see all available datasets" ) + def list_datasets( self, trans, **kwargs ): + """List all datasets that can be added as tracks""" + + + # Render the list view + # return trans.fill_template( 'tracks/add_tracks.mako', grid=data_grid( trans, status=status, message=message, **kwargs ) ) + return self.data_grid( trans, **kwargs ) + + # \ No newline at end of file diff --git a/lib/galaxy/web/framework/helpers/grids.py b/lib/galaxy/web/framework/helpers/grids.py index b6e875ba618..a362ebfefac 100644 --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -12,7 +12,7 @@ log = logging.getLogger( __name__ ) class Grid( object ): """ - Specifieds the content and format of a grid (data table). + Specifies the content and format of a grid (data table). """ title = "" exposed = True @@ -157,10 +157,10 @@ class Grid( object ): if sort_key.startswith( "-" ): sort_key = sort_key[1:] sort_order = 'desc' - query = query.order_by( self.model_class.table.c.get( sort_key ).desc() ) + query = query.order_by( func.lower( self.model_class.table.c.get( sort_key ) ).desc() ) else: sort_order = 'asc' - query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) + query = query.order_by( func.lower( self.model_class.table.c.get( sort_key ) ).asc() ) extra_url_args['sort'] = encoded_sort_key # There might be a current row @@ -230,7 +230,7 @@ class Grid( object ): else: new_kwargs[ 'id' ] = trans.security.encode_id( id ) return url_for( **new_kwargs ) - + async_request = ( ( self.use_async ) and ( 'async' in kwargs ) and ( kwargs['async'] in [ 'True', 'true'] ) ) return trans.fill_template( iff( async_request, self.async_template, self.template), grid=self, diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js index 4a47a0bb537..5e1442bc85c 100644 --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -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=$("").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};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#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));for(var c=0,a=this.tracks.length;c").text(this.name);this.content_div=$("
");this.container_div=$("
").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=$("
");this.content_div.children(":first").remove();this.content_div.append(l);var m=this.content_div.width()/f;var i=20;var h;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)
");while(a"+commatize(a)+"").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#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=$("
"+a.min_value+"
");var b=$("
"+a.max_value+"
");b.css({position:"relative",top:"25px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+55+"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;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$(""),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").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;pr[0]&&cthis.show_labels_scale){if(!this.showing_details){this.showing_details=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_detail_px+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_details){this.showing_details=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*(this.showing_details?this.vertical_detail_px:this.vertical_nodetail_px);var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_details){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left_offset,f+8)}var I=m.blocks;if(I){if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;BH){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b!==undefined&&(o<=s||H>=b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}});var ReadTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,b,d,a);this.default_font="9px Monaco, Lucida Console, monospace"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.base_color;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A").width;var w=0;for(var x=0,y=D.length;x=A){var g=Math.floor(Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l.uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.length;B").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 View=function(c,a,b){this.chrom=c;this.config=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};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},remove_track:function(a){delete this.tracks[a]},update_options:function(){for(var b in view.tracks){var a=view.tracks[b];if(a.update_options){a.update_options(b)}}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#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));for(var c=0,a=this.tracks.length;c").text(this.name);this.content_div=$("
");this.container_div=$("
").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("
");this.content_div.children(":first").remove();this.content_div.append(k);var l=this.content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)c.view.high||f
");while(a"+commatize(a)+"").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,d,b){this.track_type="LineTrack";this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.prefs={min_value:undefined,max_value:undefined};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(d){if(!d||d=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d=="no data"){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");if(a.prefs.min_value===undefined||a.prefs.max_value===undefined){a.prefs.min_value=d.min;a.prefs.max_value=d.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;var e=$("
").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var c=$("
").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);c.css({position:"relative",top:"25px"});c.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px"});e.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;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(n,p,c,e){if(!this.vertical_range){return}var q=p*DENSITY*n,a=DENSITY*n,b=$(""),s=n+"_"+p;if(!this.data_cache.get(s)){this.get_data(n,p);return}var r=this.data_cache.get(s);b.css({position:"absolute",top:0,left:(q-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var m=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,f=this.prefs.max_value,l=this.vertical_range,d=this.height_px;m.beginPath();for(var o=0;o=f){g=f}}g=Math.round(d-(g-k)/l*d);if(j){m.lineTo(h,g)}else{m.moveTo(h,g);j=true}}}m.stroke();c.append(b);return b},gen_options:function(j){var a=$("
").addClass("form-row");var e="track_"+j+"_minval",g="track_"+j+"_maxval",h=$("").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),i=$("").attr("id",e).val(b),d=$("").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("").attr("id",g).val(f);return a.append(h).append(i).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,d,b){this.track_type="FeatureTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;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.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black"};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.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.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;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var b=[],a=this.content_div.width()/(this.view.high-this.view.low),d=this.view.max_low;for(var e=0,f=this.values.length;e").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;pr[0]&&cthis.show_labels_scale){if(!this.showing_details){this.showing_details=true}for(var H in this.data_cache.obj_cache){var C=H.split("_"),z=C[0],c=C[1];if(z<=s&&c>=G){K=this.data_cache.get(H);break}}if(!K){this.data_queue[[s,G]]=true;this.get_data(s,G);return}m=this.incremental_slots(this.view.zoom_res,K)*this.vertical_detail_px+15;L=this.inc_slots[this.view.zoom_res]}else{if(this.showing_details){this.showing_details=false}m=this.height_px;L=this.zo_slots;K=this.values}var a=Math.ceil(r*M),u=$(""),D=this.prefs.label_color,e=this.prefs.block_color,x=this.left_offset,N=this.showing_details,O=(this.showing_details?this.vertical_detail_px:this.vertical_nodetail_px);u.css({position:"absolute",top:0,left:(s-this.view.low)*M-x});u.get(0).width=a+x;u.get(0).height=m;var p=u.get(0).getContext("2d");p.fillStyle=this.prefs.block_color;p.font=this.default_font;p.textAlign="right";var I=0;for(var J=0,o=K.length;J=s){var A=Math.floor(Math.max(0,(v.start-s)*M)),q=Math.ceil(Math.min(a,(v.end-s)*M)),y=L[v.uid]*O;var n,E,t=null,P=null;if(v.thick_start&&v.thick_end){t=Math.floor(Math.max(0,(v.thick_start-s)*M));P=Math.ceil(Math.min(a,(v.thick_end-s)*M))}if(!N){p.fillRect(A+x,y+5,q-A,1)}else{if(v.start>s){p.fillStyle=D;p.fillText(v.name,A-1+x,y+8);p.fillStyle=e}var Q=v.blocks;if(Q){if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND}}p.fillRect(A+x,y,q-A,10);p.fillStyle=e}for(var H=0,d=Q.length;Hw){continue}n=5;E=3;p.fillRect(b+x,y+E,w-b,n);if(t!==undefined&&!(b>P||w").addClass("form-row");var d="track_"+g+"_block_color",c=$("").attr("for",d).text("Block color:"),b=$("").attr("id",d).attr("name",d).val(this.prefs.block_color),f="track_"+g+"_label_color",h=$("").attr("for",f).text("Label color:"),e=$("").attr("id",f).attr("name",f).val(this.prefs.label_color);return a.append(c).append(b).append(h).append(e)},update_options:function(c){var a=$("#track_"+c+"_block_color").val(),b=$("#track_"+c+"_label_color").val();if(a!==this.prefs.block_color||b!==this.prefs.label_color){this.prefs.block_color=a;this.prefs.label_color=b;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,d,b){this.track_type="ReadTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,a,d,b)};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.prefs.block_color;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A").width;var w=0;for(var x=0,y=D.length;x=A){var g=Math.floor(Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l.uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.length;B0){return true}m[j]=1;l=(m[j]>0);m[j]=0;return l},isOverAxis:function(k,j,l){return(k>j)&&(k<(j+l))},isOver:function(o,k,n,m,j,l){return c.ui.isOverAxis(o,n,j)&&c.ui.isOverAxis(k,m,l)},keyCode:{BACKSPACE:8,CAPS_LOCK:20,COMMA:188,CONTROL:17,DELETE:46,DOWN:40,END:35,ENTER:13,ESCAPE:27,HOME:36,INSERT:45,LEFT:37,NUMPAD_ADD:107,NUMPAD_DECIMAL:110,NUMPAD_DIVIDE:111,NUMPAD_ENTER:108,NUMPAD_MULTIPLY:106,NUMPAD_SUBTRACT:109,PAGE_DOWN:34,PAGE_UP:33,PERIOD:190,RIGHT:39,SHIFT:16,SPACE:32,TAB:9,UP:38}};if(d){var f=c.attr,e=c.fn.removeAttr,h="http://www.w3.org/2005/07/aaa",a=/^aria-/,b=/^wairole:/;c.attr=function(k,j,l){var m=l!==undefined;return(j=="role"?(m?f.call(this,k,j,"wairole:"+l):(f.apply(this,arguments)||"").replace(b,"")):(a.test(j)?(m?k.setAttributeNS(h,j.replace(a,"aaa:"),l):f.call(this,k,j.replace(a,"aaa:"))):f.apply(this,arguments)))};c.fn.removeAttr=function(j){return(a.test(j)?this.each(function(){this.removeAttributeNS(h,j.replace(a,""))}):e.call(this,j))}}c.fn.extend({remove:function(){c("*",this).add(this).each(function(){c(this).triggerHandler("remove")});return i.apply(this,arguments)},enableSelection:function(){return this.attr("unselectable","off").css("MozUserSelect","").unbind("selectstart.ui")},disableSelection:function(){return this.attr("unselectable","on").css("MozUserSelect","none").bind("selectstart.ui",function(){return false})},scrollParent:function(){var j;if((c.browser.msie&&(/(static|relative)/).test(this.css("position")))||(/absolute/).test(this.css("position"))){j=this.parents().filter(function(){return(/(relative|absolute|fixed)/).test(c.curCSS(this,"position",1))&&(/(auto|scroll)/).test(c.curCSS(this,"overflow",1)+c.curCSS(this,"overflow-y",1)+c.curCSS(this,"overflow-x",1))}).eq(0)}else{j=this.parents().filter(function(){return(/(auto|scroll)/).test(c.curCSS(this,"overflow",1)+c.curCSS(this,"overflow-y",1)+c.curCSS(this,"overflow-x",1))}).eq(0)}return(/fixed/).test(this.css("position"))||!j.length?c(document):j}});c.extend(c.expr[":"],{data:function(l,k,j){return !!c.data(l,j[3])},focusable:function(k){var l=k.nodeName.toLowerCase(),j=c.attr(k,"tabindex");return(/input|select|textarea|button|object/.test(l)?!k.disabled:"a"==l||"area"==l?k.href||!isNaN(j):!isNaN(j))&&!c(k)["area"==l?"parents":"closest"](":hidden").length},tabbable:function(k){var j=c.attr(k,"tabindex");return(isNaN(j)||j>=0)&&c(k).is(":focusable")}});function g(m,n,o,l){function k(q){var p=c[m][n][q]||[];return(typeof p=="string"?p.split(/,?\s+/):p)}var j=k("getter");if(l.length==1&&typeof l[0]=="string"){j=j.concat(k("getterSetter"))}return(c.inArray(o,j)!=-1)}c.widget=function(k,j){var l=k.split(".")[0];k=k.split(".")[1];c.fn[k]=function(p){var n=(typeof p=="string"),o=Array.prototype.slice.call(arguments,1);if(n&&p.substring(0,1)=="_"){return this}if(n&&g(l,k,p,o)){var m=c.data(this[0],k);return(m?m[p].apply(m,o):undefined)}return this.each(function(){var q=c.data(this,k);(!q&&!n&&c.data(this,k,new c[l][k](this,p))._init());(q&&n&&c.isFunction(q[p])&&q[p].apply(q,o))})};c[l]=c[l]||{};c[l][k]=function(o,n){var m=this;this.namespace=l;this.widgetName=k;this.widgetEventPrefix=c[l][k].eventPrefix||k;this.widgetBaseClass=l+"-"+k;this.options=c.extend({},c.widget.defaults,c[l][k].defaults,c.metadata&&c.metadata.get(o)[k],n);this.element=c(o).bind("setData."+k,function(q,p,r){if(q.target==o){return m._setData(p,r)}}).bind("getData."+k,function(q,p){if(q.target==o){return m._getData(p)}}).bind("remove",function(){return m.destroy()})};c[l][k].prototype=c.extend({},c.widget.prototype,j);c[l][k].getterSetter="option"};c.widget.prototype={_init:function(){},destroy:function(){this.element.removeData(this.widgetName).removeClass(this.widgetBaseClass+"-disabled "+this.namespace+"-state-disabled").removeAttr("aria-disabled")},option:function(l,m){var k=l,j=this;if(typeof l=="string"){if(m===undefined){return this._getData(l)}k={};k[l]=m}c.each(k,function(n,o){j._setData(n,o)})},_getData:function(j){return this.options[j]},_setData:function(j,k){this.options[j]=k;if(j=="disabled"){this.element[k?"addClass":"removeClass"](this.widgetBaseClass+"-disabled "+this.namespace+"-state-disabled").attr("aria-disabled",k)}},enable:function(){this._setData("disabled",false)},disable:function(){this._setData("disabled",true)},_trigger:function(l,m,n){var p=this.options[l],j=(l==this.widgetEventPrefix?l:this.widgetEventPrefix+l);m=c.Event(m);m.type=j;if(m.originalEvent){for(var k=c.event.props.length,o;k;){o=c.event.props[--k];m[o]=m.originalEvent[o]}}this.element.trigger(m,n);return !(c.isFunction(p)&&p.call(this.element[0],m,n)===false||m.isDefaultPrevented())}};c.widget.defaults={disabled:false};c.ui.mouse={_mouseInit:function(){var j=this;this.element.bind("mousedown."+this.widgetName,function(k){return j._mouseDown(k)}).bind("click."+this.widgetName,function(k){if(j._preventClickEvent){j._preventClickEvent=false;k.stopImmediatePropagation();return false}});if(c.browser.msie){this._mouseUnselectable=this.element.attr("unselectable");this.element.attr("unselectable","on")}this.started=false},_mouseDestroy:function(){this.element.unbind("."+this.widgetName);(c.browser.msie&&this.element.attr("unselectable",this._mouseUnselectable))},_mouseDown:function(l){l.originalEvent=l.originalEvent||{};if(l.originalEvent.mouseHandled){return}(this._mouseStarted&&this._mouseUp(l));this._mouseDownEvent=l;var k=this,m=(l.which==1),j=(typeof this.options.cancel=="string"?c(l.target).parents().add(l.target).filter(this.options.cancel).length:false);if(!m||j||!this._mouseCapture(l)){return true}this.mouseDelayMet=!this.options.delay;if(!this.mouseDelayMet){this._mouseDelayTimer=setTimeout(function(){k.mouseDelayMet=true},this.options.delay)}if(this._mouseDistanceMet(l)&&this._mouseDelayMet(l)){this._mouseStarted=(this._mouseStart(l)!==false);if(!this._mouseStarted){l.preventDefault();return true}}this._mouseMoveDelegate=function(n){return k._mouseMove(n)};this._mouseUpDelegate=function(n){return k._mouseUp(n)};c(document).bind("mousemove."+this.widgetName,this._mouseMoveDelegate).bind("mouseup."+this.widgetName,this._mouseUpDelegate);(c.browser.safari||l.preventDefault());l.originalEvent.mouseHandled=true;return true},_mouseMove:function(j){if(c.browser.msie&&!j.button){return this._mouseUp(j)}if(this._mouseStarted){this._mouseDrag(j);return j.preventDefault()}if(this._mouseDistanceMet(j)&&this._mouseDelayMet(j)){this._mouseStarted=(this._mouseStart(this._mouseDownEvent,j)!==false);(this._mouseStarted?this._mouseDrag(j):this._mouseUp(j))}return !this._mouseStarted},_mouseUp:function(j){c(document).unbind("mousemove."+this.widgetName,this._mouseMoveDelegate).unbind("mouseup."+this.widgetName,this._mouseUpDelegate);if(this._mouseStarted){this._mouseStarted=false;this._preventClickEvent=(j.target==this._mouseDownEvent.target);this._mouseStop(j)}return false},_mouseDistanceMet:function(j){return(Math.max(Math.abs(this._mouseDownEvent.pageX-j.pageX),Math.abs(this._mouseDownEvent.pageY-j.pageY))>=this.options.distance)},_mouseDelayMet:function(j){return this.mouseDelayMet},_mouseStart:function(j){},_mouseDrag:function(j){},_mouseStop:function(j){},_mouseCapture:function(j){return true}};c.ui.mouse.defaults={cancel:null,distance:1,delay:0}})(jQuery); \ No newline at end of file diff --git a/static/scripts/packed/ui.sortable.js b/static/scripts/packed/ui.sortable.js new file mode 100644 index 00000000000..23de51d5f6a --- /dev/null +++ b/static/scripts/packed/ui.sortable.js @@ -0,0 +1 @@ +(function(a){a.widget("ui.sortable",a.extend({},a.ui.mouse,{_init:function(){var b=this.options;this.containerCache={};this.element.addClass("ui-sortable");this.refresh();this.floating=this.items.length?(/left|right/).test(this.items[0].item.css("float")):false;this.offset=this.element.offset();this._mouseInit()},destroy:function(){this.element.removeClass("ui-sortable ui-sortable-disabled").removeData("sortable").unbind(".sortable");this._mouseDestroy();for(var b=this.items.length-1;b>=0;b--){this.items[b].item.removeData("sortable-item")}},_mouseCapture:function(e,f){if(this.reverting){return false}if(this.options.disabled||this.options.type=="static"){return false}this._refreshItems(e);var d=null,c=this,b=a(e.target).parents().each(function(){if(a.data(this,"sortable-item")==c){d=a(this);return false}});if(a.data(e.target,"sortable-item")==c){d=a(e.target)}if(!d){return false}if(this.options.handle&&!f){var g=false;a(this.options.handle,d).find("*").andSelf().each(function(){if(this==e.target){g=true}});if(!g){return false}}this.currentItem=d;this._removeCurrentsFromItems();return true},_mouseStart:function(e,f,b){var g=this.options,c=this;this.currentContainer=this;this.refreshPositions();this.helper=this._createHelper(e);this._cacheHelperProportions();this._cacheMargins();this.scrollParent=this.helper.scrollParent();this.offset=this.currentItem.offset();this.offset={top:this.offset.top-this.margins.top,left:this.offset.left-this.margins.left};this.helper.css("position","absolute");this.cssPosition=this.helper.css("position");a.extend(this.offset,{click:{left:e.pageX-this.offset.left,top:e.pageY-this.offset.top},parent:this._getParentOffset(),relative:this._getRelativeOffset()});this.originalPosition=this._generatePosition(e);this.originalPageX=e.pageX;this.originalPageY=e.pageY;if(g.cursorAt){this._adjustOffsetFromHelper(g.cursorAt)}this.domPosition={prev:this.currentItem.prev()[0],parent:this.currentItem.parent()[0]};if(this.helper[0]!=this.currentItem[0]){this.currentItem.hide()}this._createPlaceholder();if(g.containment){this._setContainment()}if(g.cursor){if(a("body").css("cursor")){this._storedCursor=a("body").css("cursor")}a("body").css("cursor",g.cursor)}if(g.opacity){if(this.helper.css("opacity")){this._storedOpacity=this.helper.css("opacity")}this.helper.css("opacity",g.opacity)}if(g.zIndex){if(this.helper.css("zIndex")){this._storedZIndex=this.helper.css("zIndex")}this.helper.css("zIndex",g.zIndex)}if(this.scrollParent[0]!=document&&this.scrollParent[0].tagName!="HTML"){this.overflowOffset=this.scrollParent.offset()}this._trigger("start",e,this._uiHash());if(!this._preserveHelperProportions){this._cacheHelperProportions()}if(!b){for(var d=this.containers.length-1;d>=0;d--){this.containers[d]._trigger("activate",e,c._uiHash(this))}}if(a.ui.ddmanager){a.ui.ddmanager.current=this}if(a.ui.ddmanager&&!g.dropBehaviour){a.ui.ddmanager.prepareOffsets(this,e)}this.dragging=true;this.helper.addClass("ui-sortable-helper");this._mouseDrag(e);return true},_mouseDrag:function(f){this.position=this._generatePosition(f);this.positionAbs=this._convertPositionTo("absolute");if(!this.lastPositionAbs){this.lastPositionAbs=this.positionAbs}if(this.options.scroll){var g=this.options,b=false;if(this.scrollParent[0]!=document&&this.scrollParent[0].tagName!="HTML"){if((this.overflowOffset.top+this.scrollParent[0].offsetHeight)-f.pageY=0;d--){var e=this.items[d],c=e.item[0],h=this._intersectsWithPointer(e);if(!h){continue}if(c!=this.currentItem[0]&&this.placeholder[h==1?"next":"prev"]()[0]!=c&&!a.ui.contains(this.placeholder[0],c)&&(this.options.type=="semi-dynamic"?!a.ui.contains(this.element[0],c):true)){this.direction=h==1?"down":"up";if(this.options.tolerance=="pointer"||this._intersectsWithSides(e)){this._rearrange(f,e)}else{break}this._trigger("change",f,this._uiHash());break}}this._contactContainers(f);if(a.ui.ddmanager){a.ui.ddmanager.drag(this,f)}this._trigger("sort",f,this._uiHash());this.lastPositionAbs=this.positionAbs;return false},_mouseStop:function(c,d){if(!c){return}if(a.ui.ddmanager&&!this.options.dropBehaviour){a.ui.ddmanager.drop(this,c)}if(this.options.revert){var b=this;var e=b.placeholder.offset();b.reverting=true;a(this.helper).animate({left:e.left-this.offset.parent.left-b.margins.left+(this.offsetParent[0]==document.body?0:this.offsetParent[0].scrollLeft),top:e.top-this.offset.parent.top-b.margins.top+(this.offsetParent[0]==document.body?0:this.offsetParent[0].scrollTop)},parseInt(this.options.revert,10)||500,function(){b._clear(c)})}else{this._clear(c,d)}return false},cancel:function(){var b=this;if(this.dragging){this._mouseUp();if(this.options.helper=="original"){this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper")}else{this.currentItem.show()}for(var c=this.containers.length-1;c>=0;c--){this.containers[c]._trigger("deactivate",null,b._uiHash(this));if(this.containers[c].containerCache.over){this.containers[c]._trigger("out",null,b._uiHash(this));this.containers[c].containerCache.over=0}}}if(this.placeholder[0].parentNode){this.placeholder[0].parentNode.removeChild(this.placeholder[0])}if(this.options.helper!="original"&&this.helper&&this.helper[0].parentNode){this.helper.remove()}a.extend(this,{helper:null,dragging:false,reverting:false,_noFinalSort:null});if(this.domPosition.prev){a(this.domPosition.prev).after(this.currentItem)}else{a(this.domPosition.parent).prepend(this.currentItem)}return true},serialize:function(d){var b=this._getItemsAsjQuery(d&&d.connected);var c=[];d=d||{};a(b).each(function(){var e=(a(d.item||this).attr(d.attribute||"id")||"").match(d.expression||(/(.+)[-=_](.+)/));if(e){c.push((d.key||e[1]+"[]")+"="+(d.key&&d.expression?e[1]:e[2]))}});return c.join("&")},toArray:function(d){var b=this._getItemsAsjQuery(d&&d.connected);var c=[];d=d||{};b.each(function(){c.push(a(d.item||this).attr(d.attribute||"id")||"")});return c},_intersectsWith:function(m){var e=this.positionAbs.left,d=e+this.helperProportions.width,k=this.positionAbs.top,j=k+this.helperProportions.height;var f=m.left,c=f+m.width,n=m.top,i=n+m.height;var o=this.offset.click.top,h=this.offset.click.left;var g=(k+o)>n&&(k+o)f&&(e+h)m[this.floating?"width":"height"])){return g}else{return(f0?"down":"up")},_getDragHorizontalDirection:function(){var b=this.positionAbs.left-this.lastPositionAbs.left;return b!=0&&(b>0?"right":"left")},refresh:function(b){this._refreshItems(b);this.refreshPositions()},_connectWith:function(){var b=this.options;return b.connectWith.constructor==String?[b.connectWith]:b.connectWith},_getItemsAsjQuery:function(b){var l=this;var g=[];var e=[];var h=this._connectWith();if(h&&b){for(var d=h.length-1;d>=0;d--){var k=a(h[d]);for(var c=k.length-1;c>=0;c--){var f=a.data(k[c],"sortable");if(f&&f!=this&&!f.options.disabled){e.push([a.isFunction(f.options.items)?f.options.items.call(f.element):a(f.options.items,f.element).not(".ui-sortable-helper"),f])}}}}e.push([a.isFunction(this.options.items)?this.options.items.call(this.element,null,{options:this.options,item:this.currentItem}):a(this.options.items,this.element).not(".ui-sortable-helper"),this]);for(var d=e.length-1;d>=0;d--){e[d][0].each(function(){g.push(this)})}return a(g)},_removeCurrentsFromItems:function(){var d=this.currentItem.find(":data(sortable-item)");for(var c=0;c=0;e--){var m=a(l[e]);for(var d=m.length-1;d>=0;d--){var g=a.data(m[d],"sortable");if(g&&g!=this&&!g.options.disabled){f.push([a.isFunction(g.options.items)?g.options.items.call(g.element[0],b,{item:this.currentItem}):a(g.options.items,g.element),g]);this.containers.push(g)}}}}for(var e=f.length-1;e>=0;e--){var k=f[e][1];var c=f[e][0];for(var d=0,n=c.length;d=0;d--){var e=this.items[d];if(e.instance!=this.currentContainer&&this.currentContainer&&e.item[0]!=this.currentItem[0]){continue}var c=this.options.toleranceElement?a(this.options.toleranceElement,e.item):e.item;if(!b){e.width=c.outerWidth();e.height=c.outerHeight()}var f=c.offset();e.left=f.left;e.top=f.top}if(this.options.custom&&this.options.custom.refreshContainers){this.options.custom.refreshContainers.call(this)}else{for(var d=this.containers.length-1;d>=0;d--){var f=this.containers[d].element.offset();this.containers[d].containerCache.left=f.left;this.containers[d].containerCache.top=f.top;this.containers[d].containerCache.width=this.containers[d].element.outerWidth();this.containers[d].containerCache.height=this.containers[d].element.outerHeight()}}},_createPlaceholder:function(d){var b=d||this,e=b.options;if(!e.placeholder||e.placeholder.constructor==String){var c=e.placeholder;e.placeholder={element:function(){var f=a(document.createElement(b.currentItem[0].nodeName)).addClass(c||b.currentItem[0].className+" ui-sortable-placeholder").removeClass("ui-sortable-helper")[0];if(!c){f.style.visibility="hidden"}return f},update:function(f,g){if(c&&!e.forcePlaceholderSize){return}if(!g.height()){g.height(b.currentItem.innerHeight()-parseInt(b.currentItem.css("paddingTop")||0,10)-parseInt(b.currentItem.css("paddingBottom")||0,10))}if(!g.width()){g.width(b.currentItem.innerWidth()-parseInt(b.currentItem.css("paddingLeft")||0,10)-parseInt(b.currentItem.css("paddingRight")||0,10))}}}}b.placeholder=a(e.placeholder.element.call(b.element,b.currentItem));b.currentItem.after(b.placeholder);e.placeholder.update(b,b.placeholder)},_contactContainers:function(d){for(var c=this.containers.length-1;c>=0;c--){if(this._intersectsWith(this.containers[c].containerCache)){if(!this.containers[c].containerCache.over){if(this.currentContainer!=this.containers[c]){var h=10000;var g=null;var e=this.positionAbs[this.containers[c].floating?"left":"top"];for(var b=this.items.length-1;b>=0;b--){if(!a.ui.contains(this.containers[c].element[0],this.items[b].item[0])){continue}var f=this.items[b][this.containers[c].floating?"left":"top"];if(Math.abs(f-e)this.containment[2]){d=this.containment[2]+this.offset.click.left}if(e.pageY-this.offset.click.top>this.containment[3]){c=this.containment[3]+this.offset.click.top}}if(h.grid){var g=this.originalPageY+Math.round((c-this.originalPageY)/h.grid[1])*h.grid[1];c=this.containment?(!(g-this.offset.click.topthis.containment[3])?g:(!(g-this.offset.click.topthis.containment[2])?f:(!(f-this.offset.click.left=0;c--){if(a.ui.contains(this.containers[c].element[0],this.currentItem[0])&&!e){f.push((function(g){return function(h){g._trigger("receive",h,this._uiHash(this))}}).call(this,this.containers[c]));f.push((function(g){return function(h){g._trigger("update",h,this._uiHash(this))}}).call(this,this.containers[c]))}}}for(var c=this.containers.length-1;c>=0;c--){if(!e){f.push((function(g){return function(h){g._trigger("deactivate",h,this._uiHash(this))}}).call(this,this.containers[c]))}if(this.containers[c].containerCache.over){f.push((function(g){return function(h){g._trigger("out",h,this._uiHash(this))}}).call(this,this.containers[c]));this.containers[c].containerCache.over=0}}if(this._storedCursor){a("body").css("cursor",this._storedCursor)}if(this._storedOpacity){this.helper.css("opacity",this._storedOpacity)}if(this._storedZIndex){this.helper.css("zIndex",this._storedZIndex=="auto"?"":this._storedZIndex)}this.dragging=false;if(this.cancelHelperRemoval){if(!e){this._trigger("beforeStop",d,this._uiHash());for(var c=0;c *",opacity:false,placeholder:false,revert:false,scroll:true,scrollSensitivity:20,scrollSpeed:20,scope:"default",tolerance:"intersect",zIndex:1000}})})(jQuery); \ No newline at end of file diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js index fc01221f36a..cabb0122543 100644 --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -94,7 +94,18 @@ $.extend( View.prototype, { this.tracks.push( track ); if (track.init) { track.init(); } }, - redraw: function () { + remove_track: function( track ) { + delete this.tracks[track]; + }, + update_options: function() { + for (var track_id in view.tracks) { + var track = view.tracks[track_id]; + if (track.update_options) { + track.update_options(track_id); + } + } + }, + redraw: function() { var span = this.span / Math.pow(this.zoom_factor, this.zoom_level), low = this.center - (span / 2), high = low + span; @@ -252,23 +263,22 @@ $.extend( LabelTrack.prototype, Track.prototype, { } }); -var LineTrack = function ( name, dataset_id, indexer, height, minval, maxval ) { +var LineTrack = function ( name, dataset_id, indexer, prefs ) { + this.track_type = "LineTrack"; this.tile_cache = new Cache(CACHED_TILES_LINE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); this.indexer = indexer; - this.height_px = (height ? height : 100); + this.height_px = 100; this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; this.data_queue = {}; this.data_cache = new Cache(CACHED_DATA); // We need to cache some data because of // asynchronous calls - if (minval !== undefined && maxval !== undefined) { - this.min_value = minval; - this.max_value = maxval; - this.vertical_range = maxval - minval; - } + this.prefs = { 'min_value': undefined, 'max_value': undefined }; + if (prefs.min_value !== undefined) { this.prefs.min_value = prefs.min_value; } + if (prefs.max_value !== undefined) { this.prefs.max_value = prefs.max_value; } }; $.extend( LineTrack.prototype, TiledTrack.prototype, { init: function() { @@ -293,19 +303,19 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, { track.content_div.text(""); track.content_div.css( "height", track.height_px + "px" ); - if (track.min_value === undefined || track.max_value === undefined) { - track.min_value = data.min; - track.max_value = data.max; - track.vertical_range = track.max_value - track.min_value; - + if (track.prefs.min_value === undefined || track.prefs.max_value === undefined) { + track.prefs.min_value = data.min; + track.prefs.max_value = data.max; + // Update the config - $('#track_' + track_id + '_minval').val(track.min_value); - $('#track_' + track_id + '_maxval').val(track.max_value); + $('#track_' + track_id + '_minval').val(track.prefs.min_value); + $('#track_' + track_id + '_maxval').val(track.prefs.max_value); } + track.vertical_range = track.prefs.max_value - track.prefs.min_value; // Draw y-axis labels - var min_label = $("
").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.min_value); - var max_label = $("
").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.max_value); + var min_label = $("
").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value); + var max_label = $("
").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value); max_label.css({ position: "relative", top: "25px" }); max_label.prependTo(track.container_div); @@ -358,8 +368,13 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, { canvas.get(0).width = Math.ceil( tile_length * w_scale ); canvas.get(0).height = this.height_px; - var ctx = canvas.get(0).getContext("2d"); - var in_path = false; + var ctx = canvas.get(0).getContext("2d"), + in_path = false, + min_value = this.prefs.min_value, + max_value = this.prefs.max_value, + vertical_range = this.vertical_range, + height_px = this.height_px; + ctx.beginPath(); for ( var i = 0; i < data.length - 1; i++ ) { var x = data[i][0] - tile_low; @@ -371,12 +386,12 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, { // Translate x = x * w_scale; // console.log(y, this.min_value, this.vertical_range, (y - this.min_value) / this.vertical_range * this.height_px); - if (y <= this.min_value) { - y = this.min_value; - } else if (y >= this.max_value) { - y = this.max_value; + if (y <= min_value) { + y = min_value; + } else if (y >= max_value) { + y = max_value; } - y = Math.round( this.height_px - (y - this.min_value) / this.vertical_range * this.height_px ); + y = Math.round( height_px - (y - min_value) / vertical_range * height_px ); // console.log(canvas.get(0).height, canvas.get(0).width); if ( in_path ) { ctx.lineTo( x, y ); @@ -395,33 +410,37 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, { var minval = 'track_' + track_id + '_minval', maxval = 'track_' + track_id + '_maxval', min_label = $('').attr("for", minval).text("Min value:"), - min_input = $('').attr("id", minval).val(this.min_value || ""), + min_val = (this.prefs.min_value === undefined ? "" : this.prefs.min_value), + min_input = $('').attr("id", minval).val(min_val), max_label = $('').attr("for", maxval).text("Max value:"), - max_input = $('').attr("id", maxval).val(this.max_value || ""); + max_val = (this.prefs.max_value === undefined ? "" : this.prefs.max_value), + max_input = $('').attr("id", maxval).val(max_val); return container.append(min_label).append(min_input).append(max_label).append(max_input); }, update_options: function(track_id) { var min_value = $('#track_' + track_id + '_minval').val(), max_value = $('#track_' + track_id + '_maxval').val(); - if ( min_value !== this.min_value || max_value !== this.max_value) { - this.min_value = parseFloat(min_value); - this.max_value = parseFloat(max_value); - this.vertical_range = this.max_value - this.min_value; - $('#linetrack_' + track_id + '_minval').text(this.min_value); - $('#linetrack_' + track_id + '_maxval').text(this.max_value); + if ( min_value !== this.prefs.min_value || max_value !== this.prefs.max_value) { + this.prefs.min_value = parseFloat(min_value); + this.prefs.max_value = parseFloat(max_value); + this.vertical_range = this.prefs.max_value - this.prefs.min_value; + // Update the y-axis + $('#linetrack_' + track_id + '_minval').text(this.prefs.min_value); + $('#linetrack_' + track_id + '_maxval').text(this.prefs.max_value); this.tile_cache.clear(); this.draw(); } } }); -var FeatureTrack = function ( name, dataset_id, indexer, height ) { +var FeatureTrack = function ( name, dataset_id, indexer, prefs ) { + this.track_type = "FeatureTrack"; this.tile_cache = new Cache(CACHED_TILES_FEATURE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); this.indexer = indexer; - this.height_px = (height ? height : 100); + this.height_px = 100; this.container_div.addClass( "feature-track" ); this.dataset_id = dataset_id; this.zo_slots = {}; @@ -429,14 +448,16 @@ var FeatureTrack = function ( name, dataset_id, indexer, height ) { this.showing_details = false; this.vertical_detail_px = 10; this.vertical_nodetail_px = 3; - this.block_color = "black"; - this.label_color = "black"; this.default_font = "9px Monaco, Lucida Console, monospace"; this.left_offset = 200; this.inc_slots = {}; this.data_queue = {}; this.s_e_by_tile = {}; this.data_cache = new Cache(20); + this.prefs = { 'block_color': 'black', 'label_color': 'black' }; + if (prefs.block_color !== undefined) { this.prefs.block_color = prefs.block_color; } + if (prefs.label_color !== undefined) { this.prefs.label_color = prefs.label_color; } + }; $.extend( FeatureTrack.prototype, TiledTrack.prototype, { init: function() { @@ -609,18 +630,23 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, { // console.log(tile_low, tile_high, tile_length, w_scale); var width = Math.ceil( tile_span * w_scale ), - new_canvas = $(""); + new_canvas = $(""), + label_color = this.prefs.label_color, + block_color = this.prefs.block_color, + left_offset = this.left_offset, + showing_details = this.showing_details, + y_scale = (this.showing_details ? this.vertical_detail_px : this.vertical_nodetail_px); new_canvas.css({ position: "absolute", top: 0, - left: ( tile_low - this.view.low ) * w_scale - this.left_offset + left: ( tile_low - this.view.low ) * w_scale - left_offset }); - new_canvas.get(0).width = width + this.left_offset; + new_canvas.get(0).width = width + 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.block_color; + ctx.fillStyle = this.prefs.block_color; ctx.font = this.default_font; ctx.textAlign = "right"; @@ -630,22 +656,22 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, { 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.showing_details ? this.vertical_detail_px : this.vertical_nodetail_px); + y_center = slots[feature.uid] * y_scale; var thickness, y_start, thick_start = null, thick_end = null; if (feature.thick_start && feature.thick_end) { thick_start = Math.floor( Math.max(0, (feature.thick_start - tile_low) * w_scale) ); thick_end = Math.ceil( Math.min(width, (feature.thick_end - tile_low) * w_scale) ); } - if (!this.showing_details) { + if (!showing_details) { // Non-detail levels - ctx.fillRect(f_start + this.left_offset, y_center + 5, f_end - f_start, 1); + ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, 1); } else { // Showing labels, blocks, details if (feature.start > tile_low) { - ctx.fillStyle = this.label_color; - ctx.fillText(feature.name, f_start - 1 + this.left_offset, y_center + 8); - ctx.fillStyle = this.block_color; + ctx.fillStyle = label_color; + ctx.fillText(feature.name, f_start - 1 + left_offset, y_center + 8); + ctx.fillStyle = block_color; } var blocks = feature.blocks; if (blocks) { @@ -656,8 +682,8 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, { } else if (feature.strand == "-") { ctx.fillStyle = LEFT_STRAND; } - ctx.fillRect(f_start + this.left_offset, y_center, f_end - f_start, 10); - ctx.fillStyle = this.block_color; + ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, 10); + ctx.fillStyle = block_color; } for (var k = 0, k_len = blocks.length; k < k_len; k++) { @@ -668,7 +694,7 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, { // Draw the block thickness = 5; y_start = 3; - ctx.fillRect(block_start + this.left_offset, y_center + y_start, block_end - block_start, thickness); + ctx.fillRect(block_start + left_offset, y_center + y_start, block_end - block_start, thickness); // Draw thick regions: check if block intersects with thick region if (thick_start !== undefined && !(block_start > thick_end || block_end < thick_start) ) { @@ -676,7 +702,7 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, { y_start = 1; var block_thick_start = Math.max(block_start, thick_start), block_thick_end = Math.min(block_end, thick_end); - ctx.fillRect(block_thick_start + this.left_offset, y_center + y_start, block_thick_end - block_thick_start, thickness); + ctx.fillRect(block_thick_start + left_offset, y_center + y_start, block_thick_end - block_thick_start, thickness); } } @@ -684,15 +710,15 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, { // If there are no blocks, we treat the feature as one big exon thickness = 9; y_start = 1; - ctx.fillRect(f_start + this.left_offset, y_center + y_start, f_end - f_start, thickness); + ctx.fillRect(f_start + left_offset, y_center + y_start, f_end - f_start, thickness); if ( feature.strand ) { if (feature.strand == "+") { ctx.fillStyle = RIGHT_STRAND_INV; } else if (feature.strand == "-") { ctx.fillStyle = LEFT_STRAND_INV; } - ctx.fillRect(f_start + this.left_offset, y_center, f_end - f_start, 10); - ctx.fillStyle = this.block_color; + ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, 10); + ctx.fillStyle = prefs.block_color; } } } @@ -707,29 +733,29 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, { var block_color = 'track_' + track_id + '_block_color', block_color_label = $('').attr("for", block_color).text("Block color:"), - block_color_input = $('').attr("id", block_color).attr("name", block_color).val(this.block_color), + block_color_input = $('').attr("id", block_color).attr("name", block_color).val(this.prefs.block_color), label_color = 'track_' + track_id + '_label_color', label_color_label = $('').attr("for", label_color).text("Label color:"), - label_color_input = $('').attr("id", label_color).attr("name", label_color).val(this.label_color); + label_color_input = $('').attr("id", label_color).attr("name", label_color).val(this.prefs.label_color); return container.append(block_color_label).append(block_color_input).append(label_color_label).append(label_color_input); }, update_options: function(track_id) { var block_color = $('#track_' + track_id + '_block_color').val(), label_color = $('#track_' + track_id + '_label_color').val(); - if (block_color !== this.block_color || label_color !== this.label_color) { - this.block_color = block_color; - this.label_color = label_color; + if (block_color !== this.prefs.block_color || label_color !== this.prefs.label_color) { + this.prefs.block_color = block_color; + this.prefs.label_color = label_color; this.tile_cache.clear(); this.draw(); } } }); -var ReadTrack = function ( name, dataset_id, indexer, height ) { +var ReadTrack = function ( name, dataset_id, indexer, prefs ) { + this.track_type = "ReadTrack"; 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"; + FeatureTrack.call( this, name, dataset_id, indexer, prefs ); }; $.extend( ReadTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { @@ -760,7 +786,7 @@ $.extend( ReadTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { 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.block_color; + ctx.fillStyle = this.prefs.block_color; ctx.font = this.default_font; ctx.textAlign = "right"; var px_per_char = ctx.measureText("A").width; diff --git a/static/trackster.css b/static/trackster.css index 98dbfca6c21..4afa01c5907 100644 --- a/static/trackster.css +++ b/static/trackster.css @@ -1,16 +1,3 @@ -body, html { - height: 100%; -} - -body { - margin: 0 0; - padding: 0; - font-family: verdana; - font-size: 12px; - overflow: hidden; - background: #eeeeee; -} - #content { width: 100%; } @@ -24,10 +11,6 @@ body { bottom: 0; } -input { - font-size: 100%; -} - /*canvas{ border-left: 1px solid green; border-right: 1px solid red; } /* debugging */ diff --git a/templates/grid_base.mako b/templates/grid_base.mako index 1beff19e2d9..5d33a22ad97 100644 --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -205,6 +205,7 @@ var grid = this; var checkboxes = $(this).find("input.grid-row-select-checkbox"); var update = $(this).find( "span.grid-selected-count" ); + update.text(""); $(checkboxes).each( function() { $(this).change( function() { var n = $(checkboxes).filter("[checked]").size(); @@ -834,6 +835,7 @@ <% num_rows_rendered = 1 %> %endif %for i, item in enumerate( query ): + <% encoded_id = trans.security.encode_id( item.id ) %> - + %endif ## Data columns @@ -875,12 +877,12 @@ cls = "menubutton" if column.attach_popup and href: cls = "menubutton split" - + %> - %if href: + %if href:
${v} %else: -
${v}
+
%endif %endfor %endif diff --git a/templates/tracks/add_tracks.mako b/templates/tracks/add_tracks.mako new file mode 100644 index 00000000000..e5b6846d5f8 --- /dev/null +++ b/templates/tracks/add_tracks.mako @@ -0,0 +1,12 @@ +## Template generates a grid that enables user to add tracks +<%namespace file="../grid_base.mako" import="*" /> + +${javascripts()} +${stylesheets()} +${render_grid_table( grid, show_item_checkboxes=True )} + +## Initialize the grid. + diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako index 4ca3ecf1c9b..e02d314273e 100644 --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -78,16 +78,18 @@ ${h.css( "history" )} ##
    -## -
    +## + + + <%def name="javascripts()"> ${parent.javascripts()} -${h.js( "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )} +${h.js( "json2", "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )}