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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 21 May '13

21 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9bb23c38aeec/ Changeset: 9bb23c38aeec Branch: next-stable User: carlfeberhard Date: 2013-05-21 16:58:08 Summary: Fix to scatterplot to use non-dictionary hda Affected #: 1 file diff -r 0973c5acbfdac9b1de170341a19e4e57606358f8 -r 9bb23c38aeec1f26ec1c22fbcad8a098fd6ae015 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -883,48 +883,10 @@ """ Returns a page that controls and renders a scatteplot graph. """ - # Get HDA. hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) - hda_dict = hda.get_api_value() - hda_dict[ 'id' ] = dataset_id - - if( ( hda_dict[ 'metadata_column_names' ] == None ) - and ( hasattr( hda.datatype, 'column_names' ) ) ): - hda_dict[ 'metadata_column_names' ] = hda.datatype.column_names - - # try to get the first line (assuming it's a header) - #TODO: doesn't belong here - try: - num_comment_lines = 1 - if hda_dict[ 'metadata_comment_lines' ]: - num_comment_lines = hda_dict[ 'metadata_comment_lines' ] - - infile = open( hda.file_name ) - for index, line in enumerate( infile ): - if 'comment_lines' not in hda_dict: - hda_dict[ 'comment_lines' ] = [] - hda_dict[ 'comment_lines' ].append( line ) - if index >= num_comment_lines: - break - infile.close() - - except Exception, exc: - if infile: - infile.close() - log.error( str( exc ) ) - - history_id = trans.security.encode_id( hda.history.id ) - - #TODO: add column data - # Read data. - #data_provider = ColumnDataProvider( original_dataset=hda, **kwargs ) - #data = data_provider.get_data() - - # Return plot. return trans.fill_template_mako( "visualization/scatterplot.mako", - hda=hda_dict, - historyID=history_id, - kwargs=kwargs ) + hda=hda, + query_args=kwargs ) @web.expose def phyloviz( self, trans, dataset_id, tree_index=0, **kwargs ): https://bitbucket.org/galaxy/galaxy-central/commits/137dc44f2178/ Changeset: 137dc44f2178 User: carlfeberhard Date: 2013-05-21 16:58:47 Summary: merge next-stable Affected #: 1 file diff -r 4adb47c6fe35edafaf9fcf84dfda7cd098ef1686 -r 137dc44f21782c771879af1febfe962a2ea9ae6a lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -883,48 +883,10 @@ """ Returns a page that controls and renders a scatteplot graph. """ - # Get HDA. hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) - hda_dict = hda.get_api_value() - hda_dict[ 'id' ] = dataset_id - - if( ( hda_dict[ 'metadata_column_names' ] == None ) - and ( hasattr( hda.datatype, 'column_names' ) ) ): - hda_dict[ 'metadata_column_names' ] = hda.datatype.column_names - - # try to get the first line (assuming it's a header) - #TODO: doesn't belong here - try: - num_comment_lines = 1 - if hda_dict[ 'metadata_comment_lines' ]: - num_comment_lines = hda_dict[ 'metadata_comment_lines' ] - - infile = open( hda.file_name ) - for index, line in enumerate( infile ): - if 'comment_lines' not in hda_dict: - hda_dict[ 'comment_lines' ] = [] - hda_dict[ 'comment_lines' ].append( line ) - if index >= num_comment_lines: - break - infile.close() - - except Exception, exc: - if infile: - infile.close() - log.error( str( exc ) ) - - history_id = trans.security.encode_id( hda.history.id ) - - #TODO: add column data - # Read data. - #data_provider = ColumnDataProvider( original_dataset=hda, **kwargs ) - #data = data_provider.get_data() - - # Return plot. return trans.fill_template_mako( "visualization/scatterplot.mako", - hda=hda_dict, - historyID=history_id, - kwargs=kwargs ) + hda=hda, + query_args=kwargs ) @web.expose def phyloviz( self, trans, dataset_id, tree_index=0, **kwargs ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 21 May '13

21 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4adb47c6fe35/ Changeset: 4adb47c6fe35 User: dan Date: 2013-05-21 16:39:47 Summary: Fix for uploading toolshed repository via hg. Affected #: 1 file diff -r 2b456e2215824614a974f481ef22506ad99267e9 -r 4adb47c6fe35edafaf9fcf84dfda7cd098ef1686 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -74,7 +74,7 @@ fd, uploaded_file_name = tempfile.mkstemp() uploaded_file = open( uploaded_file_name, 'wb' ) while 1: - chunk = stream.read( CHUNK_SIZE ) + chunk = stream.read( util.CHUNK_SIZE ) if not chunk: break uploaded_file.write( chunk ) https://bitbucket.org/galaxy/galaxy-central/commits/0973c5acbfda/ Changeset: 0973c5acbfda Branch: next-stable User: dan Date: 2013-05-21 16:39:47 Summary: Fix for uploading toolshed repository via hg. Affected #: 1 file diff -r 632b55655358ee532777a6af0f7ed781905a67d1 -r 0973c5acbfdac9b1de170341a19e4e57606358f8 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -74,7 +74,7 @@ fd, uploaded_file_name = tempfile.mkstemp() uploaded_file = open( uploaded_file_name, 'wb' ) while 1: - chunk = stream.read( CHUNK_SIZE ) + chunk = stream.read( util.CHUNK_SIZE ) if not chunk: break uploaded_file.write( chunk ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 May '13

20 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/632b55655358/ Changeset: 632b55655358 Branch: next-stable User: Dave Bouvier Date: 2013-05-20 22:50:32 Summary: Fix for uploading repository_dependencies.xml without a changeset revision specified when the target repository's latest downloadable changeset revision is followed by two or more non-downloadable changeset revisions. Affected #: 1 file diff -r 7c42691969906be88d5ac290b3e922a19ddf54af -r 632b55655358ee532777a6af0f7ed781905a67d1 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -497,7 +497,10 @@ repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), repository_tip ) if repository_metadata and repository_metadata.downloadable: return repository_tip - return get_previous_metadata_changeset_revision( repository, repo, repository_tip, downloadable=True ) + changeset_revisions = get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) + if changeset_revisions: + return changeset_revisions[ -1 ] + return INITIAL_CHANGELOG_HASH def get_named_tmpfile_from_ctx( ctx, filename, dir ): """Return a named temporary file created from a specified file with a given name included in a repository changeset revision.""" @@ -583,7 +586,7 @@ rev = '-1' changeset_tups.append( ( rev, changeset_revision ) ) sorted_changeset_tups = sorted( changeset_tups ) - sorted_changeset_revisions = [ changeset_tup[ 1 ] for changeset_tup in sorted_changeset_tups ] + sorted_changeset_revisions = [ str( changeset_tup[ 1 ] ) for changeset_tup in sorted_changeset_tups ] return sorted_changeset_revisions def get_previous_metadata_changeset_revision( repository, repo, before_changeset_revision, downloadable=True ): https://bitbucket.org/galaxy/galaxy-central/commits/2b456e221582/ Changeset: 2b456e221582 User: Dave Bouvier Date: 2013-05-20 22:51:05 Summary: Merged in bugfix from next-stable. Affected #: 1 file diff -r 5e89080bc9fa7eccc7ec1d4c8ac6da3657ce457e -r 2b456e2215824614a974f481ef22506ad99267e9 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -497,7 +497,10 @@ repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), repository_tip ) if repository_metadata and repository_metadata.downloadable: return repository_tip - return get_previous_metadata_changeset_revision( repository, repo, repository_tip, downloadable=True ) + changeset_revisions = get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) + if changeset_revisions: + return changeset_revisions[ -1 ] + return INITIAL_CHANGELOG_HASH def get_named_tmpfile_from_ctx( ctx, filename, dir ): """Return a named temporary file created from a specified file with a given name included in a repository changeset revision.""" @@ -583,7 +586,7 @@ rev = '-1' changeset_tups.append( ( rev, changeset_revision ) ) sorted_changeset_tups = sorted( changeset_tups ) - sorted_changeset_revisions = [ changeset_tup[ 1 ] for changeset_tup in sorted_changeset_tups ] + sorted_changeset_revisions = [ str( changeset_tup[ 1 ] ) for changeset_tup in sorted_changeset_tups ] return sorted_changeset_revisions def get_previous_metadata_changeset_revision( repository, repo, before_changeset_revision, downloadable=True ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Merge in next-stable
by commits-noreply＠bitbucket.org 20 May '13

20 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5e89080bc9fa/ Changeset: 5e89080bc9fa User: jgoecks Date: 2013-05-20 22:16:56 Summary: Merge in next-stable Affected #: 3 files diff -r ebe882ab26c4abbd7b3fa85161864257a3f785a6 -r 5e89080bc9fa7eccc7ec1d4c8ac6da3657ce457e static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),j;if(this.prefs.show_sample_data){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];alt=locus_data[4].split(",");sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));ctx.fillStyle="#999999";ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=this.base_color_fn(alt[j]);allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}if(!this.prefs.show_sample_data){continue}draw_y_start=this.prefs.summary_height+this.divider_height;for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.4}if(variant){ctx.fillStyle=this.base_color_fn(variant);if(this.mode==="Squish"||w_scale<ctx.canvas.manager.char_width_px){ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}else{ctx.fillText(variant,char_x_start,draw_y_start+row_height)}}}}}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),j;if(this.prefs.show_sample_data){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];alt=locus_data[4].split(",");sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=this.base_color_fn(alt[j]);allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}if(!this.prefs.show_sample_data){continue}draw_y_start=this.prefs.summary_height+this.divider_height;for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){ctx.fillStyle=this.base_color_fn(variant);if(this.mode==="Squish"||w_scale<ctx.canvas.manager.char_width_px){ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}else{ctx.fillText(variant,char_x_start,draw_y_start+row_height)}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file diff -r ebe882ab26c4abbd7b3fa85161864257a3f785a6 -r 5e89080bc9fa7eccc7ec1d4c8ac6da3657ce457e static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -1538,6 +1538,8 @@ * as a left_offset may be present. */ draw: function(ctx, width, height, w_scale) { + ctx.save(); + var locus_data, pos, id, @@ -1568,7 +1570,7 @@ ctx.fillStyle = '#F3F3F3'; ctx.globalAlpha = 1; ctx.fillRect(0, this.prefs.summary_height - this.divider_height, width, this.divider_height); - } + } // Draw variants. ctx.textAlign = "center"; @@ -1586,6 +1588,7 @@ // Draw summary. ctx.fillStyle = '#999999'; + ctx.globalAlpha = 1; // Draw background for summary. ctx.fillRect(draw_x_start, 0, base_px, this.prefs.summary_height); draw_y_start = this.prefs.summary_height; @@ -1622,7 +1625,7 @@ else { // Heterozygous for variant. variant = (genotype[0] !== '0' ? genotype[0] : genotype[1]); variant = alt[ parseInt(variant, 10) - 1 ]; - ctx.globalAlpha = 0.4; + ctx.globalAlpha = 0.5; } // If there's a variant, draw it. @@ -1637,6 +1640,8 @@ } } } + + ctx.restore(); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Trackster: transparency and state fixes for variant painter.
by commits-noreply＠bitbucket.org 20 May '13

20 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7c4269196990/ Changeset: 7c4269196990 Branch: next-stable User: jgoecks Date: 2013-05-20 22:16:03 Summary: Trackster: transparency and state fixes for variant painter. Affected #: 2 files diff -r b1850aa88b03d9a7455e380540b7e7c23b251b29 -r 7c42691969906be88d5ac290b3e922a19ddf54af static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),j;if(this.prefs.show_sample_data){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];alt=locus_data[4].split(",");sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));ctx.fillStyle="#999999";ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=this.base_color_fn(alt[j]);allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}if(!this.prefs.show_sample_data){continue}draw_y_start=this.prefs.summary_height+this.divider_height;for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.4}if(variant){ctx.fillStyle=this.base_color_fn(variant);if(this.mode==="Squish"||w_scale<ctx.canvas.manager.char_width_px){ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}else{ctx.fillText(variant,char_x_start,draw_y_start+row_height)}}}}}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),j;if(this.prefs.show_sample_data){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];alt=locus_data[4].split(",");sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=this.base_color_fn(alt[j]);allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}if(!this.prefs.show_sample_data){continue}draw_y_start=this.prefs.summary_height+this.divider_height;for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){ctx.fillStyle=this.base_color_fn(variant);if(this.mode==="Squish"||w_scale<ctx.canvas.manager.char_width_px){ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}else{ctx.fillText(variant,char_x_start,draw_y_start+row_height)}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file diff -r b1850aa88b03d9a7455e380540b7e7c23b251b29 -r 7c42691969906be88d5ac290b3e922a19ddf54af static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -1538,6 +1538,8 @@ * as a left_offset may be present. */ draw: function(ctx, width, height, w_scale) { + ctx.save(); + var locus_data, pos, id, @@ -1568,7 +1570,7 @@ ctx.fillStyle = '#F3F3F3'; ctx.globalAlpha = 1; ctx.fillRect(0, this.prefs.summary_height - this.divider_height, width, this.divider_height); - } + } // Draw variants. ctx.textAlign = "center"; @@ -1586,6 +1588,7 @@ // Draw summary. ctx.fillStyle = '#999999'; + ctx.globalAlpha = 1; // Draw background for summary. ctx.fillRect(draw_x_start, 0, base_px, this.prefs.summary_height); draw_y_start = this.prefs.summary_height; @@ -1622,7 +1625,7 @@ else { // Heterozygous for variant. variant = (genotype[0] !== '0' ? genotype[0] : genotype[1]); variant = alt[ parseInt(variant, 10) - 1 ]; - ctx.globalAlpha = 0.4; + ctx.globalAlpha = 0.5; } // If there's a variant, draw it. @@ -1637,6 +1640,8 @@ } } } + + ctx.restore(); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 May '13

20 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1a3dc9d098e0/ Changeset: 1a3dc9d098e0 Branch: next-stable User: natefoo Date: 2013-05-20 21:54:08 Summary: Open next-stable branch for upcoming June 3, 2013 release. Affected #: 607 files diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b .hgignore --- a/.hgignore +++ b/.hgignore @@ -20,6 +20,7 @@ database/pbs database/tmp database/*.sqlite +database/openid_consumer_cache # Python bytecode *.pyc @@ -35,6 +36,11 @@ tool_shed_webapp.pid hgweb.config* +# Reports Runtime Files +reports_webapp.lock +reports_webapp.log +reports_webapp.pid + # Config files universe_wsgi.ini reports_wsgi.ini @@ -54,7 +60,7 @@ job_conf.xml data_manager_conf.xml shed_data_manager_conf.xml - +visualizations_conf.xml static/welcome.html.* static/welcome.html @@ -75,6 +81,7 @@ # Test output run_functional_tests.html +test/tool_shed/tmp/* # Project files *.kpf diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b .hgtags --- a/.hgtags +++ b/.hgtags @@ -1,1 +1,4 @@ a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 +1c717491139269651bb59687563da9410b84c65d release_2013.02.08 +75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 +2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -93,26 +93,49 @@ JARS="/galaxy/software/jars" -for link in $LINKS; do - echo "Linking $link" - rm -f tool-data/`basename $link` - ln -sf $link tool-data -done - -if [ -d "$HYPHY" ]; then - echo "Linking $HYPHY" - rm -f tool-data/HYPHY - ln -sf $HYPHY tool-data/HYPHY +if [ ! $1 ]; then + type="standard" +elif [ $1 == "-ec2" ]; then + type="external-ec2" +else + type="unknown" fi -if [ -d "$JARS" ]; then - echo "Linking $JARS" - rm -f tool-data/shared/jars - ln -sf $JARS tool-data/shared/jars -fi +case $type in + external*) + echo "Running standalone buildbot setup..." + for sample in tool-data/*.sample; do + basename=${sample%.sample} + if [ ! -f $basename ]; then + echo "Copying $sample to $basename" + cp "$sample" "$basename" + fi + done + ;; + *) + echo "Running standard buildbot setup..." + for link in $LINKS; do + echo "Linking $link" + rm -f tool-data/`basename $link` + ln -sf $link tool-data + done + + if [ -d "$HYPHY" ]; then + echo "Linking $HYPHY" + rm -f tool-data/HYPHY + ln -sf $HYPHY tool-data/HYPHY + fi + + if [ -d "$JARS" ]; then + echo "Linking $JARS" + rm -f tool-data/shared/jars + ln -sf $JARS tool-data/shared/jars + fi + ;; +esac for sample in $SAMPLES; do - file=`echo $sample | sed -e 's/\.sample$//'` + file=${sample%.sample} echo "Copying $sample to $file" cp $sample $file done diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -3,16 +3,13 @@ <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"><datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false"/> + <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true" /> + <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true" /><datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/><datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/><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"/> - <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree"/> -  + <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/><display file="ucsc/bam.xml" /><display file="ensembl/ensembl_bam.xml" /><display file="igv/bam.xml" /> @@ -20,10 +17,9 @@ </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"/><converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> - <converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/><converter file="bed_to_fli_converter.xml" target_datatype="fli"/><display file="igb/bed.xml" /> @@ -49,7 +45,7 @@ <datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="True"><converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> - <converter file="interval_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/></datatype><datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /> @@ -91,7 +87,7 @@ <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true"><converter file="gff_to_bed_converter.xml" target_datatype="bed"/><converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/> - <converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/><converter file="gff_to_fli_converter.xml" target_datatype="fli"/><display file="ensembl/ensembl_gff.xml" inherit="True"/> @@ -101,7 +97,7 @@ <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/><datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"><converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/> - <converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/></datatype><datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> @@ -113,7 +109,7 @@ <converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/><converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> - <converter file="interval_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <converter file="interval_to_bigwig_converter.xml" target_datatype="bigwig"/><display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/><display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/> @@ -154,10 +150,13 @@ <datatype extension="encodepeak" type="galaxy.datatypes.interval:ENCODEPeak" display_in_upload="True"><converter file="encodepeak_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/><converter file="encodepeak_to_bgzip_converter.xml" target_datatype="bgzip"/> - <converter file="encodepeak_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/></datatype><datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/> - <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" /> + <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true"> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + </datatype><datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/><datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /><datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> @@ -167,7 +166,7 @@ <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/><datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"><converter file="sam_to_bam.xml" target_datatype="bam"/> - <converter file="sam_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/></datatype><datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/> @@ -185,7 +184,7 @@ <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/><converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> - <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/><display file="ucsc/vcf.xml" /><display file="igv/vcf.xml" /><display file="rviewer/vcf.xml" inherit="True"/> @@ -198,7 +197,6 @@ <display file="igb/wig.xml" /></datatype> - <datatype extension="summary_tree" type="galaxy.datatypes.binary:Binary" subclass="True" /><datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="True" /><datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="True" /><datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="True" /> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/galaxy.webapps.tool_shed.api.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.api.rst @@ -0,0 +1,19 @@ +api Package +=========== + +:mod:`repositories` Module +-------------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.repositories + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_revisions` Module +---------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.repository_revisions + :members: + :undoc-members: + :show-inheritance: + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/galaxy.webapps.tool_shed.controllers.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst @@ -0,0 +1,59 @@ +controllers Package +=================== + +:mod:`controllers` Package +-------------------------- + +.. automodule:: galaxy.webapps.tool_shed.controllers + :members: + :undoc-members: + :show-inheritance: + +:mod:`admin` Module +------------------- + +.. automodule:: galaxy.webapps.tool_shed.controllers.admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`hg` Module +---------------- + +.. automodule:: galaxy.webapps.tool_shed.controllers.hg + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository` Module +------------------------ + +.. automodule:: galaxy.webapps.tool_shed.controllers.repository + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_review` Module +------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.controllers.repository_review + :members: + :undoc-members: + :show-inheritance: + +:mod:`upload` Module +-------------------- + +.. automodule:: galaxy.webapps.tool_shed.controllers.upload + :members: + :undoc-members: + :show-inheritance: + +:mod:`user` Module +------------------ + +.. automodule:: galaxy.webapps.tool_shed.controllers.user + :members: + :undoc-members: + :show-inheritance: + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst @@ -0,0 +1,27 @@ +middleware Package +================== + +:mod:`middleware` Package +------------------------- + +.. automodule:: galaxy.webapps.tool_shed.framework.middleware + :members: + :undoc-members: + :show-inheritance: + +:mod:`hg` Module +---------------- + +.. automodule:: galaxy.webapps.tool_shed.framework.middleware.hg + :members: + :undoc-members: + :show-inheritance: + +:mod:`remoteuser` Module +------------------------ + +.. automodule:: galaxy.webapps.tool_shed.framework.middleware.remoteuser + :members: + :undoc-members: + :show-inheritance: + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/galaxy.webapps.tool_shed.framework.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.rst @@ -0,0 +1,18 @@ +framework Package +================= + +:mod:`framework` Package +------------------------ + +.. automodule:: galaxy.webapps.tool_shed.framework + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.tool_shed.framework.middleware + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst @@ -0,0 +1,11 @@ +migrate Package +=============== + +:mod:`check` Module +------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.check + :members: + :undoc-members: + :show-inheritance: + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/galaxy.webapps.tool_shed.model.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.rst @@ -0,0 +1,26 @@ +model Package +============= + +:mod:`model` Package +-------------------- + +.. automodule:: galaxy.webapps.tool_shed.model + :members: + :undoc-members: + :show-inheritance: + +:mod:`mapping` Module +--------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.mapping + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.tool_shed.model.migrate + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/galaxy.webapps.tool_shed.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.rst @@ -0,0 +1,47 @@ +tool_shed Package +================= + +:mod:`tool_shed` Package +------------------------ + +.. automodule:: galaxy.webapps.tool_shed + :members: + :undoc-members: + :show-inheritance: + +:mod:`app` Module +----------------- + +.. automodule:: galaxy.webapps.tool_shed.app + :members: + :undoc-members: + :show-inheritance: + +:mod:`buildapp` Module +---------------------- + +.. automodule:: galaxy.webapps.tool_shed.buildapp + :members: + :undoc-members: + :show-inheritance: + +:mod:`config` Module +-------------------- + +.. automodule:: galaxy.webapps.tool_shed.config + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.tool_shed.api + galaxy.webapps.tool_shed.controllers + galaxy.webapps.tool_shed.framework + galaxy.webapps.tool_shed.model + galaxy.webapps.tool_shed.security + galaxy.webapps.tool_shed.util + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/galaxy.webapps.tool_shed.security.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.security.rst @@ -0,0 +1,11 @@ +security Package +================ + +:mod:`security` Package +----------------------- + +.. automodule:: galaxy.webapps.tool_shed.security + :members: + :undoc-members: + :show-inheritance: + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/galaxy.webapps.tool_shed.util.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.util.rst @@ -0,0 +1,35 @@ +util Package +============ + +:mod:`common_util` Module +------------------------- + +.. automodule:: galaxy.webapps.tool_shed.util.common_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`container_util` Module +---------------------------- + +.. automodule:: galaxy.webapps.tool_shed.util.container_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`hgweb_config` Module +-------------------------- + +.. automodule:: galaxy.webapps.tool_shed.util.hgweb_config + :members: + :undoc-members: + :show-inheritance: + +:mod:`shed_statistics` Module +----------------------------- + +.. automodule:: galaxy.webapps.tool_shed.util.shed_statistics + :members: + :undoc-members: + :show-inheritance: + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/tool_shed.galaxy_install.grids.rst --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.grids.rst @@ -0,0 +1,11 @@ +grids Package +============= + +:mod:`admin_toolshed_grids` Module +---------------------------------- + +.. automodule:: tool_shed.galaxy_install.grids.admin_toolshed_grids + :members: + :undoc-members: + :show-inheritance: + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/tool_shed.galaxy_install.migrate.rst --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.migrate.rst @@ -0,0 +1,19 @@ +migrate Package +=============== + +:mod:`check` Module +------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.check + :members: + :undoc-members: + :show-inheritance: + +:mod:`common` Module +-------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.common + :members: + :undoc-members: + :show-inheritance: + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/tool_shed.galaxy_install.rst --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.rst @@ -0,0 +1,44 @@ +galaxy_install Package +====================== + +:mod:`galaxy_install` Package +----------------------------- + +.. automodule:: tool_shed.galaxy_install + :members: + :undoc-members: + :show-inheritance: + +:mod:`install_manager` Module +----------------------------- + +.. automodule:: tool_shed.galaxy_install.install_manager + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_util` Module +----------------------------- + +.. automodule:: tool_shed.galaxy_install.repository_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`update_manager` Module +---------------------------- + +.. automodule:: tool_shed.galaxy_install.update_manager + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + tool_shed.galaxy_install.grids + tool_shed.galaxy_install.migrate + tool_shed.galaxy_install.tool_dependencies + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst @@ -0,0 +1,27 @@ +tool_dependencies Package +========================= + +:mod:`common_util` Module +------------------------- + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.common_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`fabric_util` Module +------------------------- + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.fabric_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`install_util` Module +-------------------------- + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.install_util + :members: + :undoc-members: + :show-inheritance: + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/tool_shed.grids.rst --- /dev/null +++ b/doc/source/lib/tool_shed.grids.rst @@ -0,0 +1,35 @@ +grids Package +============= + +:mod:`admin_grids` Module +------------------------- + +.. automodule:: tool_shed.grids.admin_grids + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_grids` Module +------------------------------ + +.. automodule:: tool_shed.grids.repository_grids + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_review_grids` Module +------------------------------------- + +.. automodule:: tool_shed.grids.repository_review_grids + :members: + :undoc-members: + :show-inheritance: + +:mod:`util` Module +------------------ + +.. automodule:: tool_shed.grids.util + :members: + :undoc-members: + :show-inheritance: + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/tool_shed.rst --- /dev/null +++ b/doc/source/lib/tool_shed.rst @@ -0,0 +1,20 @@ +tool_shed Package +================= + +:mod:`tool_shed_registry` Module +-------------------------------- + +.. automodule:: tool_shed.tool_shed_registry + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + tool_shed.galaxy_install + tool_shed.grids + tool_shed.util + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b doc/source/lib/tool_shed.util.rst --- /dev/null +++ b/doc/source/lib/tool_shed.util.rst @@ -0,0 +1,107 @@ +util Package +============ + +:mod:`common_install_util` Module +--------------------------------- + +.. automodule:: tool_shed.util.common_install_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`common_util` Module +------------------------- + +.. automodule:: tool_shed.util.common_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`data_manager_util` Module +------------------------------- + +.. automodule:: tool_shed.util.data_manager_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`datatype_util` Module +--------------------------- + +.. automodule:: tool_shed.util.datatype_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`encoding_util` Module +--------------------------- + +.. automodule:: tool_shed.util.encoding_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`metadata_util` Module +--------------------------- + +.. automodule:: tool_shed.util.metadata_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`readme_util` Module +------------------------- + +.. automodule:: tool_shed.util.readme_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_dependency_util` Module +---------------------------------------- + +.. automodule:: tool_shed.util.repository_dependency_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`review_util` Module +------------------------- + +.. automodule:: tool_shed.util.review_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`shed_util_common` Module +------------------------------ + +.. automodule:: tool_shed.util.shed_util_common + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_dependency_util` Module +---------------------------------- + +.. automodule:: tool_shed.util.tool_dependency_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_util` Module +----------------------- + +.. automodule:: tool_shed.util.tool_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflow_util` Module +--------------------------- + +.. automodule:: tool_shed.util.workflow_util + :members: + :undoc-members: + :show-inheritance: + diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -14,7 +14,6 @@ [eggs:platform] bx_python = 0.7.1 Cheetah = 2.2.2 -ctypes = 1.0.2 DRMAA_python = 0.2 MarkupSafe = 0.12 mercurial = 2.2.3 @@ -29,6 +28,7 @@ simplejson = 2.1.1 threadframe = 0.2 guppy = 0.1.8 +SQLAlchemy = 0.7.9 ; msgpack_python = 0.2.4 [eggs:noplatform] @@ -46,17 +46,17 @@ nose = 0.11.1 NoseHTML = 0.4.1 NoseTestDiff = 0.1 +Parsley = 1.1 Paste = 1.7.5.1 PasteDeploy = 1.5.0 pexpect = 2.4 python_openid = 2.2.5 python_daemon = 1.5.5 Routes = 1.12.3 -SQLAlchemy = 0.5.6 -sqlalchemy_migrate = 0.5.4 +sqlalchemy_migrate = 0.7.2 ssh = 1.7.14 SVGFig = 1.1.6 -Tempita = 0.1 +Tempita = 0.5.1 twill = 0.9 WebError = 0.8a WebHelpers = 0.2 @@ -75,7 +75,6 @@ MySQL_python = _5.1.41_static bx_python = _7b95ff194725 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 -SQLAlchemy = _dev_r6498 pysam = _kanwei_b10f6e722e9a ; dependency source urls, necessary for scrambling. for an explanation, see diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -6,8 +6,8 @@ --><plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/><plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/> - <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAARunner"/> - <plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr.LwrJobRunner" /> + <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/> + <plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr:LwrJobRunner" /><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /></plugins> @@ -40,7 +40,6 @@ </destination><destination id="dynamic" runner="dynamic"> - <param id="type">python</param><param id="function">foo</param></destination><destination id="secure_lwr" runner="lwr"> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/fpconst.py --- a/lib/fpconst.py +++ /dev/null @@ -1,163 +0,0 @@ -"""Utilities for handling IEEE 754 floating point special values - -This python module implements constants and functions for working with -IEEE754 double-precision special values. It provides constants for -Not-a-Number (NaN), Positive Infinity (PosInf), and Negative Infinity -(NegInf), as well as functions to test for these values. - -The code is implemented in pure python by taking advantage of the -'struct' standard module. Care has been taken to generate proper -results on both big-endian and little-endian machines. Some efficiency -could be gained by translating the core routines into C. - -See <http://babbage.cs.qc.edu/courses/cs341/IEEE-754references.html> -for reference material on the IEEE 754 floating point standard. - -Further information on this package is available at -<http://www.analytics.washington.edu/statcomp/projects/rzope/fpconst/>. - -Author: Gregory R. Warnes <gregory_r_warnes(a)groton.pfizer.com> -Date:: 2003-04-08 -Copyright: (c) 2003, Pfizer, Inc. -""" - -__version__ = "0.7.0" -ident = "$Id: fpconst.py,v 1.12 2004/05/22 04:38:17 warnes Exp $" - -import struct, operator - -# check endianess -_big_endian = struct.pack('i',1)[0] != '\x01' - -# and define appropriate constants -if(_big_endian): - NaN = struct.unpack('d', '\x7F\xF8\x00\x00\x00\x00\x00\x00')[0] - PosInf = struct.unpack('d', '\x7F\xF0\x00\x00\x00\x00\x00\x00')[0] - NegInf = -PosInf -else: - NaN = struct.unpack('d', '\x00\x00\x00\x00\x00\x00\xf8\xff')[0] - PosInf = struct.unpack('d', '\x00\x00\x00\x00\x00\x00\xf0\x7f')[0] - NegInf = -PosInf - -def _double_as_bytes(dval): - "Use struct.unpack to decode a double precision float into eight bytes" - tmp = list(struct.unpack('8B',struct.pack('d', dval))) - if not _big_endian: - tmp.reverse() - return tmp - -## -## Functions to extract components of the IEEE 754 floating point format -## - -def _sign(dval): - "Extract the sign bit from a double-precision floating point value" - bb = _double_as_bytes(dval) - return bb[0] >> 7 & 0x01 - -def _exponent(dval): - """Extract the exponentent bits from a double-precision floating - point value. - - Note that for normalized values, the exponent bits have an offset - of 1023. As a consequence, the actual exponentent is obtained - by subtracting 1023 from the value returned by this function - """ - bb = _double_as_bytes(dval) - return (bb[0] << 4 | bb[1] >> 4) & 0x7ff - -def _mantissa(dval): - """Extract the _mantissa bits from a double-precision floating - point value.""" - - bb = _double_as_bytes(dval) - mantissa = bb[1] & 0x0f << 48 - mantissa += bb[2] << 40 - mantissa += bb[3] << 32 - mantissa += bb[4] - return mantissa - -def _zero_mantissa(dval): - """Determine whether the mantissa bits of the given double are all - zero.""" - bb = _double_as_bytes(dval) - return ((bb[1] & 0x0f) | reduce(operator.or_, bb[2:])) == 0 - -## -## Functions to test for IEEE 754 special values -## - -def isNaN(value): - "Determine if the argument is a IEEE 754 NaN (Not a Number) value." - return (_exponent(value)==0x7ff and not _zero_mantissa(value)) - -def isInf(value): - """Determine if the argument is an infinite IEEE 754 value (positive - or negative inifinity)""" - return (_exponent(value)==0x7ff and _zero_mantissa(value)) - -def isFinite(value): - """Determine if the argument is an finite IEEE 754 value (i.e., is - not NaN, positive or negative inifinity)""" - return (_exponent(value)!=0x7ff) - -def isPosInf(value): - "Determine if the argument is a IEEE 754 positive infinity value" - return (_sign(value)==0 and _exponent(value)==0x7ff and \ - _zero_mantissa(value)) - -def isNegInf(value): - "Determine if the argument is a IEEE 754 negative infinity value" - return (_sign(value)==1 and _exponent(value)==0x7ff and \ - _zero_mantissa(value)) - -## -## Functions to test public functions. -## - -def test_isNaN(): - assert( not isNaN(PosInf) ) - assert( not isNaN(NegInf) ) - assert( isNaN(NaN ) ) - assert( not isNaN( 1.0) ) - assert( not isNaN( -1.0) ) - -def test_isInf(): - assert( isInf(PosInf) ) - assert( isInf(NegInf) ) - assert( not isInf(NaN ) ) - assert( not isInf( 1.0) ) - assert( not isInf( -1.0) ) - -def test_isFinite(): - assert( not isFinite(PosInf) ) - assert( not isFinite(NegInf) ) - assert( not isFinite(NaN ) ) - assert( isFinite( 1.0) ) - assert( isFinite( -1.0) ) - -def test_isPosInf(): - assert( isPosInf(PosInf) ) - assert( not isPosInf(NegInf) ) - assert( not isPosInf(NaN ) ) - assert( not isPosInf( 1.0) ) - assert( not isPosInf( -1.0) ) - -def test_isNegInf(): - assert( not isNegInf(PosInf) ) - assert( isNegInf(NegInf) ) - assert( not isNegInf(NaN ) ) - assert( not isNegInf( 1.0) ) - assert( not isNegInf( -1.0) ) - -# overall test -def test(): - test_isNaN() - test_isInf() - test_isFinite() - test_isPosInf() - test_isNegInf() - -if __name__ == "__main__": - test() - diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/__init__.py --- a/lib/galaxy/__init__.py +++ b/lib/galaxy/__init__.py @@ -95,10 +95,15 @@ pkg_resources.Distribution._insert_on = pkg_resources.Distribution.insert_on pkg_resources.Distribution.insert_on = _insert_on -# patch to add the NullHandler class to logging -if sys.version_info[:2] < ( 2, 7 ): - import logging +# compat: BadZipFile introduced in Python 2.7 +import zipfile +if not hasattr( zipfile, 'BadZipFile' ): + zipfile.BadZipFile = zipfile.error + +# compat: patch to add the NullHandler class to logging +import logging +if not hasattr( logging, 'NullHandler' ): class NullHandler( logging.Handler ): def emit( self, record ): pass - logging.NullHandler = NullHandler + logging.NullHandler = NullHandler \ No newline at end of file diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -15,6 +15,7 @@ from galaxy.tags.tag_handler import GalaxyTagHandler from galaxy.visualization.genomes import Genomes from galaxy.visualization.data_providers.registry import DataProviderRegistry +from galaxy.visualization.registry import VisualizationsRegistry from galaxy.tools.imp_exp import load_history_imp_exp_tools from galaxy.tools.genome_index import load_genome_index_tools from galaxy.sample_tracking import external_service_types @@ -120,6 +121,9 @@ load_history_imp_exp_tools( self.toolbox ) # Load genome indexer tool. load_genome_index_tools( self.toolbox ) + # visualizations registry: associates resources with visualizations, controls how to render + self.visualizations_registry = ( VisualizationsRegistry( self.config.root, self.config.visualizations_conf_path ) + if self.config.visualizations_conf_path else None ) # Load security policy. self.security_agent = self.model.security_agent self.host_security_agent = galaxy.security.HostAgent( model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions ) diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -86,7 +86,6 @@ self.galaxy_data_manager_data_path = kwargs.get( 'galaxy_data_manager_data_path', self.tool_data_path ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) - self.set_metadata_externally = string_as_bool( kwargs.get( "set_metadata_externally", "False" ) ) self.retry_metadata_internally = string_as_bool( kwargs.get( "retry_metadata_internally", "True" ) ) self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) @@ -155,6 +154,10 @@ self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) + # Configuration for the message box directly below the masthead. + self.message_box_visible = kwargs.get( 'message_box_visible', False ) + self.message_box_content = kwargs.get( 'message_box_content', None ) + self.message_box_class = kwargs.get( 'message_box_class', 'info' ) self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' ) self.wiki_url = kwargs.get( 'wiki_url', 'http://g2.trac.bx.psu.edu/' ) self.blog_url = kwargs.get( 'blog_url', None ) @@ -166,6 +169,7 @@ self.enable_whoosh_library_search = string_as_bool( kwargs.get( 'enable_whoosh_library_search', False ) ) self.whoosh_index_dir = resolve_path( kwargs.get( "whoosh_index_dir", "database/whoosh_indexes" ), self.root ) self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None ) + self.ftp_upload_dir_identifier = kwargs.get( 'ftp_upload_dir_identifier', 'email' ) # attribute on user - email, username, id, etc... self.ftp_upload_site = kwargs.get( 'ftp_upload_site', None ) self.allow_library_path_paste = kwargs.get( 'allow_library_path_paste', False ) self.disable_library_comptypes = kwargs.get( 'disable_library_comptypes', '' ).lower().split( ',' ) @@ -271,6 +275,8 @@ self.fluent_log = string_as_bool( kwargs.get( 'fluent_log', False ) ) self.fluent_host = kwargs.get( 'fluent_host', 'localhost' ) self.fluent_port = int( kwargs.get( 'fluent_port', 24224 ) ) + # visualizations registry config path + self.visualizations_conf_path = kwargs.get( 'visualizations_conf_path', None ) @property def sentry_dsn_public( self ): diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/assembly.py --- a/lib/galaxy/datatypes/assembly.py +++ b/lib/galaxy/datatypes/assembly.py @@ -5,14 +5,14 @@ """ import data +import logging +import os +import re +import sys from galaxy.datatypes import sequence -import logging, os, sys, time, tempfile, shutil, string, glob, re -import galaxy.model -from galaxy.datatypes import metadata +from galaxy.datatypes.images import Html from galaxy.datatypes.metadata import MetadataElement -from galaxy import util -from galaxy.datatypes.images import Html -from sniff import * + log = logging.getLogger(__name__) @@ -174,7 +174,6 @@ gen_msg = '' try: efp = dataset.extra_files_path - flist = os.listdir(efp) log_path = os.path.join(efp,'Log') f = open(log_path,'r') log_content = f.read(1000) @@ -223,5 +222,5 @@ self.regenerate_primary_file(dataset) if __name__ == '__main__': - import doctest, sys + import doctest doctest.testmod(sys.modules[__name__]) diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -2,18 +2,26 @@ Binary classes """ -import data, logging, binascii +import binascii +import data +import gzip +import logging +import os +import shutil +import struct +import subprocess +import tempfile +import zipfile + +from urllib import urlencode, quote_plus +from galaxy import eggs +eggs.require( "bx-python" ) + +from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE + from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes import metadata from galaxy.datatypes.sniff import * -from galaxy import eggs -import pkg_resources -pkg_resources.require( "bx-python" ) -from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE -from urllib import urlencode, quote_plus -import zipfile, gzip -import os, subprocess, tempfile -import struct log = logging.getLogger(__name__) @@ -85,9 +93,18 @@ Binary.register_unsniffable_binary_ext("ab1") +class GenericAsn1Binary( Binary ): + """Class for generic ASN.1 binary format""" + file_ext = "asn1-binary" + +Binary.register_unsniffable_binary_ext("asn1-binary") + class Bam( Binary ): """Class describing a BAM binary file""" file_ext = "bam" + track_type = "ReadTrack" + data_sources = { "data": "bai", "index": "bigwig" } + MetadataElement( name="bam_index", desc="BAM Index File", param=metadata.FileParameter, file_ext="bai", readonly=True, no_value=None, visible=False, optional=True ) def _get_samtools_version( self ): @@ -238,9 +255,7 @@ return dataset.peek except: return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) ) - def get_track_type( self ): - return "ReadTrack", { "data": "bai", "index": [ "bigwig", "summary_tree" ] } - + Binary.register_sniffable_binary_format("bam", "bam", Bam) class H5( Binary ): @@ -318,6 +333,9 @@ The supplemental info in the paper has the binary details: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq351v1 """ + track_type = "LineTrack" + data_sources = { "data_standalone": "bigwig" } + def __init__( self, **kwd ): Binary.__init__( self, **kwd ) self._magic = 0x888FFC26 @@ -342,19 +360,18 @@ return dataset.peek except: return "Binary UCSC %s file (%s)" % ( self._name, data.nice_size( dataset.get_size() ) ) - def get_track_type( self ): - return "LineTrack", {"data_standalone": "bigwig"} - + Binary.register_sniffable_binary_format("bigwig", "bigwig", BigWig) class BigBed(BigWig): """BigBed support from UCSC.""" + + data_sources = { "data_standalone": "bigbed" } + def __init__( self, **kwd ): Binary.__init__( self, **kwd ) self._magic = 0x8789F2EB self._name = "BigBed" - def get_track_type( self ): - return "LineTrack", {"data_standalone": "bigbed"} Binary.register_sniffable_binary_format("bigbed", "bigbed", BigBed) diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/checkers.py --- a/lib/galaxy/datatypes/checkers.py +++ b/lib/galaxy/datatypes/checkers.py @@ -58,7 +58,7 @@ for chars in temp: for char in chars: chars_read += 1 - if ord( char ) > 128: + if util.is_binary( char ): is_binary = True break if chars_read > 100: diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/chrominfo.py --- a/lib/galaxy/datatypes/chrominfo.py +++ b/lib/galaxy/datatypes/chrominfo.py @@ -1,7 +1,3 @@ -import data -from galaxy import util -from galaxy.datatypes.sniff import * -from galaxy.web import url_for from tabular import Tabular from galaxy.datatypes import metadata from galaxy.datatypes.metadata import MetadataElement diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml @@ -1,7 +1,14 @@ <tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.0" hidden="true"><command> - bedtools genomecov -bg -split -ibam $input -g $chromInfo | wigToBigWig stdin $chromInfo $output + bedtools genomecov -bg -split -ibam $input -g $chromInfo + + ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this + ## should only be used on systems with large RAM. + ## | wigToBigWig stdin $chromInfo $output + + ## This can be used anywhere. + > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output </command><inputs><param format="bam" name="input" type="data" label="Choose BAM file"/> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml --- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml +++ /dev/null @@ -1,14 +0,0 @@ -<tool id="CONVERTER_bam_to_summary_tree_0" name="Convert BAM to Summary Tree" version="1.0.0" hidden="true"> -  - <command interpreter="python"> - sam_or_bam_to_summary_tree_converter.py --bam $input1 $input1.metadata.bam_index $output1 - </command> - <inputs> - <param format="bam" name="input1" type="data" label="Choose BAM file"/> - </inputs> - <outputs> - <data format="summary_tree" name="output1"/> - </outputs> - <help> - </help> -</tool> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml @@ -0,0 +1,25 @@ +<tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.0" hidden="true"> +  + <command> + ## Remove comments and sort by chromosome. + grep -v '^#' $input | sort -k1,1 | + + ## Generate coverage bedgraph. + bedtools genomecov -bg -split -i stdin -g $chromInfo + + ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this + ## should only be used on systems with large RAM. + ## | wigToBigWig stdin $chromInfo $output + + ## This can be used anywhere. + > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output + </command> + <inputs> + <param format="bed,gff,vcf" name="input" type="data" label="Choose input file"/> + </inputs> + <outputs> + <data format="bigwig" name="output"/> + </outputs> + <help> + </help> +</tool> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.xml --- a/lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.xml +++ /dev/null @@ -1,14 +0,0 @@ -<tool id="CONVERTER_bed_to_summary_tree_0" name="Convert BED to Summary Tree" version="1.0.0" hidden="true"> - - <command interpreter="python">interval_to_summary_tree_converter.py $input1 $output1</command> - <inputs> - <page> - <param format="bed" name="input1" type="data" label="Choose BED file"/> - </page> - </inputs> - <outputs> - <data format="summary_tree" name="output1"/> - </outputs> - <help> - </help> -</tool> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/encodepeak_to_summary_tree_converter.xml --- a/lib/galaxy/datatypes/converters/encodepeak_to_summary_tree_converter.xml +++ /dev/null @@ -1,20 +0,0 @@ -<tool id="CONVERTER_encodepeak_to_summary_tree_0" name="Convert ENCODEPeak to Summary Tree" version="1.0.0" hidden="true"> - - <command interpreter="python">interval_to_summary_tree_converter.py - -c ${input1.metadata.chromCol} - -s ${input1.metadata.startCol} - -e ${input1.metadata.endCol} - $input1 $output1 - </command> - - <inputs> - <page> - <param format="ENCODEPeak" name="input1" type="data" label="Choose ENCODEPeak file"/> - </page> - </inputs> - <outputs> - <data format="summary_tree" name="output1"/> - </outputs> - <help> - </help> -</tool> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/gff_to_summary_tree_converter.xml --- a/lib/galaxy/datatypes/converters/gff_to_summary_tree_converter.xml +++ /dev/null @@ -1,14 +0,0 @@ -<tool id="CONVERTER_gff_to_summary_tree_0" name="Convert GFF to Summary Tree" version="1.0.0" hidden="true"> - - <command interpreter="python">interval_to_summary_tree_converter.py $input1 $output1 --gff</command> - <inputs> - <page> - <param format="gff" name="input1" type="data" label="Choose GFF file"/> - </page> - </inputs> - <outputs> - <data format="summary_tree" name="output1"/> - </outputs> - <help> - </help> -</tool> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml @@ -0,0 +1,33 @@ +<tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage"> +  +  + <command> + + ## Remove comments and sort by chromosome. + grep -v '^#' $input1 | sort -k${input1.metadata.chromCol},${input1.metadata.chromCol} | + + ## Create simple BED by cutting chrom, start, and end columns. + awk -v OFS=' ' '{print $${input1.metadata.chromCol},$${input1.metadata.startCol},$${input1.metadata.endCol} }' | + + ## Generate coverage bedgraph. + bedtools genomecov -bg -split -i stdin -g $chromInfo + + ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this + ## should only be used on systems with large RAM. + ## | wigToBigWig stdin $chromInfo $output + + ## This can be used anywhere. + > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output + + </command> + <inputs> + <page> + <param format="interval" name="input1" type="data" label="Choose intervals"/> + </page> + </inputs> + <outputs> + <data format="bigwig" name="output"/> + </outputs> + <help> + </help> +</tool> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py +++ /dev/null @@ -1,63 +0,0 @@ -#!/usr/bin/env python - -""" -Convert from interval file to summary tree file. Default input file format is BED (0-based, half-open intervals). - -usage: %prog <options> in_file out_file - -c, --chr-col: chromosome column, default=1 - -s, --start-col: start column, default=2 - -e, --end-col: end column, default=3 - -t, --strand-col: strand column, default=6 - -G, --gff: input is GFF format, meaning start and end coordinates are 1-based, closed interval -""" -from __future__ import division - -import sys, fileinput, optparse -from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -from galaxy.visualization.tracks.summary import * -from bx.intervals.io import * -from galaxy.datatypes.util.gff_util import * - -def main(): - # Read options, args. - parser = optparse.OptionParser() - parser.add_option( '-c', '--chr-col', type='int', dest='chrom_col', default=1 ) - parser.add_option( '-s', '--start-col', type='int', dest='start_col', default=2 ) - parser.add_option( '-e', '--end-col', type='int', dest='end_col', default=3 ) - parser.add_option( '-t', '--strand-col', type='int', dest='strand_col', default=6 ) - parser.add_option( '-G', '--gff', dest="gff_format", action="store_true" ) - (options, args) = parser.parse_args() - input_fname, output_fname = args - - # Convert column indices to 0-based. - options.chrom_col -= 1 - options.start_col -= 1 - options.end_col -= 1 - options.strand_col -= 1 - - # Do conversion. - if options.gff_format: - reader_wrapper_class = GFFReaderWrapper - chr_col, start_col, end_col, strand_col = ( 0, 3, 4, 6 ) - else: - reader_wrapper_class = NiceReaderWrapper - chr_col, start_col, end_col, strand_col = ( options.chrom_col, options.start_col, options.end_col, options.strand_col ) - reader_wrapper = reader_wrapper_class( fileinput.FileInput( input_fname ), - chrom_col=chr_col, - start_col=start_col, - end_col=end_col, - strand_col=strand_col, - fix_strand=True ) - st = SummaryTree() - for feature in list( reader_wrapper ): - if isinstance( feature, GenomicInterval ): - # Tree expects BED coordinates. - if type( feature ) is GFFFeature: - convert_gff_coords_to_bed( feature ) - st.insert_range( feature.chrom, long( feature.start ), long( feature.end ) ) - - st.write( output_fname ) - -if __name__ == "__main__": - main() diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.xml --- a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.xml +++ /dev/null @@ -1,20 +0,0 @@ -<tool id="CONVERTER_interval_to_summary_tree_0" name="Convert Interval to Summary Tree" version="1.0.0" hidden="true"> - - <command interpreter="python">interval_to_summary_tree_converter.py - -c ${input1.metadata.chromCol} - -s ${input1.metadata.startCol} - -e ${input1.metadata.endCol} - $input1 $output1 - </command> - - <inputs> - <page> - <param format="interval" name="input1" type="data" label="Choose Interval file"/> - </page> - </inputs> - <outputs> - <data format="summary_tree" name="output1"/> - </outputs> - <help> - </help> -</tool> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py --- /dev/null +++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py @@ -0,0 +1,39 @@ +#!/usr/bin/env python + +""" +Convert from pileup file to interval index file. + +usage: %prog <options> in_file out_file +""" + +from __future__ import division + +import sys, fileinput, optparse +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from galaxy.visualization.tracks.summary import * +from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed +from bx.interval_index_file import Indexes + +def main(): + + # Read options, args. + parser = optparse.OptionParser() + (options, args) = parser.parse_args() + input_fname, output_fname = args + + # Do conversion. + index = Indexes() + offset = 0 + for line in open( input_fname, "r" ): + chrom, start = line.split()[ 0:2 ] + # Pileup format is 1-based. + start = int( start ) - 1 + index.add( chrom, start, start + 1, offset ) + offset += len( line ) + + index.write( open(output_fname, "w") ) + +if __name__ == "__main__": + main() + \ No newline at end of file diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml @@ -0,0 +1,15 @@ +<tool id="CONVERTER_pileup_to_interval_index_0" name="Convert Pileup to Interval Index" version="1.0.0" hidden="true"> + + <command interpreter="python">pileup_to_interval_index_converter.py $input $output + </command> + <inputs> + <page> + <param format="pileup" name="input" type="data" label="Choose Pileup file"/> + </page> + </inputs> + <outputs> + <data format="interval_index" name="output"/> + </outputs> + <help> + </help> +</tool> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env python - -from __future__ import division - -import sys, os, optparse -sys.stderr = open(os.devnull, 'w') # suppress stderr as cython produces warning on some systems: - # csamtools.so:6: RuntimeWarning: __builtin__.file size changed - -from galaxy import eggs -import pkg_resources - -if sys.version_info[:2] == (2, 4): - pkg_resources.require( "ctypes" ) -pkg_resources.require( "pysam" ) - -from pysam import csamtools -from galaxy.visualization.tracks.summary import * - -def main(): - parser = optparse.OptionParser() - parser.add_option( '-S', '--sam', action="store_true", dest="is_sam" ) - parser.add_option( '-B', '--bam', action="store_true", dest="is_bam" ) - options, args = parser.parse_args() - - if options.is_bam: - input_fname = args[0] - index_fname = args[1] - out_fname = args[2] - samfile = csamtools.Samfile( filename=input_fname, mode='rb', index_filename=index_fname ) - elif options.is_sam: - input_fname = args[0] - out_fname = args[1] - samfile = csamtools.Samfile( filename=input_fname, mode='r' ) - - st = SummaryTree() - for read in samfile.fetch(): - st.insert_range( samfile.getrname( read.rname ), read.pos, read.pos + read.rlen ) - - st.write(out_fname) - -if __name__ == "__main__": - main() diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml @@ -0,0 +1,20 @@ +<tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.0" hidden="true"> + <command> + samtools view -bh $input | bedtools genomecov -bg -split -ibam stdin -g $chromInfo + + ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this + ## should only be used on systems with large RAM. + ## | wigToBigWig stdin $chromInfo $output + + ## This can be used anywhere. + > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output + </command> + <inputs> + <param format="bam" name="input" type="data" label="Choose BAM file"/> + </inputs> + <outputs> + <data format="bigwig" name="output"/> + </outputs> + <help> + </help> +</tool> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml --- a/lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml +++ /dev/null @@ -1,14 +0,0 @@ -<tool id="CONVERTER_sam_to_summary_tree_0" name="Convert SAM to Summary Tree" version="1.0.0" hidden="true"> - - <command interpreter="python">sam_or_bam_to_summary_tree_converter.py --sam $input1 $output1</command> - <inputs> - <page> - <param format="sam" name="input1" type="data" label="Choose sam file"/> - </page> - </inputs> - <outputs> - <data format="summary_tree" name="output1"/> - </outputs> - <help> - </help> -</tool> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py +++ /dev/null @@ -1,30 +0,0 @@ -#!/usr/bin/env python - -""" -Convert from VCF file to summary tree file. - -usage: %prog in_file out_file -""" -from __future__ import division - -import optparse -import galaxy_utils.sequence.vcf -from galaxy.visualization.tracks.summary import SummaryTree - -def main(): - # Read options, args. - parser = optparse.OptionParser() - (options, args) = parser.parse_args() - in_file, out_file = args - - # Do conversion. - st = SummaryTree() - for line in list( galaxy_utils.sequence.vcf.Reader( open( in_file ) ) ): - # VCF format provides a chrom and 1-based position for each variant. - # SummaryTree expects 0-based coordinates. - st.insert_range( line.chrom, long( line.pos-1 ), long( line.pos ) ) - - st.write(out_file) - -if __name__ == "__main__": - main() \ No newline at end of file diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.xml --- a/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.xml +++ /dev/null @@ -1,14 +0,0 @@ -<tool id="CONVERTER_vcf_to_summary_tree_0" name="Convert VCF to Summary Tree" version="1.0.0" hidden="true"> -  - <command interpreter="python">vcf_to_summary_tree_converter.py $input1 $output1</command> - <inputs> - <page> - <param format="vcf" name="input1" type="data" label="Choose VCF file"/> - </page> - </inputs> - <outputs> - <data format="summary_tree" name="output1"/> - </outputs> - <help> - </help> -</tool> diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/coverage.py --- a/lib/galaxy/datatypes/coverage.py +++ b/lib/galaxy/datatypes/coverage.py @@ -2,21 +2,14 @@ Coverage datatypes """ -import pkg_resources -pkg_resources.require( "bx-python" ) -import logging, os, sys, time, tempfile, shutil -import data -from galaxy import util -from galaxy.datatypes.sniff import * -from galaxy.web import url_for -from cgi import escape -import urllib -from bx.intervals.io import * +import logging +import math + +from galaxy import eggs from galaxy.datatypes import metadata from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes.tabular import Tabular -import math log = logging.getLogger(__name__) @@ -34,7 +27,7 @@ Assumes we have a numpy file. """ # Maybe if we import here people will still be able to use Galaxy when numpy kills it - pkg_resources.require("numpy>=1.2.1") + eggs.require("numpy>=1.2.1") #from numpy.lib import format import numpy diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -2,6 +2,7 @@ import metadata import mimetypes import os +import shutil import sys import tempfile import zipfile @@ -17,12 +18,6 @@ eggs.require( "Paste" ) import paste - -if sys.version_info[:2] < ( 2, 6 ): - zipfile.BadZipFile = zipfile.error -if sys.version_info[:2] < ( 2, 5 ): - zipfile.LargeZipFile = zipfile.error - log = logging.getLogger(__name__) tmpd = tempfile.mkdtemp() @@ -103,6 +98,12 @@ #A per datatype setting (inherited): max file size (in bytes) for setting optional metadata _max_optional_metadata_filesize = None + # Trackster track type. + track_type = None + + # Data sources. + data_sources = {} + def __init__(self, **kwd): """Initialize the datatype""" object.__init__(self, **kwd) @@ -343,6 +344,7 @@ max_peek_size = 1000000 # 1 MB if isinstance(data.datatype, datatypes.images.Html): max_peek_size = 10000000 # 10 MB for html + preview = util.string_as_bool( preview ) if not preview or isinstance(data.datatype, datatypes.images.Image) or os.stat( data.file_name ).st_size < max_peek_size: if trans.app.config.sanitize_all_html and trans.response.get_content_type() == "text/html": # Sanitize anytime we respond with plain text/html content. @@ -544,21 +546,21 @@ return False - def merge( split_files, output_file): """ - TODO: Do we need to merge gzip files using gzjoin? cat seems to work, - but might be brittle. Need to revisit this. + Merge files with copy.copyfileobj() will not hit the + max argument limitation of cat. gz and bz2 files are also working. """ if not split_files: raise ValueError('Asked to merge zero files as %s' % output_file) elif len(split_files) == 1: - cmd = 'mv -f %s %s' % ( split_files[0], output_file ) + shutil.copyfileobj(open(split_files[0], 'rb'), open(output_file, 'wb')) else: - cmd = 'cat %s > %s' % ( ' '.join(split_files), output_file ) - result = os.system(cmd) - if result != 0: - raise Exception('Result %s from %s' % (result, cmd)) + fdst = open(output_file, 'wb') + for fsrc in split_files: + shutil.copyfileobj(open(fsrc, 'rb'), fdst) + fdst.close() + merge = staticmethod(merge) def get_visualizations( self, dataset ): @@ -566,7 +568,7 @@ Returns a list of visualizations for datatype. """ - if hasattr( self, 'get_track_type' ): + if self.track_type: return [ 'trackster', 'circster' ] return [] @@ -739,6 +741,10 @@ f.close() split = classmethod(split) +class GenericAsn1( Text ): + """Class for generic ASN.1 text format""" + file_ext = 'asn1' + class LineCount( Text ): """ Dataset contains a single line with a single integer that denotes the @@ -859,7 +865,7 @@ text = "%s file" % file_type else: try: - text = unicode( '\n'.join( lines ), 'utf-8' ) + text = util.unicodify( '\n'.join( lines ) ) except UnicodeDecodeError: text = "binary/unknown file" return text diff -r 98055c5c428ec019eb9738db8bb6f4331c163377 -r 1a3dc9d098e053592b6a066c8344b00c12ea905b lib/galaxy/datatypes/display_applications/application.py --- a/lib/galaxy/datatypes/display_applications/application.py +++ b/lib/galaxy/datatypes/display_applications/application.py @@ -12,7 +12,7 @@ log = logging.getLogger( __name__ ) #Any basic functions that we want to provide as a basic part of parameter dict should be added to this dict -BASE_PARAMS = { 'qp': quote_plus, 'url_for':url_for } #url_for has route memory... +BASE_PARAMS = { 'qp': quote_plus, 'url_for':url_for } class DisplayApplicationLink( object ): @classmethod @@ -40,7 +40,7 @@ self.name = None def get_display_url( self, data, trans ): dataset_hash, user_hash = encode_dataset_user( trans, data, None ) - return url_for( controller='/dataset', + return url_for( controller='dataset', action="display_application", dataset_id=dataset_hash, user_id=user_hash, This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/b1850aa88b03/ Changeset: b1850aa88b03 Branch: next-stable User: natefoo Date: 2013-05-20 21:55:46 Summary: Merge stable branch to next-stable. Affected #: 1 file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Change the tool shed grid ToolsFunctionallyCorrectColumn column type.
by commits-noreply＠bitbucket.org 20 May '13

20 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ebe882ab26c4/ Changeset: ebe882ab26c4 User: greg Date: 2013-05-20 21:51:10 Summary: Change the tool shed grid ToolsFunctionallyCorrectColumn column type. Affected #: 1 file diff -r ae1fb20222cc7d075009b59295e247c00616bc15 -r ebe882ab26c4abbd7b3fa85161864257a3f785a6 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -121,7 +121,7 @@ return escape_html( repository.revision( trans.app ) ) - class ToolsFunctionallyCorrectColumn( grids.BooleanColumn ): + class ToolsFunctionallyCorrectColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): # This column will display the value associated with the currently displayed metadata revision. @@ -1130,7 +1130,7 @@ return '' - class ToolsFunctionallyCorrectColumn( grids.BooleanColumn ): + class ToolsFunctionallyCorrectColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): # This column will display the value associated with the currently displayed metadata revision. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 20 May '13

20 May '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a709ca0ea728/ Changeset: a709ca0ea728 User: jmchilton Date: 2013-05-13 20:59:16 Summary: Refactor logic for setting metadata exteranlly used local job runner out into a method on the BaseJobRunner class. This improves the readibility and allows other job runners to use this logic. Rework LWR to use this new method. Overtime the lwr.py and local.py version of that code had diverged and it had never been noticed because I guess no one had been using the LWR with set_metadata_exteranlly = True, which is no longer an option. Affected #: 3 files diff -r d92704335a2774e1bde2be72f9f78ce63c0447fd -r a709ca0ea7289833b8016613a646c88bbf04cef9 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -7,6 +7,7 @@ import string import logging import threading +import subprocess from Queue import Queue, Empty @@ -235,6 +236,30 @@ log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) return output_pairs + def _handle_metadata_externally(self, job_wrapper): + """ + Set metadata externally. Used by the local and lwr job runners where this + shouldn't be attached to command-line to execute. + """ + #run the metadata setting script here + #this is terminate-able when output dataset/job is deleted + #so that long running set_meta()s can be canceled without having to reboot the server + if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and job_wrapper.output_paths: + external_metadata_script = job_wrapper.setup_external_metadata( output_fnames=job_wrapper.get_output_fnames(), + set_extension=True, + tmp_dir=job_wrapper.working_directory, + #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior + kwds={ 'overwrite' : False } ) + log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) + external_metadata_proc = subprocess.Popen( args=external_metadata_script, + shell=True, + env=os.environ, + preexec_fn=os.setpgrp ) + job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session ) + external_metadata_proc.wait() + log.debug( 'execution of external set_meta for job %d finished' % job_wrapper.job_id ) + + class AsynchronousJobState( object ): """ Encapsulate the state of an asynchronous job, this should be subclassed as diff -r d92704335a2774e1bde2be72f9f78ce63c0447fd -r a709ca0ea7289833b8016613a646c88bbf04cef9 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -87,23 +87,7 @@ job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return - #run the metadata setting script here - #this is terminate-able when output dataset/job is deleted - #so that long running set_meta()s can be canceled without having to reboot the server - if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and job_wrapper.output_paths: - external_metadata_script = job_wrapper.setup_external_metadata( output_fnames = job_wrapper.get_output_fnames(), - set_extension = True, - tmp_dir = job_wrapper.working_directory, - kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior - log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) - external_metadata_proc = subprocess.Popen( args = external_metadata_script, - shell = True, - env = os.environ, - preexec_fn = os.setpgrp ) - job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session ) - external_metadata_proc.wait() - log.debug( 'execution of external set_meta for job %d finished' % job_wrapper.job_id ) - + self._handle_metadata_externally( job_wrapper ) # Finish the job! try: job_wrapper.finish( stdout, stderr, exit_code ) diff -r d92704335a2774e1bde2be72f9f78ce63c0447fd -r a709ca0ea7289833b8016613a646c88bbf04cef9 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -1,5 +1,4 @@ import logging -import subprocess from galaxy import model from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner @@ -7,6 +6,7 @@ import errno from time import sleep +import os from lwr_client import FileStager, Client, url_to_destination_params @@ -140,23 +140,8 @@ job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return - #run the metadata setting script here - #this is terminate-able when output dataset/job is deleted - #so that long running set_meta()s can be canceled without having to reboot the server - if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and job_wrapper.output_paths: - external_metadata_script = job_wrapper.setup_external_metadata( output_fnames = job_wrapper.get_output_fnames(), - set_extension = True, - kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior - log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) - external_metadata_proc = subprocess.Popen( args = external_metadata_script, - shell = True, - env = os.environ, - preexec_fn = os.setpgrp ) - job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session ) - external_metadata_proc.wait() - log.debug( 'execution of external set_meta finished for job %d' % job_wrapper.job_id ) - - # Finish the job + self._handle_metadata_externally( job_wrapper ) + # Finish the job try: job_wrapper.finish( stdout, stderr ) except: https://bitbucket.org/galaxy/galaxy-central/commits/e456392f0557/ Changeset: e456392f0557 User: jmchilton Date: 2013-05-16 06:37:16 Summary: Implement queued state for LWR jobs - previously all queued and running LWR jobs were marked as running in the Galaxy. Affected #: 2 files diff -r a709ca0ea7289833b8016613a646c88bbf04cef9 -r e456392f0557079488a901a2c0d90459919aa9ea lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -34,15 +34,18 @@ def check_watched_item(self, job_state): try: client = self.get_client_from_state(job_state) - complete = client.check_complete() + status = client.get_status() except Exception: # An orphaned job was put into the queue at app startup, so remote server went down # either way we are done I guess. self.mark_as_finished(job_state) return None - if complete: + if status == "complete": self.mark_as_finished(job_state) return None + if status == "running" and not job_state.running: + job_state.running = True + job_state.job_wrapper.change_state( model.Job.states.RUNNING ) return job_state def queue_job(self, job_wrapper): @@ -81,7 +84,7 @@ job_id = file_stager.job_id client.launch( rebuilt_command_line ) job_wrapper.set_job_destination( job_destination, job_id ) - job_wrapper.change_state( model.Job.states.RUNNING ) + job_wrapper.change_state( model.Job.states.QUEUED ) except Exception, exc: job_wrapper.fail( "failure running job", exception=True ) @@ -92,7 +95,7 @@ lwr_job_state.job_wrapper = job_wrapper lwr_job_state.job_id = job_id lwr_job_state.old_state = True - lwr_job_state.running = True + lwr_job_state.running = False lwr_job_state.job_destination = job_destination self.monitor_job(lwr_job_state) @@ -207,12 +210,8 @@ job_state.job_destination = job_wrapper.job_destination job_wrapper.command_line = job.get_command_line() job_state.job_wrapper = job_wrapper - if job.get_state() == model.Job.states.RUNNING: + if job.get_state() in [model.Job.states.RUNNING, model.Job.states.QUEUED]: log.debug( "(LWR/%s) is still in running state, adding to the LWR queue" % ( job.get_id()) ) job_state.old_state = True job_state.running = True self.monitor_queue.put( job_state ) - elif job.get_state() == model.Job.states.QUEUED: - # LWR doesn't queue currently, so this indicates galaxy was shutoff while - # job was being staged. Not sure how to recover from that. - job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted. Please retry the job." ) diff -r a709ca0ea7289833b8016613a646c88bbf04cef9 -r e456392f0557079488a901a2c0d90459919aa9ea lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -210,11 +210,25 @@ check_complete_response = self.__raw_execute("check_complete", {"job_id": self.job_id}) return check_complete_response - def check_complete(self): + def check_complete(self, response=None): """ Return boolean indicating whether the job is complete. """ - return self.raw_check_complete()["complete"] == "true" + if response == None: + response = self.raw_check_complete() + return response["complete"] == "true" + + def get_status(self): + check_complete_response = self.raw_check_complete() + # Older LWR instances won't set status so use 'complete', at some + # point drop backward compatibility. + complete = self.check_complete(check_complete_response) + old_status = "complete" if complete else "running" + status = check_complete_response.get("status", old_status) + # Bug in certains older LWR instances returned literal "status". + if status not in ["complete", "running", "queued"]: + status = old_status + return status def clean(self): """ https://bitbucket.org/galaxy/galaxy-central/commits/2ffd8c25e9ce/ Changeset: 2ffd8c25e9ce User: jmchilton Date: 2013-05-16 06:50:19 Summary: Fix bug that was preventing LWR jobs from entering the RUNNING state post job "recover" on Galaxy startup. Affected #: 1 file diff -r e456392f0557079488a901a2c0d90459919aa9ea -r 2ffd8c25e9cea2c0f3b7e36373eeb5cac27357d2 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -210,8 +210,9 @@ job_state.job_destination = job_wrapper.job_destination job_wrapper.command_line = job.get_command_line() job_state.job_wrapper = job_wrapper - if job.get_state() in [model.Job.states.RUNNING, model.Job.states.QUEUED]: + state = job.get_state() + if state in [model.Job.states.RUNNING, model.Job.states.QUEUED]: log.debug( "(LWR/%s) is still in running state, adding to the LWR queue" % ( job.get_id()) ) job_state.old_state = True - job_state.running = True + job_state.running = state == model.Job.states.RUNNING self.monitor_queue.put( job_state ) https://bitbucket.org/galaxy/galaxy-central/commits/ae1fb20222cc/ Changeset: ae1fb20222cc User: natefoo Date: 2013-05-20 21:00:11 Summary: Merged in jmchilton/galaxy-central-lwr (pull request #166) LWR fix for setting metadata externally. Affected #: 4 files diff -r 64c6e3dfaa2bd54f344026752f4ab7ae008a5094 -r ae1fb20222cc7d075009b59295e247c00616bc15 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -7,6 +7,7 @@ import string import logging import threading +import subprocess from Queue import Queue, Empty @@ -236,6 +237,30 @@ log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) return output_pairs + def _handle_metadata_externally(self, job_wrapper): + """ + Set metadata externally. Used by the local and lwr job runners where this + shouldn't be attached to command-line to execute. + """ + #run the metadata setting script here + #this is terminate-able when output dataset/job is deleted + #so that long running set_meta()s can be canceled without having to reboot the server + if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and job_wrapper.output_paths: + external_metadata_script = job_wrapper.setup_external_metadata( output_fnames=job_wrapper.get_output_fnames(), + set_extension=True, + tmp_dir=job_wrapper.working_directory, + #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior + kwds={ 'overwrite' : False } ) + log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) + external_metadata_proc = subprocess.Popen( args=external_metadata_script, + shell=True, + env=os.environ, + preexec_fn=os.setpgrp ) + job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session ) + external_metadata_proc.wait() + log.debug( 'execution of external set_meta for job %d finished' % job_wrapper.job_id ) + + class AsynchronousJobState( object ): """ Encapsulate the state of an asynchronous job, this should be subclassed as diff -r 64c6e3dfaa2bd54f344026752f4ab7ae008a5094 -r ae1fb20222cc7d075009b59295e247c00616bc15 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -88,23 +88,7 @@ job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return - #run the metadata setting script here - #this is terminate-able when output dataset/job is deleted - #so that long running set_meta()s can be canceled without having to reboot the server - if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and job_wrapper.output_paths: - external_metadata_script = job_wrapper.setup_external_metadata( output_fnames = job_wrapper.get_output_fnames(), - set_extension = True, - tmp_dir = job_wrapper.working_directory, - kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior - log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) - external_metadata_proc = subprocess.Popen( args = external_metadata_script, - shell = True, - env = os.environ, - preexec_fn = os.setpgrp ) - job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session ) - external_metadata_proc.wait() - log.debug( 'execution of external set_meta for job %d finished' % job_wrapper.job_id ) - + self._handle_metadata_externally( job_wrapper ) # Finish the job! try: job_wrapper.finish( stdout, stderr, exit_code ) diff -r 64c6e3dfaa2bd54f344026752f4ab7ae008a5094 -r ae1fb20222cc7d075009b59295e247c00616bc15 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -1,5 +1,4 @@ import logging -import subprocess from galaxy import model from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner @@ -7,6 +6,7 @@ import errno from time import sleep +import os from lwr_client import FileStager, Client, url_to_destination_params @@ -34,15 +34,18 @@ def check_watched_item(self, job_state): try: client = self.get_client_from_state(job_state) - complete = client.check_complete() + status = client.get_status() except Exception: # An orphaned job was put into the queue at app startup, so remote server went down # either way we are done I guess. self.mark_as_finished(job_state) return None - if complete: + if status == "complete": self.mark_as_finished(job_state) return None + if status == "running" and not job_state.running: + job_state.running = True + job_state.job_wrapper.change_state( model.Job.states.RUNNING ) return job_state def queue_job(self, job_wrapper): @@ -81,7 +84,7 @@ job_id = file_stager.job_id client.launch( rebuilt_command_line ) job_wrapper.set_job_destination( job_destination, job_id ) - job_wrapper.change_state( model.Job.states.RUNNING ) + job_wrapper.change_state( model.Job.states.QUEUED ) except Exception, exc: job_wrapper.fail( "failure running job", exception=True ) @@ -92,7 +95,7 @@ lwr_job_state.job_wrapper = job_wrapper lwr_job_state.job_id = job_id lwr_job_state.old_state = True - lwr_job_state.running = True + lwr_job_state.running = False lwr_job_state.job_destination = job_destination self.monitor_job(lwr_job_state) @@ -140,23 +143,8 @@ job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return - #run the metadata setting script here - #this is terminate-able when output dataset/job is deleted - #so that long running set_meta()s can be canceled without having to reboot the server - if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and job_wrapper.output_paths: - external_metadata_script = job_wrapper.setup_external_metadata( output_fnames = job_wrapper.get_output_fnames(), - set_extension = True, - kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior - log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) - external_metadata_proc = subprocess.Popen( args = external_metadata_script, - shell = True, - env = os.environ, - preexec_fn = os.setpgrp ) - job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session ) - external_metadata_proc.wait() - log.debug( 'execution of external set_meta finished for job %d' % job_wrapper.job_id ) - - # Finish the job + self._handle_metadata_externally( job_wrapper ) + # Finish the job try: job_wrapper.finish( stdout, stderr ) except: @@ -222,12 +210,9 @@ job_state.job_destination = job_wrapper.job_destination job_wrapper.command_line = job.get_command_line() job_state.job_wrapper = job_wrapper - if job.get_state() == model.Job.states.RUNNING: + state = job.get_state() + if state in [model.Job.states.RUNNING, model.Job.states.QUEUED]: log.debug( "(LWR/%s) is still in running state, adding to the LWR queue" % ( job.get_id()) ) job_state.old_state = True - job_state.running = True + job_state.running = state == model.Job.states.RUNNING self.monitor_queue.put( job_state ) - elif job.get_state() == model.Job.states.QUEUED: - # LWR doesn't queue currently, so this indicates galaxy was shutoff while - # job was being staged. Not sure how to recover from that. - job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted. Please retry the job." ) diff -r 64c6e3dfaa2bd54f344026752f4ab7ae008a5094 -r ae1fb20222cc7d075009b59295e247c00616bc15 lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -210,11 +210,25 @@ check_complete_response = self.__raw_execute("check_complete", {"job_id": self.job_id}) return check_complete_response - def check_complete(self): + def check_complete(self, response=None): """ Return boolean indicating whether the job is complete. """ - return self.raw_check_complete()["complete"] == "true" + if response == None: + response = self.raw_check_complete() + return response["complete"] == "true" + + def get_status(self): + check_complete_response = self.raw_check_complete() + # Older LWR instances won't set status so use 'complete', at some + # point drop backward compatibility. + complete = self.check_complete(check_complete_response) + old_status = "complete" if complete else "running" + status = check_complete_response.get("status", old_status) + # Bug in certains older LWR instances returned literal "status". + if status not in ["complete", "running", "queued"]: + status = old_status + return status def clean(self): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 20 May '13

20 May '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f6961b71d02e/ Changeset: f6961b71d02e User: natefoo Date: 2013-05-20 19:16:04 Summary: Do not abort on failures in dependency installation. Affected #: 1 file diff -r d9b308ec77f675f33d340d6f6e08000de374441c -r f6961b71d02e1032662b8d0c3d548f509e8ca68e lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -30,7 +30,8 @@ def handle_command( app, tool_dependency, install_dir, cmd ): sa_session = app.model.context.current - output = local( cmd, capture=True ) + with settings( warn_only=True ): + output = local( cmd, capture=True ) log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) if output.return_code: tool_dependency.status = app.model.ToolDependency.installation_status.ERROR https://bitbucket.org/galaxy/galaxy-central/commits/a331810bf7cf/ Changeset: a331810bf7cf User: natefoo Date: 2013-05-20 20:55:57 Summary: Changes to the setup_virtualenv tool_dependency action: - Download and use a local copy of virtualenv rather than rely on virtualenv being on the $PATH. - Do not use activate (except when installing packages e.g. with pip) since only one virtualenv can be active at a time. This allows for the use of multiple dependencies that use virtualenv. - Support setup_virtualenv with complex dependencies. Affected #: 2 files diff -r f6961b71d02e1032662b8d0c3d548f509e8ca68e -r a331810bf7cff996bde9be8b17b71dd17bb2fb90 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -6,6 +6,7 @@ import os import shutil import tempfile +import shutil from contextlib import contextmanager from galaxy import eggs @@ -22,13 +23,14 @@ log = logging.getLogger( __name__ ) INSTALLATION_LOG = 'INSTALLATION.log' +VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz' def check_fabric_version(): version = env.version if int( version.split( "." )[ 0 ] ) < 1: raise NotImplementedError( "Install Fabric version 1.0 or later." ) -def handle_command( app, tool_dependency, install_dir, cmd ): +def handle_command( app, tool_dependency, install_dir, cmd, return_output=False ): sa_session = app.model.context.current with settings( warn_only=True ): output = local( cmd, capture=True ) @@ -43,8 +45,25 @@ tool_dependency.error_message = "Unknown error occurred executing shell command %s, return_code: %s" % ( str( cmd ), str( output.return_code ) ) sa_session.add( tool_dependency ) sa_session.flush() + if return_output: + return output return output.return_code +def install_virtualenv( app, venv_dir ): + if not os.path.exists( venv_dir ): + with make_tmp_dir() as work_dir: + downloaded_filename = VIRTUALENV_URL.rsplit('/', 1)[-1] + downloaded_file_path = common_util.url_download( work_dir, downloaded_filename, VIRTUALENV_URL ) + if common_util.istar( downloaded_file_path ): + common_util.extract_tar( downloaded_file_path, work_dir ) + dir = common_util.tar_extraction_directory( work_dir, downloaded_filename ) + else: + log.error( "Failed to download virtualenv: Downloaded file '%s' is not a tar file", downloaded_filename ) + return False + full_path_to_dir = os.path.abspath( os.path.join( work_dir, dir ) ) + shutil.move( full_path_to_dir, venv_dir ) + return True + def install_and_build_package( app, tool_dependency, actions_dict ): """Install a Galaxy tool dependency package either via a url or a mercurial or git clone command.""" sa_session = app.model.context.current @@ -142,6 +161,11 @@ # tags that follow this <action type="set_environment_for_install"> tag set in the tool_dependencies.xml file. env_shell_file_paths = action_dict[ 'env_shell_file_paths' ] elif action_type == 'setup_virtualenv': + # TODO: maybe should be configurable + venv_src_directory = os.path.abspath( os.path.join( app.config.tool_dependency_dir, '__virtualenv_src' ) ) + if not install_virtualenv( app, venv_src_directory ): + log.error( 'Unable to install virtualenv' ) + return requirements = action_dict[ 'requirements' ] if os.path.exists( os.path.join( dir, requirements ) ): # requirements specified as path to a file @@ -153,7 +177,7 @@ f.write( requirements ) venv_directory = os.path.join( install_dir, "venv" ) # TODO: Consider making --no-site-packages optional. - setup_command = "virtualenv --no-site-packages '%s'" % venv_directory + setup_command = "python %s/virtualenv.py --no-site-packages '%s'" % (venv_src_directory, venv_directory) # POSIXLY_CORRECT forces shell commands . and source to have the same # and well defined behavior in bash/zsh. activate_command = "POSIXLY_CORRECT=1; . %s" % os.path.join( venv_directory, "bin", "activate" ) @@ -162,7 +186,18 @@ return_code = handle_command( app, tool_dependency, install_dir, full_setup_command ) if return_code: return - modify_env_command = common_util.create_or_update_env_shell_file_with_command( install_dir, activate_command ) + site_packages_command = "%s -c 'import os, sys; print os.path.join(sys.prefix, \"lib\", \"python\" + sys.version[:3], \"site-packages\")'" % os.path.join( venv_directory, "bin", "python" ) + output = handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True ) + if output.return_code: + return + if not os.path.exists( output.stdout ): + log.error( "virtualenv's site-packages directory '%s' does not exist", output.stdout ) + return + modify_env_command = common_util.create_or_update_env_shell_file( install_dir, dict( name="PYTHONPATH", action="prepend_to", value=output.stdout ) ) + return_code = handle_command( app, tool_dependency, install_dir, modify_env_command ) + if return_code: + return + modify_env_command = common_util.create_or_update_env_shell_file( install_dir, dict( name="PATH", action="prepend_to", value=os.path.join( venv_directory, "bin" ) ) ) return_code = handle_command( app, tool_dependency, install_dir, modify_env_command ) if return_code: return diff -r f6961b71d02e1032662b8d0c3d548f509e8ca68e -r a331810bf7cff996bde9be8b17b71dd17bb2fb90 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -137,21 +137,32 @@ for actions_elem in package_elem: for action_elem in actions_elem: action_type = action_elem.get( 'type', 'shell_command' ) + env_var_dicts = [] if action_type == 'set_environment': # <action type="set_environment"> # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> # </action> - env_var_dicts = [] for env_elem in action_elem: if env_elem.tag == 'environment_variable': env_var_dict = common_util.create_env_var_dict( env_elem, tool_dependency_install_dir=install_dir ) if env_var_dict: env_var_dicts.append( env_var_dict ) - if env_var_dicts: - action_dict[ env_elem.tag ] = env_var_dicts - actions.append( ( action_type, action_dict ) ) - return tool_dependency, actions + elif action_type == 'setup_virtualenv': + # Add the virtualenv's site-pacakges to PYTHONPATH and bin to PATH. This is a bit hackish. + site_packages_command = "%s -c 'import os, sys; print os.path.join(sys.prefix, \"lib\", \"python\" + sys.version[:3], \"site-packages\")'" % os.path.join( install_dir, "venv", "bin", "python" ) + output = fabric_util.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True ) + if output.return_code: + log.error( 'Dependency includes a setup_virtualenv action but venv python is broken:', output.stderr ) + elif not os.path.exists( output.stdout ): + log.error( "virtualenv's site-packages directory '%s' does not exist", output.stdout ) + else: + env_var_dicts.append( dict( name="PYTHONPATH", action="prepend_to", value=output.stdout ) ) + env_var_dicts.append( dict( name="PATH", action="prepend_to", value=os.path.join( install_dir, 'venv', 'bin' ) ) ) + if env_var_dicts: + action_dict[ 'environment_variable' ] = env_var_dicts + actions.append( ( 'set_environment', action_dict ) ) + return tool_dependency, actions else: raise NotImplementedError( 'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).' ) return None, actions https://bitbucket.org/galaxy/galaxy-central/commits/64c6e3dfaa2b/ Changeset: 64c6e3dfaa2b User: natefoo Date: 2013-05-20 20:56:51 Summary: Merge. Affected #: 4 files diff -r a331810bf7cff996bde9be8b17b71dd17bb2fb90 -r 64c6e3dfaa2bd54f344026752f4ab7ae008a5094 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1451,10 +1451,7 @@ def dataset_collector( hdas, parent_hid ): current_user_roles = trans.get_current_user_roles() for i, hda in enumerate( hdas ): - if len( hda.name ) > 30: - hda_name = '%s..%s' % ( hda.name[:17], hda.name[-11:] ) - else: - hda_name = hda.name + hda_name = hda.name if parent_hid is not None: hid = "%s.%d" % ( parent_hid, i + 1 ) else: diff -r a331810bf7cff996bde9be8b17b71dd17bb2fb90 -r 64c6e3dfaa2bd54f344026752f4ab7ae008a5094 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,w,k,t,L,X,i){var p=ab.extend;var m={};var j=function(ac,ad){m[ac.attr("id")]=ad};var l=function(ac,ae,ag,af){ag=".group";var ad={};m[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=m[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=m[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=m[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}m[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);m[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));m[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,n="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",R=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(y.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=o(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var Q=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);j(this.container_div,this);j(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(Q.prototype,q.prototype,y.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(af,ae,ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(af,ae,ac)}}});var Y=Backbone.View.extend({initialize:function(ac){p(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ac.prefs,onchange:function(){track.request_redraw(true)}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;j(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(o(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.values[ac.toLowerCase()+"_color"]||this.config.values.n_color}});p(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,aj,ak){var ai=this,ag=(ak?[ak]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var am=13;this.overview_box.css({left:ac,width:Math.max(am,ai)}).show();if(ai<am){this.overview_box.css("left",ac-(am-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.id=aj.id;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new O(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: 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ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new w.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:this.id,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new Q(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new X.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new k.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var O=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(O.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){O.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(e.prototype,O.prototype,{update_value:function(){O.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(k.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag,10)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ac,ag,ae,ad,af){b.call(this,ac,ag,ae,ad,af)};M.prototype.predisplay_actions=function(){};var P=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new w.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(false,true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(false,true)}).dblclick(function(ar){ar.stopPropagation()})}};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.dataset=new X.Dataset(ae.dataset);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};p(g.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset.id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw(true)},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.tiles_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(n);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;l(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new w.Cache(R);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(N.prototype,q.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw(true);this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ae,ad,ac){if(ae){this.tile_cache.clear()}this.view.request_redraw(ad,ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ac*S*ag)<ah){am=this._get_tile_bounds(ac,ag);ai=this.draw_helper(ad,am,ag,this.tiles_div,ap);aj.push(ai);$.when(ai).then(function(aq){ao.push(aq)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();if(ao[0]){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ah=ah||function(){ad.request_draw(true)},ae=this.container_div.find(".yaxislabel."+ag);if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".bs-tooltip").remove();var aj=V(parseFloat(aj),3);ad.prefs[ac]=(!isNaN(aj)?aj:null);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return !(aj instanceof M)});if(ae.length>0&&ae.length<af.length){this.max_height_px=0;var ad=this;ab.each(ae,function(aj){aj.html_elt.remove();ad.draw_helper(true,aj.region,aj.resolution,ad.tiles_div,ai,{mode:"Coverage"})});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove()}var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}},_get_drawables:function(){return[this]},draw_helper:function(ad,am,ag,ao,ap,ae){if(!ae){ae={}}var af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(aq){return(aq&&"track" in aq)},aj=ae.mode||af.mode;var ak=(ad?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ao,ap)}return ak}var al=function(){var aq=(ab.find(A,function(at){return at===aj})?"Coverage":aj);var ar=ab.map(ah,function(at){return at.data_manager.get_data(am,aq,ag,af.data_url_extra_params)});if(view.reference_track){ar.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return ar};var ac=$.Deferred();af.tile_cache.set_elt(an,ac);$.when.apply($,al()).then(function(){var aq=al(),aw=aq,aC;if(view.reference_track){aC=view.reference_track.data_manager.subset_entry(aq.pop(),am)}var ax=[],au=[];ab.each(ah,function(aH,aE){var aG=aH.mode,aF=aw[aE];if(aG==="Auto"){aG=aH.get_mode(aF);aH.update_auto_mode(aG)}ax.push(aG);au.push(aH.get_canvas_height(aF,aG,ap,ar))});var av=af.view.canvas_manager.new_canvas(),ay=am.get("start"),aD=am.get("end"),at=0,ar=Math.ceil((aD-ay)*ap)+af.left_offset,aA=ab.max(au),az;av.width=ar;av.height=(ae.height?ae.height:aA);var aB=av.getContext("2d");aB.translate(af.left_offset,0);if(ah.length>1){aB.globalAlpha=0.5;aB.globalCompositeOperation="source-over"}ab.each(ah,function(aF,aE){az=aF.draw_tile(aw[aE],aB,ax[aE],ag,am,ap,aC)});if(az!==undefined){af.tile_cache.set_elt(an,az);af.show_tile(az,ao,ap)}ac.resolve(az)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.LinePainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new M(this,ah,ag,af,ac.data)},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new k.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda")},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){this.display_modes=A;N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=o(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};p(f.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:q.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new Q(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw(true)},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw(true)},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1;for(var ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(var ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(true,af.region,af.resolution,af.html_elt.parent(),al,{height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};p(B.prototype,q.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:q.prototype.can_draw,draw_helper:function(ae,af,ac,ag,ah,ad){if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ae,af,ac,ag,ah,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(af,al,ag,ad,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ac=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,ad,ac,ae)}});var h=function(ae,ad,af){var ac=this;this.display_modes=A;this.mode="Histogram";N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:k.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.request_redraw(true)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};p(h.prototype,q.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ac,ad,ag,ae,af,ah){return this._draw_line_track_tile(ac,ad,ag,ae,af,ah)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var s=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);this.request_redraw(true)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};p(s.prototype,q.prototype,N.prototype,{draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,af,ae,ah);var ag=k.get_random_color(),ac=k.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.set_painter_from_config();ad.request_draw(true)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(c.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters;for(var aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(var aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof P){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (t.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,ar,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae,function(aD){return ap.view.get_base_color(aD)});var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new P(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="bigwig"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var Z=function(ad,ac,ae){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw(true)}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};p(Z.prototype,q.prototype,N.prototype,{draw_tile:function(ac,af,ai,ag,ah,aj){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ah,aj)}else{var ae=this.view,ad=new (this.painter)(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai,function(ak){return ae.get_base_color(ak)});ad.draw(af,af.canvas.width,af.canvas.height,aj);return new b(this,ah,ag,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=new (this.painter)(null,null,null,this.prefs,ag);var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ae,af,ah,ad){N.prototype.postdraw_actions.call(this,ae,af,ah,ad);if(!(ae[0] instanceof M)&&this.prefs.show_labels){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ag=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ag).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=k.get_random_color(),ac=k.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw(true)}});this.prefs=this.config.values;this.painter=(ae.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};p(T.prototype,q.prototype,N.prototype,c.prototype);var d={CompositeTrack:f,DrawableGroup:Q,DiagonalHeatmapTrack:s,FeatureTrack:c,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var o=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:Q,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:s,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:o}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,w,k,t,L,X,i){var p=ab.extend;var m={};var j=function(ac,ad){m[ac.attr("id")]=ad};var l=function(ac,ae,ag,af){ag=".group";var ad={};m[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=m[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=m[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=m[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}m[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);m[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));m[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,n="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",R=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(y.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=o(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var Q=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);j(this.container_div,this);j(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(Q.prototype,q.prototype,y.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(af,ae,ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(af,ae,ac)}}});var Y=Backbone.View.extend({initialize:function(ac){p(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ac.prefs,onchange:function(){track.request_redraw(true)}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;j(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(o(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.values[ac.toLowerCase()+"_color"]||this.config.values.n_color}});p(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,aj,ak){var ai=this,ag=(ak?[ak]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var am=13;this.overview_box.css({left:ac,width:Math.max(am,ai)}).show();if(ai<am){this.overview_box.css("left",ac-(am-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.id=aj.id;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new O(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new w.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:this.id,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new Q(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new X.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new k.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var O=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(O.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){O.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(e.prototype,O.prototype,{update_value:function(){O.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(k.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag,10)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ac,ag,ae,ad,af){b.call(this,ac,ag,ae,ad,af)};M.prototype.predisplay_actions=function(){};var P=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new w.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(false,true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(false,true)}).dblclick(function(ar){ar.stopPropagation()})}};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.dataset=new X.Dataset(ae.dataset);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};p(g.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset.id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw(true)},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.tiles_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(n);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;l(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new w.Cache(R);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(N.prototype,q.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw(true);this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ae,ad,ac){if(ae){this.tile_cache.clear()}this.view.request_redraw(ad,ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ac*S*ag)<ah){am=this._get_tile_bounds(ac,ag);ai=this.draw_helper(ad,am,ag,this.tiles_div,ap);aj.push(ai);$.when(ai).then(function(aq){ao.push(aq)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();if(ao[0]){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ah=ah||function(){ad.request_draw(true)},ae=this.container_div.find(".yaxislabel."+ag);if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".bs-tooltip").remove();var aj=V(parseFloat(aj),3);ad.prefs[ac]=(!isNaN(aj)?aj:null);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return !(aj instanceof M)});if(ae.length>0&&ae.length<af.length){this.max_height_px=0;var ad=this;ab.each(ae,function(aj){aj.html_elt.remove();ad.draw_helper(true,aj.region,aj.resolution,ad.tiles_div,ai,{mode:"Coverage"})});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove()}var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(ad,am,ag,ao,ap,ae){if(!ae){ae={}}var af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(aq){return(aq&&"track" in aq)},aj=ae.mode||af.mode;var ak=(ad?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ao,ap)}return ak}var al=function(){var aq=(ab.find(A,function(at){return at===aj})?"Coverage":aj);var ar=ab.map(ah,function(at){return at.data_manager.get_data(am,aq,ag,af.data_url_extra_params)});if(view.reference_track){ar.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return ar};var ac=$.Deferred();af.tile_cache.set_elt(an,ac);$.when.apply($,al()).then(function(){var aq=al(),aw=aq,aC;if(view.reference_track){aC=view.reference_track.data_manager.subset_entry(aq.pop(),am)}var ax=[],au=[];ab.each(ah,function(aH,aE){var aG=aH.mode,aF=aw[aE];if(aG==="Auto"){aG=aH.get_mode(aF);aH.update_auto_mode(aG)}ax.push(aG);au.push(aH.get_canvas_height(aF,aG,ap,ar))});var av=af.view.canvas_manager.new_canvas(),ay=am.get("start"),aD=am.get("end"),at=0,ar=Math.ceil((aD-ay)*ap)+af.left_offset,aA=ab.max(au),az;av.width=ar;av.height=(ae.height?ae.height:aA);var aB=av.getContext("2d");aB.translate(af.left_offset,0);if(ah.length>1){aB.globalAlpha=0.5;aB.globalCompositeOperation="source-over"}ab.each(ah,function(aF,aE){az=aF.draw_tile(aw[aE],aB,ax[aE],ag,am,ap,aC)});if(az!==undefined){af.tile_cache.set_elt(an,az);af.show_tile(az,ao,ap)}ac.resolve(az)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.LinePainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new M(this,ah,ag,af,ac.data)},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new k.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda")},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){this.display_modes=A;N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=o(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};p(f.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:q.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new Q(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw(true)},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw(true)},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1;for(var ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(var ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(true,af.region,af.resolution,af.html_elt.parent(),al,{height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};p(B.prototype,q.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:q.prototype.can_draw,draw_helper:function(ae,af,ac,ag,ah,ad){if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ae,af,ac,ag,ah,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(af,al,ag,ad,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ac=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,ad,ac,ae)}});var h=function(ae,ad,af){var ac=this;this.display_modes=A;this.mode="Histogram";N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:k.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.request_redraw(true)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};p(h.prototype,q.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ac,ad,ag,ae,af,ah){return this._draw_line_track_tile(ac,ad,ag,ae,af,ah)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var s=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);this.request_redraw(true)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};p(s.prototype,q.prototype,N.prototype,{draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,af,ae,ah);var ag=k.get_random_color(),ac=k.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.set_painter_from_config();ad.request_draw(true)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(c.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters;for(var aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(var aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof P){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (t.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,ar,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae,function(aD){return ap.view.get_base_color(aD)});var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new P(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="bigwig"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var Z=function(ad,ac,ae){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw(true)}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};p(Z.prototype,q.prototype,N.prototype,{draw_tile:function(ac,af,ai,ag,ah,aj){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ah,aj)}else{var ae=this.view,ad=new (this.painter)(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai,function(ak){return ae.get_base_color(ak)});ad.draw(af,af.canvas.width,af.canvas.height,aj);return new b(this,ah,ag,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=new (this.painter)(null,null,null,this.prefs,ag);var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ae,af,ah,ad){N.prototype.postdraw_actions.call(this,ae,af,ah,ad);if(!(ae[0] instanceof M)&&this.prefs.show_labels){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ag=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ag).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=k.get_random_color(),ac=k.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw(true)}});this.prefs=this.config.values;this.painter=(ae.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};p(T.prototype,q.prototype,N.prototype,c.prototype);var d={CompositeTrack:f,DrawableGroup:Q,DiagonalHeatmapTrack:s,FeatureTrack:c,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var o=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:Q,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:s,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:o}}); \ No newline at end of file diff -r a331810bf7cff996bde9be8b17b71dd17bb2fb90 -r 64c6e3dfaa2bd54f344026752f4ab7ae008a5094 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3071,6 +3071,20 @@ }, /** + * Returns appropriate display mode based on data. + */ + get_mode: function(data) { + return this.mode; + }, + + /** + * Update track interface to show display mode being used. + */ + update_auto_mode: function( display_mode ) { + // FIXME: needs to be implemented. + }, + + /** * Returns a list of drawables to draw. Defaults to current track. */ _get_drawables: function() { @@ -3925,6 +3939,9 @@ } }, + /** + * Update track interface to show display mode being used. + */ update_auto_mode: function( mode ) { var mode; if ( this.mode === "Auto" ) { diff -r a331810bf7cff996bde9be8b17b71dd17bb2fb90 -r 64c6e3dfaa2bd54f344026752f4ab7ae008a5094 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -280,20 +280,18 @@ api_url = get_api_url( base=tool_shed_url, parts=api_path ) repository_metadata = json_from_url( api_url ) tool_test_results = repository_metadata.get( 'tool_test_results', {} ) - # Compatibility code, remove before next release. - if not tool_test_results: - tool_test_results = repository_metadata.get( 'tool_test_errors', {} ) + # If, for some reason, the script that checks for functional tests has not run, tool_test_results will be None. + if tool_test_results is None: + return dict() return tool_test_results def is_latest_downloadable_revision( url, repository_info_dict ): api_url_parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] params = urllib.urlencode( dict( name=repository_info_dict[ 'name' ], owner=repository_info_dict[ 'owner' ] ) ) api_url = get_api_url( url, api_url_parts, params ) - # TODO: Remove this try/catch wrapping when the main tool shed is updated. - try: - changeset_revisions = json_from_url( api_url ) - except Exception, e: - return True + changeset_revisions = json_from_url( api_url ) + # The get_ordered_installable_revisions returns a list of changeset hashes, with the last hash in the list + # being the most recent installable revision. latest_revision = changeset_revisions.pop() return str( repository_info_dict[ 'changeset_revision' ] ) == str( latest_revision ) @@ -312,17 +310,6 @@ Update the repository metadata tool_test_results and appropriate flags using the API. ''' params[ 'tool_test_results' ] = test_results_dict - # BEGIN compatibility code. - # TODO: The repository_revisions API controller ignores any received parameter that is not present in the database schema, - # but the compatibility code here should be removed when the main tool shed is updated with the new database migration version. - params[ 'tool_test_errors' ] = test_results_dict - if test_results_dict[ 'failed_tests' ]: - params[ 'tool_test_errors' ][ 'test_errors' ] = test_results_dict[ 'failed_tests' ] - if test_results_dict[ 'passed_tests' ]: - params[ 'tool_test_errors' ][ 'tests_passed' ] = test_results_dict[ 'passed_tests' ] - # Copying the missing_test_components key is not necessary, since the main tool shed is running its own version of the - # check repositories script, which correctly updates the invalid_tests key. - # END compatibility code. if '-info_only' in sys.argv: return {} else: @@ -760,8 +747,8 @@ repository_status[ 'missing_test_components' ].append( missing_components ) # Record the status of this repository in the tool shed. set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_info_dict ) - params[ 'tools_functionally_correct' ] = 'false' - params[ 'missing_test_components' ] = 'true' + params[ 'tools_functionally_correct' ] = False + params[ 'missing_test_components' ] = True params[ 'do_not_test' ] = str( set_do_not_test ) register_test_result( galaxy_tool_shed_url, metadata_revision_id, @@ -795,9 +782,9 @@ error_message=dependency.error_message ) repository_status[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) # Record the status of this repository in the tool shed. - params[ 'tools_functionally_correct' ] = 'false' - params[ 'do_not_test' ] = 'false' - params[ 'test_install_error' ] = 'true' + params[ 'tools_functionally_correct' ] = False + params[ 'do_not_test' ] = False + params[ 'test_install_error' ] = True register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, @@ -848,8 +835,8 @@ # controller with the status of the test. This also sets the do_not_test and tools_functionally correct flags, and # updates the time_last_tested field to today's date. repositories_passed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - params[ 'tools_functionally_correct' ] = 'true' - params[ 'do_not_test' ] = 'false' + params[ 'tools_functionally_correct' ] = True + params[ 'do_not_test' ] = False register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, @@ -900,7 +887,7 @@ # field to today's date. repositories_failed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_info_dict ) - params[ 'tools_functionally_correct' ] = 'false' + params[ 'tools_functionally_correct' ] = False params[ 'do_not_test' ] = str( set_do_not_test ) register_test_result( galaxy_tool_shed_url, metadata_revision_id, @@ -933,9 +920,9 @@ changeset_revision=repository.changeset_revision, error_message=repository.error_message ) repository_status[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) - params[ 'tools_functionally_correct' ] = 'false' - params[ 'test_install_error' ] = 'true' - params[ 'do_not_test' ] = 'false' + params[ 'tools_functionally_correct' ] = False + params[ 'test_install_error' ] = True + params[ 'do_not_test' ] = False register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 May '13

20 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d9b308ec77f6/ Changeset: d9b308ec77f6 User: jmchilton Date: 2013-05-20 15:25:03 Summary: Implement setting up tool dependency action (setup_virtualenv) to automatically setup python virtual environments. Install requirements from file requirements.txt of downloaded bundle: <action type="setup_virtualenv" /> - or - Install requirements from specified file from downloaded bundle: <action type="setup_virtualenv">tools/requirements.txt</action> - or - Manually specify contents of requirements.txt file to create dynamically. <action type="setup_virtualenv">pyyaml==3.2.0 lxml==2.3.0</action> Other small refactorings to support this. Including: - Rework expansion of $INSTALL_DIR in tool_dependency.xml files to use string.Template and allow additional variables. $system_install now expands to the install dir to mimic what what we do with CloudBioLinux Galaxy tool dependency creation. Ultimately, would like to have $tool_version to expand as well, since most downloads differ only based on this version which must be set anyway. - Refactor a more general function, create_or_update_env_shell_file_with_command, out of create_or_update_env_shell_file. Use this more general function to implement Python virtualenv activation in tool dependencies. - Implement shell quoting create_or_update_env_shell_file_with_command to handle special characters in paths. Affected #: 3 files diff -r 237209336f0337ea9f47df39548df3c11900f182 -r d9b308ec77f675f33d340d6f6e08000de374441c lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -47,19 +47,28 @@ changed_value = '%s' % env_var_value elif env_var_action == 'append_to': changed_value = '$%s:%s' % ( env_var_name, env_var_value ) + line = "%s=%s; export %s" % (env_var_name, changed_value, env_var_name) + return create_or_update_env_shell_file_with_command(install_dir, line) + + +def create_or_update_env_shell_file_with_command( install_dir, command ): + """ + Return a shell expression which when executed will create or update + a Galaxy env.sh dependency file in the specified install_dir containing + the supplied command. + """ env_shell_file_path = '%s/env.sh' % install_dir if os.path.exists( env_shell_file_path ): write_action = '>>' else: write_action = '>' - cmd = "echo '%s=%s; export %s' %s %s;chmod +x %s" % ( env_var_name, - changed_value, - env_var_name, - write_action, - env_shell_file_path, - env_shell_file_path ) + cmd = "echo %s %s %s;chmod +x %s" % ( __shellquote(command), + write_action, + __shellquote(env_shell_file_path), + __shellquote(env_shell_file_path)) return cmd + def extract_tar( file_name, file_path ): if isgzip( file_name ) or isbz2( file_name ): # Open for reading with transparent compression. @@ -233,3 +242,10 @@ if not member_path.startswith( basename ): return False return True + + +def __shellquote(s): + """ + Quote and escape the supplied string for use in shell expressions. + """ + return "'" + s.replace("'", "'\\''") + "'" diff -r 237209336f0337ea9f47df39548df3c11900f182 -r d9b308ec77f675f33d340d6f6e08000de374441c lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -140,6 +140,31 @@ # the environment setting in each of which will be injected into the environment for all <action type="shell_command"> # tags that follow this <action type="set_environment_for_install"> tag set in the tool_dependencies.xml file. env_shell_file_paths = action_dict[ 'env_shell_file_paths' ] + elif action_type == 'setup_virtualenv': + requirements = action_dict[ 'requirements' ] + if os.path.exists( os.path.join( dir, requirements ) ): + # requirements specified as path to a file + requirements_path = requirements + else: + # requirements specified directly in XML, create a file with these for pip. + requirements_path = os.path.join( install_dir, "requirements.txt" ) + with open( requirements_path, "w" ) as f: + f.write( requirements ) + venv_directory = os.path.join( install_dir, "venv" ) + # TODO: Consider making --no-site-packages optional. + setup_command = "virtualenv --no-site-packages '%s'" % venv_directory + # POSIXLY_CORRECT forces shell commands . and source to have the same + # and well defined behavior in bash/zsh. + activate_command = "POSIXLY_CORRECT=1; . %s" % os.path.join( venv_directory, "bin", "activate" ) + install_command = "pip install -r '%s'" % requirements_path + full_setup_command = "%s; %s; %s" % ( setup_command, activate_command, install_command ) + return_code = handle_command( app, tool_dependency, install_dir, full_setup_command ) + if return_code: + return + modify_env_command = common_util.create_or_update_env_shell_file_with_command( install_dir, activate_command ) + return_code = handle_command( app, tool_dependency, install_dir, modify_env_command ) + if return_code: + return elif action_type == 'shell_command': with settings( warn_only=True ): cmd = '' diff -r 237209336f0337ea9f47df39548df3c11900f182 -r d9b308ec77f675f33d340d6f6e08000de374441c lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -3,6 +3,7 @@ import sys import subprocess import tempfile +from string import Template import common_util import fabric_util import tool_shed.util.shed_util_common as suc @@ -317,6 +318,17 @@ def install_via_fabric( app, tool_dependency, actions_elem, install_dir, package_name=None, proprietary_fabfile_path=None, **kwd ): """Parse a tool_dependency.xml file's <actions> tag set to gather information for the installation via fabric.""" sa_session = app.model.context.current + + def evaluate_template( text ): + """ Substitute variables defined in XML blocks obtained loaded from + dependencies file. """ + # TODO: Add tool_version substitution for compat with CloudBioLinux. + substitutions = { + "INSTALL_DIR": install_dir, + "system_install": install_dir, # Added for compat with CloudBioLinux + } + return Template( text ).safe_substitute( substitutions ) + if not os.path.exists( install_dir ): os.makedirs( install_dir ) actions_dict = dict( install_dir=install_dir ) @@ -328,7 +340,7 @@ action_type = action_elem.get( 'type', 'shell_command' ) if action_type == 'shell_command': # <action type="shell_command">make</action> - action_elem_text = action_elem.text.replace( '$INSTALL_DIR', install_dir ) + action_elem_text = evaluate_template( action_elem.text ) if action_elem_text: action_dict[ 'command' ] = action_elem_text else: @@ -351,7 +363,7 @@ elif action_type == 'make_directory': # <action type="make_directory">$INSTALL_DIR/lib/python</action> if action_elem.text: - action_dict[ 'full_path' ] = action_elem.text.replace( '$INSTALL_DIR', install_dir ) + action_dict[ 'full_path' ] = evaluate_template( action_elem.text ) else: continue elif action_type in [ 'move_directory_files', 'move_file' ]: @@ -364,7 +376,7 @@ # <destination_directory>$INSTALL_DIR/bin</destination_directory> # </action> for move_elem in action_elem: - move_elem_text = move_elem.text.replace( '$INSTALL_DIR', install_dir ) + move_elem_text = evaluate_template( move_elem.text ) if move_elem_text: action_dict[ move_elem.tag ] = move_elem_text elif action_type == 'set_environment': @@ -402,6 +414,15 @@ action_dict[ 'env_shell_file_paths' ] = all_env_shell_file_paths else: continue + elif action_type == 'setup_virtualenv': + # <action type="setup_virtualenv" /> + ## Install requirements from file requirements.txt of downloaded bundle - or - + # <action type="setup_virtualenv">tools/requirements.txt</action> + ## Install requirements from specified file from downloaded bundle -or - + # <action type="setup_virtualenv">pyyaml==3.2.0 + # lxml==2.3.0</action> + ## Manually specify contents of requirements.txt file to create dynamically. + action_dict[ 'requirements' ] = evaluate_template( action_elem.text or 'requirements.txt' ) else: log.debug( "Unsupported action type '%s'. Not proceeding." % str( action_type ) ) raise Exception( "Unsupported action type '%s' in tool dependency definition." % str( action_type ) ) https://bitbucket.org/galaxy/galaxy-central/commits/68f1441f04f5/ Changeset: 68f1441f04f5 User: natefoo Date: 2013-05-20 20:56:07 Summary: Merged in jmchilton/galaxy-central-library-refactoring (pull request #167) Implement setting up tool dependency action (setup_virtualenv) to automatically setup python virtual environments. Affected #: 3 files diff -r e620c575616470afaa3923bf5817db07e09b45bc -r 68f1441f04f557ba06d41426408dab4e98997d26 lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -47,19 +47,28 @@ changed_value = '%s' % env_var_value elif env_var_action == 'append_to': changed_value = '$%s:%s' % ( env_var_name, env_var_value ) + line = "%s=%s; export %s" % (env_var_name, changed_value, env_var_name) + return create_or_update_env_shell_file_with_command(install_dir, line) + + +def create_or_update_env_shell_file_with_command( install_dir, command ): + """ + Return a shell expression which when executed will create or update + a Galaxy env.sh dependency file in the specified install_dir containing + the supplied command. + """ env_shell_file_path = '%s/env.sh' % install_dir if os.path.exists( env_shell_file_path ): write_action = '>>' else: write_action = '>' - cmd = "echo '%s=%s; export %s' %s %s;chmod +x %s" % ( env_var_name, - changed_value, - env_var_name, - write_action, - env_shell_file_path, - env_shell_file_path ) + cmd = "echo %s %s %s;chmod +x %s" % ( __shellquote(command), + write_action, + __shellquote(env_shell_file_path), + __shellquote(env_shell_file_path)) return cmd + def extract_tar( file_name, file_path ): if isgzip( file_name ) or isbz2( file_name ): # Open for reading with transparent compression. @@ -233,3 +242,10 @@ if not member_path.startswith( basename ): return False return True + + +def __shellquote(s): + """ + Quote and escape the supplied string for use in shell expressions. + """ + return "'" + s.replace("'", "'\\''") + "'" diff -r e620c575616470afaa3923bf5817db07e09b45bc -r 68f1441f04f557ba06d41426408dab4e98997d26 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -140,6 +140,31 @@ # the environment setting in each of which will be injected into the environment for all <action type="shell_command"> # tags that follow this <action type="set_environment_for_install"> tag set in the tool_dependencies.xml file. env_shell_file_paths = action_dict[ 'env_shell_file_paths' ] + elif action_type == 'setup_virtualenv': + requirements = action_dict[ 'requirements' ] + if os.path.exists( os.path.join( dir, requirements ) ): + # requirements specified as path to a file + requirements_path = requirements + else: + # requirements specified directly in XML, create a file with these for pip. + requirements_path = os.path.join( install_dir, "requirements.txt" ) + with open( requirements_path, "w" ) as f: + f.write( requirements ) + venv_directory = os.path.join( install_dir, "venv" ) + # TODO: Consider making --no-site-packages optional. + setup_command = "virtualenv --no-site-packages '%s'" % venv_directory + # POSIXLY_CORRECT forces shell commands . and source to have the same + # and well defined behavior in bash/zsh. + activate_command = "POSIXLY_CORRECT=1; . %s" % os.path.join( venv_directory, "bin", "activate" ) + install_command = "pip install -r '%s'" % requirements_path + full_setup_command = "%s; %s; %s" % ( setup_command, activate_command, install_command ) + return_code = handle_command( app, tool_dependency, install_dir, full_setup_command ) + if return_code: + return + modify_env_command = common_util.create_or_update_env_shell_file_with_command( install_dir, activate_command ) + return_code = handle_command( app, tool_dependency, install_dir, modify_env_command ) + if return_code: + return elif action_type == 'shell_command': with settings( warn_only=True ): cmd = '' diff -r e620c575616470afaa3923bf5817db07e09b45bc -r 68f1441f04f557ba06d41426408dab4e98997d26 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -3,6 +3,7 @@ import sys import subprocess import tempfile +from string import Template import common_util import fabric_util import tool_shed.util.shed_util_common as suc @@ -317,6 +318,17 @@ def install_via_fabric( app, tool_dependency, actions_elem, install_dir, package_name=None, proprietary_fabfile_path=None, **kwd ): """Parse a tool_dependency.xml file's <actions> tag set to gather information for the installation via fabric.""" sa_session = app.model.context.current + + def evaluate_template( text ): + """ Substitute variables defined in XML blocks obtained loaded from + dependencies file. """ + # TODO: Add tool_version substitution for compat with CloudBioLinux. + substitutions = { + "INSTALL_DIR": install_dir, + "system_install": install_dir, # Added for compat with CloudBioLinux + } + return Template( text ).safe_substitute( substitutions ) + if not os.path.exists( install_dir ): os.makedirs( install_dir ) actions_dict = dict( install_dir=install_dir ) @@ -328,7 +340,7 @@ action_type = action_elem.get( 'type', 'shell_command' ) if action_type == 'shell_command': # <action type="shell_command">make</action> - action_elem_text = action_elem.text.replace( '$INSTALL_DIR', install_dir ) + action_elem_text = evaluate_template( action_elem.text ) if action_elem_text: action_dict[ 'command' ] = action_elem_text else: @@ -351,7 +363,7 @@ elif action_type == 'make_directory': # <action type="make_directory">$INSTALL_DIR/lib/python</action> if action_elem.text: - action_dict[ 'full_path' ] = action_elem.text.replace( '$INSTALL_DIR', install_dir ) + action_dict[ 'full_path' ] = evaluate_template( action_elem.text ) else: continue elif action_type in [ 'move_directory_files', 'move_file' ]: @@ -364,7 +376,7 @@ # <destination_directory>$INSTALL_DIR/bin</destination_directory> # </action> for move_elem in action_elem: - move_elem_text = move_elem.text.replace( '$INSTALL_DIR', install_dir ) + move_elem_text = evaluate_template( move_elem.text ) if move_elem_text: action_dict[ move_elem.tag ] = move_elem_text elif action_type == 'set_environment': @@ -402,6 +414,15 @@ action_dict[ 'env_shell_file_paths' ] = all_env_shell_file_paths else: continue + elif action_type == 'setup_virtualenv': + # <action type="setup_virtualenv" /> + ## Install requirements from file requirements.txt of downloaded bundle - or - + # <action type="setup_virtualenv">tools/requirements.txt</action> + ## Install requirements from specified file from downloaded bundle -or - + # <action type="setup_virtualenv">pyyaml==3.2.0 + # lxml==2.3.0</action> + ## Manually specify contents of requirements.txt file to create dynamically. + action_dict[ 'requirements' ] = evaluate_template( action_elem.text or 'requirements.txt' ) else: log.debug( "Unsupported action type '%s'. Not proceeding." % str( action_type ) ) raise Exception( "Unsupported action type '%s' in tool dependency definition." % str( action_type ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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