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February 2011

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commit/galaxy-central: jgoecks: Fix bug in extract_genomic_dna to handle non-GFF files when interpret features is true. Tweak functional test to cover new behavior.
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8ecfa22f0d98/ changeset: r5075:8ecfa22f0d98 user: jgoecks date: 2011-02-17 03:46:23 summary: Fix bug in extract_genomic_dna to handle non-GFF files when interpret features is true. Tweak functional test to cover new behavior. affected #: 2 files (16 bytes) --- a/tools/extract/extract_genomic_dna.py Wed Feb 16 13:50:30 2011 -0500 +++ b/tools/extract/extract_genomic_dna.py Wed Feb 16 21:46:23 2011 -0500 @@ -234,7 +234,7 @@ fout.write( "%s\n" % str( sequence[c:b] ) ) c = b else: # output_format == "interval" - if interpret_features: + if gff_format and interpret_features: # TODO: need better GFF Reader to capture all information needed # to produce this line. meta_data = "\t".join( --- a/tools/extract/extract_genomic_dna.xml Wed Feb 16 13:50:30 2011 -0500 +++ b/tools/extract/extract_genomic_dna.xml Wed Feb 16 21:46:23 2011 -0500 @@ -70,7 +70,7 @@ </test><test><param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> - <param name="interpret_features" value="no"/> + <param name="interpret_features" value="yes"/><param name="index_source" value="cached"/><param name="out_format" value="interval"/><output name="out_file1" file="extract_genomic_dna_out3.interval" /> 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: dannon: Quick fix for postgres9 JSONType/MetadataType hex decoding issues.
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/89190bcd1ccf/ changeset: r5074:89190bcd1ccf user: dannon date: 2011-02-16 19:50:30 summary: Quick fix for postgres9 JSONType/MetadataType hex decoding issues. Todo: Postgres9 might be configurable to do this natively, postgres8 does not have the issue. affected #: 1 file (305 bytes) --- a/lib/galaxy/model/custom_types.py Wed Feb 16 13:48:14 2011 -0500 +++ b/lib/galaxy/model/custom_types.py Wed Feb 16 13:50:30 2011 -0500 @@ -4,6 +4,7 @@ import simplejson import pickle import copy +import binascii from galaxy.util.bunch import Bunch from galaxy.util.aliaspickler import AliasPickleModule @@ -14,8 +15,20 @@ json_encoder = simplejson.JSONEncoder( sort_keys=True ) json_decoder = simplejson.JSONDecoder( ) +def _sniffnfix_pg9_hex(value): + """ + Sniff for and fix postgres 9 hex decoding issue + """ + try: + if value[0] == 'x': + return binascii.unhexlify(value[1:]) + else: + return value + except Exception, ex: + return value + class JSONType( TypeDecorator ): - """ + """ Defines a JSONType for SQLAlchemy. Takes a primitive as input and JSONifies it. This should replace PickleType throughout Galaxy. """ @@ -29,16 +42,16 @@ def process_result_value( self, value, dialect ): if value is None: return None - return json_decoder.decode( str( value ) ) - + return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) ) + def copy_value( self, value ): # return json_decoder.decode( json_encoder.encode( value ) ) return copy.deepcopy( value ) def compare_values( self, x, y ): - # return json_encoder.encode( x ) == json_encoder.encode( y ) - return ( x == y ) - + # return json_encoder.encode( x ) == json_encoder.encode( y ) + return ( x == y ) + def is_mutable( self ): return True @@ -61,11 +74,11 @@ ret = dict( ret.__dict__ ) except: try: - ret = json_decoder.decode( str( value ) ) + ret = json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) ) except: ret = None return ret - + class TrimmedString( TypeDecorator ): impl = String def process_bind_param( self, value, dialect ): @@ -73,4 +86,4 @@ if self.impl.length and value is not None: value = value[0:self.impl.length] return value - + 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: natefoo: Fix unit tests failing on missing dependencies in job runners
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9a547a8f0d49/ changeset: r5073:9a547a8f0d49 user: natefoo date: 2011-02-16 19:48:14 summary: Fix unit tests failing on missing dependencies in job runners affected #: 1 file (86 bytes) --- a/run_unit_tests.sh Wed Feb 16 13:37:13 2011 -0500 +++ b/run_unit_tests.sh Wed Feb 16 13:48:14 2011 -0500 @@ -1,7 +1,9 @@ #!/bin/sh ## Excluding controllers due to the problematic genetrack dependency +## Excluding job runners due to various external dependencies python ./scripts/nosetests.py -v -w lib \ --with-nosehtml --html-report-file run_unit_tests.html \ - --with-doctest --exclude=functional --exclude="^get" --exclude=controllers + --with-doctest --exclude=functional --exclude="^get" \ + --exclude=controllers --exclude=runners 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: natefoo: Add test data repository setup directly to the buildbot setup script.
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/53ea14cb5909/ changeset: r5072:53ea14cb5909 user: natefoo date: 2011-02-16 19:37:13 summary: Add test data repository setup directly to the buildbot setup script. affected #: 1 file (347 bytes) --- a/buildbot_setup.sh Wed Feb 16 12:56:18 2011 -0500 +++ b/buildbot_setup.sh Wed Feb 16 13:37:13 2011 -0500 @@ -115,4 +115,17 @@ cp test-data/wig_to_bigwig_hg17.len tool-data/shared/ucsc/chrom/hg17.len fi +if [ -d "test-data-repo" ]; then + echo "Updating test data repository" + cd test-data-repo + hg pull + hg update + cd .. +else + echo "Cloning test data repository" + hg clone http://bitbucket.org/natefoo/galaxy-test-data/ test-data-repo +fi +echo "Setting up test data location files" +python test-data-repo/location/make_location.py + python ./scripts/fetch_eggs.py all 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: jgoecks: Bug fix: do not fix strand in extract_genomic_dna tool.
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5f2047e0eb18/ changeset: r5071:5f2047e0eb18 user: jgoecks date: 2011-02-16 18:56:18 summary: Bug fix: do not fix strand in extract_genomic_dna tool. affected #: 1 file (1 byte) --- a/tools/extract/extract_genomic_dna.py Wed Feb 16 10:14:24 2011 -0500 +++ b/tools/extract/extract_genomic_dna.py Wed Feb 16 12:56:18 2011 -0500 @@ -120,7 +120,7 @@ twobitfile = None file_iterator = open( input_filename ) if gff_format and interpret_features: - file_iterator = gff_util.GFFReaderWrapper( file_iterator, fix_strand=True ) + file_iterator = gff_util.GFFReaderWrapper( file_iterator, fix_strand=False ) for i, feature in enumerate( file_iterator ): if gff_format and interpret_features: # Processing features. 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: greg: When rendering the contents of a data library, make sure a LibraryDataset has an associated LibraryDatasetDatasetAssociation. There should always be an ldda, but some users running their own instances have reported that some of their LibraryDatasets are missing these associations.
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ca0c4ad2bb39/ changeset: r5070:ca0c4ad2bb39 user: greg date: 2011-02-16 16:14:24 summary: When rendering the contents of a data library, make sure a LibraryDataset has an associated LibraryDatasetDatasetAssociation. There should always be an ldda, but some users running their own instances have reported that some of their LibraryDatasets are missing these associations. affected #: 1 file (554 bytes) --- a/templates/library/common/browse_library.mako Wed Feb 16 09:54:49 2011 -0500 +++ b/templates/library/common/browse_library.mako Wed Feb 16 10:14:24 2011 -0500 @@ -438,9 +438,14 @@ %for library_dataset in library_datasets: <% ldda = library_dataset.library_dataset_dataset_association - selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids + if ldda: + # There should always be an ldda, but some users running their own instances have reported that + # some of their LibraryDatasets have no associated lddas + selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids %> - ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )} + %if ldda: + ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )} + %endif %endfor %else: %for sub_folder in sub_folders: @@ -449,8 +454,13 @@ %for library_dataset in library_datasets: <% ldda = library_dataset.library_dataset_dataset_association - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ldda.dataset ) - selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids + if ldda: + # There should always be an ldda, but some users running their own instances have reported that + # some of their LibraryDatasets have no associated lddas + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ldda.dataset ) + selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids + else: + can_access = False %> %if can_access: ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )} 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: greg: Fix bug when rendering the contents of a data library - render the options for acting on multiple datasets if the library includes accessible datasets at any level in the hierarchy rather than if it only includes them in the root folder.
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9754f81fd6c4/ changeset: r5069:9754f81fd6c4 user: greg date: 2011-02-16 15:54:49 summary: Fix bug when rendering the contents of a data library - render the options for acting on multiple datasets if the library includes accessible datasets at any level in the hierarchy rather than if it only includes them in the root folder. affected #: 2 files (354 bytes) --- a/lib/galaxy/webapps/reports/controllers/sample_tracking.py Tue Feb 15 19:20:39 2011 -0500 +++ b/lib/galaxy/webapps/reports/controllers/sample_tracking.py Wed Feb 16 09:54:49 2011 -0500 @@ -143,7 +143,6 @@ row.total, row.date.strftime( "%B" ), row.date.strftime( "%Y" ) ) ) - log.debug("#######In per_month_all, requests: %s" % str( requests )) return trans.fill_template( '/webapps/reports/requests_per_month_all.mako', requests=requests, message=message ) --- a/templates/library/common/browse_library.mako Tue Feb 15 19:20:39 2011 -0500 +++ b/templates/library/common/browse_library.mako Wed Feb 16 09:54:49 2011 -0500 @@ -20,6 +20,7 @@ self.message_box_visible=False self.active_view="user" self.overlay_visible=False + self.has_accessible_datasets = False %></%def> @@ -349,7 +350,9 @@ form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE info_association, inherited = folder.get_info_association( restrict=True ) - has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False ) + if not self.has_accessible_datasets: + # If we already know the library contains accessible datasets, no need to check again (and we may set it to False if we do). + self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False ) %> %if not root_folder and ( not folder.deleted or show_deleted ): <% encoded_id = trans.security.encode_id(folder.id) %> @@ -379,7 +382,7 @@ <a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a> %endif %if not branch_deleted( folder ): - %if has_accessible_datasets: + %if self.has_accessible_datasets: <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a> %endif %if can_modify: @@ -476,7 +479,7 @@ info_association, inherited = library.get_info_association() form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE - has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False ) + self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False ) has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles ) tracked_datasets = {} @@ -523,7 +526,7 @@ %endif <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> %endif - %if has_accessible_datasets: + %if self.has_accessible_datasets: <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a> %endif %elif can_modify and not library.purged: @@ -546,7 +549,7 @@ <br/> %endif - %if has_accessible_datasets: + %if self.has_accessible_datasets: <form name="act_on_multiple_datasets" action="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}" onSubmit="javascript:return checkForm();" method="post"> %endif %if has_accessible_folders: @@ -554,7 +557,7 @@ <thead><tr class="libraryTitle"><th> - %if has_accessible_datasets: + %if self.has_accessible_datasets: <input type="checkbox" id="checkAll" name=select_all_datasets_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_datasets_checkbox value="true"/> %endif Name @@ -568,18 +571,18 @@ <% row_counter = RowCounter() %> %if cntrller in [ 'library', 'requests' ]: ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} - %if not library.deleted and has_accessible_datasets: + %if not library.deleted and self.has_accessible_datasets: ${render_actions_on_multiple_items()} %endif %elif ( trans.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ): ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} - %if not library.deleted and not show_deleted and has_accessible_datasets: + %if not library.deleted and not show_deleted and self.has_accessible_datasets: ${render_actions_on_multiple_items()} %endif %endif </table> %endif - %if has_accessible_datasets: + %if self.has_accessible_datasets: </form> %endif @@ -591,7 +594,7 @@  %endif - %if has_accessible_datasets: + %if self.has_accessible_datasets: ${render_compression_types_help( comptypes )} %endif %if not has_accessible_folders: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: fix max chrom length.
by Bitbucket 15 Feb '11

15 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/88640d4ca8f5/ changeset: r5068:88640d4ca8f5 user: jgoecks date: 2011-02-16 01:20:39 summary: Trackster: fix max chrom length. affected #: 2 files (48 bytes) --- a/static/scripts/packed/trackster.js Tue Feb 15 19:09:38 2011 -0500 +++ b/static/scripts/packed/trackster.js Tue Feb 15 19:20:39 2011 -0500 @@ -1,1 +1,1 @@ -CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,PACK_SPACING=5,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. 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/>").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var k=$("<div class='form-row' />").appendTo(a);k.append($("<label />").attr("for",c).text(d.label+":"));if(d.type=="bool"){k.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type=="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var i=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(i);var j=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(i).appendTo(k).bind("click",function(l){i.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){i.hide();$(document).unbind("click.color-picker")});l.stopPropagation()})}else{k.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.name_div.data("menu_options")["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+a.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,j=g-m,c=this.view.container.width(),f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),r=c/j;this.content_div.append(p);this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=0;while((a*DENSITY*f)<g){var n=c+"_"+r+"_"+a;var e=this.tile_cache.get(n);var k=a*DENSITY*this.view.resolution;var q=k+DENSITY*this.view.resolution;if(!b&&e){this.show_tile(e,p,k,r)}else{this.delayed_draw(b,n,k,q,a,f,p,r)}a+=1}var d=this;var o=setInterval(function(){if(l===0){var u=d.content_div.children();var t=false;for(var v=u.length-1,s=0;v>=s;v--){var x=$(u[v]);if(t){x.remove()}else{if(x.children().length!==0){t=true}}}for(var w=0;w<d.filters.length;w++){d.filters[w].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(b)}},delayed_draw:function(b,g,f,i,c,e,h,j){var d=this;var a=setTimeout(function(){if(f<=d.view.high&&i>=d.view.low){var k;if(!b){k=d.tile_cache.get(g)}if(!k){k=d.draw_tile(e,c,h,j);if(k){var l=$("<div class='track-tile'>").prepend(k);if(k.hasClass(FILTERABLE_CLASS)){l.addClass(FILTERABLE_CLASS)}k=l}}if(k){d.tile_cache.set(g,k);d.show_tile(k,h,f,j)}}},50)},show_tile:function(a,f,d,g){var b=this;var c=this.view.high-this.view.low,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>CHAR_WIDTH_PX){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.data_queue={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,j,d,q){var r=this.inc_slots[a];if(!r||(r.mode!==q)){r={};r.w_scale=a;r.mode=q;this.inc_slots[a]=r;this.start_end_dct[a]={}}var m=r.w_scale,x=[],y=[],k=0,o=this.view.max_low;for(var v=0,w=j.length;v<w;v++){var h=j[v],l=h[0];if(r[l]!==undefined){k=Math.max(k,r[l]);y.push(r[l])}else{x.push(v)}}var e=this.start_end_dct[a];var n=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=e[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var i=F[z];if(E>i[0]&&D<i[1]){A=true;break}}}if(!A){return C}}return -1};for(var v=0,w=x.length;v<w;v++){var h=j[x[v]],l=h[0],t=h[1],b=h[2],p=h[3],c=Math.floor((t-o)*m),g=Math.ceil((b-o)*m),u=CONTEXT.measureText(p).width,f;if(p!==undefined&&!d){u+=(LABEL_SPACING+PACK_SPACING);if(c-u>=0){c-=u;f="left"}else{g+=u;f="right"}}var s=n(c,g);if(s>=0){if(e[s]===undefined){e[s]=[]}e[s].push([c,g]);r[l]=s;k=Math.max(k,s)}else{}}return k},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>CHAR_WIDTH_PX){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ae,m,q,au){var K=m*DENSITY*ae,aj=(m+1)*DENSITY*ae,J=aj-K;var G=this.data_cache.get_data(K,aj,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[K,aj]]=true;this.get_data(K,aj);return}var a=Math.ceil(J*au),ag=this.prefs.label_color,g=this.prefs.block_color,p=this.mode,u=25,aa,V=this.left_offset,at,B,av;var o=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(o)}o=$(o);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(p==="Dense"){B=u;av=DENSE_TRACK_HEIGHT}else{if(p==="Squish"){av=SQUISH_TRACK_HEIGHT;aa=true}else{if(p==="Pack"){av=PACK_TRACK_HEIGHT;aa=false}else{if(G.extra_info==="no_detail"){av=(G.track_type==="bai"?SQUISH_TRACK_HEIGHT:NO_DETAIL_TRACK_HEIGHT);aa=true}else{av=PACK_TRACK_HEIGHT;aa=false}}}B=this.incremental_slots(au,G.data,aa,p)*av+u;at=this.inc_slots[au]}}o.get(0).width=a+V;o.get(0).height=B;if(G.dataset_type=="summary_tree"){o.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}q.parent().css("height",Math.max(this.height_px,B)+"px");var H=o.get(0).getContext("2d");H.fillStyle=g;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var v=B+LABEL_SPACING+CHAR_HEIGHT_PX;points=G.data,max=G.max,delta_x_px=Math.ceil(G.delta*au);var n=$("<div />").addClass("yaxislabel");n.text(max);n.css({position:"absolute",top:"22px",left:"10px"});n.prependTo(this.container_div);for(var an=0,F=points.length;an<F;an++){var Z=Math.floor((points[an][0]-K)*au);var Y=points[an][1];if(!Y){continue}var ak=Y/max*B;H.fillStyle="black";H.fillRect(Z+V,v-ak,delta_x_px,ak);var X=4;if(this.prefs.show_counts&&(H.measureText(Y).width+X)<delta_x_px){H.fillStyle="#666";H.textAlign="center";H.fillText(Y,Z+V+(delta_x_px/2),10)}}return o}if(G.message){o.css({"border-color":"red"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+V,av);if(!G.data){return o}}for(var aq=0;aq<this.filters.length;aq++){if(G.data.length&&this.filters[aq].applies_to(G.data[0])){o.addClass(FILTERABLE_CLASS);break}}var ar=G.data;var am=0;for(var an=0,F=ar.length;an<F;an++){var R=ar[an],O=R[0],ap=R[1],ac=R[2],L=R[3];if(this.mode!="Dense"&&at[O]===undefined){continue}var ab=false;var T;for(var aq=0;aq<this.filters.length;aq++){T=this.filters[aq];T.update_attrs(R);if(!T.keep(R)){ab=true;break}}if(ab){continue}if(ap<=aj&&ac>=K){if(G.dataset_type=="interval_index"){ac-=1}var ad=Math.floor(Math.max(0,(ap-K)*au)),I=Math.ceil(Math.min(a,Math.max(0,(ac-K)*au))),W=(p==="Dense"?1:(1+at[O]))*av;var E,ah,M=null,aw=null;if(G.dataset_type==="bai"){H.fillStyle=g;if(R[5] instanceof Array){var C=Math.floor(Math.max(0,(R[4][0]-K)*au)),N=Math.ceil(Math.min(a,Math.max(0,(R[4][1]-K)*au))),A=Math.floor(Math.max(0,(R[5][0]-K)*au)),t=Math.ceil(Math.min(a,Math.max(0,(R[5][1]-K)*au)));if(R[4][1]>=K&&R[4][0]<=aj&&R[4][2]){this.rect_or_text(H,au,K,aj,R[4][0],R[4][2],R[4][3],W)}if(R[5][1]>=K&&R[5][0]<=aj&&R[5][2]){this.rect_or_text(H,au,K,aj,R[5][0],R[5][2],R[5][3],W)}if(A>N){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(N+V,W+5,V+A,W+5)}}else{H.fillStyle=g;this.rect_or_text(H,au,K,aj,ap,R[4],R[5],W)}if(p!=="Dense"&&!aa&&ap>K){H.fillStyle=this.prefs.label_color;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}else{if(G.dataset_type==="interval_index"){if(p=="Auto"){if(R.length<=4){p="Squish"}else{p="Pack"}}if(p=="Dense"){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{if(R.length<=4){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{var D=R[5],U=R[6],af=R[7],e=R[8];if(U&&af){M=Math.floor(Math.max(0,(U-K)*au));aw=Math.ceil(Math.min(a,Math.max(0,(af-K)*au)))}var ao,P;if(p=="Squish"){ao=1;P=SQUISH_FEATURE_HEIGHT}else{ao=5;P=PACK_FEATURE_HEIGHT}if(!e){if(R.strand){if(R.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(R.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}}else{H.fillStyle=CONNECTOR_COLOR}H.fillRect(ad+V,W+(P-ao)/2+1,I-ad,P)}else{var z,Q;if(p=="Squish"){H.fillStyle=CONNECTOR_COLOR;z=W+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}else{if(D){var z=W;var Q=P;if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}}else{H.fillStyle=CONNECTOR_COLOR;z+=(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}}H.fillRect(ad+V,z,I-ad,Q);for(var al=0,d=e.length;al<d;al++){var s=e[al],c=Math.floor(Math.max(0,(s[0]-K)*au)),S=Math.ceil(Math.min(a,Math.max((s[1]-K)*au)));if(c>S){continue}H.fillStyle=g;H.fillRect(c+V,W+(P-ao)/2+1,S-c,ao);if(M!==undefined&&!(c>aw||S<M)){var ai=Math.max(c,M),w=Math.min(S,aw-1);H.fillRect(ai+V,W+1,w-ai,P)}}}if(p=="Pack"&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}}}else{if(G.dataset_type==="vcf"){if(aa){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,1)}else{var r=R[4],l=R[5],b=R[6];E=9;ah=1;H.fillRect(ad+V,W,I-ad,E);if(p!=="Dense"&&L!==undefined&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+2+V,W+8)}else{H.textAlign="right";H.fillText(L,ad-2+V,W+8)}H.fillStyle=g}var h=r+" / "+l;if(ap>K&&H.measureText(h).width<(I-ad)){H.fillStyle="white";H.textAlign="center";H.fillText(h,V+ad+(I-ad)/2,W+8);H.fillStyle=g}}}}}am++}}return o}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}}); \ No newline at end of file +CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,PACK_SPACING=5,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").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_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len-1;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var k=$("<div class='form-row' />").appendTo(a);k.append($("<label />").attr("for",c).text(d.label+":"));if(d.type=="bool"){k.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type=="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var i=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(i);var j=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(i).appendTo(k).bind("click",function(l){i.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){i.hide();$(document).unbind("click.color-picker")});l.stopPropagation()})}else{k.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.name_div.data("menu_options")["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+a.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,j=g-m,c=this.view.container.width(),f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),r=c/j;this.content_div.append(p);this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=0;while((a*DENSITY*f)<g){var n=c+"_"+r+"_"+a;var e=this.tile_cache.get(n);var k=a*DENSITY*this.view.resolution;var q=k+DENSITY*this.view.resolution;if(!b&&e){this.show_tile(e,p,k,r)}else{this.delayed_draw(b,n,k,q,a,f,p,r)}a+=1}var d=this;var o=setInterval(function(){if(l===0){var u=d.content_div.children();var t=false;for(var v=u.length-1,s=0;v>=s;v--){var x=$(u[v]);if(t){x.remove()}else{if(x.children().length!==0){t=true}}}for(var w=0;w<d.filters.length;w++){d.filters[w].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(b)}},delayed_draw:function(b,g,f,i,c,e,h,j){var d=this;var a=setTimeout(function(){if(f<=d.view.high&&i>=d.view.low){var k;if(!b){k=d.tile_cache.get(g)}if(!k){k=d.draw_tile(e,c,h,j);if(k){var l=$("<div class='track-tile'>").prepend(k);if(k.hasClass(FILTERABLE_CLASS)){l.addClass(FILTERABLE_CLASS)}k=l}}if(k){d.tile_cache.set(g,k);d.show_tile(k,h,f,j)}}},50)},show_tile:function(a,f,d,g){var b=this;var c=this.view.high-this.view.low,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>CHAR_WIDTH_PX){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.data_queue={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,j,d,q){var r=this.inc_slots[a];if(!r||(r.mode!==q)){r={};r.w_scale=a;r.mode=q;this.inc_slots[a]=r;this.start_end_dct[a]={}}var m=r.w_scale,x=[],y=[],k=0,o=this.view.max_low;for(var v=0,w=j.length;v<w;v++){var h=j[v],l=h[0];if(r[l]!==undefined){k=Math.max(k,r[l]);y.push(r[l])}else{x.push(v)}}var e=this.start_end_dct[a];var n=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=e[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var i=F[z];if(E>i[0]&&D<i[1]){A=true;break}}}if(!A){return C}}return -1};for(var v=0,w=x.length;v<w;v++){var h=j[x[v]],l=h[0],t=h[1],b=h[2],p=h[3],c=Math.floor((t-o)*m),g=Math.ceil((b-o)*m),u=CONTEXT.measureText(p).width,f;if(p!==undefined&&!d){u+=(LABEL_SPACING+PACK_SPACING);if(c-u>=0){c-=u;f="left"}else{g+=u;f="right"}}var s=n(c,g);if(s>=0){if(e[s]===undefined){e[s]=[]}e[s].push([c,g]);r[l]=s;k=Math.max(k,s)}else{}}return k},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>CHAR_WIDTH_PX){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ae,m,q,au){var K=m*DENSITY*ae,aj=(m+1)*DENSITY*ae,J=aj-K;var G=this.data_cache.get_data(K,aj,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[K,aj]]=true;this.get_data(K,aj);return}var a=Math.ceil(J*au),ag=this.prefs.label_color,g=this.prefs.block_color,p=this.mode,u=25,aa,V=this.left_offset,at,B,av;var o=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(o)}o=$(o);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(p==="Dense"){B=u;av=DENSE_TRACK_HEIGHT}else{if(p==="Squish"){av=SQUISH_TRACK_HEIGHT;aa=true}else{if(p==="Pack"){av=PACK_TRACK_HEIGHT;aa=false}else{if(G.extra_info==="no_detail"){av=(G.track_type==="bai"?SQUISH_TRACK_HEIGHT:NO_DETAIL_TRACK_HEIGHT);aa=true}else{av=PACK_TRACK_HEIGHT;aa=false}}}B=this.incremental_slots(au,G.data,aa,p)*av+u;at=this.inc_slots[au]}}o.get(0).width=a+V;o.get(0).height=B;if(G.dataset_type=="summary_tree"){o.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}q.parent().css("height",Math.max(this.height_px,B)+"px");var H=o.get(0).getContext("2d");H.fillStyle=g;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var v=B+LABEL_SPACING+CHAR_HEIGHT_PX;points=G.data,max=G.max,delta_x_px=Math.ceil(G.delta*au);var n=$("<div />").addClass("yaxislabel");n.text(max);n.css({position:"absolute",top:"22px",left:"10px"});n.prependTo(this.container_div);for(var an=0,F=points.length;an<F;an++){var Z=Math.floor((points[an][0]-K)*au);var Y=points[an][1];if(!Y){continue}var ak=Y/max*B;H.fillStyle="black";H.fillRect(Z+V,v-ak,delta_x_px,ak);var X=4;if(this.prefs.show_counts&&(H.measureText(Y).width+X)<delta_x_px){H.fillStyle="#666";H.textAlign="center";H.fillText(Y,Z+V+(delta_x_px/2),10)}}return o}if(G.message){o.css({"border-color":"red"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+V,av);if(!G.data){return o}}for(var aq=0;aq<this.filters.length;aq++){if(G.data.length&&this.filters[aq].applies_to(G.data[0])){o.addClass(FILTERABLE_CLASS);break}}var ar=G.data;var am=0;for(var an=0,F=ar.length;an<F;an++){var R=ar[an],O=R[0],ap=R[1],ac=R[2],L=R[3];if(this.mode!="Dense"&&at[O]===undefined){continue}var ab=false;var T;for(var aq=0;aq<this.filters.length;aq++){T=this.filters[aq];T.update_attrs(R);if(!T.keep(R)){ab=true;break}}if(ab){continue}if(ap<=aj&&ac>=K){if(G.dataset_type=="interval_index"){ac-=1}var ad=Math.floor(Math.max(0,(ap-K)*au)),I=Math.ceil(Math.min(a,Math.max(0,(ac-K)*au))),W=(p==="Dense"?1:(1+at[O]))*av;var E,ah,M=null,aw=null;if(G.dataset_type==="bai"){H.fillStyle=g;if(R[5] instanceof Array){var C=Math.floor(Math.max(0,(R[4][0]-K)*au)),N=Math.ceil(Math.min(a,Math.max(0,(R[4][1]-K)*au))),A=Math.floor(Math.max(0,(R[5][0]-K)*au)),t=Math.ceil(Math.min(a,Math.max(0,(R[5][1]-K)*au)));if(R[4][1]>=K&&R[4][0]<=aj&&R[4][2]){this.rect_or_text(H,au,K,aj,R[4][0],R[4][2],R[4][3],W)}if(R[5][1]>=K&&R[5][0]<=aj&&R[5][2]){this.rect_or_text(H,au,K,aj,R[5][0],R[5][2],R[5][3],W)}if(A>N){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(N+V,W+5,V+A,W+5)}}else{H.fillStyle=g;this.rect_or_text(H,au,K,aj,ap,R[4],R[5],W)}if(p!=="Dense"&&!aa&&ap>K){H.fillStyle=this.prefs.label_color;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}else{if(G.dataset_type==="interval_index"){if(p=="Auto"){if(R.length<=4){p="Squish"}else{p="Pack"}}if(p=="Dense"){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{if(R.length<=4){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{var D=R[5],U=R[6],af=R[7],e=R[8];if(U&&af){M=Math.floor(Math.max(0,(U-K)*au));aw=Math.ceil(Math.min(a,Math.max(0,(af-K)*au)))}var ao,P;if(p=="Squish"){ao=1;P=SQUISH_FEATURE_HEIGHT}else{ao=5;P=PACK_FEATURE_HEIGHT}if(!e){if(R.strand){if(R.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(R.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}}else{H.fillStyle=CONNECTOR_COLOR}H.fillRect(ad+V,W+(P-ao)/2+1,I-ad,P)}else{var z,Q;if(p=="Squish"){H.fillStyle=CONNECTOR_COLOR;z=W+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}else{if(D){var z=W;var Q=P;if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}}else{H.fillStyle=CONNECTOR_COLOR;z+=(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}}H.fillRect(ad+V,z,I-ad,Q);for(var al=0,d=e.length;al<d;al++){var s=e[al],c=Math.floor(Math.max(0,(s[0]-K)*au)),S=Math.ceil(Math.min(a,Math.max((s[1]-K)*au)));if(c>S){continue}H.fillStyle=g;H.fillRect(c+V,W+(P-ao)/2+1,S-c,ao);if(M!==undefined&&!(c>aw||S<M)){var ai=Math.max(c,M),w=Math.min(S,aw-1);H.fillRect(ai+V,W+1,w-ai,P)}}}if(p=="Pack"&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}}}else{if(G.dataset_type==="vcf"){if(aa){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,1)}else{var r=R[4],l=R[5],b=R[6];E=9;ah=1;H.fillRect(ad+V,W,I-ad,E);if(p!=="Dense"&&L!==undefined&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+2+V,W+8)}else{H.textAlign="right";H.fillText(L,ad-2+V,W+8)}H.fillStyle=g}var h=r+" / "+l;if(ap>K&&H.measureText(h).width<(I-ad)){H.fillStyle="white";H.textAlign="center";H.fillText(h,V+ad+(I-ad)/2,W+8);H.fillStyle=g}}}}}am++}}return o}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}}); \ No newline at end of file --- a/static/scripts/trackster.js Tue Feb 15 19:09:38 2011 -0500 +++ b/static/scripts/trackster.js Tue Feb 15 19:20:39 2011 -0500 @@ -523,7 +523,7 @@ view.intro_div.hide(); } view.chrom_select.val(view.chrom); - view.max_high = found.len; + view.max_high = found.len-1; // -1 because we're using 0-based indexing. view.reset(); view.redraw(true); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: trackster: For feature/bam tracks, new option in dropdown to list chroms/contigs that have data for that dataset. Tweak popup menu system to use a $.data variable that is bound to the anchor link, allowing options to be modified after the first initialization.
by Bitbucket 15 Feb '11

15 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/83b5c59076a5/ changeset: r5067:83b5c59076a5 user: kanwei date: 2011-02-16 01:09:38 summary: trackster: For feature/bam tracks, new option in dropdown to list chroms/contigs that have data for that dataset. Tweak popup menu system to use a $.data variable that is bound to the anchor link, allowing options to be modified after the first initialization. affected #: 6 files (1.2 KB) --- a/lib/galaxy/visualization/tracks/data_providers.py Tue Feb 15 17:24:24 2011 -0500 +++ b/lib/galaxy/visualization/tracks/data_providers.py Tue Feb 15 19:09:38 2011 -0500 @@ -47,6 +47,12 @@ """ # Override. pass + + def valid_chroms( self ): + """ + Returns chroms/contigs that the dataset contains + """ + return None # by default def has_data( self, chrom, start, end, **kwargs ): """ @@ -109,6 +115,11 @@ CACHE = LRUCache(20) # Store 20 recently accessed indices for performance + def valid_chroms( self ): + st = summary_tree_from_file( self.converted_dataset.file_name ) + return st.chrom_blocks.keys() + + def get_summary( self, chrom, start, end, **kwargs): filename = self.converted_dataset.file_name st = self.CACHE[filename] @@ -410,6 +421,10 @@ f = open( self.original_dataset.file_name ) return f + def valid_chroms( self ): + # No way to return this info as of now + return None + def has_data( self, chrom ): f = self._get_dataset() bw = BigWigFile(file=f) --- a/lib/galaxy/web/controllers/tracks.py Tue Feb 15 17:24:24 2011 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Tue Feb 15 19:09:38 2011 -0500 @@ -386,7 +386,7 @@ def reference( self, trans, dbkey, chrom, low, high, **kwargs ): if self.available_genomes is None: self._init_references(trans) - if dbkey not in self.available_genomes: + if dbkey not in self.available_genomes: return None try: @@ -434,10 +434,10 @@ return msg @web.json - def converted_datasets_state( self, trans, hda_ldda, dataset_id, chrom=None, low=None, high=None ): - """ - Returns state of dataset's converted datasets. If a genome window is - specified, method checks whether dataset has data in the window. + def converted_datasets_state( self, trans, hda_ldda, dataset_id, chrom=None ): + """ + Init-like method that returns state of dataset's converted datasets. Returns valid chroms + for that dataset as well. """ # TODO: this code is copied from data() -- should refactor. @@ -457,19 +457,24 @@ if msg: return msg + valid_chroms = None # Check for data in the genome window. if data_sources.get( 'index' ): tracks_dataset_type = data_sources['index']['name'] indexer = get_data_provider( tracks_dataset_type )( dataset.get_converted_dataset( trans, tracks_dataset_type ), dataset ) if not indexer.has_data( chrom ): return messages.NO_DATA + valid_chroms = indexer.valid_chroms() else: # Standalone data provider standalone_provider = get_data_provider(data_sources['data_standalone']['name'])( dataset ) kwargs = {"stats": True} if not standalone_provider.has_data( chrom ): return messages.NO_DATA - return messages.DATA + valid_chroms = standalone_provider.valid_chroms() + + # Have data if we get here + return { "status": messages.DATA, "valid_chroms": valid_chroms } @web.json def data( self, trans, hda_ldda, dataset_id, chrom, low, high, **kwargs ): --- a/static/scripts/galaxy.base.js Tue Feb 15 17:24:24 2011 -0500 +++ b/static/scripts/galaxy.base.js Tue Feb 15 19:09:38 2011 -0500 @@ -54,16 +54,21 @@ }); } -function make_popupmenu( button_element, options ) { +function make_popupmenu( button_element, initial_options ) { + + /* Use the $.data feature to store options with the link element. + This allows options to be changed at a later time + */ + button_element.data("menu_options", initial_options); button_element.bind("click.show_popup", function(e) { // Close existing visible menus $(".popmenu-wrapper").remove(); - // Need setTimeouts so clicks don't interfere with each other setTimeout( function() { // Dynamically generate the wrapper holding all the selectable options of the menu. var menu_element = $( "<ul id='" + button_element.attr('id') + "-menu'></ul>" ); + var options = button_element.data("menu_options"); if (obj_length(options) <= 0) { $("<li>No Options.</li>").appendTo(menu_element); } --- a/static/scripts/packed/galaxy.base.js Tue Feb 15 17:24:24 2011 -0500 +++ 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c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return 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DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,PACK_SPACING=5,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").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_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var k=$("<div class='form-row' />").appendTo(a);k.append($("<label />").attr("for",c).text(d.label+":"));if(d.type=="bool"){k.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type=="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var i=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(i);var j=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(i).appendTo(k).bind("click",function(l){i.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){i.hide();$(document).unbind("click.color-picker")});l.stopPropagation()})}else{k.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,j=g-m,c=this.view.container.width(),f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),r=c/j;this.content_div.append(p);this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=0;while((a*DENSITY*f)<g){var n=c+"_"+r+"_"+a;var e=this.tile_cache.get(n);var k=a*DENSITY*this.view.resolution;var q=k+DENSITY*this.view.resolution;if(!b&&e){this.show_tile(e,p,k,r)}else{this.delayed_draw(b,n,k,q,a,f,p,r)}a+=1}var d=this;var o=setInterval(function(){if(l===0){var u=d.content_div.children();var t=false;for(var v=u.length-1,s=0;v>=s;v--){var x=$(u[v]);if(t){x.remove()}else{if(x.children().length!==0){t=true}}}for(var w=0;w<d.filters.length;w++){d.filters[w].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(b)}},delayed_draw:function(b,g,f,i,c,e,h,j){var d=this;var a=setTimeout(function(){if(f<=d.view.high&&i>=d.view.low){var k;if(!b){k=d.tile_cache.get(g)}if(!k){k=d.draw_tile(e,c,h,j);if(k){var l=$("<div class='track-tile'>").prepend(k);if(k.hasClass(FILTERABLE_CLASS)){l.addClass(FILTERABLE_CLASS)}k=l}}if(k){d.tile_cache.set(g,k);d.show_tile(k,h,f,j)}}},50)},show_tile:function(a,f,d,g){var b=this;var c=this.view.high-this.view.low,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>CHAR_WIDTH_PX){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.data_queue={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,j,d,q){var r=this.inc_slots[a];if(!r||(r.mode!==q)){r={};r.w_scale=a;r.mode=q;this.inc_slots[a]=r;this.start_end_dct[a]={}}var m=r.w_scale,x=[],y=[],k=0,o=this.view.max_low;for(var v=0,w=j.length;v<w;v++){var h=j[v],l=h[0];if(r[l]!==undefined){k=Math.max(k,r[l]);y.push(r[l])}else{x.push(v)}}var e=this.start_end_dct[a];var n=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=e[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var i=F[z];if(E>i[0]&&D<i[1]){A=true;break}}}if(!A){return C}}return -1};for(var v=0,w=x.length;v<w;v++){var h=j[x[v]],l=h[0],t=h[1],b=h[2],p=h[3],c=Math.floor((t-o)*m),g=Math.ceil((b-o)*m),u=CONTEXT.measureText(p).width,f;if(p!==undefined&&!d){u+=(LABEL_SPACING+PACK_SPACING);if(c-u>=0){c-=u;f="left"}else{g+=u;f="right"}}var s=n(c,g);if(s>=0){if(e[s]===undefined){e[s]=[]}e[s].push([c,g]);r[l]=s;k=Math.max(k,s)}else{}}return k},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>CHAR_WIDTH_PX){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ae,m,q,au){var K=m*DENSITY*ae,aj=(m+1)*DENSITY*ae,J=aj-K;var G=this.data_cache.get_data(K,aj,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[K,aj]]=true;this.get_data(K,aj);return}var a=Math.ceil(J*au),ag=this.prefs.label_color,g=this.prefs.block_color,p=this.mode,u=25,aa,V=this.left_offset,at,B,av;var o=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(o)}o=$(o);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(p==="Dense"){B=u;av=DENSE_TRACK_HEIGHT}else{if(p==="Squish"){av=SQUISH_TRACK_HEIGHT;aa=true}else{if(p==="Pack"){av=PACK_TRACK_HEIGHT;aa=false}else{if(G.extra_info==="no_detail"){av=(G.track_type==="bai"?SQUISH_TRACK_HEIGHT:NO_DETAIL_TRACK_HEIGHT);aa=true}else{av=PACK_TRACK_HEIGHT;aa=false}}}B=this.incremental_slots(au,G.data,aa,p)*av+u;at=this.inc_slots[au]}}o.get(0).width=a+V;o.get(0).height=B;if(G.dataset_type=="summary_tree"){o.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}q.parent().css("height",Math.max(this.height_px,B)+"px");var H=o.get(0).getContext("2d");H.fillStyle=g;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var v=B+LABEL_SPACING+CHAR_HEIGHT_PX;points=G.data,max=G.max,delta_x_px=Math.ceil(G.delta*au);var n=$("<div />").addClass("yaxislabel");n.text(max);n.css({position:"absolute",top:"22px",left:"10px"});n.prependTo(this.container_div);for(var an=0,F=points.length;an<F;an++){var Z=Math.floor((points[an][0]-K)*au);var Y=points[an][1];if(!Y){continue}var ak=Y/max*B;H.fillStyle="black";H.fillRect(Z+V,v-ak,delta_x_px,ak);var X=4;if(this.prefs.show_counts&&(H.measureText(Y).width+X)<delta_x_px){H.fillStyle="#666";H.textAlign="center";H.fillText(Y,Z+V+(delta_x_px/2),10)}}return o}if(G.message){o.css({"border-color":"red"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+V,av);if(!G.data){return o}}for(var aq=0;aq<this.filters.length;aq++){if(G.data.length&&this.filters[aq].applies_to(G.data[0])){o.addClass(FILTERABLE_CLASS);break}}var ar=G.data;var am=0;for(var an=0,F=ar.length;an<F;an++){var R=ar[an],O=R[0],ap=R[1],ac=R[2],L=R[3];if(this.mode!="Dense"&&at[O]===undefined){continue}var ab=false;var T;for(var aq=0;aq<this.filters.length;aq++){T=this.filters[aq];T.update_attrs(R);if(!T.keep(R)){ab=true;break}}if(ab){continue}if(ap<=aj&&ac>=K){if(G.dataset_type=="interval_index"){ac-=1}var ad=Math.floor(Math.max(0,(ap-K)*au)),I=Math.ceil(Math.min(a,Math.max(0,(ac-K)*au))),W=(p==="Dense"?1:(1+at[O]))*av;var E,ah,M=null,aw=null;if(G.dataset_type==="bai"){H.fillStyle=g;if(R[5] instanceof Array){var C=Math.floor(Math.max(0,(R[4][0]-K)*au)),N=Math.ceil(Math.min(a,Math.max(0,(R[4][1]-K)*au))),A=Math.floor(Math.max(0,(R[5][0]-K)*au)),t=Math.ceil(Math.min(a,Math.max(0,(R[5][1]-K)*au)));if(R[4][1]>=K&&R[4][0]<=aj&&R[4][2]){this.rect_or_text(H,au,K,aj,R[4][0],R[4][2],R[4][3],W)}if(R[5][1]>=K&&R[5][0]<=aj&&R[5][2]){this.rect_or_text(H,au,K,aj,R[5][0],R[5][2],R[5][3],W)}if(A>N){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(N+V,W+5,V+A,W+5)}}else{H.fillStyle=g;this.rect_or_text(H,au,K,aj,ap,R[4],R[5],W)}if(p!=="Dense"&&!aa&&ap>K){H.fillStyle=this.prefs.label_color;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}else{if(G.dataset_type==="interval_index"){if(p=="Auto"){if(R.length<=4){p="Squish"}else{p="Pack"}}if(p=="Dense"){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{if(R.length<=4){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{var D=R[5],U=R[6],af=R[7],e=R[8];if(U&&af){M=Math.floor(Math.max(0,(U-K)*au));aw=Math.ceil(Math.min(a,Math.max(0,(af-K)*au)))}var ao,P;if(p=="Squish"){ao=1;P=SQUISH_FEATURE_HEIGHT}else{ao=5;P=PACK_FEATURE_HEIGHT}if(!e){if(R.strand){if(R.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(R.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}}else{H.fillStyle=CONNECTOR_COLOR}H.fillRect(ad+V,W+(P-ao)/2+1,I-ad,P)}else{var z,Q;if(p=="Squish"){H.fillStyle=CONNECTOR_COLOR;z=W+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}else{if(D){var z=W;var Q=P;if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}}else{H.fillStyle=CONNECTOR_COLOR;z+=(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}}H.fillRect(ad+V,z,I-ad,Q);for(var al=0,d=e.length;al<d;al++){var s=e[al],c=Math.floor(Math.max(0,(s[0]-K)*au)),S=Math.ceil(Math.min(a,Math.max((s[1]-K)*au)));if(c>S){continue}H.fillStyle=g;H.fillRect(c+V,W+(P-ao)/2+1,S-c,ao);if(M!==undefined&&!(c>aw||S<M)){var ai=Math.max(c,M),w=Math.min(S,aw-1);H.fillRect(ai+V,W+1,w-ai,P)}}}if(p=="Pack"&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}}}else{if(G.dataset_type==="vcf"){if(aa){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,1)}else{var r=R[4],l=R[5],b=R[6];E=9;ah=1;H.fillRect(ad+V,W,I-ad,E);if(p!=="Dense"&&L!==undefined&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+2+V,W+8)}else{H.textAlign="right";H.fillText(L,ad-2+V,W+8)}H.fillStyle=g}var h=r+" / "+l;if(ap>K&&H.measureText(h).width<(I-ad)){H.fillStyle="white";H.textAlign="center";H.fillText(h,V+ad+(I-ad)/2,W+8);H.fillStyle=g}}}}}am++}}return o}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}}); \ No newline at end of file +CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,PACK_SPACING=5,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").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_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var k=$("<div class='form-row' />").appendTo(a);k.append($("<label />").attr("for",c).text(d.label+":"));if(d.type=="bool"){k.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type=="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var i=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(i);var j=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(i).appendTo(k).bind("click",function(l){i.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){i.hide();$(document).unbind("click.color-picker")});l.stopPropagation()})}else{k.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.name_div.data("menu_options")["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+a.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,j=g-m,c=this.view.container.width(),f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),r=c/j;this.content_div.append(p);this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=0;while((a*DENSITY*f)<g){var n=c+"_"+r+"_"+a;var e=this.tile_cache.get(n);var k=a*DENSITY*this.view.resolution;var q=k+DENSITY*this.view.resolution;if(!b&&e){this.show_tile(e,p,k,r)}else{this.delayed_draw(b,n,k,q,a,f,p,r)}a+=1}var d=this;var o=setInterval(function(){if(l===0){var u=d.content_div.children();var t=false;for(var v=u.length-1,s=0;v>=s;v--){var x=$(u[v]);if(t){x.remove()}else{if(x.children().length!==0){t=true}}}for(var w=0;w<d.filters.length;w++){d.filters[w].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(b)}},delayed_draw:function(b,g,f,i,c,e,h,j){var d=this;var a=setTimeout(function(){if(f<=d.view.high&&i>=d.view.low){var k;if(!b){k=d.tile_cache.get(g)}if(!k){k=d.draw_tile(e,c,h,j);if(k){var l=$("<div class='track-tile'>").prepend(k);if(k.hasClass(FILTERABLE_CLASS)){l.addClass(FILTERABLE_CLASS)}k=l}}if(k){d.tile_cache.set(g,k);d.show_tile(k,h,f,j)}}},50)},show_tile:function(a,f,d,g){var b=this;var c=this.view.high-this.view.low,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>CHAR_WIDTH_PX){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.data_queue={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,j,d,q){var r=this.inc_slots[a];if(!r||(r.mode!==q)){r={};r.w_scale=a;r.mode=q;this.inc_slots[a]=r;this.start_end_dct[a]={}}var m=r.w_scale,x=[],y=[],k=0,o=this.view.max_low;for(var v=0,w=j.length;v<w;v++){var h=j[v],l=h[0];if(r[l]!==undefined){k=Math.max(k,r[l]);y.push(r[l])}else{x.push(v)}}var e=this.start_end_dct[a];var n=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=e[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var i=F[z];if(E>i[0]&&D<i[1]){A=true;break}}}if(!A){return C}}return -1};for(var v=0,w=x.length;v<w;v++){var h=j[x[v]],l=h[0],t=h[1],b=h[2],p=h[3],c=Math.floor((t-o)*m),g=Math.ceil((b-o)*m),u=CONTEXT.measureText(p).width,f;if(p!==undefined&&!d){u+=(LABEL_SPACING+PACK_SPACING);if(c-u>=0){c-=u;f="left"}else{g+=u;f="right"}}var s=n(c,g);if(s>=0){if(e[s]===undefined){e[s]=[]}e[s].push([c,g]);r[l]=s;k=Math.max(k,s)}else{}}return k},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>CHAR_WIDTH_PX){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ae,m,q,au){var K=m*DENSITY*ae,aj=(m+1)*DENSITY*ae,J=aj-K;var G=this.data_cache.get_data(K,aj,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[K,aj]]=true;this.get_data(K,aj);return}var a=Math.ceil(J*au),ag=this.prefs.label_color,g=this.prefs.block_color,p=this.mode,u=25,aa,V=this.left_offset,at,B,av;var o=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(o)}o=$(o);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(p==="Dense"){B=u;av=DENSE_TRACK_HEIGHT}else{if(p==="Squish"){av=SQUISH_TRACK_HEIGHT;aa=true}else{if(p==="Pack"){av=PACK_TRACK_HEIGHT;aa=false}else{if(G.extra_info==="no_detail"){av=(G.track_type==="bai"?SQUISH_TRACK_HEIGHT:NO_DETAIL_TRACK_HEIGHT);aa=true}else{av=PACK_TRACK_HEIGHT;aa=false}}}B=this.incremental_slots(au,G.data,aa,p)*av+u;at=this.inc_slots[au]}}o.get(0).width=a+V;o.get(0).height=B;if(G.dataset_type=="summary_tree"){o.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}q.parent().css("height",Math.max(this.height_px,B)+"px");var H=o.get(0).getContext("2d");H.fillStyle=g;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var v=B+LABEL_SPACING+CHAR_HEIGHT_PX;points=G.data,max=G.max,delta_x_px=Math.ceil(G.delta*au);var n=$("<div />").addClass("yaxislabel");n.text(max);n.css({position:"absolute",top:"22px",left:"10px"});n.prependTo(this.container_div);for(var an=0,F=points.length;an<F;an++){var Z=Math.floor((points[an][0]-K)*au);var Y=points[an][1];if(!Y){continue}var ak=Y/max*B;H.fillStyle="black";H.fillRect(Z+V,v-ak,delta_x_px,ak);var X=4;if(this.prefs.show_counts&&(H.measureText(Y).width+X)<delta_x_px){H.fillStyle="#666";H.textAlign="center";H.fillText(Y,Z+V+(delta_x_px/2),10)}}return o}if(G.message){o.css({"border-color":"red"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+V,av);if(!G.data){return o}}for(var aq=0;aq<this.filters.length;aq++){if(G.data.length&&this.filters[aq].applies_to(G.data[0])){o.addClass(FILTERABLE_CLASS);break}}var ar=G.data;var am=0;for(var an=0,F=ar.length;an<F;an++){var R=ar[an],O=R[0],ap=R[1],ac=R[2],L=R[3];if(this.mode!="Dense"&&at[O]===undefined){continue}var ab=false;var T;for(var aq=0;aq<this.filters.length;aq++){T=this.filters[aq];T.update_attrs(R);if(!T.keep(R)){ab=true;break}}if(ab){continue}if(ap<=aj&&ac>=K){if(G.dataset_type=="interval_index"){ac-=1}var ad=Math.floor(Math.max(0,(ap-K)*au)),I=Math.ceil(Math.min(a,Math.max(0,(ac-K)*au))),W=(p==="Dense"?1:(1+at[O]))*av;var E,ah,M=null,aw=null;if(G.dataset_type==="bai"){H.fillStyle=g;if(R[5] instanceof Array){var C=Math.floor(Math.max(0,(R[4][0]-K)*au)),N=Math.ceil(Math.min(a,Math.max(0,(R[4][1]-K)*au))),A=Math.floor(Math.max(0,(R[5][0]-K)*au)),t=Math.ceil(Math.min(a,Math.max(0,(R[5][1]-K)*au)));if(R[4][1]>=K&&R[4][0]<=aj&&R[4][2]){this.rect_or_text(H,au,K,aj,R[4][0],R[4][2],R[4][3],W)}if(R[5][1]>=K&&R[5][0]<=aj&&R[5][2]){this.rect_or_text(H,au,K,aj,R[5][0],R[5][2],R[5][3],W)}if(A>N){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(N+V,W+5,V+A,W+5)}}else{H.fillStyle=g;this.rect_or_text(H,au,K,aj,ap,R[4],R[5],W)}if(p!=="Dense"&&!aa&&ap>K){H.fillStyle=this.prefs.label_color;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}else{if(G.dataset_type==="interval_index"){if(p=="Auto"){if(R.length<=4){p="Squish"}else{p="Pack"}}if(p=="Dense"){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{if(R.length<=4){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{var D=R[5],U=R[6],af=R[7],e=R[8];if(U&&af){M=Math.floor(Math.max(0,(U-K)*au));aw=Math.ceil(Math.min(a,Math.max(0,(af-K)*au)))}var ao,P;if(p=="Squish"){ao=1;P=SQUISH_FEATURE_HEIGHT}else{ao=5;P=PACK_FEATURE_HEIGHT}if(!e){if(R.strand){if(R.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(R.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}}else{H.fillStyle=CONNECTOR_COLOR}H.fillRect(ad+V,W+(P-ao)/2+1,I-ad,P)}else{var z,Q;if(p=="Squish"){H.fillStyle=CONNECTOR_COLOR;z=W+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}else{if(D){var z=W;var Q=P;if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}}else{H.fillStyle=CONNECTOR_COLOR;z+=(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}}H.fillRect(ad+V,z,I-ad,Q);for(var al=0,d=e.length;al<d;al++){var s=e[al],c=Math.floor(Math.max(0,(s[0]-K)*au)),S=Math.ceil(Math.min(a,Math.max((s[1]-K)*au)));if(c>S){continue}H.fillStyle=g;H.fillRect(c+V,W+(P-ao)/2+1,S-c,ao);if(M!==undefined&&!(c>aw||S<M)){var ai=Math.max(c,M),w=Math.min(S,aw-1);H.fillRect(ai+V,W+1,w-ai,P)}}}if(p=="Pack"&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}}}else{if(G.dataset_type==="vcf"){if(aa){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,1)}else{var r=R[4],l=R[5],b=R[6];E=9;ah=1;H.fillRect(ad+V,W,I-ad,E);if(p!=="Dense"&&L!==undefined&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+2+V,W+8)}else{H.textAlign="right";H.fillText(L,ad-2+V,W+8)}H.fillStyle=g}var h=r+" / "+l;if(ap>K&&H.measureText(h).width<(I-ad)){H.fillStyle="white";H.textAlign="center";H.fillText(h,V+ad+(I-ad)/2,W+8);H.fillStyle=g}}}}}am++}}return o}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}}); \ No newline at end of file --- a/static/scripts/trackster.js Tue Feb 15 17:24:24 2011 -0500 +++ b/static/scripts/trackster.js Tue Feb 15 19:09:38 2011 -0500 @@ -903,7 +903,7 @@ }); return container; }, - update_from_form : function( container ) { + update_from_form: function( container ) { var track_config = this; var changed = false; $.each( this.params, function( index, param ) { @@ -1002,8 +1002,7 @@ if ( track.view.chrom != null ) { // Get dataset state; if state is fine, enable and draw track. Otherwise, show message // about track status. - $.getJSON(this.dataset_check_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, - chrom: track.view.chrom, low: track.view.max_low, high: track.view.max_high}, + $.getJSON(converted_datasets_state_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, chrom: track.view.chrom}, function (result) { if (!result || result === "error" || result.kind === "error") { track.container_div.addClass("error"); @@ -1025,8 +1024,13 @@ track.container_div.addClass("pending"); track.content_div.text(DATA_PENDING); setTimeout(function() { track.init(); }, track.data_query_wait); - } else if (result === "data") { - // Only draw in user has selected a chromosome. + } else if (result['status'] === "data") { + if (result['valid_chroms']) { + track.valid_chroms = result['valid_chroms']; + track.name_div.data("menu_options")["List chrom/contigs with data"] = function() { + show_modal("Chrom/contigs with data", "<p>" + track.valid_chroms.join("<br/>") + "</p>", { "Close": function() { hide_modal(); } }); + }; + } track.content_div.text(DATA_OK); if (track.view.chrom) { track.content_div.text(""); @@ -1297,7 +1301,7 @@ "OK": ok_fn }); }; - + /* track_dropdown["Set as overview"] = function() { view.overview_viewport.find("canvas").remove(); track.is_overview = true; @@ -1307,7 +1311,7 @@ view.tracks[track_id].is_overview = false; } } - }; + };*/ if (track.filters.length > 0) { // Show/hide filters menu item. 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: dan: Add a Line/Word/Character count Text Manipulation tool.
by Bitbucket 15 Feb '11

15 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/93b1bbecbed8/ changeset: r5066:93b1bbecbed8 user: dan date: 2011-02-15 23:24:24 summary: Add a Line/Word/Character count Text Manipulation tool. affected #: 4 files (39 bytes) --- a/tool_conf.xml.sample Tue Feb 15 16:52:16 2011 -0500 +++ b/tool_conf.xml.sample Tue Feb 15 17:24:24 2011 -0500 @@ -55,6 +55,7 @@ <tool file="filters/headWrapper.xml" /><tool file="filters/tailWrapper.xml" /><tool file="filters/trimmer.xml" /> + <tool file="filters/wc_gnu.xml" /><tool file="stats/dna_filtering.xml" /><tool file="new_operations/tables_arithmetic_operations.xml" /></section> 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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