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August 2013

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commit/galaxy-central: dannon: Update select2 to 3.4.2. Pack scripts. Build styles.
by commits-noreply＠bitbucket.org 15 Aug '13

15 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0977d06f1b82/ Changeset: 0977d06f1b82 User: dannon Date: 2013-08-15 23:01:59 Summary: Update select2 to 3.4.2. Pack scripts. Build styles. Affected #: 4 files This diff is so big that we needed to truncate the remainder. 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: carlfeberhard: History panel: more fixes
by commits-noreply＠bitbucket.org 15 Aug '13

15 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d390aadad2aa/ Changeset: d390aadad2aa User: carlfeberhard Date: 2013-08-15 20:03:40 Summary: History panel: more fixes Affected #: 2 files diff -r a926267deade171d97a39cccc9ffa680d8ef0822 -r d390aadad2aa74d938c3b08062f710daf12f07ce static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -49,7 +49,7 @@ this.model.bind( 'change', function( model, options ){ // if more than the display apps have changed: render everything var nonDisplayAppChanges = _.omit( this.model.changedAttributes(), 'display_apps', 'display_types' ); - if( nonDisplayAppChanges.length ){ + if( _.keys( nonDisplayAppChanges ).length ){ this.render(); // if just the display links, and it's already expanded: render the links only diff -r a926267deade171d97a39cccc9ffa680d8ef0822 -r d390aadad2aa74d938c3b08062f710daf12f07ce static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(d,c){var b=_.omit(this.model.changedAttributes(),"display_apps","display_types");if(b.length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var b={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){b.enabled=false;b.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD){b.enabled=false;b.title=_l("This dataset must finish uploading before it can be viewed")}else{b.title=_l("View data");b.href=this.urls.display;var a=this;b.on_click=function(){parent.frame_manager.frame_new({title:"Data Viewer",type:"url",location:"center",content:a.urls.display})}}}this.displayButton=new IconButtonView({model:new IconButton(b)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(d,c){var b=_.omit(this.model.changedAttributes(),"display_apps","display_types");if(_.keys(b).length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var b={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){b.enabled=false;b.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD){b.enabled=false;b.title=_l("This dataset must finish uploading before it can be viewed")}else{b.title=_l("View data");b.href=this.urls.display;var a=this;b.on_click=function(){parent.frame_manager.frame_new({title:"Data Viewer",type:"url",location:"center",content:a.urls.display})}}}this.displayButton=new IconButtonView({model:new IconButton(b)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: History panel: fix for backbone update
by commits-noreply＠bitbucket.org 15 Aug '13

15 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a926267deade/ Changeset: a926267deade User: carlfeberhard Date: 2013-08-15 19:48:23 Summary: History panel: fix for backbone update Affected #: 7 files diff -r fe5a566cb0d8419d17fae52dfe88f2c9822261ab -r a926267deade171d97a39cccc9ffa680d8ef0822 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -46,18 +46,15 @@ this.expanded = attributes.expanded || false; // re-rendering on any model changes - this.model.bind( 'change', function( event, changed ){ - // find out if more has changed than just the display applications - //TODO: need a better handler for these sorts of partial rendering cases - var nonDisplayAppChanges = _.without( _.keys( changed.changes ), 'display_apps', 'display_types' ); + this.model.bind( 'change', function( model, options ){ + // if more than the display apps have changed: render everything + var nonDisplayAppChanges = _.omit( this.model.changedAttributes(), 'display_apps', 'display_types' ); if( nonDisplayAppChanges.length ){ - // if it's more, render everything this.render(); - // if it's just the display links, and it's already expanded + // if just the display links, and it's already expanded: render the links only } else { if( this.expanded ){ - // render the links only this._render_displayApps(); } } diff -r fe5a566cb0d8419d17fae52dfe88f2c9822261ab -r a926267deade171d97a39cccc9ffa680d8ef0822 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -245,7 +245,7 @@ for( var i=endingIndex; i>=0; i-- ){ var hdaHid = this.at( i ).get( 'hid' ); //this.log( i, 'hdaHid:', hdaHid ); - if( hdaHid == hid ){ + if( hdaHid === hid ){ //this.log( '\t match:', hdaHid, hid, ' returning:', i ); return i; } @@ -297,24 +297,6 @@ return idList; }, - /** Set ea - * Precondition: each data_array object must have an id - * @param {Object[]} data_array an array of attribute objects to update the models with - * @see HistoryDatasetAssociation#set - */ - set : function( data_array ){ - var collection = this; - if( !data_array || !_.isArray( data_array ) ){ return; } - - //TODO: remove when updated backbone >= 1.0 - data_array.forEach( function( hda_data ){ - var model = collection.get( hda_data.id ); - if( model ){ - model.set( hda_data ); - } - }); - }, - /** Update (fetch) the data of the hdas with the given ids. * @param {String[]} ids an array of hda ids to update * @returns {HistoryDatasetAssociation[]} hda models that were updated diff -r fe5a566cb0d8419d17fae52dfe88f2c9822261ab -r a926267deade171d97a39cccc9ffa680d8ef0822 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -51,7 +51,7 @@ // if we've got hdas passed in the constructor, load them and set up updates if needed if( initialHdas && _.isArray( initialHdas ) ){ - this.hdas.reset( initialHdas ); + this.hdas.add( initialHdas ); this.checkForUpdates(); //TODO: don't call if force_history_refresh if( this.hdas.length > 0 ){ @@ -279,8 +279,12 @@ history.log( this + ': fetching display application data' ); jQuery.ajax( 'history/get_display_application_links', { data : data, - success : function( data, status, xhr ){ - history.hdas.set( data ); + success : function( displayAppList, status, xhr ){ + //history.hdas.set( data, { merge: true } ); // doesn't work - clears all other attributes + _.each( displayAppList, function( displayAppData ){ + var hda = history.hdas.get( displayAppData.id ); + if( hda ){ hda.set( displayAppData ); } + }); }, error : function( xhr, status, error ){ if( !( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ) ){ diff -r fe5a566cb0d8419d17fae52dfe88f2c9822261ab -r a926267deade171d97a39cccc9ffa680d8ef0822 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(c,d){var b=_.without(_.keys(d.changes),"display_apps","display_types");if(b.length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var b={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){b.enabled=false;b.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD){b.enabled=false;b.title=_l("This dataset must finish uploading before it can be viewed")}else{b.title=_l("View data");b.href=this.urls.display;var a=this;b.on_click=function(){parent.frame_manager.frame_new({title:"Data Viewer",type:"url",location:"center",content:a.urls.display})}}}this.displayButton=new IconButtonView({model:new IconButton(b)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(d,c){var b=_.omit(this.model.changedAttributes(),"display_apps","display_types");if(b.length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var b={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){b.enabled=false;b.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD){b.enabled=false;b.title=_l("This dataset must finish uploading before it can be viewed")}else{b.title=_l("View data");b.href=this.urls.display;var a=this;b.on_click=function(){parent.frame_manager.frame_new({title:"Data Viewer",type:"url",location:"center",content:a.urls.display})}}}this.displayButton=new IconButtonView({model:new IconButton(b)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file diff -r fe5a566cb0d8419d17fae52dfe88f2c9822261ab -r a926267deade171d97a39cccc9ffa680d8ef0822 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -var HistoryDatasetAssociation=Backbone.Model.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:true,accessible:true},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",b,a,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return(this.isDeletedOrPurged()||(a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a=this.get("hid")+' :"'+this.get("name")+'",'+a}return"HDA("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},set:function(a){var b=this;if(!a||!_.isArray(a)){return}a.forEach(function(c){var d=b.get(c.id);if(d){d.set(c)}})},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file +var HistoryDatasetAssociation=Backbone.Model.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:true,accessible:true},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",b,a,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return(this.isDeletedOrPurged()||(a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a=this.get("hid")+' :"'+this.get("name")+'",'+a}return"HDA("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c===a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file diff -r fe5a566cb0d8419d17fae52dfe88f2c9822261ab -r a926267deade171d97a39cccc9ffa680d8ef0822 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();if(c&&_.isArray(c)){this.hdas.reset(c);this.checkForUpdates();if(this.hdas.length>0){this.updateDisplayApplications()}}this.hdas.bind("state:ready",function(e,g,d){if(e.get("force_history_refresh")){var f=this;setTimeout(function(){f.stateUpdater()},History.UPDATE_DELAY)}},this);if(this.logger){this.bind("all",function(d){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{a.log("Error updating hdas from api history contents",b,h,c,d,f);var g=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",g,h,c,d)}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(e,d,f){c.hdas.set(e)},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.updateDisplayApplications()}}this.hdas.bind("state:ready",function(e,g,d){if(e.get("force_history_refresh")){var f=this;setTimeout(function(){f.stateUpdater()},History.UPDATE_DELAY)}},this);if(this.logger){this.bind("all",function(d){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{a.log("Error updating hdas from api history contents",b,h,c,d,f);var g=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",g,h,c,d)}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file diff -r fe5a566cb0d8419d17fae52dfe88f2c9822261ab -r a926267deade171d97a39cccc9ffa680d8ef0822 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(config.root+"visualization/list_current_history_datasets",config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=Backbone.RelationalModel.extend({defaults:{track:null,tool:null,},relations:[{type:Backbone.HasOne,key:"tool",relatedModel:R.Tool}]});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({render:function(){var ae=this;tool=this.model.get("tool"),parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()})},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},state_dict:function(){var ad=this.model.get("tool").get_param_values_dict();ad.visible=this.parent_div.is(":visible");return ad},run_on_dataset:function(){var ad=this.model.get("tool");this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){show_modal(ad.get("name")+" is Running",ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model.get("tool"),aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get("tool").get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".bs-tooltip").removeClass("in");var ax=$(this).siblings(".bs-tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ah,af,ae,ag){this.track=ad;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.resolution=af;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ah,af,ae,ag){b.call(this,ad,ah,af,ae,ag)};M.prototype.predisplay_actions=function(){};var O=function(ag,ao,ah,af,aj,aq,ak,ar,ae,an){b.call(this,ag,ao,ah,af,aj);this.mode=ak;this.all_slotted=ae;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var am=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()});ad.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=new X.Dataset(af.dataset);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.dynamic_tool_div.toggle();if(ad.dynamic_tool_div.is(":visible")){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset.id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q({track:this,tool:ah.tool,tool_state:ah.tool_state}):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ad*S*ag)<ah){am=this._get_tile_bounds(ad,ag);ai=this.draw_helper(am,ag,ap,aq);aj.push(ai);$.when(ai).then(function(ar){ao.push(ar)});ad+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ao=ac.filter(ao,function(ar){return ar!==null});if(ao.length!==0){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".bs-tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,ak.resolution,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ag,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],ag,am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.LinePainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new M(this,ai,ah,ag,ad.data)},draw_tile:function(ad,ae,ai,ag,ah,aj,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(ad,ae){var ag=Math.floor(ad*S*ae),ah=Math.ceil(S*ae),af=(ag+ah<=this.view.max_high?ag+ah:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:ag,end:af})},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get("tool").get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.dataset_type==="bigwig"||ad.message||ad.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(af,ag,ai,ad){var ae=this;ae.normal_postdraw_actions(af,ag,ai,ad);ae.dataset_check_type="converted_datasets_state";ae.data_query_wait=K;var ah=new j.ServerStateDeferred({url:ae.dataset_state_url,url_params:{dataset_id:ae.dataset.id,hda_ldda:ae.dataset.get("hda_ldda")},interval:ae.data_query_wait,success_fn:function(aj){return aj!=="pending"}});$.when(ah.go()).then(function(){ae.data_manager.set("data_type","data")});ae.postdraw_actions=ae.normal_postdraw_actions}}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,ag.resolution,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ae,ag,ad){if(ag>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,af,ae,ag,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(ag,am,ah,ae,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ad=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;ai<ak;ai++){am.fillStyle=this.view.get_base_color(al[ai]);am.fillText(al[ai],Math.floor(ai*an),10)}return new b(this,aj,ae,ad,af)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ah,af,ag,ai){return this._draw_line_track_tile(ad,ae,ah,af,ag,ai)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new b(this,ai,ah,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,at,ag,ak,af){var aq=this,ae=ar.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,at,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.prefs,ap,aC,aA,af,function(aE){return aq.view.get_base_color(aE)});var ax=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ax=aB.draw(ar,ae.width,ae.height,ak,ao);ax.translation=-ah}return new O(aq,ag,at,ae,an.data,ak,ap,an.message,all_slotted,ax)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,aj,ah,ai,ak){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,ai,ak)}else{var af=this.view,ae=new (this.painter)(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj,function(al){return af.get_base_color(al)});ae.draw(ag,ag.canvas.width,ag.canvas.height,ak);return new b(this,ai,ah,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(config.root+"visualization/list_current_history_datasets",config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=Backbone.RelationalModel.extend({defaults:{track:null,tool:null,},relations:[{type:Backbone.HasOne,key:"tool",relatedModel:R.Tool}]});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({render:function(){var ae=this;tool=this.model.get("tool"),parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()})},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},state_dict:function(){var ad=this.model.get("tool").get_param_values_dict();ad.visible=this.parent_div.is(":visible");return ad},run_on_dataset:function(){var ad=this.model.get("tool");this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){show_modal(ad.get("name")+" is Running",ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model.get("tool"),aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get("tool").get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".bs-tooltip").removeClass("in");var ax=$(this).siblings(".bs-tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ah,af,ae,ag){this.track=ad;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.resolution=af;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ah,af,ae,ag){b.call(this,ad,ah,af,ae,ag)};M.prototype.predisplay_actions=function(){};var O=function(ag,ao,ah,af,aj,aq,ak,ar,ae,an){b.call(this,ag,ao,ah,af,aj);this.mode=ak;this.all_slotted=ae;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var am=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()});ad.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=(af.dataset?new X.Dataset(af.dataset):null);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.dynamic_tool_div.toggle();if(ad.dynamic_tool_div.is(":visible")){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset.id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q({track:this,tool:ah.tool,tool_state:ah.tool_state}):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ad*S*ag)<ah){am=this._get_tile_bounds(ad,ag);ai=this.draw_helper(am,ag,ap,aq);aj.push(ai);$.when(ai).then(function(ar){ao.push(ar)});ad+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ao=ac.filter(ao,function(ar){return ar!==null});if(ao.length!==0){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".bs-tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,ak.resolution,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ag,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],ag,am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.LinePainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new M(this,ai,ah,ag,ad.data)},draw_tile:function(ad,ae,ai,ag,ah,aj,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(ad,ae){var ag=Math.floor(ad*S*ae),ah=Math.ceil(S*ae),af=(ag+ah<=this.view.max_high?ag+ah:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:ag,end:af})},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get("tool").get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.dataset_type==="bigwig"||ad.message||ad.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(af,ag,ai,ad){var ae=this;ae.normal_postdraw_actions(af,ag,ai,ad);ae.dataset_check_type="converted_datasets_state";ae.data_query_wait=K;var ah=new j.ServerStateDeferred({url:ae.dataset_state_url,url_params:{dataset_id:ae.dataset.id,hda_ldda:ae.dataset.get("hda_ldda")},interval:ae.data_query_wait,success_fn:function(aj){return aj!=="pending"}});$.when(ah.go()).then(function(){ae.data_manager.set("data_type","data")});ae.postdraw_actions=ae.normal_postdraw_actions}}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,ag.resolution,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ae,ag,ad){if(ag>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,af,ae,ag,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(ag,am,ah,ae,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ad=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;ai<ak;ai++){am.fillStyle=this.view.get_base_color(al[ai]);am.fillText(al[ai],Math.floor(ai*an),10)}return new b(this,aj,ae,ad,af)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ah,af,ag,ai){return this._draw_line_track_tile(ad,ae,ah,af,ag,ai)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new b(this,ai,ah,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,at,ag,ak,af){var aq=this,ae=ar.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,at,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.prefs,ap,aC,aA,af,function(aE){return aq.view.get_base_color(aE)});var ax=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ax=aB.draw(ar,ae.width,ae.height,ak,ao);ax.translation=-ah}return new O(aq,ag,at,ae,an.data,ak,ap,an.message,all_slotted,ax)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,aj,ah,ai,ak){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,ai,ak)}else{var af=this.view,ae=new (this.painter)(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj,function(al){return af.get_base_color(al)});ae.draw(ag,ag.canvas.width,ag.canvas.height,ak);return new b(this,ai,ah,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Branch close
by commits-noreply＠bitbucket.org 15 Aug '13

15 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/53c6769dcff4/ Changeset: 53c6769dcff4 Branch: cleanup_datasets_unicode_fix User: dannon Date: 2013-08-15 17:20:55 Summary: Branch close Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Aug '13

15 Aug '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b245b46ec4c0/ Changeset: b245b46ec4c0 Branch: cleanup_datasets_unicode_fix User: lance_parsons Date: 2013-07-22 20:24:13 Summary: Fix unicode issue when printing history names in cleanup_datasets.py script Affected #: 1 file diff -r b72d967e0cf4a506f0bfbcef0f068fe1709659e9 -r b245b46ec4c09947613477cf1839070f91ce5a86 scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py +++ b/scripts/cleanup_datasets/cleanup_datasets.py @@ -175,7 +175,7 @@ app.model.History.table.c.update_time < cutoff_time ) ) \ .options( eagerload( 'datasets' ) ) for history in histories: - print "### Processing history id %d (%s)" % (history.id, history.name) + print ("### Processing history id %d (%s)" % (history.id, history.name)).encode('utf-8') for dataset_assoc in history.datasets: _purge_dataset_instance( dataset_assoc, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable if not info_only: https://bitbucket.org/galaxy/galaxy-central/commits/fe5a566cb0d8/ Changeset: fe5a566cb0d8 User: dannon Date: 2013-08-15 17:18:37 Summary: Merged in lance_parsons/galaxy-central-pull-requests/cleanup_datasets_unicode_fix (pull request #196) Fix unicode issue when printing history names in cleanup_datasets.py script Affected #: 1 file diff -r 57348d7dcddfecf058916b3ff4d04fecb6a15301 -r fe5a566cb0d8419d17fae52dfe88f2c9822261ab scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py +++ b/scripts/cleanup_datasets/cleanup_datasets.py @@ -175,7 +175,7 @@ app.model.History.table.c.update_time < cutoff_time ) ) \ .options( eagerload( 'datasets' ) ) for history in histories: - print "### Processing history id %d (%s)" % (history.id, history.name) + print ("### Processing history id %d (%s)" % (history.id, history.name)).encode('utf-8') for dataset_assoc in history.datasets: _purge_dataset_instance( dataset_assoc, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable if not info_only: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Make trackster compatible with backbone-relational v0.8.5
by commits-noreply＠bitbucket.org 15 Aug '13

15 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/57348d7dcddf/ Changeset: 57348d7dcddf User: jgoecks Date: 2013-08-15 15:46:04 Summary: Make trackster compatible with backbone-relational v0.8.5 Affected #: 1 file diff -r ebf6033a1cd4416602294b674628eb73da6fa663 -r 57348d7dcddfecf058916b3ff4d04fecb6a15301 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2308,7 +2308,9 @@ // // Attribute init. // - this.dataset = new data.Dataset(obj_dict.dataset); + + // Only create dataset if it is defined. + this.dataset = (obj_dict.dataset ? new data.Dataset(obj_dict.dataset) : null); this.dataset_check_type = 'converted_datasets_state'; this.data_url_extra_params = {}; this.data_query_wait = ('data_query_wait' in obj_dict ? obj_dict.data_query_wait : DEFAULT_DATA_QUERY_WAIT); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 14 Aug '13

14 Aug '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/84c88d3644c0/ Changeset: 84c88d3644c0 User: jgoecks Date: 2013-08-14 21:15:13 Summary: Update Backbone to v1.0.0 and Backbone-relational to v0.8.5 Affected #: 4 files This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/ebf6033a1cd4/ Changeset: ebf6033a1cd4 User: jgoecks Date: 2013-08-14 21:20:23 Summary: Tool panel refactoring: (a) make client-side code compatible with newest Backbone and Backbone-relational libraries; (b) use mixin rather than a base model on client; (c) add spacing between methods of server-side definition. Pack scripts. Affected #: 4 files diff -r 84c88d3644c0edc925fe2583276fbd32711f30a9 -r ebf6033a1cd4416602294b674628eb73da6fa663 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -94,6 +94,7 @@ class ToolBox( object ): """Container for a collection of tools""" + def __init__( self, config_filenames, tool_root_dir, app ): """ Create a toolbox from the config files named by `config_filenames`, using @@ -144,6 +145,7 @@ # config files, adding or removing locally developed tools or workflows. The value of integrated_tool_panel # will be False when things like functional tests are the caller. self.write_integrated_tool_panel_config_file() + def init_tools( self, config_filename ): """ Read the configuration file and load each tool. The following tags are currently supported: @@ -199,11 +201,13 @@ tool_path=tool_path, config_elems=config_elems ) self.shed_tool_confs.append( shed_tool_conf_dict ) + def get_shed_config_dict_by_filename( self, filename, default=None ): for shed_config_dict in self.shed_tool_confs: if shed_config_dict[ 'config_filename' ] == filename: return shed_config_dict return default + def __add_tool_to_tool_panel( self, tool_id, panel_component, section=False ): # See if a version of this tool is already loaded into the tool panel. The value of panel_component # will be a ToolSection (if the value of section=True) or self.tool_panel (if section=False). @@ -239,6 +243,7 @@ del panel_dict[ loaded_version_key ] panel_dict.insert( index, key, tool ) log.debug( "Loaded tool id: %s, version: %s into tool panel." % ( tool.id, tool.version ) ) + def load_tool_panel( self ): for key, val in self.integrated_tool_panel.items(): if key.startswith( 'tool_' ): @@ -276,6 +281,7 @@ section.elems[ section_key ] = section_val log.debug( "Loaded label: %s" % ( section_val.text ) ) self.tool_panel[ key ] = section + def load_integrated_tool_panel_keys( self ): """ Load the integrated tool panel keys, setting values for tools and workflows to None. The values will @@ -308,6 +314,7 @@ elif elem.tag == 'label': key = 'label_%s' % elem.get( 'id' ) self.integrated_tool_panel[ key ] = None + def write_integrated_tool_panel_config_file( self ): """ Write the current in-memory version of the integrated_tool_panel.xml file to disk. Since Galaxy administrators @@ -350,6 +357,7 @@ os.close( fd ) shutil.move( filename, os.path.abspath( self.integrated_tool_panel_config ) ) os.chmod( self.integrated_tool_panel_config, 0644 ) + def get_tool( self, tool_id, tool_version=None, get_all_versions=False ): """Attempt to locate a tool in the tool box.""" if tool_id in self.tools_by_id and not get_all_versions: @@ -380,6 +388,7 @@ #No tool matches by version, simply return the first available tool found return rval[0] return None + def get_loaded_tools_by_lineage( self, tool_id ): """Get all loaded tools associated by lineage to the tool whose id is tool_id.""" tv = self.__get_tool_version( tool_id ) @@ -395,6 +404,7 @@ tool = self.tools_by_id[ tool_id ] return [ tool ] return [] + def __get_tool_version( self, tool_id ): """Return a ToolVersion if one exists for the tool_id""" return self.sa_session.query( self.app.model.ToolVersion ) \ @@ -527,6 +537,7 @@ integrated_panel_dict.insert( index, key, tool ) except: log.exception( "Error reading tool from path: %s" % path ) + def load_workflow_tag_set( self, elem, panel_dict, integrated_panel_dict, load_panel_dict, index=None ): try: # TODO: should id be encoded? @@ -543,6 +554,7 @@ integrated_panel_dict.insert( index, key, workflow ) except: log.exception( "Error loading workflow: %s" % workflow_id ) + def load_label_tag_set( self, elem, panel_dict, integrated_panel_dict, load_panel_dict, index=None ): label = ToolSectionLabel( elem ) key = 'label_' + label.id @@ -552,6 +564,7 @@ integrated_panel_dict[ key ] = label else: integrated_panel_dict.insert( index, key, label ) + def load_section_tag_set( self, elem, tool_path, load_panel_dict, index=None ): key = 'section_' + elem.get( "id" ) if key in self.tool_panel: @@ -580,6 +593,7 @@ self.integrated_tool_panel[ key ] = integrated_section else: self.integrated_tool_panel.insert( index, key, integrated_section ) + def load_tool( self, config_file, guid=None, repository_id=None, **kwds ): """Load a single tool from the file named by `config_file` and return an instance of `Tool`.""" # Parse XML configuration file and get the root element @@ -597,6 +611,7 @@ else: ToolClass = Tool return ToolClass( config_file, root, self.app, guid=guid, repository_id=repository_id, **kwds ) + def reload_tool_by_id( self, tool_id ): """ Attempt to reload the tool identified by 'tool_id', if successful @@ -634,6 +649,7 @@ message += "<b>version:</b> %s" % old_tool.version status = 'done' return message, status + def remove_tool_by_id( self, tool_id ): """ Attempt to remove the tool identified by 'tool_id'. @@ -662,6 +678,7 @@ message += "<b>version:</b> %s" % tool.version status = 'done' return message, status + def load_workflow( self, workflow_id ): """ Return an instance of 'Workflow' identified by `id`, @@ -670,11 +687,13 @@ id = self.app.security.decode_id( workflow_id ) stored = self.app.model.context.query( self.app.model.StoredWorkflow ).get( id ) return stored.latest_workflow + def init_dependency_manager( self ): if self.app.config.use_tool_dependencies: self.dependency_manager = DependencyManager( [ self.app.config.tool_dependency_dir ] ) else: self.dependency_manager = None + @property def sa_session( self ): """ @@ -683,9 +702,10 @@ return self.app.model.context def to_dict( self, trans, in_panel=True, **kwds ): - # - # Dictify toolbox. - # + """ + Dictify toolbox. + """ + context = Bunch( toolbox=self, trans=trans, **kwds ) if in_panel: panel_elts = [ val for val in self.tool_panel.itervalues() ] @@ -705,8 +725,8 @@ rval.append( elt.to_dict( trans, for_link=True ) ) else: tools = [] - for id, tool in self.toolbox.tools_by_id.items(): - tools.append( tool.to_dict( trans ) ) + for id, tool in self.tools_by_id.items(): + tools.append( tool.to_dict( trans, for_link=True ) ) rval = tools return rval diff -r 84c88d3644c0edc925fe2583276fbd32711f30a9 -r ebf6033a1cd4416602294b674628eb73da6fa663 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -8,17 +8,13 @@ define( ["libs/underscore", "viz/trackster/util", "mvc/data", "libs/backbone/backbone-relational" ], function(_, util, data) { - + /** - * Simple base model for any visible element. Includes useful attributes and ability - * to set and track visibility. + * Mixin to enable model to track visibility. */ -var BaseModel = Backbone.RelationalModel.extend({ - defaults: { - name: null, - hidden: false - }, - +var VisibilityMixin = { + hidden: false, + show: function() { this.set("hidden", false); }, @@ -30,7 +26,8 @@ is_visible: function() { return !this.attributes.hidden; } -}); + +}; /** * A tool parameter. @@ -121,7 +118,7 @@ /** * A Galaxy tool. */ -var Tool = BaseModel.extend({ +var Tool = Backbone.RelationalModel.extend({ // Default attributes. defaults: { id: null, @@ -252,6 +249,7 @@ return run_deferred; } }); +_.extend(Tool.prototype, VisibilityMixin); /** * Tool view. @@ -270,12 +268,12 @@ /** * Label or section header in tool panel. */ -var ToolPanelLabel = BaseModel.extend({}); +var ToolPanelLabel = Backbone.Model.extend(VisibilityMixin); /** * Section of tool panel with elements (labels and tools). */ -var ToolPanelSection = BaseModel.extend({ +var ToolPanelSection = Backbone.Model.extend({ defaults: { elems: [], open: false @@ -317,13 +315,14 @@ } } }); +_.extend(ToolPanelSection.prototype, VisibilityMixin); /** * Tool search that updates results when query is changed. Result value of null * indicates that query was not run; if not null, results are from search using * query. */ -var ToolSearch = BaseModel.extend({ +var ToolSearch = Backbone.Model.extend({ defaults: { search_hint_string: "search tools", min_chars_for_search: 3, @@ -378,65 +377,48 @@ } }); +_.extend(ToolSearch.prototype, VisibilityMixin); /** - * A collection of ToolPanelSections, Tools, and ToolPanelLabels. Collection - * applies search results as they become available. + * Tool Panel. */ -var ToolPanel = Backbone.Collection.extend({ - // TODO: need to generate this using url_for - url: "/tools", - tools: new ToolCollection(), - +var ToolPanel = Backbone.Model.extend({ + + initialize: function(options) { + this.attributes.tool_search = options.tool_search; + this.attributes.tool_search.on("change:results", this.apply_search_results, this); + this.attributes.tools = options.tools; + this.attributes.layout = new Backbone.Collection( this.parse(options.layout) ); + }, + + /** + * Parse tool panel dictionary and return collection of tool panel elements. + */ parse: function(response) { // Recursive function to parse tool panel elements. - var parse_elt = function(elt_dict) { - var type = elt_dict.type; - if (type === 'tool') { - return new Tool(elt_dict); - } - else if (type === 'section') { - // Parse elements. - var elems = _.map(elt_dict.elems, parse_elt); - elt_dict.elems = elems; - return new ToolPanelSection(elt_dict); - } - else if (type === 'label') { - return new ToolPanelLabel(elt_dict); - } - }; + var self = this, + // Helper to recursively parse tool panel. + parse_elt = function(elt_dict) { + var type = elt_dict.type; + if (type === 'tool') { + return self.attributes.tools.get(elt_dict.id); + } + else if (type === 'section') { + // Parse elements. + var elems = _.map(elt_dict.elems, parse_elt); + elt_dict.elems = elems; + return new ToolPanelSection(elt_dict); + } + else if (type === 'label') { + return new ToolPanelLabel(elt_dict); + } + }; return _.map(response, parse_elt); }, - - initialize: function(options) { - this.tool_search = options.tool_search; - this.tool_search.on("change:results", this.apply_search_results, this); - this.on("reset", this.populate_tools, this); - }, - - /** - * Populate tool collection from panel elements. - */ - populate_tools: function() { - var self = this; - self.tools = new ToolCollection(); - this.each(function(panel_elt) { - if (panel_elt instanceof ToolPanelSection) { - _.each(panel_elt.attributes.elems, function (section_elt) { - if (section_elt instanceof Tool) { - self.tools.push(section_elt); - } - }); - } - else if (panel_elt instanceof Tool) { - self.tools.push(panel_elt); - } - }); - }, - + clear_search_results: function() { - this.each(function(panel_elt) { + this.get('layout').each(function(panel_elt) { if (panel_elt instanceof ToolPanelSection) { panel_elt.clear_search_results(); } @@ -448,14 +430,14 @@ }, apply_search_results: function() { - var results = this.tool_search.attributes.results; + var results = this.get('tool_search').get('results'); if (results === null) { this.clear_search_results(); return; } var cur_label = null; - this.each(function(panel_elt) { + this.get('layout').each(function(panel_elt) { if (panel_elt instanceof ToolPanelLabel) { cur_label = panel_elt; cur_label.hide(); @@ -635,19 +617,19 @@ * Set up view. */ initialize: function() { - this.collection.tool_search.on("change:results", this.handle_search_results, this); + this.model.get('tool_search').on("change:results", this.handle_search_results, this); }, render: function() { var self = this; // Render search. - var search_view = new ToolSearchView( {model: this.collection.tool_search} ); + var search_view = new ToolSearchView( { model: this.model.get('tool_search') } ); search_view.render(); self.$el.append(search_view.$el); // Render panel. - this.collection.each(function(panel_elt) { + this.model.get('layout').each(function(panel_elt) { if (panel_elt instanceof ToolPanelSection) { var section_title_view = new ToolPanelSectionView({model: panel_elt}); section_title_view.render(); @@ -670,7 +652,7 @@ // Tool id is always the first class. var tool_id = $(this).attr('class').split(/\s+/)[0], - tool = self.collection.tools.get(tool_id); + tool = self.model.get('tools').get(tool_id); self.trigger("tool_link_click", e, tool); }); @@ -679,7 +661,7 @@ }, handle_search_results: function() { - var results = this.collection.tool_search.attributes.results; + var results = this.model.get('tool_search').get('results'); if (results && results.length === 0) { $("#search-no-results").show(); } @@ -752,6 +734,7 @@ ToolParameter: ToolParameter, IntegerToolParameter: IntegerToolParameter, Tool: Tool, + ToolCollection: ToolCollection, ToolSearch: ToolSearch, ToolPanel: ToolPanel, ToolPanelView: ToolPanelView, diff -r 84c88d3644c0edc925fe2583276fbd32711f30a9 -r ebf6033a1cd4416602294b674628eb73da6fa663 static/scripts/packed/mvc/tools.js --- a/static/scripts/packed/mvc/tools.js +++ b/static/scripts/packed/mvc/tools.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(t,a,u){var h=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var d=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new d(this.toJSON())},get_samples:function(){var w=this.get("type"),v=null;if(w==="number"){v=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(w==="select"){v=t.map(this.get("options"),function(x){return x[0]})}}return v},set_value:function(v){this.set("value",v||"")}},{TYPE_DICT:{number:c},create:function(v){var w=d.TYPE_DICT[v.type]||d;return new w(v)}});var c=d.extend({defaults:t.extend({},d.prototype.defaults,{min:null,max:null}),initialize:function(){d.prototype.initialize.call(this);if(this.attributes.min){this.attributes.min=parseInt(this.attributes.min,10)}if(this.attributes.max){this.attributes.max=parseInt(this.attributes.max,10)}},set_value:function(v){this.set("value",parseInt(v,10))}});var g=h.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[]},initialize:function(v){this.attributes.inputs=new Backbone.Collection(t.map(v.inputs,function(w){return d.create(w)}))},urlRoot:galaxy_paths.get("tool_url"),copy:function(w){var x=new g(this.toJSON());if(w){var v=new Backbone.Collection();x.get("inputs").each(function(y){if(y.get_samples()){v.push(y)}});x.set("inputs",v)}return x},apply_search_results:function(v){(t.indexOf(v,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(v,w){this.get("inputs").find(function(x){return x.get("name")===v}).set("value",w)},set_input_values:function(w){var v=this;t.each(t.keys(w),function(x){v.set_input_value(x,w[x])})},run:function(){return this._run()},rerun:function(w,v){return this._run({action:"rerun",target_dataset_id:w.id,regions:v})},get_inputs_dict:function(){var v={};this.get("inputs").each(function(w){v[w.get("name")]=w.get("value")});return v},_run:function(x){var y=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},x);var w=$.Deferred(),v=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(y),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(z){return z!=="pending"}});$.when(v.go()).then(function(z){w.resolve(new u.DatasetCollection().reset(z))});return w}});var n=Backbone.View.extend({});var k=Backbone.Collection.extend({model:g});var o=h.extend({});var r=h.extend({defaults:{elems:[],open:false},clear_search_results:function(){t.each(this.attributes.elems,function(v){v.show()});this.show();this.set("open",false)},apply_search_results:function(w){var x=true,v;t.each(this.attributes.elems,function(y){if(y instanceof o){v=y;v.hide()}else{if(y instanceof g){if(y.apply_search_results(w)){x=false;if(v){v.show()}}}}});if(x){this.hide()}else{this.show();this.set("open",true)}}});var b=h.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var x=this.attributes.query;if(x.length<this.attributes.min_chars_for_search){this.set("results",null);return}var w=x+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var v=this;this.timer=setTimeout(function(){$.get(v.attributes.search_url,{query:w},function(y){v.set("results",y);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});var l=Backbone.Collection.extend({url:"/tools",tools:new k(),parse:function(v){var w=function(z){var y=z.type;if(y==="tool"){return new g(z)}else{if(y==="section"){var x=t.map(z.elems,w);z.elems=x;return new r(z)}else{if(y==="label"){return new o(z)}}}};return t.map(v,w)},initialize:function(v){this.tool_search=v.tool_search;this.tool_search.on("change:results",this.apply_search_results,this);this.on("reset",this.populate_tools,this)},populate_tools:function(){var v=this;v.tools=new k();this.each(function(w){if(w instanceof r){t.each(w.attributes.elems,function(x){if(x instanceof g){v.tools.push(x)}})}else{if(w instanceof g){v.tools.push(w)}}})},clear_search_results:function(){this.each(function(v){if(v instanceof r){v.clear_search_results()}else{v.show()}})},apply_search_results:function(){var w=this.tool_search.attributes.results;if(w===null){this.clear_search_results();return}var v=null;this.each(function(x){if(x instanceof o){v=x;v.hide()}else{if(x instanceof g){if(x.apply_search_results(w)){if(v){v.show()}}}else{v=null;x.apply_search_results(w)}}})}});var p=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var j=p.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var e=p.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.name));return this}});var i=p.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){p.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var v=this.$el.find(".toolSectionBody");t.each(this.model.attributes.elems,function(w){if(w instanceof g){var x=new j({model:w,className:"toolTitle"});x.render();v.append(x.$el)}else{if(w instanceof o){var y=new e({model:w});y.render();v.append(y.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var m=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(v){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===v.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var v=this;var w=new m({model:this.collection.tool_search});w.render();v.$el.append(w.$el);this.collection.each(function(y){if(y instanceof r){var x=new i({model:y});x.render();v.$el.append(x.$el)}else{if(y instanceof g){var z=new j({model:y,className:"toolTitleNoSection"});z.render();v.$el.append(z.$el)}else{if(y instanceof o){var A=new e({model:y});A.render();v.$el.append(A.$el)}}}});v.$el.find("a.tool-link").click(function(z){var y=$(this).attr("class").split(/\s+/)[0],x=v.collection.tools.get(y);v.trigger("tool_link_click",z,x)});return this},handle_search_results:function(){var v=this.collection.tool_search.attributes.results;if(v&&v.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var q=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var f=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new q()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var v=this;this.tool_panel_view.on("tool_link_click",function(x,w){x.preventDefault();v.show_tool(w)})},show_tool:function(w){var v=this;w.fetch().done(function(){v.tool_form_view.model=w;v.tool_form_view.render();v.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:d,IntegerToolParameter:c,Tool:g,ToolSearch:b,ToolPanel:l,ToolPanelView:s,ToolFormView:q}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(t,a,u){var e={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}};var d=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new d(this.toJSON())},get_samples:function(){var w=this.get("type"),v=null;if(w==="number"){v=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(w==="select"){v=t.map(this.get("options"),function(x){return x[0]})}}return v},set_value:function(v){this.set("value",v||"")}},{TYPE_DICT:{number:c},create:function(v){var w=d.TYPE_DICT[v.type]||d;return new w(v)}});var c=d.extend({defaults:t.extend({},d.prototype.defaults,{min:null,max:null}),initialize:function(){d.prototype.initialize.call(this);if(this.attributes.min){this.attributes.min=parseInt(this.attributes.min,10)}if(this.attributes.max){this.attributes.max=parseInt(this.attributes.max,10)}},set_value:function(v){this.set("value",parseInt(v,10))}});var h=Backbone.RelationalModel.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[]},initialize:function(v){this.attributes.inputs=new Backbone.Collection(t.map(v.inputs,function(w){return d.create(w)}))},urlRoot:galaxy_paths.get("tool_url"),copy:function(w){var x=new h(this.toJSON());if(w){var v=new Backbone.Collection();x.get("inputs").each(function(y){if(y.get_samples()){v.push(y)}});x.set("inputs",v)}return x},apply_search_results:function(v){(t.indexOf(v,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(v,w){this.get("inputs").find(function(x){return x.get("name")===v}).set("value",w)},set_input_values:function(w){var v=this;t.each(t.keys(w),function(x){v.set_input_value(x,w[x])})},run:function(){return this._run()},rerun:function(w,v){return this._run({action:"rerun",target_dataset_id:w.id,regions:v})},get_inputs_dict:function(){var v={};this.get("inputs").each(function(w){v[w.get("name")]=w.get("value")});return v},_run:function(x){var y=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},x);var w=$.Deferred(),v=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(y),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(z){return z!=="pending"}});$.when(v.go()).then(function(z){w.resolve(new u.DatasetCollection().reset(z))});return w}});t.extend(h.prototype,e);var n=Backbone.View.extend({});var k=Backbone.Collection.extend({model:h});var o=Backbone.Model.extend(e);var r=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){t.each(this.attributes.elems,function(v){v.show()});this.show();this.set("open",false)},apply_search_results:function(w){var x=true,v;t.each(this.attributes.elems,function(y){if(y instanceof o){v=y;v.hide()}else{if(y instanceof h){if(y.apply_search_results(w)){x=false;if(v){v.show()}}}}});if(x){this.hide()}else{this.show();this.set("open",true)}}});t.extend(r.prototype,e);var b=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var x=this.attributes.query;if(x.length<this.attributes.min_chars_for_search){this.set("results",null);return}var w=x+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var v=this;this.timer=setTimeout(function(){$.get(v.attributes.search_url,{query:w},function(y){v.set("results",y);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});t.extend(b.prototype,e);var l=Backbone.Model.extend({initialize:function(v){this.attributes.tool_search=v.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=v.tools;this.attributes.layout=new Backbone.Collection(this.parse(v.layout))},parse:function(w){var v=this,x=function(A){var z=A.type;if(z==="tool"){return v.attributes.tools.get(A.id)}else{if(z==="section"){var y=t.map(A.elems,x);A.elems=y;return new r(A)}else{if(z==="label"){return new o(A)}}}};return t.map(w,x)},clear_search_results:function(){this.get("layout").each(function(v){if(v instanceof r){v.clear_search_results()}else{v.show()}})},apply_search_results:function(){var w=this.get("tool_search").get("results");if(w===null){this.clear_search_results();return}var v=null;this.get("layout").each(function(x){if(x instanceof o){v=x;v.hide()}else{if(x instanceof h){if(x.apply_search_results(w)){if(v){v.show()}}}else{v=null;x.apply_search_results(w)}}})}});var p=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var j=p.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var f=p.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.name));return this}});var i=p.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){p.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var v=this.$el.find(".toolSectionBody");t.each(this.model.attributes.elems,function(w){if(w instanceof h){var x=new j({model:w,className:"toolTitle"});x.render();v.append(x.$el)}else{if(w instanceof o){var y=new f({model:w});y.render();v.append(y.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var m=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(v){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===v.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var v=this;var w=new m({model:this.model.get("tool_search")});w.render();v.$el.append(w.$el);this.model.get("layout").each(function(y){if(y instanceof r){var x=new i({model:y});x.render();v.$el.append(x.$el)}else{if(y instanceof h){var z=new j({model:y,className:"toolTitleNoSection"});z.render();v.$el.append(z.$el)}else{if(y instanceof o){var A=new f({model:y});A.render();v.$el.append(A.$el)}}}});v.$el.find("a.tool-link").click(function(z){var y=$(this).attr("class").split(/\s+/)[0],x=v.model.get("tools").get(y);v.trigger("tool_link_click",z,x)});return this},handle_search_results:function(){var v=this.model.get("tool_search").get("results");if(v&&v.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var q=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var g=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new q()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var v=this;this.tool_panel_view.on("tool_link_click",function(x,w){x.preventDefault();v.show_tool(w)})},show_tool:function(w){var v=this;w.fetch().done(function(){v.tool_form_view.model=w;v.tool_form_view.render();v.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:d,IntegerToolParameter:c,Tool:h,ToolCollection:k,ToolSearch:b,ToolPanel:l,ToolPanelView:s,ToolFormView:q}}); \ No newline at end of file diff -r 84c88d3644c0edc925fe2583276fbd32711f30a9 -r ebf6033a1cd4416602294b674628eb73da6fa663 templates/webapps/galaxy/root/tool_menu.mako --- a/templates/webapps/galaxy/root/tool_menu.mako +++ b/templates/webapps/galaxy/root/tool_menu.mako @@ -12,40 +12,45 @@ } }); - require(["mvc/tools"], function(tools) { + require(["mvc/tools"], function(tools_mod) { // Init. on document load. $(function() { - // Create tool search, tool panel, and tool panel view. - var tool_search = new tools.ToolSearch({ - spinner_url: "${h.url_for('/static/images/loading_small_white_bg.gif')}", - search_url: "${h.url_for( controller='root', action='tool_search' )}", - hidden: false - }), - tool_panel = new tools.ToolPanel({ tool_search: tool_search }), - tool_panel_view = new tools.ToolPanelView({ collection: tool_panel }); - - // Add tool panel to Galaxy object. - Galaxy.toolPanel = tool_panel; - ## Populate tool panel if (a) anonymous use possible or (b) user is logged in. %if trans.user or not trans.app.config.require_login: - tool_panel.reset( tool_panel.parse( ${h.to_json_string( trans.app.toolbox.to_dict( trans ) )} ) ); + // Create tool search, tool panel, and tool panel view. + var tool_search = new tools_mod.ToolSearch({ + spinner_url: "${h.url_for('/static/images/loading_small_white_bg.gif')}", + search_url: "${h.url_for( controller='root', action='tool_search' )}", + hidden: false + }), + tools = new tools_mod.ToolCollection( + ${ h.to_json_string( trans.app.toolbox.to_dict( trans, in_panel=False ) ) } + ), + tool_panel = new tools_mod.ToolPanel({ + tool_search: tool_search, + tools: tools, + layout: ${h.to_json_string( trans.app.toolbox.to_dict( trans ) )} + }), + tool_panel_view = new tools_mod.ToolPanelView({ model: tool_panel }); + + // Add tool panel to Galaxy object. + Galaxy.toolPanel = tool_panel; + + // If there are tools, render panel and display everything. + if (tool_panel.get('layout').size() > 1) { + tool_panel_view.render(); + $('.toolMenu').show(); + } + $('.toolMenuContainer').prepend(tool_panel_view.$el); + + // Minsize init hint. + $( "a[minsizehint]" ).click( function() { + if ( parent.handle_minwidth_hint ) { + parent.handle_minwidth_hint( $(this).attr( "minsizehint" ) ); + } + }); %endif - - // If there are tools, render panel and display everything. - if (tool_panel.length > 1) { // > 1 because tool_search counts as a model - tool_panel_view.render(); - $('.toolMenu').show(); - } - $('.toolMenuContainer').prepend(tool_panel_view.$el); - - // Minsize init hint. - $( "a[minsizehint]" ).click( function() { - if ( parent.handle_minwidth_hint ) { - parent.handle_minwidth_hint( $(this).attr( "minsizehint" ) ); - } - }); }); }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: UI: change load order of user-related JS; pack scripts
by commits-noreply＠bitbucket.org 14 Aug '13

14 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2c3f4163da4e/ Changeset: 2c3f4163da4e User: carlfeberhard Date: 2013-08-14 19:09:51 Summary: UI: change load order of user-related JS; pack scripts Affected #: 8 files diff -r 3f85113b7476767ef1dc76c7f3312b423ff743db -r 2c3f4163da4ef47bb3f04da580e5015961dc0c67 static/scripts/packed/galaxy.autocom_tagging.js --- a/static/scripts/packed/galaxy.autocom_tagging.js +++ b/static/scripts/packed/galaxy.autocom_tagging.js @@ -1,1 +1,1 @@ -function init_tag_click_function(b,a){$(b).find(".tag-name").each(function(){$(this).click(function(){var d=$(this).text();var c=d.split(":");a(c[0],c[1]);return true})})}jQuery.fn.autocomplete_tagging=function(m){var f={get_toggle_link_text_fn:function(n){var p="";var o=obj_length(n);if(o>0){p=o+(o>1?" Tags":" Tag")}else{p="Add tags"}return p},tag_click_fn:function(n,o){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var d=jQuery.extend(f,m);var g=$(this);var b=g.find(".tag-area");var e=g.find(".toggle-link");var a=g.find(".tag-input");var l=g.find(".add-tag-button");e.click(function(){var n;if(b.is(":hidden")){n=function(){var o=$(this).find(".tag-button").length;if(o===0){b.click()}}}else{n=function(){b.blur()}}b.slideToggle("fast",n);return $(this)});if(d.editable){a.hide()}a.keyup(function(t){if(t.keyCode===27){$(this).trigger("blur")}else{if((t.keyCode===13)||(t.keyCode===188)||(t.keyCode===32)){var s=this.value;if(return_key_pressed_for_autocomplete===true){return_key_pressed_for_autocomplete=false;return false}if(s.indexOf(": ",s.length-2)!==-1){this.value=s.substring(0,s.length-1);return false}if((t.keyCode===188)||(t.keyCode===32)){s=s.substring(0,s.length-1)}s=$.trim(s);if(s.length<2){return false}this.value="";var q=j(s);var p=b.children(".tag-button");if(p.length!==0){var u=p.slice(p.length-1);u.after(q)}else{b.prepend(q)}var o=s.split(":");d.tags[o[0]]=o[1];var r=d.get_toggle_link_text_fn(d.tags);e.text(r);var n=$(this);$.ajax({url:d.ajax_add_tag_url,data:{new_tag:s},error:function(){q.remove();delete d.tags[o[0]];var v=d.get_toggle_link_text_fn(d.tags);e.text(v);alert("Add tag failed")},success:function(){n.flushCache()}});return false}}});var i=function(q,p,o,s,r){var n=s.split(":");return(n.length===1?n[0]:n[1])};var h={selectFirst:false,formatItem:i,autoFill:false,highlight:false};a.autocomplete(d.ajax_autocomplete_tag_url,h);g.find(".delete-tag-img").each(function(){c($(this))});init_tag_click_function($(this),d.tag_click_fn);l.click(function(){$(this).hide();b.click();return false});if(d.editable){b.bind("blur",function(n){if(obj_length(d.tags)>0){l.show();a.hide();b.removeClass("active-tag-area");b.addClass("tooltip")}else{}});b.click(function(p){var o=$(this).hasClass("active-tag-area");if($(p.target).hasClass("delete-tag-img")&&!o){return false}if($(p.target).hasClass("tag-name")&&!o){return false}$(this).removeClass("tooltip");$(this).addClass("active-tag-area");l.hide();a.show();a.focus();var n=function(r){var q=function(s,u){var t=s.attr("id");if(u!==s){s.blur();$(window).unbind("click.tagging_blur");$(this).addClass("tooltip")}};q(b,$(r.target))};$(window).bind("click.tagging_blur",n);return false})}if(d.use_toggle_link){b.hide()}function k(o,n){return o+(n?":"+n:"")}function c(n){$(n).mouseenter(function(){$(this).attr("src",d.delete_tag_img_rollover)});$(n).mouseleave(function(){$(this).attr("src",d.delete_tag_img)});$(n).click(function(){var t=$(this).parent();var s=t.find(".tag-name").eq(0);var r=s.text();var p=r.split(":");var v=p[0];var o=p[1];var u=t.prev();t.remove();delete d.tags[v];var q=d.get_toggle_link_text_fn(d.tags);e.text(q);$.ajax({url:d.ajax_delete_tag_url,data:{tag_name:v},error:function(){d.tags[v]=o;if(u.hasClass("tag-button")){u.after(t)}else{b.prepend(t)}alert("Remove tag failed");e.text(d.get_toggle_link_text_fn(d.tags));n.mouseenter(function(){$(this).attr("src",d.delete_tag_img_rollover)});n.mouseleave(function(){$(this).attr("src",d.delete_tag_img)})},success:function(){}});return true})}function j(n){var o=$("<img/>").attr("src",d.delete_tag_img).addClass("delete-tag-img");c(o);var p=$("<span>").text(n).addClass("tag-name");p.click(function(){var r=n.split(":");d.tag_click_fn(r[0],r[1]);return true});var q=$("<span></span>").addClass("tag-button");q.append(p);if(d.editable){q.append(o)}return q}}; \ No newline at end of file +function init_tag_click_function(b,a){$(b).find(".tag-name").each(function(){$(this).click(function(){var d=$(this).text();var c=d.split(":");a(c[0],c[1]);return true})})}jQuery.fn.autocomplete_tagging=function(m){var f={get_toggle_link_text_fn:function(n){var p="";var o=obj_length(n);if(o>0){p=o+(o>1?" Tags":" Tag")}else{p="Add tags"}return p},tag_click_fn:function(n,o){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var d=jQuery.extend(f,m);var g=$(this);var b=g.find(".tag-area");var e=g.find(".toggle-link");var a=g.find(".tag-input");var l=g.find(".add-tag-button");e.click(function(){var n;if(b.is(":hidden")){n=function(){var o=$(this).find(".tag-button").length;if(o===0){b.click()}}}else{n=function(){b.blur()}}b.slideToggle("fast",n);return $(this)});if(d.editable){a.hide()}a.keyup(function(t){if(t.keyCode===27){$(this).trigger("blur")}else{if((t.keyCode===13)||(t.keyCode===188)||(t.keyCode===32)){var s=this.value;if(s.indexOf(": ",s.length-2)!==-1){this.value=s.substring(0,s.length-1);return false}if((t.keyCode===188)||(t.keyCode===32)){s=s.substring(0,s.length-1)}s=$.trim(s);if(s.length<2){return false}this.value="";var q=j(s);var p=b.children(".tag-button");if(p.length!==0){var u=p.slice(p.length-1);u.after(q)}else{b.prepend(q)}var o=s.split(":");d.tags[o[0]]=o[1];var r=d.get_toggle_link_text_fn(d.tags);e.text(r);var n=$(this);$.ajax({url:d.ajax_add_tag_url,data:{new_tag:s},error:function(){q.remove();delete d.tags[o[0]];var v=d.get_toggle_link_text_fn(d.tags);e.text(v);alert("Add tag failed")},success:function(){n.data("autocompleter").cacheFlush()}});return false}}});var i=function(q,p,o,s,r){var n=s.split(":");return(n.length===1?n[0]:n[1])};var h={selectFirst:false,formatItem:i,autoFill:false,highlight:false};a.autocomplete(d.ajax_autocomplete_tag_url,h);g.find(".delete-tag-img").each(function(){c($(this))});init_tag_click_function($(this),d.tag_click_fn);l.click(function(){$(this).hide();b.click();return false});if(d.editable){b.bind("blur",function(n){if(obj_length(d.tags)>0){l.show();a.hide();b.removeClass("active-tag-area");b.addClass("tooltip")}else{}});b.click(function(p){var o=$(this).hasClass("active-tag-area");if($(p.target).hasClass("delete-tag-img")&&!o){return false}if($(p.target).hasClass("tag-name")&&!o){return false}$(this).removeClass("tooltip");$(this).addClass("active-tag-area");l.hide();a.show();a.focus();var n=function(r){var q=function(s,u){var t=s.attr("id");if(u!==s){s.blur();$(window).unbind("click.tagging_blur");$(this).addClass("tooltip")}};q(b,$(r.target))};$(window).bind("click.tagging_blur",n);return false})}if(d.use_toggle_link){b.hide()}function k(o,n){return o+(n?":"+n:"")}function c(n){$(n).mouseenter(function(){$(this).attr("src",d.delete_tag_img_rollover)});$(n).mouseleave(function(){$(this).attr("src",d.delete_tag_img)});$(n).click(function(){var t=$(this).parent();var s=t.find(".tag-name").eq(0);var r=s.text();var p=r.split(":");var v=p[0];var o=p[1];var u=t.prev();t.remove();delete d.tags[v];var q=d.get_toggle_link_text_fn(d.tags);e.text(q);$.ajax({url:d.ajax_delete_tag_url,data:{tag_name:v},error:function(){d.tags[v]=o;if(u.hasClass("tag-button")){u.after(t)}else{b.prepend(t)}alert("Remove tag failed");e.text(d.get_toggle_link_text_fn(d.tags));n.mouseenter(function(){$(this).attr("src",d.delete_tag_img_rollover)});n.mouseleave(function(){$(this).attr("src",d.delete_tag_img)})},success:function(){}});return true})}function j(n){var o=$("<img/>").attr("src",d.delete_tag_img).addClass("delete-tag-img");c(o);var p=$("<span>").text(n).addClass("tag-name");p.click(function(){var r=n.split(":");d.tag_click_fn(r[0],r[1]);return true});var q=$("<span></span>").addClass("tag-button");q.append(p);if(d.editable){q.append(o)}return q}}; \ No newline at end of file diff -r 3f85113b7476767ef1dc76c7f3312b423ff743db -r 2c3f4163da4ef47bb3f04da580e5015961dc0c67 static/scripts/packed/libs/jquery/jquery.autocomplete.js --- a/static/scripts/packed/libs/jquery/jquery.autocomplete.js +++ b/static/scripts/packed/libs/jquery/jquery.autocomplete.js @@ -1,1 +1,1 @@ -String.prototype.endsWith=function(a){return(this.match(a+"$")==a)};var return_key_pressed_for_autocomplete=false;(function(a){a.fn.extend({autocomplete:function(b,c){var d=typeof b=="string";c=a.extend({},a.Autocompleter.defaults,{url:d?b:null,data:d?null:b,delay:d?a.Autocompleter.defaults.delay:10,max:c&&!c.scroll?10:150},c);c.highlight=c.highlight||function(e){return e};c.formatMatch=c.formatMatch||c.formatItem;return this.each(function(){new a.Autocompleter(this,c)})},result:function(b){return this.bind("result",b)},search:function(b){return this.trigger("search",[b])},flushCache:function(){return this.trigger("flushCache")},setOptions:function(b){return this.trigger("setOptions",[b])},unautocomplete:function(){return this.trigger("unautocomplete")},showAllInCache:function(){return this.trigger("showAllInCache")}});a.Autocompleter=function(l,g){var c={UP:38,DOWN:40,DEL:46,TAB:9,RETURN:13,ESC:27,COMMA:188,PAGEUP:33,PAGEDOWN:34,BACKSPACE:8,COLON:16};var b=a(l).attr("autocomplete","off").addClass(g.inputClass);var j;var p="";var m=a.Autocompleter.Cache(g);var e=0;var u;var x={mouseDownOnSelect:false};var r=a.Autocompleter.Select(g,l,d,x);var w;a.browser.opera&&a(l.form).bind("submit.autocomplete",function(){if(w){w=false;return false}});b.bind((a.browser.mozilla?"keypress":"keydown")+".autocomplete",function(y){u=y.keyCode;switch(y.keyCode){case c.UP:y.preventDefault();if(r.visible()){r.prev()}else{t(0,true)}break;case c.DOWN:y.preventDefault();if(r.visible()){r.next()}else{t(0,true)}break;case c.PAGEUP:y.preventDefault();if(r.visible()){r.pageUp()}else{t(0,true)}break;case c.PAGEDOWN:y.preventDefault();if(r.visible()){r.pageDown()}else{t(0,true)}break;case g.multiple&&a.trim(g.multipleSeparator)==","&&c.COMMA:case c.TAB:case 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q(y,z){if(g.autoFill&&(i(b.val()).toLowerCase()==y.toLowerCase())&&u!=c.BACKSPACE){b.val(b.val()+z.substring(i(p).length));a.Autocompleter.Selection(l,p.length,p.length+z.length)}}function s(){clearTimeout(j);j=setTimeout(v,200)}function v(){var y=r.visible();r.hide();clearTimeout(j);n();if(g.mustMatch){b.search(function(z){if(!z){if(g.multiple){var A=h(b.val()).slice(0,-1);b.val(A.join(g.multipleSeparator)+(A.length?g.multipleSeparator:""))}else{b.val("")}}})}if(y){a.Autocompleter.Selection(l,l.value.length,l.value.length)}}function k(z,y){if(y&&y.length&&e){n();r.display(y,z);q(z,y[0].value);r.show()}else{v()}}function f(z,B,y){if(!g.matchCase){z=z.toLowerCase()}var A=m.load(z);if(z.endsWith(":")){A=null}if(A&&A.length){B(z,A)}else{if((typeof g.url=="string")&&(g.url.length>0)){var C={timestamp:+new Date()};a.each(g.extraParams,function(D,E){C[D]=typeof 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RegExp("(?![^&;]+;)(?!<[^<>]*)("+b.replace(/([\^\$\[\]\{\}\*\.\+\?\|\\])/gi,"\\$1")+")(?![^<>]*>)(?![^&;]+;)","gi"),"<strong>$1</strong>")},scroll:true,scrollHeight:180};a.Autocompleter.Cache=function(c){var f={};var d=0;function h(l,k){if(!c.matchCase){l=l.toLowerCase()}var j=l.indexOf(k);if(j==-1){return false}return j==0||c.matchContains}function g(j,i){if(d>c.cacheLength){b()}if(!f[j]){d++}f[j]=i}function e(){if(!c.data){return false}var k={},j=0;if(!c.url){c.cacheLength=1}k[""]=[];for(var m=0,l=c.data.length;m<l;m++){var o=c.data[m];o=(typeof o=="string")?[o]:o;var n=c.formatMatch(o,m+1,c.data.length);if(n===false){continue}if(!k[n]){k[n]=[]}var p={value:n,data:o,result:c.formatResult&&c.formatResult(o)||n};k[n].push(p);if(j++<c.max){k[""].push(p)}}a.each(k,function(q,r){c.cacheLength++;g(q,r)})}setTimeout(e,25);function b(){f={};d=0}return{flush:b,add:g,populate:e,load:function(n){if(!c.cacheLength||!d){return null}if(!c.url&&c.matchContains){var m=[];for(var j in 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u=a("<li/>").html(s[w].data[1]).addClass("ac_header").appendTo(p)[0]}}else{var u=a("<li/>").html(e.highlight(x,m)).addClass(w%2==0?"ac_even":"ac_odd").appendTo(p)[0]}a.data(u,"ac_data",s[w])}k=p.find("li");if(e.selectFirst){k.slice(0,1).addClass(i.ACTIVE);f=0}if(a.fn.bgiframe){p.bgiframe()}}return{display:function(v,u){o();s=v;m=u;d()},next:function(){h(1)},prev:function(){h(-1)},pageUp:function(){if(f!=0&&f-8<0){h(-f)}else{h(-8)}},pageDown:function(){if(f!=k.size()-1&&f+8>k.size()){h(k.size()-1-f)}else{h(8)}},hide:function(){c&&c.hide();k&&k.removeClass(i.ACTIVE);f=-1},visible:function(){return c&&c.is(":visible")},current:function(){return this.visible()&&(k.filter("."+i.ACTIVE)[0]||e.selectFirst&&k[0])},show:function(){var w=a(j).offset();c.css({width:typeof e.width=="string"||e.width>0?e.width:a(j).width(),top:w.top+j.offsetHeight,left:w.left}).show();if(e.scroll){p.scrollTop(0);p.css({maxHeight:e.scrollHeight,overflow:"auto"});if(a.browser.msie&&typeof 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h;if(i==="string"){k=h;j={}}else{if(e.isArray(h)){k=h[0];j=h.slice(1)}else{if(i==="object"){k=h.value;j=h.data}}}k=String(k);if(typeof j!=="object"){j={}}return{value:k,data:j}};var g=function(k,h,j){var i=parseInt(k,10);j=j||{};if(isNaN(i)||(j.min&&i<j.min)){i=h}return i};var b=function(h,i){return[h,encodeURIComponent(i)].join("=")};var c=function(h,j){var i=[];e.each(j,function(k,l){i.push(b(k,l))});if(i.length){h+=h.indexOf("?")===-1?"?":"&";h+=i.join("&")}return h};var f=function(i,h,j){i=String(i.value);h=String(h.value);if(!j){i=i.toLowerCase();h=h.toLowerCase()}if(i>h){return 1}if(i<h){return -1}return 0};var a=function(q,k,h){var n=[];var o,l,m,s,p,r;r=String(q).replace("\r\n","\n").split(k);for(o=0;o<r.length;o++){s=r[o].split(h);m=[];for(l=0;l<s.length;l++){m.push(decodeURIComponent(s[l]))}p=m.shift();n.push({value:p,data:m})}return n};e.Autocompleter=function(i,j){if(!i||!(i instanceof e)||i.length!==1||(i.get(0).tagName.toUpperCase()!=="INPUT"&&i.get(0).tagName.toUpperCase()!=="TEXTAREA")){throw new Error("Invalid parameter for jquery.Autocompleter, jQuery object with one element with INPUT or TEXTAREA tag expected.")}var h=this;this.options=j;this.cacheData_={};this.cacheLength_=0;this.selectClass_="jquery-autocomplete-selected-item";this.keyTimeout_=null;this.finishTimeout_=null;this.lastKeyPressed_=null;this.lastProcessedValue_=null;this.lastSelectedValue_=null;this.active_=false;this.finishOnBlur_=true;this.options.minChars=g(this.options.minChars,e.fn.autocomplete.defaults.minChars,{min:0});this.options.maxItemsToShow=g(this.options.maxItemsToShow,e.fn.autocomplete.defaults.maxItemsToShow,{min:0});this.options.maxCacheLength=g(this.options.maxCacheLength,e.fn.autocomplete.defaults.maxCacheLength,{min:1});this.options.delay=g(this.options.delay,e.fn.autocomplete.defaults.delay,{min:0});if(this.options.preventDefaultReturn!=2){this.options.preventDefaultReturn=this.options.preventDefaultReturn?1:0}if(this.options.preventDefaultTab!=2){this.options.preventDefaultTab=this.options.preventDefaultTab?1:0}this.dom={};this.dom.$elem=i;this.dom.$elem.attr("autocomplete","off").addClass(this.options.inputClass);this.dom.$results=e("<div></div>").hide().addClass(this.options.resultsClass).css({position:"absolute"});e("body").append(this.dom.$results);i.keydown(function(l){h.lastKeyPressed_=l.keyCode;switch(h.lastKeyPressed_){case h.options.delimiterKeyCode:if(h.options.useDelimiter&&h.active_){h.selectCurrent()}break;case 35:case 36:case 16:case 17:case 18:case 37:case 39:break;case 38:l.preventDefault();if(h.active_){h.focusPrev()}else{h.activate()}return false;case 40:l.preventDefault();if(h.active_){h.focusNext()}else{h.activate()}return false;case 9:if(h.active_){h.selectCurrent();if(h.options.preventDefaultTab){l.preventDefault();return false}}if(h.options.preventDefaultTab===2){l.preventDefault();return false}break;case 13:if(h.active_){h.selectCurrent();if(h.options.preventDefaultReturn){l.preventDefault();return false}}if(h.options.preventDefaultReturn===2){l.preventDefault();return false}break;case 27:if(h.active_){l.preventDefault();h.deactivate(true);return false}break;default:h.activate()}});i.on("paste",function(){h.activate()});var k=function(){h.deactivate(true)};i.blur(function(){if(h.finishOnBlur_){h.finishTimeout_=setTimeout(k,200)}});i.parents("form").on("submit",k)};e.Autocompleter.prototype.position=function(){var n=this.dom.$elem.offset();var i=this.dom.$results.outerHeight();var k=e(window).outerHeight();var m=n.top+this.dom.$elem.outerHeight();var l=m+i;var h={top:m,left:n.left};if(l>k){var j=n.top-i;if(j>=0){h.top=j}}this.dom.$results.css(h)};e.Autocompleter.prototype.cacheRead=function(k){var m,j,i,h,l;if(this.options.useCache){k=String(k);m=k.length;if(this.options.matchSubset){j=1}else{j=m}while(j<=m){if(this.options.matchInside){h=m-j}else{h=0}l=0;while(l<=h){i=k.substr(0,j);if(this.cacheData_[i]!==undefined){return this.cacheData_[i]}l++}j++}}return false};e.Autocompleter.prototype.cacheWrite=function(h,i){if(this.options.useCache){if(this.cacheLength_>=this.options.maxCacheLength){this.cacheFlush()}h=String(h);if(this.cacheData_[h]!==undefined){this.cacheLength_++}this.cacheData_[h]=i;return this.cacheData_[h]}return false};e.Autocompleter.prototype.cacheFlush=function(){this.cacheData_={};this.cacheLength_=0};e.Autocompleter.prototype.callHook=function(j,i){var h=this.options[j];if(h&&e.isFunction(h)){return h(i,this)}return false};e.Autocompleter.prototype.activate=function(){if(!this.options.enabled){return}var h=this;if(this.keyTimeout_){clearTimeout(this.keyTimeout_)}this.keyTimeout_=setTimeout(function(){h.activateNow()},this.options.delay)};e.Autocompleter.prototype.activateNow=function(){var h=this.beforeUseConverter(this.dom.$elem.val());if(h!==this.lastProcessedValue_&&h!==this.lastSelectedValue_){this.fetchData(h)}};e.Autocompleter.prototype.fetchData=function(j){var i=this;var h=function(k,l){if(i.options.processData){k=i.options.processData(k)}i.showResults(i.filterResults(k,l),l)};this.lastProcessedValue_=j;if(j.length<this.options.minChars){h([],j)}else{if(this.options.data){h(this.options.data,j)}else{this.fetchRemoteData(j,function(k){h(k,j)})}}};e.Autocompleter.prototype.fetchRemoteData=function(k,m){var l=this.cacheRead(k);if(l){m(l)}else{var i=this;var h=i.options.remoteDataType==="json"?"json":"text";var j=function(o){var n=false;if(o!==false){n=i.parseRemoteData(o);i.cacheWrite(k,n)}i.dom.$elem.removeClass(i.options.loadingClass);m(n)};this.dom.$elem.addClass(this.options.loadingClass);e.ajax({url:this.makeUrl(k),success:j,error:function(n,p,o){if(e.isFunction(i.options.onError)){i.options.onError(n,p,o)}else{j(false)}},dataType:h})}};e.Autocompleter.prototype.setExtraParam=function(i,j){var h=e.trim(String(i));if(h){if(!this.options.extraParams){this.options.extraParams={}}if(this.options.extraParams[h]!==j){this.options.extraParams[h]=j;this.cacheFlush()}}return this};e.Autocompleter.prototype.makeUrl=function(k){var h=this;var i=this.options.url;var j=e.extend({},this.options.extraParams);if(this.options.queryParamName===false){i+=encodeURIComponent(k)}else{j[this.options.queryParamName]=k}return c(i,j)};e.Autocompleter.prototype.parseRemoteData=function(i){var h;var j=i;if(this.options.remoteDataType==="json"){h=typeof(i);switch(h){case"object":j=i;break;case"string":j=e.parseJSON(i);break;default:throw new Error("Unexpected remote data type: "+h)}return j}return a(j,this.options.lineSeparator,this.options.cellSeparator)};e.Autocompleter.prototype.defaultFilter=function(h,j){if(!h.value){return false}if(this.options.filterResults){var k=this.matchStringConverter(j);var l=this.matchStringConverter(h.value);if(!this.options.matchCase){k=k.toLowerCase();l=l.toLowerCase()}var i=l.indexOf(k);if(this.options.matchInside){return i>-1}else{return i===0}}return true};e.Autocompleter.prototype.filterResult=function(h,i){if(this.options.filter===false){return true}if(e.isFunction(this.options.filter)){return this.options.filter(h,i)}return this.defaultFilter(h,i)};e.Autocompleter.prototype.filterResults=function(l,m){var j=[];var k,h;for(k=0;k<l.length;k++){h=d(l[k]);if(this.filterResult(h,m)){j.push(h)}}if(this.options.sortResults){j=this.sortResults(j,m)}if(this.options.maxItemsToShow>0&&this.options.maxItemsToShow<j.length){j.length=this.options.maxItemsToShow}return j};e.Autocompleter.prototype.sortResults=function(j,k){var i=this;var h=this.options.sortFunction;if(!e.isFunction(h)){h=function(m,l,n){return f(m,l,i.options.matchCase)}}j.sort(function(m,l){return h(m,l,k,i.options)});return j};e.Autocompleter.prototype.matchStringConverter=function(k,i,h){var j=this.options.matchStringConverter;if(e.isFunction(j)){k=j(k,i,h)}return k};e.Autocompleter.prototype.beforeUseConverter=function(i){i=this.getValue(i);var h=this.options.beforeUseConverter;if(e.isFunction(h)){i=h(i)}return i};e.Autocompleter.prototype.enableFinishOnBlur=function(){this.finishOnBlur_=true};e.Autocompleter.prototype.disableFinishOnBlur=function(){this.finishOnBlur_=false};e.Autocompleter.prototype.createItemFromResult=function(h){var i=this;var j=e("<li/>");j.html(this.showResult(h.value,h.data));j.data({value:h.value,data:h.data}).click(function(){i.selectItem(j)}).mousedown(i.disableFinishOnBlur).mouseup(i.enableFinishOnBlur);return j};e.Autocompleter.prototype.getItems=function(){return e(">ul>li",this.dom.$results)};e.Autocompleter.prototype.showResults=function(l,h){var j=l.length;var r=this;var n=e("<ul></ul>");var m,s,p,q,o=false,k=false;if(j){for(m=0;m<j;m++){s=l[m];p=this.createItemFromResult(s);n.append(p);if(o===false){o=String(s.value);k=p;p.addClass(this.options.firstItemClass)}if(m===j-1){p.addClass(this.options.lastItemClass)}}this.dom.$results.html(n).show();this.position();if(this.options.autoWidth){q=this.dom.$elem.outerWidth()-this.dom.$results.outerWidth()+this.dom.$results.width();this.dom.$results.css(this.options.autoWidth,q)}this.getItems().hover(function(){r.focusItem(this)},function(){});if(this.autoFill(o,h)||this.options.selectFirst||(this.options.selectOnly&&j===1)){this.focusItem(k)}this.active_=true}else{this.hideResults();this.active_=false}};e.Autocompleter.prototype.showResult=function(i,h){if(e.isFunction(this.options.showResult)){return this.options.showResult(i,h)}else{return e("<p></p>").text(i).html()}};e.Autocompleter.prototype.autoFill=function(p,i){var m,n,q,k;if(this.options.autoFill&&this.lastKeyPressed_!==8){m=String(p).toLowerCase();n=String(i).toLowerCase();q=p.length;k=i.length;if(m.substr(0,k)===n){var o=this.getDelimiterOffsets();var j=o.start?" ":"";this.setValue(j+p);var h=k+o.start+j.length;var l=q+o.start+j.length;this.selectRange(h,l);return true}}return false};e.Autocompleter.prototype.focusNext=function(){this.focusMove(+1)};e.Autocompleter.prototype.focusPrev=function(){this.focusMove(-1)};e.Autocompleter.prototype.focusMove=function(h){var k=this.getItems();h=g(h,0);if(h){for(var j=0;j<k.length;j++){if(e(k[j]).hasClass(this.selectClass_)){this.focusItem(j+h);return}}}this.focusItem(0)};e.Autocompleter.prototype.focusItem=function(i){var h,j=this.getItems();if(j.length){j.removeClass(this.selectClass_).removeClass(this.options.selectClass);if(typeof i==="number"){if(i<0){i=0}else{if(i>=j.length){i=j.length-1}}h=e(j[i])}else{h=e(i)}if(h){h.addClass(this.selectClass_).addClass(this.options.selectClass)}}};e.Autocompleter.prototype.selectCurrent=function(){var h=e("li."+this.selectClass_,this.dom.$results);if(h.length===1){this.selectItem(h)}else{this.deactivate(false)}};e.Autocompleter.prototype.selectItem=function(n){var p=n.data("value");var j=n.data("data");var m=this.displayValue(p,j);var k=this.beforeUseConverter(m);this.lastProcessedValue_=k;this.lastSelectedValue_=k;var l=this.getDelimiterOffsets();var h=this.options.delimiterChar;var i=this.dom.$elem;var o=0;if(this.options.useDelimiter){if(i.val().substring(l.start-1,l.start)==h&&h!=" "){m=" "+m}if(i.val().substring(l.end,l.end+1)!=h&&this.lastKeyPressed_!=this.options.delimiterKeyCode){m=m+h}else{o=1}}this.setValue(m);this.setCaret(l.start+m.length+o);this.callHook("onItemSelect",{value:p,data:j});this.deactivate(true);i.focus()};e.Autocompleter.prototype.displayValue=function(i,h){if(e.isFunction(this.options.displayValue)){return this.options.displayValue(i,h)}return i};e.Autocompleter.prototype.hideResults=function(){this.dom.$results.hide()};e.Autocompleter.prototype.deactivate=function(h){if(this.finishTimeout_){clearTimeout(this.finishTimeout_)}if(this.keyTimeout_){clearTimeout(this.keyTimeout_)}if(h){if(this.lastProcessedValue_!==this.lastSelectedValue_){if(this.options.mustMatch){this.setValue("")}this.callHook("onNoMatch")}if(this.active_){this.callHook("onFinish")}this.lastKeyPressed_=null;this.lastProcessedValue_=null;this.lastSelectedValue_=null;this.active_=false}this.hideResults()};e.Autocompleter.prototype.selectRange=function(k,h){var j=this.dom.$elem.get(0);if(j.setSelectionRange){j.focus();j.setSelectionRange(k,h)}else{if(j.createTextRange){var i=j.createTextRange();i.collapse(true);i.moveEnd("character",h);i.moveStart("character",k);i.select()}}};e.Autocompleter.prototype.setCaret=function(h){this.selectRange(h,h)};e.Autocompleter.prototype.getCaret=function(){var j=this.dom.$elem;var m=j[0];var n,l,i,o,h,k;if(m.createTextRange){l=document.selection;if(m.tagName.toLowerCase()!="textarea"){n=j.val();i=l.createRange().duplicate();i.moveEnd("character",n.length);if(i.text===""){o=n.length}else{o=n.lastIndexOf(i.text)}i=l.createRange().duplicate();i.moveStart("character",-n.length);h=i.text.length}else{i=l.createRange();k=i.duplicate();k.moveToElementText(m);k.setEndPoint("EndToEnd",i);o=k.text.length-i.text.length;h=o+i.text.length}}else{o=j[0].selectionStart;h=j[0].selectionEnd}return{start:o,end:h}};e.Autocompleter.prototype.setValue=function(j){if(this.options.useDelimiter){var l=this.dom.$elem.val();var k=this.getDelimiterOffsets();var h=l.substring(0,k.start);var i=l.substring(k.end);j=h+j+i}this.dom.$elem.val(j)};e.Autocompleter.prototype.getValue=function(h){if(this.options.useDelimiter){var i=this.getDelimiterOffsets();return h.substring(i.start,i.end).trim()}else{return h}};e.Autocompleter.prototype.getDelimiterOffsets=function(){var k=this.dom.$elem.val();if(this.options.useDelimiter){var j=k.substring(0,this.getCaret().start);var l=j.lastIndexOf(this.options.delimiterChar)+1;var i=k.substring(this.getCaret().start);var h=i.indexOf(this.options.delimiterChar);if(h==-1){h=k.length}h+=this.getCaret().start}else{l=0;h=k.length}return{start:l,end:h}}})(jQuery); \ No newline at end of file diff -r 3f85113b7476767ef1dc76c7f3312b423ff743db -r 2c3f4163da4ef47bb3f04da580e5015961dc0c67 static/scripts/packed/libs/jquery/jquery.mousewheel.js --- a/static/scripts/packed/libs/jquery/jquery.mousewheel.js +++ b/static/scripts/packed/libs/jquery/jquery.mousewheel.js @@ -1,1 +1,12 @@ -(function(c){var a=["DOMMouseScroll","mousewheel"];c.event.special.mousewheel={setup:function(){if(this.addEventListener){for(var d=a.length;d;){this.addEventListener(a[--d],b,false)}}else{this.onmousewheel=b}},teardown:function(){if(this.removeEventListener){for(var d=a.length;d;){this.removeEventListener(a[--d],b,false)}}else{this.onmousewheel=null}}};c.fn.extend({mousewheel:function(d){return d?this.bind("mousewheel",d):this.trigger("mousewheel")},unmousewheel:function(d){return this.unbind("mousewheel",d)}});function b(i){var g=i||window.event,f=[].slice.call(arguments,1),j=0,h=true,e=0,d=0;i=c.event.fix(g);i.type="mousewheel";if(i.wheelDelta){j=i.wheelDelta/120}if(i.detail){j=-i.detail/3}d=j;if(g.axis!==undefined&&g.axis===g.HORIZONTAL_AXIS){d=0;e=-1*j}if(g.wheelDeltaY!==undefined){d=g.wheelDeltaY/120}if(g.wheelDeltaX!==undefined){e=-1*g.wheelDeltaX/120}f.unshift(i,j,e,d);return c.event.handle.apply(this,f)}})(jQuery); \ No newline at end of file +/* Copyright (c) 2013 Brandon Aaron (http://brandonaaron.net) + * Licensed under the MIT License (LICENSE.txt). + * + * Thanks to: http://adomas.org/javascript-mouse-wheel/ for some pointers. + * Thanks to: Mathias Bank(http://www.mathias-bank.de) for a scope bug fix. + * Thanks to: Seamus Leahy for adding deltaX and deltaY + * + * Version: 3.1.3 + * + * Requires: 1.2.2+ + */ +(function(a){a(jQuery)}(function(e){var d=["wheel","mousewheel","DOMMouseScroll","MozMousePixelScroll"];var g="onwheel" in document||document.documentMode>=9?["wheel"]:["mousewheel","DomMouseScroll","MozMousePixelScroll"];var f,a;if(e.event.fixHooks){for(var b=d.length;b;){e.event.fixHooks[d[--b]]=e.event.mouseHooks}}e.event.special.mousewheel={setup:function(){if(this.addEventListener){for(var h=g.length;h;){this.addEventListener(g[--h],c,false)}}else{this.onmousewheel=c}},teardown:function(){if(this.removeEventListener){for(var h=g.length;h;){this.removeEventListener(g[--h],c,false)}}else{this.onmousewheel=null}}};e.fn.extend({mousewheel:function(h){return h?this.bind("mousewheel",h):this.trigger("mousewheel")},unmousewheel:function(h){return this.unbind("mousewheel",h)}});function c(h){var i=h||window.event,n=[].slice.call(arguments,1),p=0,k=0,j=0,m=0,l=0,o;h=e.event.fix(i);h.type="mousewheel";if(i.wheelDelta){p=i.wheelDelta}if(i.detail){p=i.detail*-1}if(i.deltaY){j=i.deltaY*-1;p=j}if(i.deltaX){k=i.deltaX;p=k*-1}if(i.wheelDeltaY!==undefined){j=i.wheelDeltaY}if(i.wheelDeltaX!==undefined){k=i.wheelDeltaX*-1}m=Math.abs(p);if(!f||m<f){f=m}l=Math.max(Math.abs(j),Math.abs(k));if(!a||l<a){a=l}o=p>0?"floor":"ceil";p=Math[o](p/f);k=Math[o](k/a);j=Math[o](j/a);n.unshift(h,p,k,j);return(e.event.dispatch||e.event.handle).apply(this,n)}})); \ No newline at end of file diff -r 3f85113b7476767ef1dc76c7f3312b423ff743db -r 2c3f4163da4ef47bb3f04da580e5015961dc0c67 static/scripts/packed/mvc/tools.js --- a/static/scripts/packed/mvc/tools.js +++ b/static/scripts/packed/mvc/tools.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(q,a,r){var g=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var c=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new c(this.toJSON())},get_samples:function(){var u=this.get("type"),t=null;if(u==="number"){t=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(u==="select"){t=q.map(this.get("options"),function(v){return v[0]})}}return t}});var f=g.extend({defaults:{description:null,target:null,inputs:[]},relations:[{type:Backbone.HasMany,key:"inputs",relatedModel:c,reverseRelation:{key:"tool",includeInJSON:false}}],urlRoot:galaxy_paths.get("tool_url"),copy:function(u){var v=new f(this.toJSON());if(u){var t=new Backbone.Collection();v.get("inputs").each(function(w){if(w.get_samples()){t.push(w)}});v.set("inputs",t)}return v},apply_search_results:function(t){(q.indexOf(t,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(t,u){this.get("inputs").find(function(v){return v.get("name")===t}).set("value",u)},set_input_values:function(u){var t=this;q.each(q.keys(u),function(v){t.set_input_value(v,u[v])})},run:function(){return this._run()},rerun:function(u,t){return this._run({action:"rerun",target_dataset_id:u.id,regions:t})},get_inputs_dict:function(){var t={};this.get("inputs").each(function(u){t[u.get("name")]=u.get("value")});return t},_run:function(v){var w=q.extend({tool_id:this.id,inputs:this.get_inputs_dict()},v);var u=$.Deferred(),t=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(w),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(x){return x!=="pending"}});$.when(t.go()).then(function(x){u.resolve(new r.DatasetCollection().reset(x))});return u}});var j=Backbone.Collection.extend({model:f});var m=g.extend({});var p=g.extend({defaults:{elems:[],open:false},clear_search_results:function(){q.each(this.attributes.elems,function(t){t.show()});this.show();this.set("open",false)},apply_search_results:function(u){var v=true,t;q.each(this.attributes.elems,function(w){if(w instanceof m){t=w;t.hide()}else{if(w instanceof f){if(w.apply_search_results(u)){v=false;if(t){t.show()}}}}});if(v){this.hide()}else{this.show();this.set("open",true)}}});var b=g.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var v=this.attributes.query;if(v.length<this.attributes.min_chars_for_search){this.set("results",null);return}var u=v+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var t=this;this.timer=setTimeout(function(){$.get(t.attributes.search_url,{query:u},function(w){t.set("results",w);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});var k=Backbone.Collection.extend({url:"/tools",tools:new j(),parse:function(t){var u=function(x){var w=x.type;if(w==="tool"){return new f(x)}else{if(w==="section"){var v=q.map(x.elems,u);x.elems=v;return new p(x)}else{if(w==="label"){return new m(x)}}}};return q.map(t,u)},initialize:function(t){this.tool_search=t.tool_search;this.tool_search.on("change:results",this.apply_search_results,this);this.on("reset",this.populate_tools,this)},populate_tools:function(){var t=this;t.tools=new j();this.each(function(u){if(u instanceof p){q.each(u.attributes.elems,function(v){if(v instanceof f){t.tools.push(v)}})}else{if(u instanceof f){t.tools.push(u)}}})},clear_search_results:function(){this.each(function(t){if(t instanceof p){t.clear_search_results()}else{t.show()}})},apply_search_results:function(){var u=this.tool_search.attributes.results;if(u===null){this.clear_search_results();return}var t=null;this.each(function(v){if(v instanceof m){t=v;t.hide()}else{if(v instanceof f){if(v.apply_search_results(u)){if(t){t.show()}}}else{t=null;v.apply_search_results(u)}}})}});var n=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var i=n.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var d=n.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.name));return this}});var h=n.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){n.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var t=this.$el.find(".toolSectionBody");q.each(this.model.attributes.elems,function(u){if(u instanceof f){var v=new i({model:u,className:"toolTitle"});v.render();t.append(v.$el)}else{if(u instanceof m){var w=new d({model:u});w.render();t.append(w.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var l=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(t){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===t.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var t=this;var u=new l({model:this.collection.tool_search});u.render();t.$el.append(u.$el);this.collection.each(function(w){if(w instanceof p){var v=new h({model:w});v.render();t.$el.append(v.$el)}else{if(w instanceof f){var x=new i({model:w,className:"toolTitleNoSection"});x.render();t.$el.append(x.$el)}else{if(w instanceof m){var y=new d({model:w});y.render();t.$el.append(y.$el)}}}});t.$el.find("a.tool-link").click(function(x){var w=$(this).attr("class").split(/\s+/)[0],v=t.collection.tools.get(w);t.trigger("tool_link_click",x,v)});return this},handle_search_results:function(){var t=this.collection.tool_search.attributes.results;if(t&&t.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var o=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var e=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new o()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(v,u){v.preventDefault();t.show_tool(u)})},show_tool:function(u){var t=this;u.fetch().done(function(){t.tool_form_view.model=u;t.tool_form_view.render();t.tool_form_view.$el.show();$("#left").width("650px")})}});return{Tool:f,ToolSearch:b,ToolPanel:k,ToolPanelView:s,ToolFormView:o}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(t,a,u){var h=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var d=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new d(this.toJSON())},get_samples:function(){var w=this.get("type"),v=null;if(w==="number"){v=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(w==="select"){v=t.map(this.get("options"),function(x){return x[0]})}}return v},set_value:function(v){this.set("value",v||"")}},{TYPE_DICT:{number:c},create:function(v){var w=d.TYPE_DICT[v.type]||d;return new w(v)}});var c=d.extend({defaults:t.extend({},d.prototype.defaults,{min:null,max:null}),initialize:function(){d.prototype.initialize.call(this);if(this.attributes.min){this.attributes.min=parseInt(this.attributes.min,10)}if(this.attributes.max){this.attributes.max=parseInt(this.attributes.max,10)}},set_value:function(v){this.set("value",parseInt(v,10))}});var g=h.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[]},initialize:function(v){this.attributes.inputs=new Backbone.Collection(t.map(v.inputs,function(w){return d.create(w)}))},urlRoot:galaxy_paths.get("tool_url"),copy:function(w){var x=new g(this.toJSON());if(w){var v=new Backbone.Collection();x.get("inputs").each(function(y){if(y.get_samples()){v.push(y)}});x.set("inputs",v)}return x},apply_search_results:function(v){(t.indexOf(v,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(v,w){this.get("inputs").find(function(x){return x.get("name")===v}).set("value",w)},set_input_values:function(w){var v=this;t.each(t.keys(w),function(x){v.set_input_value(x,w[x])})},run:function(){return this._run()},rerun:function(w,v){return this._run({action:"rerun",target_dataset_id:w.id,regions:v})},get_inputs_dict:function(){var v={};this.get("inputs").each(function(w){v[w.get("name")]=w.get("value")});return v},_run:function(x){var y=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},x);var w=$.Deferred(),v=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(y),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(z){return z!=="pending"}});$.when(v.go()).then(function(z){w.resolve(new u.DatasetCollection().reset(z))});return w}});var n=Backbone.View.extend({});var k=Backbone.Collection.extend({model:g});var o=h.extend({});var r=h.extend({defaults:{elems:[],open:false},clear_search_results:function(){t.each(this.attributes.elems,function(v){v.show()});this.show();this.set("open",false)},apply_search_results:function(w){var x=true,v;t.each(this.attributes.elems,function(y){if(y instanceof o){v=y;v.hide()}else{if(y instanceof g){if(y.apply_search_results(w)){x=false;if(v){v.show()}}}}});if(x){this.hide()}else{this.show();this.set("open",true)}}});var b=h.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var x=this.attributes.query;if(x.length<this.attributes.min_chars_for_search){this.set("results",null);return}var w=x+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var v=this;this.timer=setTimeout(function(){$.get(v.attributes.search_url,{query:w},function(y){v.set("results",y);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});var l=Backbone.Collection.extend({url:"/tools",tools:new k(),parse:function(v){var w=function(z){var y=z.type;if(y==="tool"){return new g(z)}else{if(y==="section"){var x=t.map(z.elems,w);z.elems=x;return new r(z)}else{if(y==="label"){return new o(z)}}}};return t.map(v,w)},initialize:function(v){this.tool_search=v.tool_search;this.tool_search.on("change:results",this.apply_search_results,this);this.on("reset",this.populate_tools,this)},populate_tools:function(){var v=this;v.tools=new k();this.each(function(w){if(w instanceof r){t.each(w.attributes.elems,function(x){if(x instanceof g){v.tools.push(x)}})}else{if(w instanceof g){v.tools.push(w)}}})},clear_search_results:function(){this.each(function(v){if(v instanceof r){v.clear_search_results()}else{v.show()}})},apply_search_results:function(){var w=this.tool_search.attributes.results;if(w===null){this.clear_search_results();return}var v=null;this.each(function(x){if(x instanceof o){v=x;v.hide()}else{if(x instanceof g){if(x.apply_search_results(w)){if(v){v.show()}}}else{v=null;x.apply_search_results(w)}}})}});var p=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var j=p.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var e=p.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.name));return this}});var i=p.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){p.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var v=this.$el.find(".toolSectionBody");t.each(this.model.attributes.elems,function(w){if(w instanceof g){var x=new j({model:w,className:"toolTitle"});x.render();v.append(x.$el)}else{if(w instanceof o){var y=new e({model:w});y.render();v.append(y.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var m=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(v){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===v.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var v=this;var w=new m({model:this.collection.tool_search});w.render();v.$el.append(w.$el);this.collection.each(function(y){if(y instanceof r){var x=new i({model:y});x.render();v.$el.append(x.$el)}else{if(y instanceof g){var z=new j({model:y,className:"toolTitleNoSection"});z.render();v.$el.append(z.$el)}else{if(y instanceof o){var A=new e({model:y});A.render();v.$el.append(A.$el)}}}});v.$el.find("a.tool-link").click(function(z){var y=$(this).attr("class").split(/\s+/)[0],x=v.collection.tools.get(y);v.trigger("tool_link_click",z,x)});return this},handle_search_results:function(){var v=this.collection.tool_search.attributes.results;if(v&&v.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var q=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var f=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new q()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var v=this;this.tool_panel_view.on("tool_link_click",function(x,w){x.preventDefault();v.show_tool(w)})},show_tool:function(w){var v=this;w.fetch().done(function(){v.tool_form_view.model=w;v.tool_form_view.render();v.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:d,IntegerToolParameter:c,Tool:g,ToolSearch:b,ToolPanel:l,ToolPanelView:s,ToolFormView:q}}); \ No newline at end of file diff -r 3f85113b7476767ef1dc76c7f3312b423ff743db -r 2c3f4163da4ef47bb3f04da580e5015961dc0c67 static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -define(["libs/underscore","libs/d3","viz/visualization"],function(g,l,i){var m=Backbone.Model.extend({is_visible:function(q,n){var o=q.getBoundingClientRect(),p=$("svg")[0].getBoundingClientRect();if(o.right<0||o.left>p.right||o.bottom<0||o.top>p.bottom){return false}return true}});var h={drawTicks:function(r,q,v,p,n){var u=r.append("g").selectAll("g").data(q).enter().append("g").selectAll("g").data(v).enter().append("g").attr("class","tick").attr("transform",function(w){return"rotate("+(w.angle*180/Math.PI-90)+")translate("+w.radius+",0)"});var t=[],s=[],o=function(w){return w.angle>Math.PI?"end":null};if(n){t=[0,0,0,-4];s=[4,0,"",".35em"];o=null}else{t=[1,0,4,0];s=[0,4,".35em",""]}u.append("line").attr("x1",t[0]).attr("y1",t[1]).attr("x2",t[2]).attr("y1",t[3]).style("stroke","#000");u.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",o).attr("transform",p).text(function(w){return w.label})},formatNum:function(o,n){if(n===undefined){n=2}var q=null;if(o<1){q=o.toPrecision(n)}else{var p=Math.round(o.toPrecision(n));if(o<1000){q=p}else{if(o<1000000){q=Math.round((p/1000).toPrecision(3)).toFixed(0)+"K"}else{if(o<1000000000){q=Math.round((p/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return q}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(n){this.total_gap=n.total_gap;this.genome=n.genome;this.dataset_arc_height=n.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var o=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-o.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=l.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var n=this;return g.map(tracks_start_radii,function(p){return[p,p+n.dataset_arc_height]})},render:function(){var w=this,q=this.dataset_arc_height,n=w.$el.width(),v=w.$el.height(),s=this.get_circular_tracks(),p=this.get_chord_tracks(),r=this.get_tracks_bounds(),o=l.select(w.$el[0]).append("svg").attr("width",n).attr("height",v).attr("pointer-events","all").append("svg:g").call(l.behavior.zoom().on("zoom",function(){var x=l.event.scale;o.attr("transform","translate("+l.event.translate+") scale("+x+")");if(w.scale!==x){if(w.zoom_drag_timeout){clearTimeout(w.zoom_drag_timeout)}w.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+n/2+","+v/2+")").append("svg:g").attr("class","tracks");this.circular_views=s.map(function(y,z){var x=new d({el:o.append("g")[0],track:y,radius_bounds:r[z],genome:w.genome,total_gap:w.total_gap});x.render();return x});this.chords_views=p.map(function(y){var x=new j({el:o.append("g")[0],track:y,radius_bounds:r[0],genome:w.genome,total_gap:w.total_gap});x.render();return x});var u=this.circular_views[this.circular_views.length-1].radius_bounds[1],t=[u,u+this.label_arc_height];this.label_track_view=new b({el:o.append("g")[0],track:new c(),radius_bounds:t,genome:w.genome,total_gap:w.total_gap});this.label_track_view.render()},add_track:function(t){if(t.get("track_type")==="DiagonalHeatmapTrack"){var p=this.circular_views[0].radius_bounds,s=new j({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:p,genome:this.genome,total_gap:this.total_gap});s.render();this.chords_views.push(s)}else{var r=this.get_tracks_bounds();g.each(this.circular_views,function(u,v){u.update_radius_bounds(r[v])});g.each(this.chords_views,function(u){u.update_radius_bounds(r[0])});var q=this.circular_views.length,n=new d({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:r[q],genome:this.genome,total_gap:this.total_gap});n.render();this.circular_views.push(n);var o=r[r.length-1];o[1]=o[0];this.label_track_view.update_radius_bounds(o)}},remove_track:function(o,q,p){var n=this.circular_views[p.index];this.circular_views.splice(p.index,1);n.$el.remove();var r=this.get_tracks_bounds();g.each(this.circular_views,function(s,t){s.update_radius_bounds(r[t])})}});var k=Backbone.View.extend({tagName:"g",initialize:function(n){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=n.total_gap;this.track=n.track;this.radius_bounds=n.radius_bounds;this.genome=n.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=l.select(this.$el[0])},get_fill_color:function(){var n=this.track.get("config").get_value("block_color");if(!n){n=this.track.get("config").get_value("color")}return n},render:function(){var r=this.parent_elt;if(!r){console.log("no parent elt")}var q=this.chroms_layout,t=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),n=r.selectAll("g").data(q).enter().append("svg:g"),p=n.append("path").attr("d",t).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);p.append("title").text(function(v){return v.data.chrom});var o=this,s=o.track.get("data_manager"),u=(s?s.data_is_ready():true);$.when(u).then(function(){$.when(o._render_data(r)).then(function(){p.style("fill",o.bg_fill);o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(o){this.radius_bounds=o;var n=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",n);this._transition_chrom_data();this._transition_labels()},update_scale:function(q){var p=this.scale;this.scale=q;if(q<=p){return}var o=this,n=new m();this.parent_elt.selectAll("path.chrom-data").filter(function(s,r){return n.is_visible(this)}).each(function(x,t){var w=l.select(this),s=w.attr("chrom"),v=o.genome.get_chrom_region(s),u=o.track.get("data_manager"),r;if(!u.can_get_more_detailed_data(v)){return}r=o.track.get("data_manager").get_more_detailed_data(v,"Coverage",0,q);$.when(r).then(function(A){w.remove();o._update_data_bounds();var z=g.find(o.chroms_layout,function(B){return B.data.chrom===s});var y=o.get_fill_color();o._render_chrom_data(o.parent_elt,z,A).style("stroke",y).style("fill",y)})});return o},_transition_chrom_data:function(){var o=this.track,q=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data"),r=n[0].length;if(r>0){var p=this;$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){var s=g.reject(g.map(t,function(u,v){var w=null,x=p._get_path_function(q[v],u);if(x){w=x(u.data)}return w}),function(u){return u===null});n.each(function(v,u){l.select(this).transition().duration(1000).attr("d",s[u])})})}},_transition_labels:function(){},_update_data_bounds:function(){var n=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<n[0]||this.data_bounds[1]>n[1]){this._transition_chrom_data()}},_render_data:function(q){var p=this,o=this.chroms_layout,n=this.track,r=$.Deferred();$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){p.data_bounds=p.get_data_bounds(t);layout_and_data=g.zip(o,t),chroms_data_layout=g.map(layout_and_data,function(u){var v=u[0],w=u[1];return p._render_chrom_data(q,v,w)});var s=p.get_fill_color();p.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s);r.resolve(q)});return r},_render_chrom_data:function(n,o,p){},_get_path_function:function(o,n){},_chroms_layout:function(){var o=this.genome.get_chroms_info(),q=l.layout.pie().value(function(s){return s.len}).sort(null),r=q(o),n=this.total_gap/o.length,p=g.map(r,function(u,t){var s=u.endAngle-n;u.endAngle=(s>u.startAngle?s:u.startAngle);return u});return p}});var b=k.extend({initialize:function(n){k.prototype.initialize.call(this,n);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.08},_render_data:function(p){var o=this,n=p.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom});n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>o.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").attr("font-weight","bold").text(function(t){return t.data.chrom});var q=function(v){var t=(v.endAngle-v.startAngle)/v.value,u=l.range(0,v.value,25000000).map(function(w,x){return{radius:o.innerRadius,angle:w*t+v.startAngle,label:x===0?0:(x%3?null:o.formatNum(w))}});if(u.length<4){u[u.length-1].label=o.formatNum(Math.round((u[u.length-1].angle-v.startAngle)/t))}return u};var s=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null};var r=g.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>o.min_arc_len});this.drawTicks(this.parent_elt,r,q,s)}});g.extend(b.prototype,h);var f=k.extend({_quantile:function(o,n){o.sort(l.ascending);return l.quantile(o,n)},_render_chrom_data:function(n,q,o){var r=this._get_path_function(q,o);if(!r){return null}var p=n.datum(o.data),s=p.append("path").attr("class","chrom-data").attr("chrom",q.data.chrom).attr("d",r);return s},_get_path_function:function(q,p){if(typeof p==="string"||!p.data||p.data.length===0){return null}var n=l.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var r=l.scale.linear().domain([0,p.data.length]).range([q.startAngle,q.endAngle]);var o=l.svg.line.radial().interpolate("linear").radius(function(s){return n(s[1])}).angle(function(t,s){return r(s)});return l.svg.area.radial().interpolate(o.interpolate()).innerRadius(n(0)).outerRadius(o.radius()).angle(o.angle())},render_labels:function(){var n=this,q=function(){return"rotate(90)"};var p=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),o=g.filter(p,function(s,r){return r%3===0});this.drawTicks(this.parent_elt,o,this._data_bounds_ticks_fn(),q,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var o=this,q=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),p=g.filter(q,function(s,r){return r%3===0}),n=g.flatten(g.map(p,function(r){return o._data_bounds_ticks_fn()(r)}));this.parent_elt.selectAll("g.tick").data(n).transition().attr("transform",function(r){return"rotate("+(r.angle*180/Math.PI-90)+")translate("+r.radius+",0)"})},_data_bounds_ticks_fn:function(){var n=this;visibleChroms=0;return function(o){return[{radius:n.radius_bounds[0],angle:o.startAngle,label:n.formatNum(n.data_bounds[0])},{radius:n.radius_bounds[1],angle:o.startAngle,label:n.formatNum(n.data_bounds[1])}]}},get_data_bounds:function(n){}});g.extend(f.prototype,h);var d=f.extend({get_data_bounds:function(o){var n=g.flatten(g.map(o,function(p){if(p){return g.map(p.data,function(q){return q[1]})}else{return 0}}));return[g.min(n),this._quantile(n,0.98)]}});var j=k.extend({render:function(){var n=this;$.when(n.track.get("data_manager").data_is_ready()).then(function(){$.when(n.track.get("data_manager").get_genome_wide_data(n.genome)).then(function(q){var p=[],o=n.genome.get_chroms_info();g.each(q,function(u,t){var r=o[t].chrom;var s=g.map(u.data,function(w){var v=n._get_region_angle(r,w[1]),x=n._get_region_angle(w[3],w[4]);return{source:{startAngle:v,endAngle:v+0.01},target:{startAngle:x,endAngle:x+0.01}}});p=p.concat(s)});n.parent_elt.append("g").attr("class","chord").selectAll("path").data(p).enter().append("path").style("fill",n.get_fill_color()).attr("d",l.svg.chord().radius(n.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(n){this.radius_bounds=n;this.parent_elt.selectAll("path").transition().attr("d",l.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(p,n){var o=g.find(this.chroms_layout,function(q){return q.data.chrom===p});return o.endAngle-((o.endAngle-o.startAngle)*(o.data.len-n)/o.data.len)}});var e=Backbone.View.extend({initialize:function(){var n=new i.Genome(config.app.genome),o=new i.GenomeVisualization(config.app.viz_config),q=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.1,genome:n,model:o,dataset_arc_height:25});q.render();$("#center .unified-panel-header-inner").append(config.app.viz_config.title+" "+config.app.viz_config.dbkey);var p=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){i.select_datasets(config.root+"visualization/list_current_history_datasets",config.root+"api/datasets",o.get("dbkey"),function(r){o.add_tracks(r)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){show_modal("Saving...","progress");var r=config.app.viz_config;$.ajax({url:config.root+"visualization/save",type:"POST",dataType:"json",data:{id:r.vis_id,title:r.title,dbkey:r.dbkey,type:"trackster",vis_json:JSON.stringify(r)}}).success(function(s){hide_modal();r.vis_id=s.vis_id;r.has_changes=false;window.history.pushState({},"",s.url+window.location.hash)}).error(function(){show_modal("Could Not Save","Could not save visualization. Please try again later.",{Close:hide_modal})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});p.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(p.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/visualization"],function(g,l,i){var m=Backbone.Model.extend({is_visible:function(q,n){var o=q.getBoundingClientRect(),p=$("svg")[0].getBoundingClientRect();if(o.right<0||o.left>p.right||o.bottom<0||o.top>p.bottom){return false}return true}});var h={drawTicks:function(r,q,v,p,n){var u=r.append("g").selectAll("g").data(q).enter().append("g").selectAll("g").data(v).enter().append("g").attr("class","tick").attr("transform",function(w){return"rotate("+(w.angle*180/Math.PI-90)+")translate("+w.radius+",0)"});var t=[],s=[],o=function(w){return w.angle>Math.PI?"end":null};if(n){t=[0,0,0,-4];s=[4,0,"",".35em"];o=null}else{t=[1,0,4,0];s=[0,4,".35em",""]}u.append("line").attr("x1",t[0]).attr("y1",t[1]).attr("x2",t[2]).attr("y1",t[3]).style("stroke","#000");u.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",o).attr("transform",p).text(function(w){return w.label})},formatNum:function(o,n){if(n===undefined){n=2}if(o===null){return null}var q=null;if(o<1){q=o.toPrecision(n)}else{var p=Math.round(o.toPrecision(n));if(o<1000){q=p}else{if(o<1000000){q=Math.round((p/1000).toPrecision(3)).toFixed(0)+"K"}else{if(o<1000000000){q=Math.round((p/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return q}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(n){this.total_gap=n.total_gap;this.genome=n.genome;this.dataset_arc_height=n.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var o=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-o.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=l.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var n=this;return g.map(tracks_start_radii,function(p){return[p,p+n.dataset_arc_height]})},render:function(){var w=this,q=this.dataset_arc_height,n=w.$el.width(),v=w.$el.height(),s=this.get_circular_tracks(),p=this.get_chord_tracks(),r=this.get_tracks_bounds(),o=l.select(w.$el[0]).append("svg").attr("width",n).attr("height",v).attr("pointer-events","all").append("svg:g").call(l.behavior.zoom().on("zoom",function(){var x=l.event.scale;o.attr("transform","translate("+l.event.translate+") scale("+x+")");if(w.scale!==x){if(w.zoom_drag_timeout){clearTimeout(w.zoom_drag_timeout)}w.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+n/2+","+v/2+")").append("svg:g").attr("class","tracks");this.circular_views=s.map(function(y,z){var x=new d({el:o.append("g")[0],track:y,radius_bounds:r[z],genome:w.genome,total_gap:w.total_gap});x.render();return x});this.chords_views=p.map(function(y){var x=new j({el:o.append("g")[0],track:y,radius_bounds:r[0],genome:w.genome,total_gap:w.total_gap});x.render();return x});var u=this.circular_views[this.circular_views.length-1].radius_bounds[1],t=[u,u+this.label_arc_height];this.label_track_view=new b({el:o.append("g")[0],track:new c(),radius_bounds:t,genome:w.genome,total_gap:w.total_gap});this.label_track_view.render()},add_track:function(t){if(t.get("track_type")==="DiagonalHeatmapTrack"){var p=this.circular_views[0].radius_bounds,s=new j({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:p,genome:this.genome,total_gap:this.total_gap});s.render();this.chords_views.push(s)}else{var r=this.get_tracks_bounds();g.each(this.circular_views,function(u,v){u.update_radius_bounds(r[v])});g.each(this.chords_views,function(u){u.update_radius_bounds(r[0])});var q=this.circular_views.length,n=new d({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:r[q],genome:this.genome,total_gap:this.total_gap});n.render();this.circular_views.push(n);var o=r[r.length-1];o[1]=o[0];this.label_track_view.update_radius_bounds(o)}},remove_track:function(o,q,p){var n=this.circular_views[p.index];this.circular_views.splice(p.index,1);n.$el.remove();var r=this.get_tracks_bounds();g.each(this.circular_views,function(s,t){s.update_radius_bounds(r[t])})}});var k=Backbone.View.extend({tagName:"g",initialize:function(n){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=n.total_gap;this.track=n.track;this.radius_bounds=n.radius_bounds;this.genome=n.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=l.select(this.$el[0])},get_fill_color:function(){var n=this.track.get("config").get_value("block_color");if(!n){n=this.track.get("config").get_value("color")}return n},render:function(){var r=this.parent_elt;if(!r){console.log("no parent elt")}var q=this.chroms_layout,t=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),n=r.selectAll("g").data(q).enter().append("svg:g"),p=n.append("path").attr("d",t).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);p.append("title").text(function(v){return v.data.chrom});var o=this,s=o.track.get("data_manager"),u=(s?s.data_is_ready():true);$.when(u).then(function(){$.when(o._render_data(r)).then(function(){p.style("fill",o.bg_fill);o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(o){this.radius_bounds=o;var n=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",n);this._transition_chrom_data();this._transition_labels()},update_scale:function(q){var p=this.scale;this.scale=q;if(q<=p){return}var o=this,n=new m();this.parent_elt.selectAll("path.chrom-data").filter(function(s,r){return n.is_visible(this)}).each(function(x,t){var w=l.select(this),s=w.attr("chrom"),v=o.genome.get_chrom_region(s),u=o.track.get("data_manager"),r;if(!u.can_get_more_detailed_data(v)){return}r=o.track.get("data_manager").get_more_detailed_data(v,"Coverage",0,q);$.when(r).then(function(A){w.remove();o._update_data_bounds();var z=g.find(o.chroms_layout,function(B){return B.data.chrom===s});var y=o.get_fill_color();o._render_chrom_data(o.parent_elt,z,A).style("stroke",y).style("fill",y)})});return o},_transition_chrom_data:function(){var o=this.track,q=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data"),r=n[0].length;if(r>0){var p=this;$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){var s=g.reject(g.map(t,function(u,v){var w=null,x=p._get_path_function(q[v],u);if(x){w=x(u.data)}return w}),function(u){return u===null});n.each(function(v,u){l.select(this).transition().duration(1000).attr("d",s[u])})})}},_transition_labels:function(){},_update_data_bounds:function(){var n=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<n[0]||this.data_bounds[1]>n[1]){this._transition_chrom_data()}},_render_data:function(q){var p=this,o=this.chroms_layout,n=this.track,r=$.Deferred();$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){p.data_bounds=p.get_data_bounds(t);layout_and_data=g.zip(o,t),chroms_data_layout=g.map(layout_and_data,function(u){var v=u[0],w=u[1];return p._render_chrom_data(q,v,w)});var s=p.get_fill_color();p.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s);r.resolve(q)});return r},_render_chrom_data:function(n,o,p){},_get_path_function:function(o,n){},_chroms_layout:function(){var o=this.genome.get_chroms_info(),q=l.layout.pie().value(function(s){return s.len}).sort(null),r=q(o),n=this.total_gap/o.length,p=g.map(r,function(u,t){var s=u.endAngle-n;u.endAngle=(s>u.startAngle?s:u.startAngle);return u});return p}});var b=k.extend({initialize:function(n){k.prototype.initialize.call(this,n);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.08},_render_data:function(p){var o=this,n=p.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom});n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>o.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").attr("font-weight","bold").text(function(t){return t.data.chrom});var q=function(v){var t=(v.endAngle-v.startAngle)/v.value,u=l.range(0,v.value,25000000).map(function(w,x){return{radius:o.innerRadius,angle:w*t+v.startAngle,label:x===0?0:(x%3?null:o.formatNum(w))}});if(u.length<4){u[u.length-1].label=o.formatNum(Math.round((u[u.length-1].angle-v.startAngle)/t))}return u};var s=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null};var r=g.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>o.min_arc_len});this.drawTicks(this.parent_elt,r,q,s)}});g.extend(b.prototype,h);var f=k.extend({_quantile:function(o,n){o.sort(l.ascending);return l.quantile(o,n)},_render_chrom_data:function(n,q,o){var r=this._get_path_function(q,o);if(!r){return null}var p=n.datum(o.data),s=p.append("path").attr("class","chrom-data").attr("chrom",q.data.chrom).attr("d",r);return s},_get_path_function:function(q,p){if(typeof p==="string"||!p.data||p.data.length===0){return null}var n=l.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var r=l.scale.linear().domain([0,p.data.length]).range([q.startAngle,q.endAngle]);var o=l.svg.line.radial().interpolate("linear").radius(function(s){return n(s[1])}).angle(function(t,s){return r(s)});return l.svg.area.radial().interpolate(o.interpolate()).innerRadius(n(0)).outerRadius(o.radius()).angle(o.angle())},render_labels:function(){var n=this,q=function(){return"rotate(90)"};var p=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),o=g.filter(p,function(s,r){return r%3===0});this.drawTicks(this.parent_elt,o,this._data_bounds_ticks_fn(),q,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var o=this,q=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),p=g.filter(q,function(s,r){return r%3===0}),n=g.flatten(g.map(p,function(r){return o._data_bounds_ticks_fn()(r)}));this.parent_elt.selectAll("g.tick").data(n).transition().attr("transform",function(r){return"rotate("+(r.angle*180/Math.PI-90)+")translate("+r.radius+",0)"})},_data_bounds_ticks_fn:function(){var n=this;visibleChroms=0;return function(o){return[{radius:n.radius_bounds[0],angle:o.startAngle,label:n.formatNum(n.data_bounds[0])},{radius:n.radius_bounds[1],angle:o.startAngle,label:n.formatNum(n.data_bounds[1])}]}},get_data_bounds:function(n){}});g.extend(f.prototype,h);var d=f.extend({get_data_bounds:function(o){var n=g.flatten(g.map(o,function(p){if(p){return g.map(p.data,function(q){return q[1]})}else{return 0}}));return[g.min(n),this._quantile(n,0.98)]}});var j=k.extend({render:function(){var n=this;$.when(n.track.get("data_manager").data_is_ready()).then(function(){$.when(n.track.get("data_manager").get_genome_wide_data(n.genome)).then(function(q){var p=[],o=n.genome.get_chroms_info();g.each(q,function(u,t){var r=o[t].chrom;var s=g.map(u.data,function(w){var v=n._get_region_angle(r,w[1]),x=n._get_region_angle(w[3],w[4]);return{source:{startAngle:v,endAngle:v+0.01},target:{startAngle:x,endAngle:x+0.01}}});p=p.concat(s)});n.parent_elt.append("g").attr("class","chord").selectAll("path").data(p).enter().append("path").style("fill",n.get_fill_color()).attr("d",l.svg.chord().radius(n.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(n){this.radius_bounds=n;this.parent_elt.selectAll("path").transition().attr("d",l.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(p,n){var o=g.find(this.chroms_layout,function(q){return q.data.chrom===p});return o.endAngle-((o.endAngle-o.startAngle)*(o.data.len-n)/o.data.len)}});var e=Backbone.View.extend({initialize:function(){var n=new i.Genome(config.app.genome),o=new i.GenomeVisualization(config.app.viz_config),q=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.1,genome:n,model:o,dataset_arc_height:25});q.render();$("#center .unified-panel-header-inner").append(config.app.viz_config.title+" "+config.app.viz_config.dbkey);var p=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){i.select_datasets(config.root+"visualization/list_current_history_datasets",config.root+"api/datasets",o.get("dbkey"),function(r){o.add_tracks(r)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){show_modal("Saving...","progress");var r=config.app.viz_config;$.ajax({url:config.root+"visualization/save",type:"POST",dataType:"json",data:{id:r.vis_id,title:r.title,dbkey:r.dbkey,type:"trackster",vis_json:JSON.stringify(r)}}).success(function(s){hide_modal();r.vis_id=s.vis_id;r.has_changes=false;window.history.pushState({},"",s.url+window.location.hash)}).error(function(){show_modal("Could Not Save","Could not save visualization. Please try again later.",{Close:hide_modal})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});p.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(p.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}}); \ No newline at end of file diff -r 3f85113b7476767ef1dc76c7f3312b423ff743db -r 2c3f4163da4ef47bb3f04da580e5015961dc0c67 static/scripts/packed/viz/trackster.js --- a/static/scripts/packed/viz/trackster.js +++ b/static/scripts/packed/viz/trackster.js @@ -1,1 +1,1 @@ -var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.css","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/jquery-ui-combobox","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.load_file("/static/style/jquery.rating.css");a.load_file("/static/style/history.css");a.load_file("/static/style/autocomplete_tagging.css");a.load_file("/static/style/jquery-ui/smoothness/jquery-ui.css");a.load_file("/static/style/library.css");a.load_file("/static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){show_modal("New Visualization",e.template_view_new(f),{Cancel:function(){window.location=config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val())}});if(config.app.default_dbkey){$("#new-dbkey option[value='"+config.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").combobox({appendTo:$("#overlay"),size:40});$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here?<br><a href="'+config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},config.app.gene_region);this.init_editor();view.editor=true;hide_modal()},init_editor:function(){$("#center .unified-panel-title").text(view.name+" ("+view.dbkey+")");if(config.app.add_dataset){$.ajax({url:config.root+"api/datasets/"+config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}}); \ No newline at end of file +var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.css","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/jquery-ui-combobox","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.load_file("/static/style/jquery.rating.css");a.load_file("/static/style/history.css");a.load_file("/static/style/autocomplete_tagging.css");a.load_file("/static/style/jquery-ui/smoothness/jquery-ui.css");a.load_file("/static/style/library.css");a.load_file("/static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){show_modal("New Visualization",e.template_view_new(f),{Cancel:function(){window.location=config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val())}});if(config.app.default_dbkey){$("#new-dbkey option[value='"+config.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").combobox({appendTo:$("#overlay"),size:40});$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},config.app.gene_region);this.init_editor();view.editor=true;hide_modal()},init_editor:function(){$("#center .unified-panel-title").text(view.name+" ("+view.dbkey+")");if(config.app.add_dataset){$.ajax({url:config.root+"api/datasets/"+config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}}); \ No newline at end of file diff -r 3f85113b7476767ef1dc76c7f3312b423ff743db -r 2c3f4163da4ef47bb3f04da580e5015961dc0c67 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,w,k,t,L,X,i){var p=ab.extend;var m={};var j=function(ac,ad){m[ac.attr("id")]=ad};var l=function(ac,ae,ag,af){ag=".group";var ad={};m[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=m[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=m[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=m[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}m[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);m[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));m[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,n="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",R=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(y.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=o(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var Q=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);j(this.container_div,this);j(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(Q.prototype,q.prototype,y.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){p(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;j(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(config.root+"visualization/list_current_history_datasets",config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(o(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.values[ac.toLowerCase()+"_color"]||this.config.values.n_color}});p(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.id=aj.id;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new O(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: 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ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new w.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:this.id,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new Q(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new X.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new k.ServerStateDeferred({ajax_settings:{url:config.root+"/api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var O=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(O.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){O.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(e.prototype,O.prototype,{update_value:function(){O.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(F.prototype,{set_param_default_value:function(ad,ac){var ae=ab.find(this.params,function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.params,function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.values[ac]!==ad){this.values[ac]=ad;return true}else{return false}},restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(k.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ad=ae.set_param_value(ah.key,ag)||ad}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ac,ag,ae,ad,af){b.call(this,ac,ag,ae,ad,af)};M.prototype.predisplay_actions=function(){};var P=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new w.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw()}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.dataset=new X.Dataset(ae.dataset);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};p(g.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset.id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.tiles_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(n);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;l(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new w.Cache(R);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(N.prototype,q.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,ag=this.view.high,aj=ag-ak,ad=this.view.container.width(),ao=this.view.resolution_px_b,af=this.view.resolution_b_px;if(this.is_overview){ak=this.view.max_low;ag=this.view.max_high;af=(view.max_high-view.max_low)/ad;ao=1/af}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(ak/(af*S)),al,ah,ai=[],an=[];while((ac*S*af)<ag){al=this._get_tile_bounds(ac,af);ah=this.draw_helper(al,af,ao,ap);ai.push(ah);$.when(ah).then(function(aq){an.push(aq)});ac+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();an=ab.filter(an,function(aq){return aq!==null});if(an.length!==0){ae.postdraw_actions(an,ad,ao,am)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ah=ah||function(){ad.request_draw({clear_tile_cache:true})},ae=this.container_div.find(".yaxislabel."+ag);if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".bs-tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,aj.resolution,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,af,ao,ap){if(!ap){ap={}}var ad=ap.force,an=!(ap.data_fetch===false),ai=ap.mode||this.mode,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(ao,al),ah=function(aq){return(aq&&"track" in aq)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,ao)}return aj}if(!an){return null}var ak=function(){var aq=(ab.find(A,function(at){return at===ai})?"Coverage":ai);var ar=ab.map(ag,function(at){return at.data_manager.get_data(al,aq,af,ae.data_url_extra_params)});if(view.reference_track){ar.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return ar};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var aq=ak(),aw=aq,aC;if(view.reference_track){aC=view.reference_track.data_manager.subset_entry(aq.pop(),al)}var ax=[],au=[];ab.each(ag,function(aH,aE){var aG=aH.mode,aF=aw[aE];if(aG==="Auto"){aG=aH.get_mode(aF);aH.update_auto_mode(aG)}ax.push(aG);au.push(aH.get_canvas_height(aF,aG,ao,ar))});var av=ae.view.canvas_manager.new_canvas(),ay=al.get("start"),aD=al.get("end"),at=0,ar=Math.ceil((aD-ay)*ao)+ae.left_offset,aA=ab.max(au),az;av.width=ar;av.height=(ap.height||aA);var aB=av.getContext("2d");aB.translate(ae.left_offset,0);if(ag.length>1){aB.globalAlpha=0.5;aB.globalCompositeOperation="source-over"}ab.each(ag,function(aF,aE){az=aF.draw_tile(aw[aE],aB,ax[aE],af,al,ao,aC)});if(az!==undefined){ae.tile_cache.set_elt(am,az);ae.show_tile(az,ao)}ac.resolve(az)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.LinePainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new M(this,ah,ag,af,ac.data)},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="bigwig"||ac.message||ac.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new k.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda")},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ai-1}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){this.display_modes=A;N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=o(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};p(f.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:q.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new Q(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1;for(var ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(var ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,af.resolution,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};p(B.prototype,q.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:q.prototype.can_draw,draw_helper:function(ae,ad,af,ac){if(af>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ae,ad,af,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(af,al,ag,ad,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ac=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,ad,ac,ae)}});var h=function(ae,ad,af){var ac=this;this.display_modes=A;this.mode="Histogram";N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:k.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};p(h.prototype,q.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ac,ad,ag,ae,af,ah){return this._draw_line_track_tile(ac,ad,ag,ae,af,ah)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var s=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};p(s.prototype,q.prototype,N.prototype,{draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,af,ae,ah);var ag=k.get_random_color(),ac=k.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.set_painter_from_config();ad.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(c.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters;for(var aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(var aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof P){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (t.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,ar,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae,function(aD){return ap.view.get_base_color(aD)});var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new P(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)}});var Z=function(ad,ac,ae){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:k.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};p(Z.prototype,q.prototype,N.prototype,{draw_tile:function(ac,af,ai,ag,ah,aj){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ah,aj)}else{var ae=this.view,ad=new (this.painter)(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai,function(ak){return ae.get_base_color(ak)});ad.draw(af,af.canvas.width,af.canvas.height,aj);return new b(this,ah,ag,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=new (this.painter)(null,null,null,this.prefs,ag);var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(af,ag,ai,ad){N.prototype.postdraw_actions.call(this,af,ag,ai,ad);var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length===0&&this.prefs.show_labels){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ah=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=k.get_random_color(),ac=k.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(ae.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};p(T.prototype,q.prototype,N.prototype,c.prototype);var d={CompositeTrack:f,DrawableGroup:Q,DiagonalHeatmapTrack:s,FeatureTrack:c,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var o=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:Q,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:s,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:o}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(config.root+"visualization/list_current_history_datasets",config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=Backbone.RelationalModel.extend({defaults:{track:null,tool:null,},relations:[{type:Backbone.HasOne,key:"tool",relatedModel:R.Tool}]});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({render:function(){var ae=this;tool=this.model.get("tool"),parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()})},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},state_dict:function(){var ad=this.model.get("tool").get_param_values_dict();ad.visible=this.parent_div.is(":visible");return ad},run_on_dataset:function(){var ad=this.model.get("tool");this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){show_modal(ad.get("name")+" is Running",ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model.get("tool"),aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get("tool").get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".bs-tooltip").removeClass("in");var ax=$(this).siblings(".bs-tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ah,af,ae,ag){this.track=ad;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.resolution=af;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ah,af,ae,ag){b.call(this,ad,ah,af,ae,ag)};M.prototype.predisplay_actions=function(){};var O=function(ag,ao,ah,af,aj,aq,ak,ar,ae,an){b.call(this,ag,ao,ah,af,aj);this.mode=ak;this.all_slotted=ae;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var am=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()});ad.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=new X.Dataset(af.dataset);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.dynamic_tool_div.toggle();if(ad.dynamic_tool_div.is(":visible")){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset.id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q({track:this,tool:ah.tool,tool_state:ah.tool_state}):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ad*S*ag)<ah){am=this._get_tile_bounds(ad,ag);ai=this.draw_helper(am,ag,ap,aq);aj.push(ai);$.when(ai).then(function(ar){ao.push(ar)});ad+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ao=ac.filter(ao,function(ar){return ar!==null});if(ao.length!==0){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".bs-tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,ak.resolution,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ag,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],ag,am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.LinePainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new M(this,ai,ah,ag,ad.data)},draw_tile:function(ad,ae,ai,ag,ah,aj,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(ad,ae){var ag=Math.floor(ad*S*ae),ah=Math.ceil(S*ae),af=(ag+ah<=this.view.max_high?ag+ah:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:ag,end:af})},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get("tool").get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.dataset_type==="bigwig"||ad.message||ad.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(af,ag,ai,ad){var ae=this;ae.normal_postdraw_actions(af,ag,ai,ad);ae.dataset_check_type="converted_datasets_state";ae.data_query_wait=K;var ah=new j.ServerStateDeferred({url:ae.dataset_state_url,url_params:{dataset_id:ae.dataset.id,hda_ldda:ae.dataset.get("hda_ldda")},interval:ae.data_query_wait,success_fn:function(aj){return aj!=="pending"}});$.when(ah.go()).then(function(){ae.data_manager.set("data_type","data")});ae.postdraw_actions=ae.normal_postdraw_actions}}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,ag.resolution,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ae,ag,ad){if(ag>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,af,ae,ag,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(ag,am,ah,ae,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ad=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;ai<ak;ai++){am.fillStyle=this.view.get_base_color(al[ai]);am.fillText(al[ai],Math.floor(ai*an),10)}return new b(this,aj,ae,ad,af)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ah,af,ag,ai){return this._draw_line_track_tile(ad,ae,ah,af,ag,ai)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new b(this,ai,ah,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,at,ag,ak,af){var aq=this,ae=ar.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,at,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.prefs,ap,aC,aA,af,function(aE){return aq.view.get_base_color(aE)});var ax=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ax=aB.draw(ar,ae.width,ae.height,ak,ao);ax.translation=-ah}return new O(aq,ag,at,ae,an.data,ak,ap,an.message,all_slotted,ax)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,aj,ah,ai,ak){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,ai,ak)}else{var af=this.view,ae=new (this.painter)(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj,function(al){return af.get_base_color(al)});ae.draw(ag,ag.canvas.width,ag.canvas.height,ak);return new 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d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r 3f85113b7476767ef1dc76c7f3312b423ff743db -r 2c3f4163da4ef47bb3f04da580e5015961dc0c67 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -4,7 +4,11 @@ <%def name="title()">Galaxy</%def><%def name="javascripts()"> - ${parent.javascripts()} +${parent.javascripts()} + + +${h.templates( "helpers-common-templates", "template-user-quotaMeter-quota", "template-user-quotaMeter-usage" )} +${h.js( "mvc/base-mvc", "mvc/user/user-model", "mvc/user/user-quotameter" )} </%def><%def name="get_user_json()"> @@ -35,10 +39,6 @@ <%def name="late_javascripts()"> ${parent.late_javascripts()} - - -${h.templates( "helpers-common-templates", "template-user-quotaMeter-quota", "template-user-quotaMeter-usage" )} -${h.js( "mvc/base-mvc", "mvc/user/user-model", "mvc/user/user-quotameter" )} <script type="text/javascript"> // start a Galaxy namespace for objects created Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Dataproviders, QA: fix counters in FilteredDataProvider, rewrite BlockDataProvider, remove instance checks from dataset dprovs to prevent circular imports; Add unit tests for line dprovs
by commits-noreply＠bitbucket.org 14 Aug '13

14 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3f85113b7476/ Changeset: 3f85113b7476 User: carlfeberhard Date: 2013-08-14 17:42:25 Summary: Dataproviders, QA: fix counters in FilteredDataProvider, rewrite BlockDataProvider, remove instance checks from dataset dprovs to prevent circular imports; Add unit tests for line dprovs Affected #: 5 files diff -r 009088d5e76fb00794da78dc0ee3cdaa8524b7d8 -r 3f85113b7476767ef1dc76c7f3312b423ff743db lib/galaxy/datatypes/dataproviders/base.py --- a/lib/galaxy/datatypes/dataproviders/base.py +++ b/lib/galaxy/datatypes/dataproviders/base.py @@ -247,17 +247,22 @@ `offset`, begin providing datat, and stop when `num_data_returned` is greater than `offset`. """ + if self.limit != None and self.limit <= 0: + return + yield + parent_gen = super( LimitedOffsetDataProvider, self ).__iter__() for datum in parent_gen: - - if self.limit != None and self.num_data_returned > self.limit: - break + self.num_data_returned -= 1 + #print 'self.num_data_returned:', self.num_data_returned + #print 'self.num_valid_data_read:', self.num_valid_data_read if self.num_valid_data_read > self.offset: + self.num_data_returned += 1 yield datum - else: - # wot a cheezy way of doing this... - self.num_data_returned -= 1 + + if self.limit != None and self.num_data_returned >= self.limit: + break #TODO: skipping lines is inefficient - somehow cache file position/line_num pair and allow provider # to seek to a pos/line and then begin providing lines diff -r 009088d5e76fb00794da78dc0ee3cdaa8524b7d8 -r 3f85113b7476767ef1dc76c7f3312b423ff743db lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -6,19 +6,13 @@ (e.g. parsing genomic regions from their source) """ +from galaxy import eggs + import pkg_resources pkg_resources.require( 'bx-python' ) from bx import seq as bx_seq from bx import wiggle as bx_wig -import galaxy.model -import galaxy.datatypes -import galaxy.datatypes.data - -#TODO: can't import these due to circular ref in model/registry -#import galaxy.datatypes.binary -#import galaxy.datatypes.tabular - import exceptions import base import line @@ -27,8 +21,9 @@ _TODO = """ use bx as much as possible -the use of DatasetInstance seems to create some import problems gff3 hierarchies + +change SamtoolsDataProvider to use pysam """ import logging @@ -50,11 +45,8 @@ """ :param dataset: the Galaxy dataset whose file will be the source :type dataset: model.DatasetInstance - - :raises exceptions.InvalidDataProviderSource: if not a DatsetInstance """ - if not isinstance( dataset, galaxy.model.DatasetInstance ): - raise exceptions.InvalidDataProviderSource( "Data provider can only be used with a DatasetInstance" ) + #precondition: dataset is a galaxy.model.DatasetInstance self.dataset = dataset # this dataset file is obviously the source #TODO: this might be a good place to interface with the object_store... @@ -615,13 +607,7 @@ """ #TODO: into validate_source - #TODO: have to import these here due to circular ref in model/datatypes - import galaxy.datatypes.binary - import galaxy.datatypes.tabular - if( not( isinstance( dataset.datatype, galaxy.datatypes.tabular.Sam ) - or isinstance( dataset.datatype, galaxy.datatypes.binary.Bam ) ) ): - raise exceptions.InvalidDataProviderSource( - 'dataset must be a Sam or Bam datatype: %s' %( str( dataset.datatype ) ) ) + #precondition: dataset.datatype is a tabular.Sam or binary.Bam self.dataset = dataset options_dict = options_dict or {} @@ -661,8 +647,9 @@ validated_flag_list = set([ flag for flag in options_string if flag in self.FLAGS_WO_ARGS ]) # if sam add -S - if( ( isinstance( self.dataset.datatype, galaxy.datatypes.tabular.Sam ) - and ( 'S' not in validated_flag_list ) ) ): + #TODO: not the best test in the world... + if( ( self.dataset.ext == 'sam' ) + and ( 'S' not in validated_flag_list ) ): validated_flag_list.append( 'S' ) if validated_flag_list: diff -r 009088d5e76fb00794da78dc0ee3cdaa8524b7d8 -r 3f85113b7476767ef1dc76c7f3312b423ff743db lib/galaxy/datatypes/dataproviders/line.py --- a/lib/galaxy/datatypes/dataproviders/line.py +++ b/lib/galaxy/datatypes/dataproviders/line.py @@ -28,18 +28,25 @@ """ DEFAULT_COMMENT_CHAR = '#' settings = { - 'string_lines' : 'bool', + 'strip_lines' : 'bool', + 'strip_newlines': 'bool', 'provide_blank' : 'bool', 'comment_char' : 'str', } - def __init__( self, source, strip_lines=True, provide_blank=False, comment_char=DEFAULT_COMMENT_CHAR, **kwargs ): + def __init__( self, source, strip_lines=True, strip_newlines=False, provide_blank=False, + comment_char=DEFAULT_COMMENT_CHAR, **kwargs ): """ :param strip_lines: remove whitespace from the beginning an ending of each line (or not). Optional: defaults to True :type strip_lines: bool + :param strip_newlines: remove newlines only + (only functions when ``strip_lines`` is false) + Optional: defaults to False + :type strip_lines: bool + :param provide_blank: are empty lines considered valid and provided? Optional: defaults to False :type provide_blank: bool @@ -51,6 +58,7 @@ """ super( FilteredLineDataProvider, self ).__init__( source, **kwargs ) self.strip_lines = strip_lines + self.strip_newlines = strip_newlines self.provide_blank = provide_blank self.comment_char = comment_char @@ -62,17 +70,18 @@ :type line: str :returns: a line or `None` """ - line = super( FilteredLineDataProvider, self ).filter( line ) if line != None: - # is this the proper order? + #??: shouldn't it strip newlines regardless, if not why not use on of the base.dprovs if self.strip_lines: line = line.strip() + elif self.strip_newlines: + line = line.strip( '\n' ) if not self.provide_blank and line == '': return None elif line.startswith( self.comment_char ): return None - return line + return super( FilteredLineDataProvider, self ).filter( line ) class RegexLineDataProvider( FilteredLineDataProvider ): @@ -108,6 +117,7 @@ #NOTE: no support for flags def filter( self, line ): + #NOTE: filter_fn will occur BEFORE any matching line = super( RegexLineDataProvider, self ).filter( line ) if line != None and self.compiled_regex_list: line = self.filter_by_regex( line ) @@ -144,16 +154,15 @@ :type block_filter_fn: function """ # composition - not inheritance - #TODO: don't pass any? - line_provider = FilteredLineDataProvider( source ) - super( BlockDataProvider, self ).__init__( line_provider, **kwargs ) + #TODO: not a fan of this: + ( filter_fn, limit, offset ) = ( kwargs.pop( 'filter_fn', None ), + kwargs.pop( 'limit', None ), kwargs.pop( 'offset', 0 ) ) + line_provider = FilteredLineDataProvider( source, **kwargs ) + super( BlockDataProvider, self ).__init__( line_provider, filter_fn=filter_fn, limit=limit, offset=offset ) self.new_block_delim_fn = new_block_delim_fn self.block_filter_fn = block_filter_fn self.init_new_block() - # ...well, this is kinda lame - but prevents returning first empty block - #TODO: maybe better way in iter - self.is_inside_block = False def init_new_block( self ): """ @@ -161,7 +170,6 @@ """ # called in __init__ and after yielding the prev. block self.block_lines = collections.deque([]) - self.block = {} def __iter__( self ): """ @@ -171,8 +179,8 @@ for block in parent_gen: yield block - last_block = self.filter_block( self.assemble_current_block() ) - if last_block != None and self.num_data_returned < self.limit: + last_block = self.handle_last_block() + if last_block != None: self.num_data_returned += 1 yield last_block @@ -186,26 +194,23 @@ :returns: a block or `None` """ line = super( BlockDataProvider, self ).filter( line ) + #HACK + self.num_data_read -= 1 if line == None: return None + block_to_return = None if self.is_new_block( line ): # if we're already in a block, return the prev. block and add the line to a new block - #TODO: maybe better way in iter - if self.is_inside_block: - filtered_block = self.filter_block( self.assemble_current_block() ) + if self.block_lines: + block_to_return = self.assemble_current_block() + block_to_return = self.filter_block( block_to_return ) + self.num_data_read += 1 + self.init_new_block() - self.add_line_to_block( line ) - - # return an assembled block datum if it passed the filter - if filtered_block != None: - return filtered_block - - else: - self.is_inside_block = True self.add_line_to_block( line ) - return None + return block_to_return def is_new_block( self, line ): """ @@ -239,7 +244,6 @@ Called per block (just before providing). """ # empty block_lines and assemble block - # NOTE: we don't want to have mem == 2*data here so - careful return list( ( self.block_lines.popleft() for i in xrange( len( self.block_lines ) ) ) ) def filter_block( self, block ): @@ -251,3 +255,20 @@ if self.block_filter_fn: return self.block_filter_fn( block ) return block + + def handle_last_block( self ): + """ + Handle any blocks remaining after the main loop. + """ + if self.limit != None and self.num_data_returned >= self.limit: + return None + + last_block = self.assemble_current_block() + self.num_data_read += 1 + + last_block = self.filter_block( last_block ) + if last_block != None: + self.num_valid_data_read += 1 + + return last_block + diff -r 009088d5e76fb00794da78dc0ee3cdaa8524b7d8 -r 3f85113b7476767ef1dc76c7f3312b423ff743db test/unit/datatypes/dataproviders/test_base_dataproviders.py --- a/test/unit/datatypes/dataproviders/test_base_dataproviders.py +++ b/test/unit/datatypes/dataproviders/test_base_dataproviders.py @@ -15,8 +15,9 @@ log = utility.set_up_filelogger( __name__ + '.log' ) -utility.add_galaxy_lib_to_path( '/test/unit/datatypes/dataproviders' ) -from galaxy.datatypes import dataproviders +utility.add_galaxy_lib_to_path( 'test/unit/datatypes/dataproviders' ) +from galaxy.datatypes.dataproviders import base, exceptions +from galaxy import eggs class BaseTestCase( unittest.TestCase ): @@ -53,9 +54,12 @@ log.debug( 'file contents:\n%s', contents ) return contents + def parses_default_content_as( self ): + return [ 'One\n', 'Two\n', 'Three\n' ] + class Test_BaseDataProvider( BaseTestCase ): - provider_class = dataproviders.base.DataProvider + provider_class = base.DataProvider def contents_provider_and_data( self, filename=None, contents=None, source=None, *provider_args, **provider_kwargs ): @@ -74,38 +78,38 @@ return ( contents, provider, data ) def test_iterators( self ): - source = ( x for x in xrange( 1, 10 ) ) + source = ( str( x ) for x in xrange( 1, 10 ) ) provider = self.provider_class( source ) data = list( provider ) log.debug( 'data: %s', str( data ) ) - self.assertEqual( data, [ x for x in xrange( 1, 10 ) ] ) + self.assertEqual( data, [ str( x ) for x in xrange( 1, 10 ) ] ) - source = [ x for x in xrange( 1, 10 ) ] + source = ( str( x ) for x in xrange( 1, 10 ) ) provider = self.provider_class( source ) data = list( provider ) log.debug( 'data: %s', str( data ) ) - self.assertEqual( data, [ x for x in xrange( 1, 10 ) ] ) + self.assertEqual( data, [ str( x ) for x in xrange( 1, 10 ) ] ) - source = ( x for x in xrange( 1, 10 ) ) + source = ( str( x ) for x in xrange( 1, 10 ) ) provider = self.provider_class( source ) data = list( provider ) log.debug( 'data: %s', str( data ) ) - self.assertEqual( data, [ x for x in xrange( 1, 10 ) ] ) + self.assertEqual( data, [ str( x ) for x in xrange( 1, 10 ) ] ) def test_validate_source( self ): """validate_source should throw an error if the source doesn't have attr '__iter__' """ def non_iterator_dprov( source ): return self.provider_class( source ) - self.assertRaises( dataproviders.exceptions.InvalidDataProviderSource, + self.assertRaises( exceptions.InvalidDataProviderSource, non_iterator_dprov, 'one two three' ) - self.assertRaises( dataproviders.exceptions.InvalidDataProviderSource, + self.assertRaises( exceptions.InvalidDataProviderSource, non_iterator_dprov, 40 ) def test_writemethods( self ): """should throw an error if any write methods are called """ - source = ( x for x in xrange( 1, 10 ) ) + source = ( str( x ) for x in xrange( 1, 10 ) ) provider = self.provider_class( source ) # should throw error def call_method( provider, method_name, *args ): @@ -118,11 +122,11 @@ def test_readlines( self ): """readlines should return all the data in list form """ - source = ( x for x in xrange( 1, 10 ) ) + source = ( str( x ) for x in xrange( 1, 10 ) ) provider = self.provider_class( source ) data = provider.readlines() log.debug( 'data: %s', str( data ) ) - self.assertEqual( data, [ x for x in xrange( 1, 10 ) ] ) + self.assertEqual( data, [ str( x ) for x in xrange( 1, 10 ) ] ) def test_stringio( self ): """should work with StringIO @@ -137,21 +141,21 @@ data = list( provider ) log.debug( 'data: %s', str( data ) ) # provider should call close on file - self.assertEqual( ''.join( data ), contents ) + self.assertEqual( data, self.parses_default_content_as() ) self.assertTrue( source.closed ) def test_file( self ): """should work with files """ ( contents, provider, data ) = self.contents_provider_and_data() - self.assertEqual( ''.join( data ), contents ) + self.assertEqual( data, self.parses_default_content_as() ) # provider should call close on file self.assertTrue( isinstance( provider.source, file ) ) self.assertTrue( provider.source.closed ) class Test_FilteredDataProvider( Test_BaseDataProvider ): - provider_class = dataproviders.base.FilteredDataProvider + provider_class = base.FilteredDataProvider def assertCounters( self, provider, read, valid, returned ): self.assertEqual( provider.num_data_read, read ) @@ -177,13 +181,13 @@ class Test_LimitedOffsetDataProvider( Test_FilteredDataProvider ): - provider_class = dataproviders.base.LimitedOffsetDataProvider + provider_class = base.LimitedOffsetDataProvider def test_offset_1( self ): """when offset is 1, should skip first """ ( contents, provider, data ) = self.contents_provider_and_data( offset=1 ) - self.assertEqual( data, [ 'Two\n', 'Three\n' ] ) + self.assertEqual( data, self.parses_default_content_as()[1:] ) self.assertCounters( provider, 3, 3, 2 ) def test_offset_all( self ): @@ -197,29 +201,28 @@ """when offset is 0, should return all """ ( contents, provider, data ) = self.contents_provider_and_data( offset=0 ) - self.assertEqual( ''.join( data ), contents ) + self.assertEqual( data, self.parses_default_content_as() ) self.assertCounters( provider, 3, 3, 3 ) def test_offset_negative( self ): """when offset is negative, should return all """ ( contents, provider, data ) = self.contents_provider_and_data( offset=-1 ) - self.assertEqual( ''.join( data ), contents ) + self.assertEqual( data, self.parses_default_content_as() ) self.assertCounters( provider, 3, 3, 3 ) def test_limit_1( self ): """when limit is one, should return first """ ( contents, provider, data ) = self.contents_provider_and_data( limit=1 ) - self.assertEqual( data, [ 'One\n' ] ) - #TODO: currently reads 2 in all counters before ending - #self.assertCounters( provider, 1, 1, 1 ) + self.assertEqual( data, self.parses_default_content_as()[:1] ) + self.assertCounters( provider, 1, 1, 1 ) def test_limit_all( self ): """when limit >= num lines, should return all """ ( contents, provider, data ) = self.contents_provider_and_data( limit=4 ) - self.assertEqual( ''.join( data ), contents ) + self.assertEqual( data, self.parses_default_content_as() ) self.assertCounters( provider, 3, 3, 3 ) def test_limit_zero( self ): @@ -227,14 +230,13 @@ """ ( contents, provider, data ) = self.contents_provider_and_data( limit=0 ) self.assertEqual( data, [] ) - #TODO: currently reads 1 before ending - self.assertCounters( provider, 3, 0, 0 ) + self.assertCounters( provider, 0, 0, 0 ) def test_limit_zero( self ): """when limit is None, should return all """ ( contents, provider, data ) = self.contents_provider_and_data( limit=None ) - self.assertEqual( ''.join( data ), contents ) + self.assertEqual( data, self.parses_default_content_as() ) self.assertCounters( provider, 3, 3, 3 ) #TODO: somehow re-use tmpfile here @@ -243,17 +245,18 @@ ( contents, provider, data ) = self.contents_provider_and_data( limit=limit, offset=offset ) self.assertEqual( data, data_should_be ) #self.assertCounters( provider, read, valid, returned ) + result_data = self.parses_default_content_as() test_data = [ ( 0, 0, [], 0, 0, 0 ), - ( 1, 0, [ 'One\n' ], 1, 1, 1 ), - ( 2, 0, [ 'One\n', 'Two\n' ], 2, 2, 2 ), - ( 3, 0, [ 'One\n', 'Two\n', 'Three\n' ], 3, 3, 3 ), - ( 1, 1, [ 'Two\n' ], 1, 1, 1 ), - ( 2, 1, [ 'Two\n', 'Three\n' ], 2, 2, 2 ), - ( 3, 1, [ 'Two\n', 'Three\n' ], 2, 2, 2 ), - ( 1, 2, [ 'Three\n' ], 1, 1, 1 ), - ( 2, 2, [ 'Three\n' ], 1, 1, 1 ), - ( 3, 2, [ 'Three\n' ], 1, 1, 1 ), + ( 1, 0, self.parses_default_content_as()[:1], 1, 1, 1 ), + ( 2, 0, self.parses_default_content_as()[:2], 2, 2, 2 ), + ( 3, 0, self.parses_default_content_as()[:3], 3, 3, 3 ), + ( 1, 1, self.parses_default_content_as()[1:2], 1, 1, 1 ), + ( 2, 1, self.parses_default_content_as()[1:3], 2, 2, 2 ), + ( 3, 1, self.parses_default_content_as()[1:3], 2, 2, 2 ), + ( 1, 2, self.parses_default_content_as()[2:3], 1, 1, 1 ), + ( 2, 2, self.parses_default_content_as()[2:3], 1, 1, 1 ), + ( 3, 2, self.parses_default_content_as()[2:3], 1, 1, 1 ), ] for test in test_data: log.debug( 'limit_offset_combo: %s', ', '.join([ str( e ) for e in test ]) ) @@ -269,14 +272,15 @@ limit=limit, offset=offset, filter_fn=only_ts ) self.assertEqual( data, data_should_be ) #self.assertCounters( provider, read, valid, returned ) + result_data = [ c for c in self.parses_default_content_as() if c.lower().startswith( 't' ) ] test_data = [ ( 0, 0, [], 0, 0, 0 ), - ( 1, 0, [ 'Two\n' ], 1, 1, 1 ), - ( 2, 0, [ 'Two\n', 'Three\n' ], 2, 2, 2 ), - ( 3, 0, [ 'Two\n', 'Three\n' ], 2, 2, 2 ), - ( 1, 1, [ 'Three\n' ], 1, 1, 1 ), - ( 2, 1, [ 'Three\n' ], 1, 1, 1 ), - ( 1, 2, [], 0, 0, 0 ), + ( 1, 0, result_data[:1], 1, 1, 1 ), + ( 2, 0, result_data[:2], 2, 2, 2 ), + ( 3, 0, result_data[:3], 2, 2, 2 ), + ( 1, 1, result_data[1:2], 1, 1, 1 ), + ( 2, 1, result_data[1:3], 1, 1, 1 ), + ( 1, 2, result_data[2:3], 0, 0, 0 ), ] for test in test_data: log.debug( 'limit_offset_combo: %s', ', '.join([ str( e ) for e in test ]) ) @@ -284,7 +288,7 @@ class Test_MultiSourceDataProvider( BaseTestCase ): - provider_class = dataproviders.base.MultiSourceDataProvider + provider_class = base.MultiSourceDataProvider def contents_and_tmpfile( self, contents=None ): #TODO: hmmmm... @@ -355,9 +359,9 @@ def no_youtube( string ): return None if ( 'youtu.be' in string ) else string source_list = [ - dataproviders.base.LimitedOffsetDataProvider( source_list[0], filter_fn=no_Fs, limit=2, offset=1 ), - dataproviders.base.LimitedOffsetDataProvider( source_list[1], limit=1, offset=3 ), - dataproviders.base.FilteredDataProvider( source_list[2], filter_fn=no_youtube ), + base.LimitedOffsetDataProvider( source_list[0], filter_fn=no_Fs, limit=2, offset=1 ), + base.LimitedOffsetDataProvider( source_list[1], limit=1, offset=3 ), + base.FilteredDataProvider( source_list[2], filter_fn=no_youtube ), ] provider = self.provider_class( source_list ) log.debug( 'provider: %s', provider ) diff -r 009088d5e76fb00794da78dc0ee3cdaa8524b7d8 -r 3f85113b7476767ef1dc76c7f3312b423ff743db test/unit/datatypes/dataproviders/test_line_dataproviders.py --- /dev/null +++ b/test/unit/datatypes/dataproviders/test_line_dataproviders.py @@ -0,0 +1,298 @@ +""" +Unit tests for base DataProviders. +.. seealso:: galaxy.datatypes.dataproviders.base +""" +# currently because of dataproviders.dataset importing galaxy.model this doesn't work +#TODO: fix imports there after dist and retry + +#TODO: fix off by ones in FilteredDataProvider counters + +import unittest +import StringIO + +import tempfilecache +import utility + +import test_base_dataproviders + +log = utility.set_up_filelogger( __name__ + '.log' ) + +utility.add_galaxy_lib_to_path( 'test/unit/datatypes/dataproviders' ) +from galaxy import eggs +from galaxy.datatypes.dataproviders import line + +_TODO = """ +TestCase hierarchy is a bit of mess here. +""" + + +class Test_FilteredLineDataProvider( test_base_dataproviders.Test_FilteredDataProvider ): + provider_class = line.FilteredLineDataProvider + default_file_contents = """ + # this should be stripped out + One + # as should blank lines + + # preceding/trailing whitespace too + Two + Three + """ + + def parses_default_content_as( self ): + return [ 'One', 'Two', 'Three' ] + + def test_counters( self ): + """should count: lines read, lines that passed the filter, lines returned + """ + ( contents, provider, data ) = self.contents_provider_and_data() + self.assertCounters( provider, 7, 3, 3 ) + + def test_filter_fn( self ): + """should filter out lines using filter_fn and set counters properly + based on filter + """ + def filter_ts( string ): + if string.lower().startswith( 't' ): + return None + return string + ( contents, provider, data ) = self.contents_provider_and_data( filter_fn=filter_ts ) + self.assertCounters( provider, 7, 1, 1 ) + + def test_limit_with_offset( self ): + def limit_offset_combo( limit, offset, data_should_be, read, valid, returned ): + ( contents, provider, data ) = self.contents_provider_and_data( limit=limit, offset=offset ) + self.assertEqual( data, data_should_be ) + #self.assertCounters( provider, read, valid, returned ) + result_data = self.parses_default_content_as() + test_data = [ + ( 0, 0, [], 0, 0, 0 ), + ( 1, 0, self.parses_default_content_as()[:1], 1, 1, 1 ), + ( 2, 0, self.parses_default_content_as()[:2], 2, 2, 2 ), + ( 3, 0, self.parses_default_content_as()[:3], 3, 3, 3 ), + ( 1, 1, self.parses_default_content_as()[1:2], 1, 1, 1 ), + ( 2, 1, self.parses_default_content_as()[1:3], 2, 2, 2 ), + ( 3, 1, self.parses_default_content_as()[1:3], 2, 2, 2 ), + ( 1, 2, self.parses_default_content_as()[2:3], 1, 1, 1 ), + ( 2, 2, self.parses_default_content_as()[2:3], 1, 1, 1 ), + ( 3, 2, self.parses_default_content_as()[2:3], 1, 1, 1 ), + ] + for test in test_data: + log.debug( 'limit_offset_combo: %s', ', '.join([ str( e ) for e in test ]) ) + limit_offset_combo( *test ) + + def test_provide_blank( self ): + """should return blank lines if ``provide_blank`` is true. + """ + ( contents, provider, data ) = self.contents_provider_and_data( provide_blank=True ) + self.assertEqual( data, [ 'One', '', 'Two', 'Three' ] ) + self.assertCounters( provider, 7, 4, 4 ) + + def test_strip_lines( self ): + """should return unstripped lines if ``strip_lines`` is false. + """ + ( contents, provider, data ) = self.contents_provider_and_data( strip_lines=False ) + self.assertEqual( data, ['One\n', '\n', ' Two\n', 'Three\n'] ) + self.assertCounters( provider, 7, 4, 4 ) + + def test_comment_char( self ): + """should return unstripped lines if ``strip_lines`` is false. + """ + ( contents, provider, data ) = self.contents_provider_and_data( comment_char='T' ) + self.assertEqual( data, [ '# this should be stripped out', 'One', + '# as should blank lines', '# preceding/trailing whitespace too' ] ) + self.assertCounters( provider, 7, 4, 4 ) + + +class Test_RegexLineDataProvider( Test_FilteredLineDataProvider ): + provider_class = line.RegexLineDataProvider + default_file_contents = """ + # this should be stripped out + One + # as should blank lines + + # preceding/trailing whitespace too + Two + Three + """ + + def test_regex( self ): + """should return lines matching regex (AFTER strip, comments, blanks). + """ + ( contents, provider, data ) = self.contents_provider_and_data( regex_list=[ r'^O' ] ) + self.assertEqual( data, [ 'One' ] ) + self.assertCounters( provider, 7, 1, 1 ) + + def test_regex_list( self ): + """should return regex matches using more than one regex by ORing them. + """ + ( contents, provider, data ) = self.contents_provider_and_data( regex_list=[ r'^O', r'T' ] ) + self.assertEqual( data, [ 'One', 'Two', 'Three' ] ) + self.assertCounters( provider, 7, 3, 3 ) + + def test_inverse( self ): + """should return inverse matches when ``invert`` is true. + """ + ( contents, provider, data ) = self.contents_provider_and_data( regex_list=[ r'^O' ], invert=True ) + self.assertEqual( data, [ 'Two', 'Three' ] ) + self.assertCounters( provider, 7, 2, 2 ) + + def test_regex_no_match( self ): + """should return empty if no regex matches. + """ + ( contents, provider, data ) = self.contents_provider_and_data( regex_list=[ r'^Z' ] ) + self.assertEqual( data, [] ) + self.assertCounters( provider, 7, 0, 0 ) + + def test_regex_w_limit_offset( self ): + """regex should play well with limit and offset + """ + ( contents, provider, data ) = self.contents_provider_and_data( regex_list=[ r'^T' ], limit=1 ) + self.assertEqual( data, [ 'Two' ] ) + #TODO: once again, valid data, returned data is off + self.assertCounters( provider, 6, 1, 1 ) + + ( contents, provider, data ) = self.contents_provider_and_data( regex_list=[ r'^T' ], limit=1, offset=1 ) + self.assertEqual( data, [ 'Three' ] ) + self.assertCounters( provider, 7, 2, 1 ) + + +class Test_BlockDataProvider( test_base_dataproviders.Test_FilteredDataProvider ): + provider_class = line.BlockDataProvider + default_file_contents = """ + One + ABCD + Two + ABCD + EFGH + Three + """ + + def parses_default_content_as( self ): + return [ ['One'], ['ABCD'], ['Two'], ['ABCD'], ['EFGH'], ['Three'] ] + + #TODO: well, this is ham-handed... + def test_stringio( self ): pass + def test_iterators( self ): pass + def test_readlines( self ): pass + + def test_file( self ): + """should work with files + """ + ( contents, provider, data ) = self.contents_provider_and_data() + self.assertEqual( data, self.parses_default_content_as() ) + self.assertTrue( isinstance( provider.source, line.FilteredLineDataProvider ) ) + self.assertTrue( isinstance( provider.source.source, file ) ) + # provider should call close on file + self.assertTrue( provider.source.source.closed ) + + def test_counters( self ): + """should count: lines read, lines that passed the filter, lines returned + """ + ( contents, provider, data ) = self.contents_provider_and_data() + self.assertCounters( provider, 6, 6, 6 ) + + def test_filter_fn( self ): + """should filter out lines using filter_fn and set counters properly + based on filter + """ + def filter_ts( string ): + if string.lower().startswith( 't' ): + return None + return string + ( contents, provider, data ) = self.contents_provider_and_data( filter_fn=filter_ts ) + # no block fns here, so will parse as lines + self.assertEqual( data, [ ['One'], ['ABCD'], ['ABCD'], ['EFGH'] ] ) + self.assertCounters( provider, 4, 4, 4 ) + + def test_new_block_delim_fn( self ): + """should return blocks based on ``new_block_delim_fn`` + """ + def is_not_indented( line ): + strip_diff = len( line ) - len( line.lstrip() ) + return ( strip_diff == 0 ) + # in order to use indentation as a delimiter, we need to strip the newlines only + ( contents, provider, data ) = self.contents_provider_and_data( strip_lines=False, strip_newlines=True, + new_block_delim_fn=is_not_indented ) + self.assertEqual( data, [[ 'One', ' ABCD' ], [ 'Two', ' ABCD', ' EFGH' ], [ 'Three' ]] ) + self.assertCounters( provider, 3, 3, 3 ) + + def test_block_filter_fn( self ): + """should return blocks only blocks that pass ``block_filter_fn`` + """ + def is_not_indented( line ): + strip_diff = len( line ) - len( line.lstrip() ) + return ( strip_diff == 0 ) + #def empty_block( block ): + # if len( block ) <= 1: + # return None + # return block + def no_tw( block ): + if block[0].startswith( 'Tw' ): + return None + return block + ( contents, provider, data ) = self.contents_provider_and_data( strip_lines=False, strip_newlines=True, + new_block_delim_fn=is_not_indented, block_filter_fn=no_tw ) + self.assertEqual( data, [[ 'One', ' ABCD' ], [ 'Three' ]] ) + self.assertCounters( provider, 3, 2, 2 ) + + def test_hack_block_filter_fn( self ): + """should allow other aggregating/mod use in filter_fn + + Although, it would be better to subclass and override assemble_current_block + """ + def is_not_indented( line ): + strip_diff = len( line ) - len( line.lstrip() ) + return ( strip_diff == 0 ) + def empty_block( block ): + if len( block ) <= 1: + return None + return { 'header': block[0].strip(), 'data': [ b.strip() for b in block[1:] if b.strip() ] } + ( contents, provider, data ) = self.contents_provider_and_data( + strip_lines=False, strip_newlines=True, + new_block_delim_fn=is_not_indented, block_filter_fn=empty_block ) + self.assertEqual( data, [ { 'header': 'One', 'data': [ 'ABCD' ]}, + { 'header': 'Two', 'data': [ 'ABCD', 'EFGH' ]} ]) + self.assertCounters( provider, 3, 2, 2 ) + + def test_block_filter_fn_w_limit_offset( self ): + """should allow both block fns and limit, offset + """ + def is_not_indented( line ): + strip_diff = len( line ) - len( line.lstrip() ) + return ( strip_diff == 0 ) + def empty_block( block ): + if len( block ) <= 1: + return None + return block + ( contents, provider, data ) = self.contents_provider_and_data( strip_lines=False, strip_newlines=True, + new_block_delim_fn=is_not_indented, block_filter_fn=empty_block, limit=1 ) + self.assertEqual( data, [[ 'One', ' ABCD' ]] ) + self.assertCounters( provider, 1, 1, 1 ) + ( contents, provider, data ) = self.contents_provider_and_data( strip_lines=False, strip_newlines=True, + new_block_delim_fn=is_not_indented, block_filter_fn=empty_block, limit=2, offset=1 ) + self.assertEqual( data, [[ 'Two', ' ABCD', ' EFGH' ]] ) + self.assertCounters( provider, 3, 2, 1 ) + + def test_simple_example( self ): + """ + """ + file_contents = """ + >One + ABCD + + # this comment (and the blank line above) won't be included + >Two + ABCD + EFGH + """ + def fasta_header( line ): + return line.startswith( '>' ) + def id_seq( block ): + return { 'id': block[0][1:], 'seq': ( ''.join( block[1:] ) ) } + ( contents, provider, data ) = self.contents_provider_and_data( contents=file_contents, + new_block_delim_fn=fasta_header, block_filter_fn=id_seq ) + self.assertEqual( data, [{ 'id': 'One', 'seq': 'ABCD' }, { 'id': 'Two', 'seq': 'ABCDEFGH' }] ) + self.assertCounters( provider, 2, 2, 2 ) + +if __name__ == '__main__': + unittest.main() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 12 Aug '13

12 Aug '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1e7ce74fe941/ Changeset: 1e7ce74fe941 Branch: next-stable User: natefoo Date: 2013-08-12 17:53:34 Summary: Close next-stable branch for merge to stable. Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/1ae95b3aa98d/ Changeset: 1ae95b3aa98d Branch: stable User: natefoo Date: 2013-08-12 17:54:39 Summary: Merge next-stable to stable. Affected #: 340 files diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 .coveragerc --- /dev/null +++ b/.coveragerc @@ -0,0 +1,3 @@ +[run] +branch = True +include = lib/galaxy/* diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 .hgignore --- a/.hgignore +++ b/.hgignore @@ -60,7 +60,7 @@ job_conf.xml data_manager_conf.xml shed_data_manager_conf.xml -visualizations_conf.xml +config/visualizations/*.xml static/welcome.html.* static/welcome.html @@ -82,6 +82,9 @@ # Test output run_functional_tests.html test/tool_shed/tmp/* +.coverage +htmlcov +run_unit_tests.html # Project files *.kpf diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 README.txt --- a/README.txt +++ b/README.txt @@ -7,7 +7,7 @@ HOW TO START ============ -Galaxy requires Python 2.5, 2.6 or 2.7. To check your python version, run: +Galaxy requires Python 2.6 or 2.7. To check your python version, run: % python -V Python 2.7.3 diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -65,6 +65,7 @@ " SAMPLES=" +tool_conf.xml.sample datatypes_conf.xml.sample universe_wsgi.ini.sample tool_data_table_conf.xml.sample diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 config/visualizations/circster.xml.sample --- /dev/null +++ b/config/visualizations/circster.xml.sample @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="circster"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="hda">hda_ldda</to_param> + </data_source> + <data_source> + <model_class>LibraryDatasetDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="ldda">hda_ldda</to_param> + </data_source> + </data_sources> + <params> + <param type="visualization">id</param> + <param type="hda_or_ldda">dataset_id</param> + <param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier> + <param type="dbkey">dbkey</param> + </params> + <template>circster.mako</template> + <render_location>_top</render_location> +</visualization> diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 config/visualizations/phyloviz.xml.sample --- /dev/null +++ b/config/visualizations/phyloviz.xml.sample @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="phyloviz"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Newick</test> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Nexus</test> + <to_param param_attr="id">dataset_id</to_param> + </data_source> + </data_sources> + <params> + <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> + <param type="integer" default="0">tree_index</param> + </params> + <template>phyloviz.mako</template> + <render_location>_top</render_location> +</visualization> diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 config/visualizations/scatterplot.xml.sample --- /dev/null +++ b/config/visualizations/scatterplot.xml.sample @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="scatterplot"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test> + <to_param param_attr="id">dataset_id</to_param> + </data_source> + </data_sources> + <params> + <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> + </params> + <template>scatterplot.mako</template> +</visualization> diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 config/visualizations/sweepster.xml.sample --- /dev/null +++ b/config/visualizations/sweepster.xml.sample @@ -0,0 +1,25 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="sweepster"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="hda">hda_ldda</to_param> + </data_source> + <data_source> + <model_class>LibraryDatasetDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="ldda">hda_ldda</to_param> + </data_source> + </data_sources> + <params> + <param type="visualization" var_name_in_template="viz">visualization</param> + <param type="hda_or_ldda" var_name_in_template="dataset">dataset_id</param> + <param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier> + </params> + <template>sweepster.mako</template> + <render_location>_top</render_location> +</visualization> diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 config/visualizations/trackster.xml.sample --- /dev/null +++ b/config/visualizations/trackster.xml.sample @@ -0,0 +1,29 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="trackster"> +  + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="hda">hda_ldda</to_param> + <to_param param_attr="dbkey">dbkey</to_param> + </data_source> + <data_source> + <model_class>LibraryDatasetDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="ldda">hda_ldda</to_param> + </data_source> + </data_sources> + <params> + <param type="visualization">id</param> + <param type="dataset">dataset_id</param> + <param type="genome_region">genome_region</param> + <param type="dbkey">dbkey</param> + </params> + <template_root>tracks</template_root> + <template>browser.mako</template> + <render_location>_top</render_location> +</visualization> diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 config/visualizations/visualization.dtd --- /dev/null +++ b/config/visualizations/visualization.dtd @@ -0,0 +1,132 @@ + + + +<!ELEMENT visualization (data_sources*,params*,template_root*,template,link_text*,render_location*)> + +<!ATTLIST visualization + name CDATA #REQUIRED +> + +<!ELEMENT data_sources (data_source*)> + + <!ELEMENT data_source (model_class,(test|to_param)*)> + <!ELEMENT model_class (#PCDATA)> +  + <!ELEMENT test (#PCDATA)> +  + <!ATTLIST test + type CDATA #IMPLIED + test_attr CDATA #IMPLIED + result_type CDATA #IMPLIED + > + + <!ELEMENT to_param (#PCDATA)> +  + <!ATTLIST to_param + param_attr CDATA #IMPLIED + assign CDATA #IMPLIED + > + +<!ELEMENT params ((param|param_modifier)*)> + + <!ELEMENT param (#PCDATA)> +  + <!ATTLIST param + type CDATA #IMPLIED + default CDATA #IMPLIED + required CDATA #IMPLIED + csv CDATA #IMPLIED + constrain_to CDATA #IMPLIED + var_name_in_template CDATA #IMPLIED + > +  + <!ELEMENT param_modifier (#PCDATA)> + <!ATTLIST param_modifier + modifies CDATA #REQUIRED + type CDATA #IMPLIED + default CDATA #IMPLIED + required CDATA #IMPLIED + csv CDATA #IMPLIED + constrain_to CDATA #IMPLIED + var_name_in_template CDATA #IMPLIED + > + + +<!ELEMENT template_root (#PCDATA)> + +<!ELEMENT template (#PCDATA)> + +<!ELEMENT link_text (#PCDATA)> + + +<!ELEMENT render_location (#PCDATA)> diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -19,7 +19,7 @@ mercurial = 2.2.3 MySQL_python = 1.2.3c1 numpy = 1.6.0 -pbs_python = 4.1.0 +pbs_python = 4.3.5 psycopg2 = 2.0.13 pycrypto = 2.5 pysam = 0.4.2 diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -54,7 +54,15 @@ <param id="shell_hostname">foo.example.org</param><param id="Job_Execution_Time">24:00:00</param></destination> - <destination id="condor" runner="condor"/> + <destination id="condor" runner="condor"> +  + <param id="request_cpus">8</param> + </destination></destinations><tools> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> bedtools genomecov -bg -split -ibam $input -g $chromInfo diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml @@ -1,5 +1,9 @@ <tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.0" hidden="true"> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> ## Remove comments and sort by chromosome. grep -v '^#' $input | sort -k1,1 | diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml @@ -1,6 +1,10 @@ <tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage"> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> ## Remove comments and sort by chromosome. diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py @@ -11,15 +11,13 @@ from __future__ import division -import sys, fileinput, optparse +import optparse from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -from galaxy.visualization.tracks.summary import * -from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed +eggs.require( "bx-python" ) from bx.interval_index_file import Indexes def main(): - + # Read options, args. parser = optparse.OptionParser() parser.add_option( '-c', '--chr-col', type='int', dest='chrom_col', default=1 ) @@ -27,12 +25,12 @@ parser.add_option( '-e', '--end-col', type='int', dest='end_col', default=3 ) (options, args) = parser.parse_args() input_fname, output_fname = args - + # Make column indices 0-based. options.chrom_col -= 1 options.start_col -= 1 options.end_col -= 1 - + # Do conversion. index = Indexes() offset = 0 @@ -46,9 +44,9 @@ chrom_end = int( feature[ options.end_col ] ) index.add( chrom, chrom_start, chrom_end, offset ) offset += len(line) - + index.write( open(output_fname, "w") ) -if __name__ == "__main__": +if __name__ == "__main__": main() - \ No newline at end of file + diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py --- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py +++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py @@ -8,20 +8,18 @@ from __future__ import division -import sys, fileinput, optparse +import optparse from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -from galaxy.visualization.tracks.summary import * -from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed +eggs.require( "bx-python" ) from bx.interval_index_file import Indexes def main(): - + # Read options, args. parser = optparse.OptionParser() (options, args) = parser.parse_args() input_fname, output_fname = args - + # Do conversion. index = Indexes() offset = 0 @@ -31,9 +29,9 @@ start = int( start ) - 1 index.add( chrom, start, start + 1, offset ) offset += len( line ) - + index.write( open(output_fname, "w") ) -if __name__ == "__main__": +if __name__ == "__main__": main() - \ No newline at end of file + diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml @@ -1,4 +1,9 @@ <tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.0" hidden="true"> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">samtools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> samtools view -bh $input | bedtools genomecov -bg -split -ibam stdin -g $chromInfo diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -7,6 +7,7 @@ import tempfile import zipfile from cgi import escape +from inspect import isclass from galaxy import util from galaxy.datatypes.metadata import MetadataElement #import directly to maintain ease of use in Datatype class definitions from galaxy.util import inflector @@ -14,6 +15,8 @@ from galaxy.util.odict import odict from galaxy.util.sanitize_html import sanitize_html +import dataproviders + from galaxy import eggs eggs.require( "Paste" ) import paste @@ -56,6 +59,7 @@ cls.metadata_spec.update( base.metadata_spec ) #add contents of metadata spec of base class to cls metadata.Statement.process( cls ) +(a)dataproviders.decorators.has_dataproviders class Data( object ): """ Base class for all datatypes. Implements basic interfaces as well @@ -545,7 +549,13 @@ def has_resolution(self): return False - + def matches_any( self, target_datatypes ): + """ + Check if this datatype is of any of the target_datatypes or is + a subtype thereof. + """ + datatype_classes = tuple( [ datatype if isclass( datatype ) else datatype.__class__ for datatype in target_datatypes ] ) + return isinstance( self, datatype_classes ) def merge( split_files, output_file): """ Merge files with copy.copyfileobj() will not hit the @@ -572,6 +582,39 @@ return [ 'trackster', 'circster' ] return [] + # ------------- Dataproviders + def has_dataprovider( self, data_format ): + """ + Returns True if `data_format` is available in `dataproviders`. + """ + return ( data_format in self.dataproviders ) + + def dataprovider( self, dataset, data_format, **settings ): + """ + Base dataprovider factory for all datatypes that returns the proper provider + for the given `data_format` or raises a `NoProviderAvailable`. + """ + if self.has_dataprovider( data_format ): + return self.dataproviders[ data_format ]( self, dataset, **settings ) + raise dataproviders.exceptions.NoProviderAvailable( self, data_format ) + + @dataproviders.decorators.dataprovider_factory( 'base' ) + def base_dataprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.base.DataProvider( dataset_source, **settings ) + + @dataproviders.decorators.dataprovider_factory( 'chunk', dataproviders.chunk.ChunkDataProvider.settings ) + def chunk_dataprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.chunk.ChunkDataProvider( dataset_source, **settings ) + + @dataproviders.decorators.dataprovider_factory( 'chunk64', dataproviders.chunk.Base64ChunkDataProvider.settings ) + def chunk64_dataprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.chunk.Base64ChunkDataProvider( dataset_source, **settings ) + + +(a)dataproviders.decorators.has_dataproviders class Text( Data ): file_ext = 'txt' line_class = 'line' @@ -741,10 +784,31 @@ f.close() split = classmethod(split) + # ------------- Dataproviders + @dataproviders.decorators.dataprovider_factory( 'line', dataproviders.line.FilteredLineDataProvider.settings ) + def line_dataprovider( self, dataset, **settings ): + """ + Returns an iterator over the dataset's lines (that have been `strip`ed) + optionally excluding blank lines and lines that start with a comment character. + """ + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.line.FilteredLineDataProvider( dataset_source, **settings ) + + @dataproviders.decorators.dataprovider_factory( 'regex-line', dataproviders.line.RegexLineDataProvider.settings ) + def regex_line_dataprovider( self, dataset, **settings ): + """ + Returns an iterator over the dataset's lines + optionally including/excluding lines that match one or more regex filters. + """ + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.line.RegexLineDataProvider( dataset_source, **settings ) + + class GenericAsn1( Text ): """Class for generic ASN.1 text format""" file_ext = 'asn1' + class LineCount( Text ): """ Dataset contains a single line with a single integer that denotes the @@ -752,6 +816,7 @@ """ pass + class Newick( Text ): """New Hampshire/Newick Format""" file_ext = "nhx" diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 lib/galaxy/datatypes/dataproviders/__init__.py --- /dev/null +++ b/lib/galaxy/datatypes/dataproviders/__init__.py @@ -0,0 +1,28 @@ + +#TODO: ---- This is a work in progress ---- +""" +Dataproviders are iterators with context managers that provide data to some +consumer datum by datum. + +As well as subclassing and overriding to get the proper data, Dataproviders +can be piped from one to the other. +..example:: + +.. note:: be careful to NOT pipe providers into subclasses of those providers. + Subclasses provide all the functionality of their superclasses, + so there's generally no need. + +.. note:: be careful to when using piped providers that accept the same keywords + in their __init__ functions (such as limit or offset) to pass those + keywords to the proper (often final) provider. These errors that result + can be hard to diagnose. +""" +import decorators +import exceptions + +import base +import chunk +import line +import column +import external +import dataset diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 lib/galaxy/datatypes/dataproviders/base.py --- /dev/null +++ b/lib/galaxy/datatypes/dataproviders/base.py @@ -0,0 +1,305 @@ +""" +Base class(es) for all DataProviders. +""" +# there's a blurry line between functionality here and functionality in datatypes module +# attempting to keep parsing to a minimum here and focus on chopping/pagination/reformat(/filtering-maybe?) +# and using as much pre-computed info/metadata from the datatypes module as possible +# also, this shouldn't be a replacement/re-implementation of the tool layer +# (which provides traceability/versioning/reproducibility) + +from collections import deque +import exceptions + +_TODO = """ +hooks into datatypes (define providers inside datatype modules) as factories +capture tell() when provider is done + def stop( self ): self.endpoint = source.tell(); raise StopIteration() +implement __len__ sensibly where it can be (would be good to have where we're giving some progress - '100 of 300') + seems like sniffed files would have this info +unit tests +add datum entry/exit point methods: possibly decode, encode + or create a class that pipes source through - how would decode work then? + +icorporate existing visualization/dataproviders +some of the sources (esp. in datasets) don't need to be re-created +YAGNI: InterleavingMultiSourceDataProvider, CombiningMultiSourceDataProvider + +datasets API entry point: + kwargs should be parsed from strings 2 layers up (in the DatasetsAPI) - that's the 'proper' place for that. + but how would it know how/what to parse if it doesn't have access to the classes used in the provider? + Building a giant list by sweeping all possible dprov classes doesn't make sense + For now - I'm burying them in the class __init__s - but I don't like that +""" + +import logging +log = logging.getLogger( __name__ ) + + +# ----------------------------------------------------------------------------- base classes +class HasSettings( type ): + """ + Metaclass for data providers that allows defining and inheriting + a dictionary named 'settings'. + + Useful for allowing class level access to expected variable types + passed to class `__init__` functions so they can be parsed from a query string. + """ + # yeah - this is all too acrobatic + def __new__( cls, name, base_classes, attributes ): + settings = {} + # get settings defined in base classes + for base_class in base_classes: + base_settings = getattr( base_class, 'settings', None ) + if base_settings: + settings.update( base_settings ) + # get settings defined in this class + new_settings = attributes.pop( 'settings', None ) + if new_settings: + settings.update( new_settings ) + attributes[ 'settings' ] = settings + return type.__new__( cls, name, base_classes, attributes ) + + +# ----------------------------------------------------------------------------- base classes +class DataProvider( object ): + """ + Base class for all data providers. Data providers: + (a) have a source (which must be another file-like object) + (b) implement both the iterator and context manager interfaces + (c) do not allow write methods + (but otherwise implement the other file object interface methods) + """ + # a definition of expected types for keyword arguments sent to __init__ + # useful for controlling how query string dictionaries can be parsed into correct types for __init__ + # empty in this base class + __metaclass__ = HasSettings + settings = {} + + def __init__( self, source, **kwargs ): + """ + :param source: the source that this iterator will loop over. + (Should implement the iterable interface and ideally have the + context manager interface as well) + """ + self.source = self.validate_source( source ) + + def validate_source( self, source ): + """ + Is this a valid source for this provider? + + :raises InvalidDataProviderSource: if the source is considered invalid. + + Meant to be overridden in subclasses. + """ + if not source or not hasattr( source, '__iter__' ): + # that's by no means a thorough check + raise exceptions.InvalidDataProviderSource( source ) + return source + + #TODO: (this might cause problems later...) + #TODO: some providers (such as chunk's seek and read) rely on this... remove + def __getattr__( self, name ): + if name == 'source': + # if we're inside this fn, source hasn't been set - provide some safety just for this attr + return None + # otherwise, try to get the attr from the source - allows us to get things like provider.encoding, etc. + if hasattr( self.source, name ): + return getattr( self.source, name ) + # raise the proper error + return self.__getattribute__( name ) + + # write methods should not be allowed + def truncate( self, size ): + raise NotImplementedError( 'Write methods are purposely disabled' ) + def write( self, string ): + raise NotImplementedError( 'Write methods are purposely disabled' ) + def writelines( self, sequence ): + raise NotImplementedError( 'Write methods are purposely disabled' ) + + #TODO: route read methods through next? + #def readline( self ): + # return self.next() + def readlines( self ): + return [ line for line in self ] + + # iterator interface + def __iter__( self ): + # it's generators all the way up, Timmy + with self as source: + for datum in self.source: + yield datum + def next( self ): + return self.source.next() + + # context manager interface + def __enter__( self ): + # make the source's context manager interface optional + if hasattr( self.source, '__enter__' ): + self.source.__enter__() + return self + def __exit__( self, *args ): + # make the source's context manager interface optional, call on source if there + if hasattr( self.source, '__exit__' ): + self.source.__exit__( *args ) + # alternately, call close() + elif hasattr( self.source, 'close' ): + self.source.close() + + def __str__( self ): + """ + String representation for easier debugging. + + Will call `__str__` on it's source so this will display piped dataproviders. + """ + # we need to protect against recursion (in __getattr__) if self.source hasn't been set + source_str = str( self.source ) if hasattr( self, 'source' ) else '' + return '%s(%s)' %( self.__class__.__name__, str( source_str ) ) + + +class FilteredDataProvider( DataProvider ): + """ + Passes each datum through a filter function and yields it if that function + returns a non-`None` value. + + Also maintains counters: + - `num_data_read`: how many data have been consumed from the source. + - `num_valid_data_read`: how many data have been returned from `filter`. + - `num_data_returned`: how many data has this provider yielded. + """ + # not useful here - we don't want functions over the query string + #settings.update({ 'filter_fn': 'function' }) + + def __init__( self, source, filter_fn=None, **kwargs ): + """ + :param filter_fn: a lambda or function that will be passed a datum and + return either the (optionally modified) datum or None. + """ + super( FilteredDataProvider, self ).__init__( source, **kwargs ) + self.filter_fn = filter_fn if hasattr( filter_fn, '__call__' ) else None + # count how many data we got from the source + self.num_data_read = 0 + # how many valid data have we gotten from the source + # IOW, data that's passed the filter and been either provided OR have been skipped due to offset + self.num_valid_data_read = 0 + # how many lines have been provided/output + self.num_data_returned = 0 + + def __iter__( self ): + parent_gen = super( FilteredDataProvider, self ).__iter__() + for datum in parent_gen: + self.num_data_read += 1 + datum = self.filter( datum ) + if datum != None: + self.num_valid_data_read += 1 + self.num_data_returned += 1 + yield datum + + #TODO: may want to squash this into DataProvider + def filter( self, datum ): + """ + When given a datum from the provider's source, return None if the datum + 'does not pass' the filter or is invalid. Return the datum if it's valid. + + :param datum: the datum to check for validity. + :returns: the datum, a modified datum, or None + + Meant to be overridden. + """ + if self.filter_fn: + return self.filter_fn( datum ) + # also can be overriden entirely + return datum + + +class LimitedOffsetDataProvider( FilteredDataProvider ): + """ + A provider that uses the counters from FilteredDataProvider to limit the + number of data and/or skip `offset` number of data before providing. + + Useful for grabbing sections from a source (e.g. pagination). + """ + # define the expected types of these __init__ arguments so they can be parsed out from query strings + settings = { + 'limit' : 'int', + 'offset': 'int' + } + + #TODO: may want to squash this into DataProvider + def __init__( self, source, offset=0, limit=None, **kwargs ): + """ + :param offset: the number of data to skip before providing. + :param limit: the final number of data to provide. + """ + super( LimitedOffsetDataProvider, self ).__init__( source, **kwargs ) + + # how many valid data to skip before we start outputing data - must be positive + # (diff to support neg. indeces - must be pos.) + self.offset = max( offset, 0 ) + + # how many valid data to return - must be positive (None indicates no limit) + self.limit = limit + if self.limit != None: + self.limit = max( self.limit, 0 ) + + def __iter__( self ): + """ + Iterate over the source until `num_valid_data_read` is greater than + `offset`, begin providing datat, and stop when `num_data_returned` + is greater than `offset`. + """ + parent_gen = super( LimitedOffsetDataProvider, self ).__iter__() + for datum in parent_gen: + + if self.limit != None and self.num_data_returned > self.limit: + break + + if self.num_valid_data_read > self.offset: + yield datum + else: + # wot a cheezy way of doing this... + self.num_data_returned -= 1 + + #TODO: skipping lines is inefficient - somehow cache file position/line_num pair and allow provider + # to seek to a pos/line and then begin providing lines + # the important catch here is that we need to have accurate pos/line pairs + # in order to preserve the functionality of limit and offset + #if file_seek and len( file_seek ) == 2: + # seek_pos, new_line_num = file_seek + # self.seek_and_set_curr_line( seek_pos, new_line_num ) + + #def seek_and_set_curr_line( self, file_seek, new_curr_line_num ): + # self.seek( file_seek, os.SEEK_SET ) + # self.curr_line_num = new_curr_line_num + + +class MultiSourceDataProvider( DataProvider ): + """ + A provider that iterates over a list of given sources and provides data + from one after another. + + An iterator over iterators. + """ + def __init__( self, source_list, **kwargs ): + """ + :param source_list: an iterator of iterables + """ + self.source_list = deque( source_list ) + + def __iter__( self ): + """ + Iterate over the source_list, then iterate over the data in each source. + + Skip a given source in `source_list` if it is `None` or invalid. + """ + for source in self.source_list: + # just skip falsy sources + if not source: + continue + try: + self.source = self.validate_source( source ) + except exceptions.InvalidDataProviderSource, invalid_source: + continue + + parent_gen = super( MultiSourceDataProvider, self ).__iter__() + for datum in parent_gen: + yield datum diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 lib/galaxy/datatypes/dataproviders/chunk.py --- /dev/null +++ b/lib/galaxy/datatypes/dataproviders/chunk.py @@ -0,0 +1,84 @@ +""" +Chunk (N number of bytes at M offset to a source's beginning) provider. + +Primarily for file sources but usable by any iterator that has both +seek and read( N ). +""" +import os +import base64 + +import base +import exceptions + +_TODO = """ +""" + +import logging +log = logging.getLogger( __name__ ) + + +# ----------------------------------------------------------------------------- +class ChunkDataProvider( base.DataProvider ): + """ + Data provider that yields chunks of data from it's file. + + Note: this version does not account for lines and works with Binary datatypes. + """ + MAX_CHUNK_SIZE = 2**16 + DEFAULT_CHUNK_SIZE = MAX_CHUNK_SIZE + settings = { + 'chunk_index' : 'int', + 'chunk_size' : 'int' + } + + #TODO: subclass from LimitedOffsetDataProvider? + # see web/framework/base.iterate_file, util/__init__.file_reader, and datatypes.tabular + def __init__( self, source, chunk_index=0, chunk_size=DEFAULT_CHUNK_SIZE, **kwargs ): + """ + :param chunk_index: if a source can be divided into N number of + `chunk_size` sections, this is the index of which section to + return. + :param chunk_size: how large are the desired chunks to return + (gen. in bytes). + """ + super( ChunkDataProvider, self ).__init__( source, **kwargs ) + self.chunk_size = int( chunk_size ) + self.chunk_pos = int( chunk_index ) * self.chunk_size + + def validate_source( self, source ): + """ + Does the given source have both the methods `seek` and `read`? + :raises InvalidDataProviderSource: if not. + """ + source = super( ChunkDataProvider, self ).validate_source( source ) + if( ( not hasattr( source, 'seek' ) ) + or ( not hasattr( source, 'read' ) ) ): + raise exceptions.InvalidDataProviderSource( source ) + return source + + def __iter__( self ): + # not reeeally an iterator per se + self.__enter__() + self.source.seek( self.chunk_pos, os.SEEK_SET ) + chunk = self.encode( self.source.read( self.chunk_size ) ) + yield chunk + self.__exit__() + + def encode( self, chunk ): + """ + Called on the chunk before returning. + + Overrride to modify, encode, or decode chunks. + """ + return chunk + + +class Base64ChunkDataProvider( ChunkDataProvider ): + """ + Data provider that yields chunks of base64 encoded data from it's file. + """ + def encode( self, chunk ): + """ + Return chunks encoded in base 64. + """ + return base64.b64encode( chunk ) diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 lib/galaxy/datatypes/dataproviders/column.py --- /dev/null +++ b/lib/galaxy/datatypes/dataproviders/column.py @@ -0,0 +1,254 @@ +""" +Providers that provide lists of lists generally where each line of a source +is further subdivided into multiple data (e.g. columns from a line). +""" + +import line + +_TODO = """ +move ColumnarDataProvider parsers to more sensible location + +TransposedColumnarDataProvider: provides each column as a single array + - see existing visualizations/dataprovider/basic.ColumnDataProvider +""" + +import logging +log = logging.getLogger( __name__ ) + + +# ----------------------------------------------------------------------------- base classes +class ColumnarDataProvider( line.RegexLineDataProvider ): + """ + Data provider that provide a list of columns from the lines of it's source. + + Columns are returned in the order given in indeces, so this provider can + re-arrange columns. + + If any desired index is outside the actual number of columns + in the source, this provider will None-pad the output and you are guaranteed + the same number of columns as the number of indeces asked for (even if they + are filled with None). + """ + settings = { + 'indeces' : 'list:int', + 'column_count' : 'int', + 'column_types' : 'list:str', + 'parse_columns' : 'bool', + 'deliminator' : 'str' + } + + def __init__( self, source, indeces=None, + column_count=None, column_types=None, parsers=None, parse_columns=True, + deliminator='\t', **kwargs ): + """ + :param indeces: a list of indeces of columns to gather from each row + Optional: will default to `None`. + If `None`, this provider will return all rows (even when a + particular row contains more/less than others). + If a row/line does not contain an element at a given index, the + provider will-return/fill-with a `None` value as the element. + :type indeces: list or None + + :param column_count: an alternate means of defining indeces, use an int + here to effectively provide the first N columns. + Optional: will default to `None`. + :type column_count: int + + :param column_types: a list of string names of types that the + provider will use to look up an appropriate parser for the column. + (e.g. 'int', 'float', 'str', 'bool') + Optional: will default to parsing all columns as strings. + :type column_types: list of strings + + :param parsers: a dictionary keyed with column type strings + and with values that are functions to use when parsing those + types. + Optional: will default to using the function `_get_default_parsers`. + :type parsers: dictionary + + :param parse_columns: attempt to parse columns? + Optional: defaults to `True`. + :type parse_columns: bool + + :param deliminator: character(s) used to split each row/line of the source. + Optional: defaults to the tab character. + :type deliminator: str + + .. note: that the subclass constructors are passed kwargs - so they're + params (limit, offset, etc.) are also applicable here. + """ + #TODO: other columnar formats: csv, etc. + super( ColumnarDataProvider, self ).__init__( source, **kwargs ) + + #IMPLICIT: if no indeces, column_count, or column_types passed: return all columns + self.selected_column_indeces = indeces + self.column_count = column_count + self.column_types = column_types or [] + # if no column count given, try to infer from indeces or column_types + if not self.column_count: + if self.selected_column_indeces: + self.column_count = len( self.selected_column_indeces ) + elif self.column_types: + self.column_count = len( self.column_types ) + # if no indeces given, infer from column_count + if not self.selected_column_indeces and self.column_count: + self.selected_column_indeces = list( xrange( self.column_count ) ) + + self.deliminator = deliminator + + # how/whether to parse each column value + self.parsers = {} + if parse_columns: + self.parsers = self.get_default_parsers() + # overwrite with user desired parsers + self.parsers.update( parsers or {} ) + + def get_default_parsers( self ): + """ + Return parser dictionary keyed for each columnar type + (as defined in datatypes). + + .. note: primitives only by default (str, int, float, boolean, None). + Other (more complex) types are retrieved as strings. + :returns: a dictionary of the form: + `{ <parser type name> : <function used to parse type> }` + """ + #TODO: move to module level (or datatypes, util) + return { + # str is default and not needed here + 'int' : int, + 'float' : float, + 'bool' : bool, + + # unfortunately, 'list' is used in dataset metadata both for + # query style maps (9th col gff) AND comma-sep strings. + # (disabled for now) + #'list' : lambda v: v.split( ',' ), + #'csv' : lambda v: v.split( ',' ), + ## i don't like how urlparses does sub-lists... + #'querystr' : lambda v: dict([ ( p.split( '=', 1 ) if '=' in p else ( p, True ) ) + # for p in v.split( ';', 1 ) ]) + + #'scifloat': #floating point which may be in scientific notation + + # always with the 1 base, biologists? + #'int1' : ( lambda i: int( i ) - 1 ), + + #'gffval': string or '.' for None + #'gffint': # int or '.' for None + #'gffphase': # 0, 1, 2, or '.' for None + #'gffstrand': # -, +, ?, or '.' for None, etc. + } + + def parse_value( self, val, type ): + """ + Attempt to parse and return the given value based on the given type. + + :param val: the column value to parse (often a string) + :param type: the string type 'name' used to find the appropriate parser + :returns: the parsed value + or `value` if no `type` found in `parsers` + or `None` if there was a parser error (ValueError) + """ + if type == 'str' or type == None: return val + try: + return self.parsers[ type ]( val ) + except KeyError, err: + # no parser - return as string + pass + except ValueError, err: + # bad value - return None + return None + return val + + def get_column_type( self, index ): + """ + Get the column type for the parser from `self.column_types` or `None` + if the type is unavailable. + :param index: the column index + :returns: string name of type (e.g. 'float', 'int', etc.) + """ + try: + return self.column_types[ index ] + except IndexError, ind_err: + return None + + def parse_column_at_index( self, columns, parser_index, index ): + """ + Get the column type for the parser from `self.column_types` or `None` + if the type is unavailable. + """ + try: + return self.parse_value( columns[ index ], self.get_column_type( parser_index ) ) + # if a selected index is not within columns, return None + except IndexError, index_err: + return None + + def parse_columns_from_line( self, line ): + """ + Returns a list of the desired, parsed columns. + :param line: the line to parse + :type line: str + """ + #TODO: too much going on in this loop - the above should all be precomputed AMAP... + all_columns = line.split( self.deliminator ) + # if no indeces were passed to init, return all columns + selected_indeces = self.selected_column_indeces or list( xrange( len( all_columns ) ) ) + parsed_columns = [] + for parser_index, column_index in enumerate( selected_indeces ): + parsed_columns.append( self.parse_column_at_index( all_columns, parser_index, column_index ) ) + return parsed_columns + + def __iter__( self ): + parent_gen = super( ColumnarDataProvider, self ).__iter__() + for line in parent_gen: + columns = self.parse_columns_from_line( line ) + yield columns + + #TODO: implement column filters here and not below - flatten hierarchy + +class FilteredByColumnDataProvider( ColumnarDataProvider ): + """ + Data provider that provide a list of columns from the lines of it's source + _only_ if they pass a given filter function. + + e.g. column #3 is type int and > N + """ + # TODO: how to do this and still have limit and offset work? + def __init__( self, source, **kwargs ): + raise NotImplementedError() + super( FilteredByColumnDataProvider, self ).__init__( source, **kwargs ) + + +class DictDataProvider( ColumnarDataProvider ): + """ + Data provider that zips column_names and columns from the source's contents + into a dictionary. + + A combination use of both `column_names` and `indeces` allows 'picking' + key/value pairs from the source. + + .. note: that the subclass constructors are passed kwargs - so they're + params (limit, offset, etc.) are also applicable here. + """ + settings = { + 'column_names' : 'list:str', + } + + def __init__( self, source, column_names=None, **kwargs ): + """ + :param column_names: an ordered list of strings that will be used as the keys + for each column in the returned dictionaries. + The number of key, value pairs each returned dictionary has will + be as short as the number of column names provided. + :type column_names: + """ + #TODO: allow passing in a map instead of name->index { 'name1': index1, ... } + super( DictDataProvider, self ).__init__( source, **kwargs ) + self.column_names = column_names or [] + + def __iter__( self ): + parent_gen = super( DictDataProvider, self ).__iter__() + for column_values in parent_gen: + map = dict( zip( self.column_names, column_values ) ) + yield map This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/d05bf67aefa6/ Changeset: d05bf67aefa6 Branch: stable User: natefoo Date: 2013-08-12 17:55:41 Summary: Added tag release_2013.08.12 for changeset 1ae95b3aa98d Affected #: 1 file diff -r 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 -r d05bf67aefa670f4d004db3c1494e9052c0c0d9c .hgtags --- a/.hgtags +++ b/.hgtags @@ -3,3 +3,4 @@ 75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 +1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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