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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| ApolloLabelProc is a JBrowse plugin. | ||
| Update location bar with 'label' (if it exists), when the locationBar content is JSON, which is expected from Apollo. | ||
| Install / Activate: | ||
|
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| For JBrowse 1.11.6+, copy the ApolloLabelProc directory to the 'plugins' directory. | ||
| Add this to appropriate trackList.json under the plugins section (create one if it doesn't exist): | ||
|
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| "plugins": [ | ||
| "ApolloLabelProc" | ||
| ], | ||
|
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| For Apollo 2.x, copy the ApolloLabelProc directory to the web-apps/jbrowse/plugins directory. | ||
| Add this to web-apps/jbrowse/plugins/WebApollo/json/annot.json: | ||
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| "plugins" : [ | ||
| { | ||
| "location" : "./plugins/WebApollo", | ||
| "name" : "WebApollo" | ||
| }, | ||
| { | ||
| "location" : "./plugins/ApolloLabelProc", | ||
| "name" : "ApolloLabelProc" | ||
| } | ||
| ], |
Empty file.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| /* | ||
| * ApolloLabelProc | ||
| * Update location bar with label (if it exists), when the locationBar content is JSON, which is expected from Apollo. | ||
| */ | ||
|
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| define([ | ||
| 'dojo/_base/declare', | ||
| 'dojo/_base/lang', | ||
| 'dojo/Deferred', | ||
| 'JBrowse/Plugin', | ||
| 'JBrowse/Util' | ||
| ], | ||
| function( | ||
| declare, | ||
| lang, | ||
| Deferred, | ||
| JBrowsePlugin, | ||
| Util | ||
| ) { | ||
| return declare( JBrowsePlugin, | ||
| { | ||
| constructor: function( args ) { | ||
| console.log("plugin: ApolloLabelProc"); | ||
| var counter = 0 ; | ||
|
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| var thisB = this; | ||
|
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| var currentBookmark ; | ||
|
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| // this traps the event that happens directly after onCoarseMove function, where the label gets updates. | ||
| dojo.subscribe("/jbrowse/v1/n/navigate", function(currRegion){ | ||
| var locationStr = Util.assembleLocStringWithLength( currRegion ); | ||
| //console.log("locationStr="+locationStr); | ||
|
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| // is locationStr JSON? | ||
| if (locationStr.charAt(0)=='{') { | ||
| locationStr = locationStr.substring(0,locationStr.lastIndexOf('}')+1); | ||
| var obj = JSON.parse(locationStr); | ||
|
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| // look for the "label" property | ||
| if(obj.hasOwnProperty('sequenceList')) { | ||
| //console.log("label="+obj.label); | ||
| currentBookmark = obj ; | ||
|
|
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| // if( thisB.browser.locationBox ){ | ||
| // // thisB.browser.locationBox.set('value',obj.label, false); | ||
| // // dojo.style(dojo.byId('widget_location'), "display", "none"); | ||
| // dojo.style(dojo.byId('widget_location'), "width", "0"); | ||
| // } | ||
|
|
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| dojo.addOnLoad(function() { | ||
| // console.log(borderContainer); | ||
|
|
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| if(counter==0){ | ||
| var searchBox = dojo.byId('search-box'); | ||
| dojo.style(searchBox, "display", "none"); | ||
| if(obj.hasOwnProperty("label")){ | ||
| // TODO: add something next to search-box that displays something slightly different | ||
| // bookmark name + location . . . pasting it in should call browser "GO" function | ||
| // should call Browser.navigateTo . . with the browser location stuff | ||
| // we cann actually store the bookmark data here | ||
|
|
||
| } | ||
| var borderContainer = dijit.byId('GenomeBrowser'); | ||
| borderContainer.resize(); | ||
| } | ||
| counter = 1 ; | ||
|
|
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| // dojo.style(dojo.byId('search-refseq'), "display", "none"); | ||
| }); | ||
|
|
||
| } | ||
| else{ | ||
| currentBookmark = null ; | ||
| } | ||
| } | ||
|
|
||
| }); | ||
| } | ||
| }); | ||
| }); |
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