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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,116 @@ | ||
| const BlobFilehandleWrapper = cjsRequire('../../Model/BlobFilehandleWrapper') | ||
|
|
||
| define( [ 'dojo/_base/declare', | ||
| 'dojo/_base/lang', | ||
| 'dojo/Deferred', | ||
| 'JBrowse/Store/SeqFeature', | ||
| 'JBrowse/Model/XHRBlob', | ||
| 'JBrowse/Store/DeferredFeaturesMixin' | ||
| ], | ||
| function( | ||
| declare, | ||
| lang, | ||
| Deferred, | ||
| SeqFeatureStore, | ||
| XHRBlob, | ||
| DeferredFeaturesMixin | ||
| ) { | ||
|
|
||
| return declare( [ SeqFeatureStore, DeferredFeaturesMixin ], | ||
| { | ||
|
|
||
| /** | ||
| * Storage backend for sequences in indexed fasta files | ||
| * served as static text files. | ||
| * @constructs | ||
| */ | ||
| constructor: function(args) { | ||
| let dataBlob | ||
| if (args.blob) | ||
| dataBlob = new BlobFilehandleWrapper(args.blob) | ||
| else if (args.urlTemplate) | ||
| dataBlob = new BlobFilehandleWrapper(new XHRBlob(this.resolveUrl(args.urlTemplate), { expectRanges: true })) | ||
|
|
||
| this.source = dataBlob.toString() | ||
| this.data = dataBlob | ||
| this.refSeqs = {} | ||
|
|
||
| this.init({ | ||
| success: () => this._deferred.features.resolve({success:true}), | ||
| error: () => this._failAllDeferred() | ||
| }) | ||
| }, | ||
|
|
||
| hasRefSeq: function( seqName, callback, errorCallback ) { | ||
| this.getSequenceSize(seqName) | ||
| .then( | ||
| size => { | ||
| callback(size !== undefined) | ||
| }, | ||
| errorCallback, | ||
| ) | ||
| }, | ||
| getRefSeqs: function( callback, errorCallback ) { | ||
| this.getSequenceSizes() | ||
| .then(sizes => Object.entries(this.refSeqs).map(([name,length]) => { | ||
| return { | ||
| name, | ||
| length, | ||
| end: length, | ||
| start: 0, | ||
| } | ||
| })) | ||
| .then(callback, errorCallback) | ||
| }, | ||
| getSequenceSize: function(refSeq) { | ||
| return this._deferred.features.then(() => { | ||
| return this.refSeqs[refSeq] | ||
| }) | ||
| }, | ||
| getSequenceSizes: function() { | ||
| return this._deferred.features.then(() => { | ||
| return this.refSeqs | ||
| }) | ||
| }, | ||
| init: function( args ) { | ||
| var fasta = this.data; | ||
| var successCallback = args.success || function() {}; | ||
| var failCallback = args.failure || function(e) { console.error(e, e.stack); }; | ||
| this.parseFile(fasta, data => { | ||
| data.split('\n').forEach(line => { | ||
| if(line.length) { | ||
| const [name, length] = line.split('\t') | ||
| this.refSeqs[name] = length | ||
| } | ||
| }) | ||
| successCallback(); | ||
| }, failCallback ); | ||
| }, | ||
|
|
||
|
|
||
| parseFile: function(fastaFile, successCallback, failCallback ) { | ||
| fastaFile.readFile().then(text => { | ||
| var chromSizes = ""; | ||
| var bytes = new Uint8Array(text); | ||
| var length = bytes.length; | ||
| for (var i = 0; i < length; i++) { | ||
| chromSizes += String.fromCharCode(bytes[i]); | ||
| } | ||
|
|
||
| if (!(chromSizes && chromSizes.length)) | ||
| failCallback ("Could not read file: " + fastaFile.name); | ||
| else { | ||
| successCallback(chromSizes); | ||
| } | ||
|
|
||
| }, failCallback ); | ||
| }, | ||
|
|
||
| saveStore: function() { | ||
| return { | ||
| urlTemplate: (this.config.file||this.config.blob).url, | ||
| }; | ||
| } | ||
|
|
||
| }); | ||
| }); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| define([ | ||
| 'dojo/_base/declare', | ||
| 'JBrowse/Util', | ||
| 'JBrowse/Model/FileBlob', | ||
| 'JBrowse/Model/XHRBlob' | ||
| ], | ||
| function( declare, Util, FileBlob, XHRBlob ) { | ||
| var uniqCounter = 0; | ||
| return declare( null, { | ||
|
|
||
| storeType: 'JBrowse/Store/SeqFeature/ChromSizes', | ||
|
|
||
| tryResource: function( configs, resource ) { | ||
| if( resource.type == 'chrom.sizes' ) { | ||
| var basename = Util.basename( | ||
| resource.file ? resource.file.name : | ||
| resource.url ? resource.url : | ||
| '', | ||
| ['.sizes'] | ||
| ); | ||
| if( !basename ) | ||
| return false; | ||
|
|
||
| var newName = 'REF_'+basename+'_'+uniqCounter++; | ||
| configs[newName] = { | ||
| type: this.storeType, | ||
| fileBasename: basename, | ||
| blob: this._makeBlob( resource ), | ||
| name: newName | ||
| }; | ||
| return true; | ||
| } | ||
| else | ||
| return false; | ||
| }, | ||
|
|
||
| finalizeConfiguration: function( configs ) { | ||
| }, | ||
|
|
||
| _makeBlob: function( resource ) { | ||
| var r = resource.file ? new FileBlob( resource.file ) : | ||
| resource.url ? new XHRBlob( resource.url ) : | ||
| null; | ||
| if( ! r ) | ||
| throw 'unknown resource type'; | ||
| return r; | ||
|
|
||
| }, | ||
|
|
||
| confIsValid: function( conf ) { | ||
| return conf.blob || conf.urlTemplate; | ||
| } | ||
| }); | ||
| }); |