@gmod/jbrowse/src/JBrowse/View/FileDialog/TrackList/BgzipIndexedFASTADriver.js

JBrowse - client-side genome browser

define([
           'dojo/_base/declare',
           'JBrowse/Util',
           'JBrowse/Model/FileBlob',
           'JBrowse/Model/XHRBlob'
       ],
       function( declare, Util, FileBlob, XHRBlob ) {
var uniqCounter = 0;
return declare( null, {
    name: 'BGZFASTA',
    storeType: 'JBrowse/Store/SeqFeature/BgzipIndexedFasta',
    fileExtension: 'fasta.gz',
    fileExtensionMap: ['.fasta.gz', '.fa.gz', '.fna.gz', '.mfa.gz'],
    fileConfKey: 'bgzfa',
    fileUrlConfKey: 'urlTemplate',

    indexExtension: 'fasta.gz.fai',
    indexExtensionMap: ['.fasta.gz.fai', '.fa.gz.fai', '.fna.gz.fai', '.mfa.gz.fai'],
    indexConfKey: 'fai',
    indexUrlConfKey: 'faiUrlTemplate',

    doubleIndexExtension: 'gzi',
    doubleIndexExtensionMap: ['.fasta.gz.gzi', '.fa.gz.gzi', '.fna.gz.gzi', '.mfa.gz.gzi'],
    doubleIndexConfKey: 'gzi',
    doubleIndexUrlConfKey: 'gziUrlTemplate',


    tryResource: function( configs, resource ) {
        if( resource.type == this.fileExtension ) {
            var basename = Util.basename(
                resource.file ? resource.file.name :
                resource.url  ? resource.url       :
                                '',
                this.fileExtensionMap
            );
            if( !basename )
                return false;

            // go through the configs and see if there is one for an index that seems to match
            for( var n in configs ) {
                var c = configs[n];
                if( Util.basename( c[this.indexConfKey] ? c[this.indexConfKey ].url || c[this.indexConfKey].blob.name : c[this.indexUrlConfKey], this.indexExtensionMap ) == basename ||
                    Util.basename( c[this.doubleIndexConfKey] ? c[this.doubleIndexConfKey ].url || c[this.doubleIndexConfKey].blob.name : c[this.doubleIndexUrlConfKey], this.doubleIndexExtensionMap ) == basename ) {

                    // it's a match, put it in
                    c[this.fileConfKey] = this._makeBlob( resource );
                    return true;
                }
            }
            // otherwise make a new store config for it
            var newName = this.name+'_'+basename+'_'+uniqCounter++;
            configs[newName] = {
                type: this.storeType,
                name: newName,
                fileBasename: basename
            };
            configs[newName][this.fileConfKey] = this._makeBlob( resource );

            return true;
        } else if( resource.type == this.indexExtension ) {
            var basename = Util.basename(
                resource.file ? resource.file.name :
                resource.url  ? resource.url       :
                                '',
                this.indexExtensionMap
            );
            if( !basename )
                return false;

            for( var n in configs ) {
                var c = configs[n];
                if( Util.basename( c[this.fileConfKey] ? c[this.fileConfKey ].url || c[this.fileConfKey].blob.name : c[this.fileConfKey], this.fileExtensionMap ) == basename ||
                    Util.basename( c[this.doubleIndexConfKey] ? c[this.doubleIndexConfKey ].url || c[this.doubleIndexConfKey].blob.name : c[this.doubleIndexUrlConfKey], this.doubleIndexExtensionMap ) == basename ) {

                    // it's a match, put it in
                    c[this.indexConfKey] = this._makeBlob( resource );
                    return true;
                }
            }

            // otherwise make a new store
            var newName = this.name+'_'+Util.basename(basename,'.'+this.fileExtension)+'_'+uniqCounter++;
            configs[newName] = {
                name: newName,
                type: this.storeType
            };

            configs[newName][this.indexConfKey] = this._makeBlob( resource );
            return true;
        } else if( resource.type == this.doubleIndexExtension ) {
            var basename = Util.basename(
                resource.file ? resource.file.name :
                resource.url  ? resource.url       :
                                '',
                this.doubleIndexExtensionMap
            );
            if( !basename )
                return false;

            for( var n in configs ) {
                var c = configs[n];
                if( Util.basename( c[this.fileConfKey] ? c[this.fileConfKey ].url || c[this.fileConfKey].blob.name : c[this.fileConfKey], this.fileExtensionMap ) == basename ||
                    Util.basename( c[this.indexConfKey] ? c[this.indexConfKey ].url || c[this.indexConfKey].blob.name : c[this.indexUrlConfKey], this.indexExtensionMap ) == basename ) {

                    // it's a match, put it in
                    c[this.doubleIndexConfKey] = this._makeBlob( resource );
                    return true;
                }
            }


            // otherwise make a new store
            var newName = this.name+'_'+Util.basename(basename,'.'+this.fileExtension)+'_'+uniqCounter++;
            configs[newName] = {
                name: newName,
                type: this.storeType
            };

            configs[newName][this.doubleIndexConfKey] = this._makeBlob( resource );
            return true;
        }
        else
            return false;
    },

    // try to merge any singleton file and index stores.  currently can only do this if there is one of each
    finalizeConfiguration: function( configs ) {

        for( var n in configs ) {
            var conf = configs[n];
            if( conf.type === this.storeType ) {
                var v1 = (conf[this.indexConfKey] || conf[this.indexUrlConfKey])
                var v2 = (conf[this.fileConfKey] || conf[this.fileUrlConfKey])
                var v3 = (conf[this.doubleIndexConfKey] || conf[this.doubleIndexUrlConfKey])
                if(!(v1 && v2 && v3)) {
                    delete configs[n]
                }
            }
        }
    },

    _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[this.fileConfKey] || conf[this.fileUrlConfKey]) && ( conf[this.indexConfKey] || conf[this.indexUrlConfKey] ) && ( conf[this.doubleIndexConfKey] || conf[this.doubleIndexUrlConfKey] );
    }
});
});