@gmod/jbrowse/src/JBrowse/Store/SeqFeature/FromConfig.js

JBrowse - client-side genome browser

/**
 * Store that shows features defined in its `features` configuration
 * key, like:
 *   "features": [ { "seq_id": "ctgA", "start":1, "end":20 },
 *                 ...
 *               ]
 */

define( [
            'dojo/_base/declare',
            'dojo/_base/array',
            'JBrowse/Store/SeqFeature',
            'JBrowse/Model/SimpleFeature'
        ],
        function(
            declare,
            array,
            SeqFeatureStore,
            SimpleFeature
        ) {

return declare( SeqFeatureStore,
{
    constructor: function( args ) {
        this.features = this._makeFeatures( this.config.features || [] );
    },

    _makeFeatures: function( fdata ) {
        var features = {};
        for( var i=0; i<fdata.length; i++ ) {
            if( fdata[i] ) {
                var f = this._makeFeature( fdata[i] );
                var refName = this.browser.regularizeReferenceName( f.get('seq_id') );
                var refFeatures = features[ refName ] || function() {
                    return features[ refName ] = [];
                }.call();
                refFeatures.push( f );
            }
        }
        return features;
    },

    _parseInt: function( data ) {
        array.forEach(['start','end','strand'], function( field ) {
            if( field in data )
                data[field] = parseInt( data[field] );
        });
        if( 'score' in data )
            data.score = parseFloat( data.score );
        if( 'subfeatures' in data )
            for( var i=0; i<data.subfeatures.length; i++ )
                this._parseInt( data.subfeatures[i] );
    },

    _makeFeature: function( data, parent ) {
        this._parseInt( data );
        return new SimpleFeature( { data: data, parent: parent } );
    },

    getGlobalStats: function( cb, errorCb ) {
        this.getRegionStats( { ref: this.refSeq.name, start: this.refSeq.start, end: this.refSeq.end }, cb, errorCb );
    },

    getFeatures: function( query, featCallback, endCallback, errorCallback ) {
        var start = query.start;
        var end = query.end;
        var features = this.features[ this.browser.regularizeReferenceName( query.ref ) ] || {};
        for( var id in features ) {
            var f = features[id];
            if(! ( f.get('end') < start  || f.get('start') > end ) ) {
                featCallback( f );
            }
        }
        endCallback();
    }
});
});