@gmod/jbrowse/src/JBrowse/Store/SeqFeature/BigWig/Window.js

JBrowse - client-side genome browser

define( [
            'dojo/_base/declare',
            'dojo/_base/lang',
            'dojo/_base/array',
            'JBrowse/Store/LRUCache',
            './RequestWorker'
        ],
        function( declare, lang, array, LRUCache, RequestWorker ) {

var dlog = function(){ console.log.apply(console, arguments); };

return declare( null,
 /**
  * @lends JBrowse.Store.BigWig.Window.prototype
  */
{

    /**
     * View into a subset of the data in a BigWig file.
     *
     * Adapted by Robert Buels from bigwig.js in the Dalliance Genome
     * Explorer by Thomas Down.
     * @constructs
     */
    constructor: function(bwg, cirTreeOffset, cirTreeLength, isSummary, autoSql) {
        this.bwg = bwg;
        this.autoSql = autoSql;
        if( !( cirTreeOffset >= 0 ) )
            throw "invalid cirTreeOffset!";
        if( !( cirTreeLength > 0 ) )
            throw "invalid cirTreeLength!";

        this.cirTreeOffset = cirTreeOffset;
        this.cirTreeLength = cirTreeLength;
        this.isSummary = isSummary;

        function countFeatures(features) {
            if (!features) return 0
            let total = features.length
            features.forEach( feature => {
                total += countFeatures(feature.children())
            })
            return total
        }
        this.featureCache = new LRUCache({
            name: 'feature cache',
            fillCallback: (query, callback) => {
                this.readWigDataById(...query, callback, err => {console.error(err)})
            },
            sizeFunction: countFeatures,
            maxSize: 500000 // cache up to 50000 features and subfeatures
        });
    },

    BED_COLOR_REGEXP: /^[0-9]+,[0-9]+,[0-9]+/,

    readWigData: function(chrName, min, max, callback, errorCallback ) {
        // console.log( 'reading wig data from '+chrName+':'+min+'..'+max);
        var chr = this.bwg.refsByName[chrName];
        if ( ! chr ) {
            // Not an error because some .bwgs won't have data for all chromosomes.

            // dlog("Couldn't find chr " + chrName);
            // dlog('Chroms=' + miniJSONify(this.bwg.refsByName));
            callback([]);
        } else {
            this.readWigDataByIdWithCache( chr.id, min, max, callback, errorCallback );
        }
    },

    readWigDataByIdWithCache(chr, min, max, callback, errorCallback) {
        this.featureCache.get([chr, min, max], (result,error) => {
            if (error)
                errorCallback(error)
            else
                callback(result)
        })
    },

    readWigDataById: function(chr, min, max, callback, errorCallback ) {
        if( !this.cirHeader ) {
            var readCallback = lang.hitch( this, 'readWigDataById', chr, min, max, callback, errorCallback );
            if( this.cirHeaderLoading ) {
                this.cirHeaderLoading.push( readCallback );
            }
            else {
                this.cirHeaderLoading = [ readCallback ];
                // dlog('No CIR yet, fetching');
                this.bwg.data
                    .read( this.cirTreeOffset, 48, lang.hitch( this, function(result) {
                                this.cirHeader = result;
                                this.cirBlockSize = this.bwg.newDataView( result, 4, 4 ).getUint32();
                                array.forEach( this.cirHeaderLoading, function(c) { c(); });
                                delete this.cirHeaderLoading;
                            }), errorCallback );
            }
            return;
        }

        //dlog('_readWigDataById', chr, min, max, callback);

        var worker = new RequestWorker( this, chr, min, max, callback, errorCallback );
        worker.cirFobRecur([this.cirTreeOffset + 48], 1);
    }
});

});