@gmod/jbrowse/src/JBrowse/Store/Names/Hash.js

JBrowse - client-side genome browser

define( [
            'dojo/_base/declare',
            'dojo/_base/array',
            'dojo/store/util/QueryResults',
            'JBrowse/Util',
            'JBrowse/Store/Hash',
            'JBrowse/Model/Location'
        ],
        function(
            declare,
            array,
            QueryResults,
            Util,
            HashStore,
            Location
        ) {

return declare( HashStore,
{

    constructor: function( args ) {

        this.tooManyMatchesMessage = args.tooManyMatchesMessage || '(too many matches to display)';

        // generate stopPrefixes
        var stopPrefixes = this.stopPrefixes = {};
        // make our stopPrefixes an object as { prefix: true, ... }
        // with all possible prefixes of our stop prefixes
        if( args.stopPrefixes ) {
            var prefixesInput = typeof args.stopPrefixes == 'string'
                ? [ args.stopPrefixes ] : args.stopPrefixes;

            dojo.forEach( prefixesInput, function(prefix) {
                while( prefix.length ) {
                    stopPrefixes[prefix] = true;
                    prefix = prefix.substr( 0, prefix.length - 1 );
                }
            });
        }
    },

    _nameRecordToItem: function( nameRecord ) {
        if( nameRecord.hitLimit ) {
            // it's a too-many-matches marker
            return { name: this.tooManyMatchesMessage, hitLimit: true };
        }
        else {
            // it's an actual name record
            var item = {};
            if( typeof nameRecord == 'object' ) {
                item.name = nameRecord[0];
                var trackConfig = this._findTrackConfig( ((this.meta||{}).track_names||{})[ nameRecord[1] ] );
                item.location = new Location({
                    ref: nameRecord[3],
                    start: parseInt( nameRecord[4] ),
                    end: parseInt( nameRecord[5] ),
                    tracks: trackConfig ? [ trackConfig  ] : null,
                    objectName: nameRecord[0]
                });
            } else {
                item.name = nameRecord;
            }
            return item;
        }
    },

    // look in the browser's track configuration for the track with the given label
    _findTrackConfig: function( trackLabel ) {
        if( ! trackLabel )
            return null;

        var track = null;
        var i = array.some( this.browser.config.tracks, function( t ) {
            if( t.label == trackLabel ) {
                track = t;
                return true;
            }
            return false;
        });

        return track;
    },

    _makeResults: function( nameRecords ) {
        // convert the name records into dojo.store-compliant data
        // items, sort them by name and location
        var results = array.map( nameRecords, dojo.hitch(this,'_nameRecordToItem') )
                           .sort( function( a, b ) {
                                      return a.name.localeCompare( b.name )
                                          || a.location.localeCompare( b.location );
                                  });

        var last;
        var hitLimit;

        // aggregate them and make labels for them.  for names with
        // multiple locations, make a multipleLocations member.
        results = array.filter( results, function( i ) {
            if( i.hitLimit ) {
                hitLimit = i;
                if( ! hitLimit.label )
                    hitLimit.label = hitLimit.name || 'too many matches';
                return false;
            }
            else if( last && last.name == i.name ) {
                last.label = last.name + ' <span class="multipleLocations">multiple locations</span>';
                if( last.multipleLocations ) {
                    last.multipleLocations.push( i.location );
                } else {
                    last.multipleLocations = [last.location,i.location];
                    delete last.location;
                }
                return false;
            }
            last = i;
            last.label = last.name
                + ( last.location ? ' <span class="locString">'+last.location+'</span>'
                                  : ''
                  );
            return true;
        });

        if( hitLimit )
            results.push( hitLimit );

        return QueryResults( results );
    },

    // case-insensitive, and supports prefix queries like 'foo*'
    query: function( query, options ) {
        // remove trailing asterisks from query.name
        var thisB = this;
        var name = ( query.name || '' ).toString();

        // lowercase the name if the store is all-lowercase
        if( this.meta.lowercase_keys )
            name = name.toLowerCase();

        var trailingStar = /\*$/;
        if( trailingStar.test( name ) ) {
            name = name.replace( trailingStar, '' );
            return this._getEntry( name )
                       .then( function( value ) {
                            value = value || {};
                            return thisB._makeResults( ( value.exact || [] ).concat( value.prefix || [] ) );
                        });
        }
        else {
            return this._getEntry( name )
                       .then( function( value ) {
                           return thisB._makeResults( (value||{}).exact || [] );
                       });
        }
    },

    get: function( id ) {
        // lowercase the id if the store is all-lowercase
        if( this.meta.lowercase_keys )
            id = id.toLowerCase();

        return this._getEntry( id )
                   .then( function( bucket ) {
                       var nameRec = (bucket.exact||[])[0];
                       return nameRec ? this._nameRecordToItem( nameRec ) : null;
                   });
    },

    _getEntry: function( key ) {
        return this._getBucket(key)
                   .then( function( bucket ) {
                        return bucket[key];
                    });
    }

});
});