@gmod/jbrowse
Version:
JBrowse - client-side genome browser
78 lines (69 loc) • 2.42 kB
JavaScript
/**
* Support for Sequin Feature table export. See
* http://www.ncbi.nlm.nih.gov/Sequin/table.html.
*/
define([ 'dojo/_base/declare',
'dojo/_base/array',
'JBrowse/View/Export'
],
function( declare, array, ExportBase ) {
return declare( ExportBase,
{
/**
* Data export driver for BED format.
* @constructs
*/
// constructor: function( args ) {
// },
/**
* print the BED track definition line
* @private
*/
_printHeader: function( feature ) {
// print the BED header
this.print( '>Feature '+(feature.get('seq_id') || this.refSeq.name)+"\n" );
return true;
},
/**
* Format a feature into a string.
* @param {Object} feature feature object (like those returned from JBrowse/Store/SeqFeature/*)
* @returns {String} BED string representation of the feature
*/
formatFeature: function( feature ) {
var thisB = this;
if( ! this.headerPrinted )
this.headerPrinted = this._printHeader( feature );
var featLine = [ feature.get('start')+1,
feature.get('end'),
feature.get('type') || 'region'
];
if( feature.get('strand') == -1 ) {
var t = featLine[0];
featLine[0] = featLine[1];
featLine[1] = t;
}
// make the qualifiers
var qualifiers = array.map(
array.filter( feature.tags(), function(t) {
return ! { start: 1, end: 1, type: 1, strand: 1, seq_id: 1 }[ t.toLowerCase() ];
}),
function( tag ) {
return [ tag.toLowerCase(), thisB.stringifyAttributeValue( feature.get(tag) ) ];
});
return featLine.join("\t")+"\n" + array.map( qualifiers, function( q ) { return "\t\t\t"+q.join("\t")+"\n"; } ).join('');
},
stringifyAttributeValue: function( val ) {
return val.hasOwnProperty( 'toString' )
? val.toString() :
val.values
? function(val) {
return val instanceof Array
? val.join(',')
: val;
}.call(this,val.values) :
val instanceof Array
? val.join(',')
: val;
}
});
});