/*
* Copyright (c) 2007-2013 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.cli_plugin;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.feature.tribble.GFFCodec;
import org.broad.igv.track.GFFFeatureSource;
import java.io.IOException;
import java.io.InputStream;
import java.util.Iterator;
/**
* @author jacob
* @date 2013-Apr-29
*/
public class CufflinksTranscriptDecoder extends RenameDecoder{
public CufflinksTranscriptDecoder() {
super(new GFFCodec(GenomeManager.getInstance().getCurrentGenome()));
}
@Override
public Iterator decodeAll(InputStream is, boolean strictParsing) throws IOException {
Iterator iter = super.decodeAll(is, strictParsing);
GFFFeatureSource.GFFCombiner combiner = new GFFFeatureSource.GFFCombiner();
combiner.addFeatures(iter);
return combiner.combineFeatures().iterator();
}
}