/*
* Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
*
* 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.
*
* THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
* WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
* WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
* PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
* OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
* TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
* OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
* ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
* THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
* SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*/
package org.broad.igv.sam.reader;
import org.broad.igv.feature.BasicFeature;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.peaks.Peak;
import org.broad.igv.sam.Alignment;
import org.broad.igv.sam.FeatureWrappedAlignment;
import org.broad.igv.feature.tribble.PSLCodec;
import htsjdk.tribble.Feature;
import htsjdk.tribble.readers.AsciiLineReader;
import java.io.IOException;
/**
* @author jrobinso
* @date Aug 5, 2010
*/
public class PSLAlignmentParser implements AlignmentParser {
PSLCodec codec;
public PSLAlignmentParser() {
codec = new PSLCodec(); //genome);
}
public Alignment readNextRecord(AsciiLineReader reader) throws IOException {
String nextLine;
while ((nextLine = reader.readLine()) != null) {
Feature f = codec.decode(nextLine);
if(f != null && f instanceof BasicFeature) {
return new FeatureWrappedAlignment((BasicFeature) f);
}
}
return null;
}
}