/*
* 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.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.sam.reader;
import htsjdk.samtools.util.SortingCollection;
import htsjdk.samtools.util.SortingCollection.Codec;
import org.apache.log4j.Logger;
import org.broad.igv.sam.DotAlignedAlignment;
import java.io.*;
/**
* private String chromosome;
* private int start;
* private int end;
* boolean negativeStrand;
*
* @author jrobinso
*/
public class DotAlignedCodec implements SortingCollection.Codec<DotAlignedAlignment> {
private static Logger log = Logger.getLogger(DotAlignedCodec.class);
DataOutputStream outputStream;
DataInputStream inputStream;
public void setOutputStream(OutputStream outputStream) {
this.outputStream = new DataOutputStream(outputStream);
}
public void setInputStream(InputStream inputStream) {
this.inputStream = new DataInputStream(inputStream);
}
public void encode(DotAlignedAlignment alignment) {
try {
outputStream.writeUTF(alignment.getChr());
outputStream.writeInt(alignment.getStart());
outputStream.writeInt(alignment.getEnd());
outputStream.writeBoolean(alignment.isNegativeStrand());
} catch (IOException ex) {
log.error("Error encoding alignment", ex);
}
}
public DotAlignedAlignment decode() {
try {
String chr = inputStream.readUTF();
int start = inputStream.readInt();
int end = inputStream.readInt();
boolean negativeStrand = inputStream.readBoolean();
return new DotAlignedAlignment(chr, start, end, negativeStrand);
} catch (EOFException ex) {
return null;
} catch (IOException ex) {
log.error("Error decoding alignment", ex);
return null;
}
}
public Codec<DotAlignedAlignment> clone() {
DotAlignedCodec other = new DotAlignedCodec();
return other;
}
}