/*
* 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.apache.log4j.Logger;
import htsjdk.tribble.Feature;
import htsjdk.tribble.FeatureCodec;
import htsjdk.tribble.readers.PositionalBufferedStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
/**
* @author jacob
* @date 2013-Jun-14
*/
public class FeatureCodecDecoder<D extends Feature> implements FeatureDecoder<D> {
private static Logger log = Logger.getLogger(PluginSource.class);
private FeatureCodec<D, PositionalBufferedStream> codec;
public FeatureCodecDecoder(FeatureCodec<D, PositionalBufferedStream> codec) {
this.codec = codec;
}
@Override
public Iterator<D> decodeAll(InputStream is, boolean strictParsing) throws IOException {
PositionalBufferedStream pis = new PositionalBufferedStream(is);
this.codec.readHeader(pis);
List<D> features = new ArrayList<D>();
while (!pis.isDone()) {
try {
D feature = this.codec.decode(pis);
if (feature != null) {
features.add(feature);
}
} catch (Exception e) {
log.error(e.getMessage(), e);
if (strictParsing) {
throw new RuntimeException(e);
}
} finally {
pis.close();
}
}
return features.iterator();
}
@Override
public void setAttributes(List<Map<String, Object>> attributes) {
//pass
}
@Override
public void setInputs(List<String> commands, Map<Argument, Object> argumentMap) {
//pass
}
}