/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
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
}
}