/*
* Copyright (c) 2007-2012 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.feature.tribble;
import org.apache.log4j.Logger;
import org.broad.igv.feature.AbstractCacher;
import htsjdk.tribble.CloseableTribbleIterator;
import htsjdk.tribble.Feature;
import htsjdk.tribble.FeatureReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
* @author jrobinso
* @date Jun 24, 2010
*/
public class CachingFeatureReader extends AbstractCacher implements IGVFeatureReader {
private static Logger log = Logger.getLogger(CachingFeatureReader.class);
private static int maxBinCount = 1000;
private static int defaultBinSize = 16000; // <= 16 kb
private FeatureReader tribbleFeatureReader;
public CachingFeatureReader(FeatureReader tribbleFeatureReader) {
this(tribbleFeatureReader, maxBinCount, defaultBinSize);
}
public CachingFeatureReader(FeatureReader tribbleFeatureReader, int binCount, int binSize) {
super(binCount, binSize);
this.tribbleFeatureReader = tribbleFeatureReader;
}
@Override
protected Iterator<Feature> queryRaw(String chr, int start, int end) throws IOException {
// Tribble iterators must be closed, so we need to copy the features and insure closure before exiting.
CloseableTribbleIterator<Feature> iter = null;
try {
iter = tribbleFeatureReader.query(chr, start, end);
List<Feature> featureList = new ArrayList<Feature>();
while (iter.hasNext()) {
Feature f = iter.next();
if (f.getStart() > end) {
break;
} else if (f.getEnd() < start) {
continue;
} else {
featureList.add(f);
}
}
return featureList.iterator();
} finally {
if (iter != null) iter.close();
}
}
@Override
public List<String> getSequenceNames() {
return tribbleFeatureReader.getSequenceNames();
}
@Override
public Object getHeader() {
return tribbleFeatureReader.getHeader();
}
@Override
public Iterator query(String chr, int start, int end) throws IOException {
return queryCached(chr, start, end);
}
/**
* Return an iterator over the entire file. Nothing to cache, just delegate to the wrapped reader
*
* @throws java.io.IOException
*/
@Override
public Iterator iterator() throws IOException {
return tribbleFeatureReader.iterator();
}
}