/*
* 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.feature.tribble;
import htsjdk.tribble.TribbleIndexedFeatureReader;
import htsjdk.tribble.index.Index;
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();
}
}