package org.broad.igv.feature.tribble;
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: 5/8/13
* Time: 11:02 AM
*/
public class TribbleReaderWrapper implements IGVFeatureReader {
FeatureReader<Feature> wrappedReader;
public TribbleReaderWrapper(FeatureReader<Feature> wrappedReader) {
this.wrappedReader = wrappedReader;
}
@Override
public Iterator<Feature> query(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 = wrappedReader.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 Iterator<Feature> iterator() throws IOException {
// Note: Technically this is a file handle leak as the "close" method of the tribble iterator is not called.
// In practice this is not a problem as the iterator() method is only called by batch programs transversing
// the entire file. It is none-the-less a file handle leak that should be addressed at some point.
return wrappedReader.iterator();
}
@Override
public List<String> getSequenceNames() {
return wrappedReader.getSequenceNames();
}
@Override
public Object getHeader() {
return wrappedReader.getHeader();
}
}