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/*
* Copyright (C) 2009-2010 Institute for Computational Biomedicine,
* Weill Medical College of Cornell University
*
* This file is part of the Goby IO API.
*
* The Goby IO API is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The Goby IO API is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the Goby IO API. If not, see <http://www.gnu.org/licenses/>.
*/
package org.campagnelab.goby.alignments;
import it.unimi.dsi.fastutil.objects.ObjectArrayList;
import java.io.Closeable;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.util.zip.GZIPOutputStream;
/**
* Writes the too many hit data structure Protocol Buffer format.
* See Alignements.proto for the specification of this format.
*
* @author Fabien Campagne
* Date: May 5, 2009
* Time: 2:03 PM
*/
public class AlignmentTooManyHitsWriter implements Closeable {
private boolean tooManyHitsWritten;
private final OutputStream tooManyHitsOutput;
private final Alignments.AlignmentTooManyHits.Builder tooManyHits;
private Alignments.AmbiguousLocation.Builder newAmbiguousLocation;
/**
* A collection where the append AmbiguousLocation until it is time to write the PB messages. We use a fastutil collection
* for performance upon add when the list becomes large.
*/
private ObjectArrayList<Alignments.AmbiguousLocation>localCachedCollection=new ObjectArrayList<Alignments.AmbiguousLocation>();
public AlignmentTooManyHitsWriter(final String outputBasename, final int alignerThreshold) throws IOException {
tooManyHitsOutput = new GZIPOutputStream(new FileOutputStream(outputBasename + ".tmh"));
newAmbiguousLocation = Alignments.AmbiguousLocation.newBuilder();
tooManyHits = Alignments.AlignmentTooManyHits.newBuilder();
tooManyHits.setAlignerThreshold(alignerThreshold);
}
/**
* Update the aligner threshold.
* @param alignerThreshold the new threshold to write in the too many hits file.
*/
public void setAlignerThreshold(final int alignerThreshold) {
tooManyHits.setAlignerThreshold(alignerThreshold);
}
/**
* {@inheritDoc}
*/
public void close() throws IOException {
if (!localCachedCollection.isEmpty()) {
tooManyHits.addAllHits(localCachedCollection);
localCachedCollection.clear();
}
write();
}
public void write() throws IOException {
if (!tooManyHitsWritten) {
tooManyHits.build().writeTo(tooManyHitsOutput);
tooManyHitsOutput.close();
tooManyHitsWritten = true;
//recover the memory:
tooManyHits.clear();
}
}
public Alignments.AmbiguousLocation.Builder getNewAmbiguousLocation() {
return newAmbiguousLocation;
}
/**
* Append record defined by 3 arguments.
* previously called appendTooManyHits()
*/
public void append(final int queryIndex, final int howManyHits, final int lengthOfMatch) {
newAmbiguousLocation.setQueryIndex(queryIndex);
newAmbiguousLocation.setAtLeastNumberOfHits(howManyHits);
newAmbiguousLocation.setLengthOfMatch(lengthOfMatch);
append();
}
/**
* Append the current too many hits record.
*/
public void append() {
assert tooManyHits.hasAlignerThreshold() : "append> writer missing aligner threshold";
assert newAmbiguousLocation.hasAtLeastNumberOfHits() : "append> new record missing atLeastNumberOfHits";
if (newAmbiguousLocation.getAtLeastNumberOfHits() > tooManyHits.getAlignerThreshold()) {
final Alignments.AmbiguousLocation builder = newAmbiguousLocation.build();
localCachedCollection.add(builder);
}
//tooManyHits.addHits(newAmbiguousLocation.build());
// whether or not the hit was added, reset/create a new one
newAmbiguousLocation = Alignments.AmbiguousLocation.newBuilder();
}
}
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