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/*
* Copyright (C) 2009-2011 Institute for Computational Biomedicine,
* Weill Medical College of Cornell University
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* This program 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.campagnelab.goby.counts;
import it.unimi.dsi.fastutil.io.FastByteArrayInputStream;
import org.campagnelab.goby.counts.compound.*;
import java.io.DataInputStream;
import java.io.IOException;
import java.io.InputStream;
/**
* A count archive reader that caches the last chromosome accessed.
*
* @author Fabien Campagne
* Date: 6/12/11
* Time: 2:09 PM
*/
public class CachingCountsArchiveReader extends CountsArchiveReader {
private byte[] bytes;
private String previousId;
private byte[] indexBytes;
private boolean hasIndex;
public CachingCountsArchiveReader(final String basename) throws IOException {
super(basename);
}
int previousIndex = -1;
/**
* Determine if the previous counts reader returned supports position().
* @return
*/
public boolean hasIndex() {
return hasIndex;
}
/**
* Obtain the count reader over the count information identified by id.
*
* @param identifier The indentifier of the count information to retrieve.
* @return A countReader over count information associated with the id.
* @throws IOException If an error occurs reading count information.
*/
@Override
public CountsReader getCountReader(final String identifier) throws IOException {
if (identifier == null || previousId == null || !identifier.equals(previousId)) {
String name = makeFileIdentifier(identifier);
final CompoundDataInput input = compoundReader.readFile(name);
bytes = new byte[(int) input.length()];
input.readFully(bytes);
String indexName = "#index:" + name;
if (compoundReader.containsFile(indexName)) {
final CompoundDataInput indexInput = compoundReader.readFile(indexName);
indexBytes = new byte[(int) indexInput.length()];
indexInput.readFully(indexBytes);
hasIndex = true;
}
previousId = identifier;
}
final InputStream stream = new FastByteArrayInputStream(bytes);
if (hasIndex) {
final DataInputStream indexDataInput = new DataInputStream(new FastByteArrayInputStream(indexBytes));
return new CountsReader(stream, indexDataInput);
} else {
return new CountsReader(stream);
}
}
}
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