/*
* The MIT License
*
* Copyright (c) 2013 The 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 htsjdk.tribble.example;
import htsjdk.tribble.AbstractFeatureReader;
import htsjdk.tribble.BasicFeature;
import htsjdk.tribble.BinaryFeatureCodec;
import htsjdk.tribble.Feature;
import htsjdk.tribble.FeatureCodec;
import htsjdk.tribble.FeatureCodecHeader;
import htsjdk.tribble.FeatureReader;
import htsjdk.tribble.readers.AsciiLineReader;
import htsjdk.tribble.readers.LineIterator;
import htsjdk.tribble.readers.PositionalBufferedStream;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
* An example binary codec that encodes / decodes contig / start / stop values via DataInputStreams
*
* @author Mark DePristo
*/
public class ExampleBinaryCodec extends BinaryFeatureCodec<Feature> {
public final static String HEADER_LINE = "# BinaryTestFeature";
@Override
public Feature decodeLoc(final PositionalBufferedStream stream) throws IOException {
return decode(stream);
}
@Override
public Feature decode(final PositionalBufferedStream stream) throws IOException {
DataInputStream dis = new DataInputStream(stream);
String contig = dis.readUTF();
int start = dis.readInt();
int stop = dis.readInt();
return new BasicFeature(contig, start, stop);
}
@Override
public FeatureCodecHeader readHeader(final PositionalBufferedStream stream) throws IOException {
// Construct a reader that does not read ahead (because we don't want to consume data from the stream that is not the header)
final AsciiLineReader nonReadAheadLineReader = new AsciiLineReader(stream);
final List<String> headerLines = new ArrayList<String>();
long headerLengthInBytes = 0;
while (stream.peek() == ('#' & 0xff)) { // Look for header lines, which are prefixed by '#'.
headerLines.add(nonReadAheadLineReader.readLine());
headerLengthInBytes = stream.getPosition();
}
return new FeatureCodecHeader(headerLines, headerLengthInBytes);
}
@Override
public Class<Feature> getFeatureType() {
return Feature.class;
}
@Override
public boolean canDecode(final String path) {
return false;
}
/**
* Convenience method that creates an ExampleBinaryCodec file from another feature file.
*
* For testing purposes really
*
* @param source file containing the features
* @param dest the place to write the binary features
* @param codec of the source file features
* @throws IOException
*/
public static <FEATURE_TYPE extends Feature> void convertToBinaryTest(final File source, final File dest, final FeatureCodec<FEATURE_TYPE, LineIterator> codec) throws IOException {
final FeatureReader<FEATURE_TYPE> reader = AbstractFeatureReader.getFeatureReader(source.getAbsolutePath(), codec, false); // IndexFactory.loadIndex(idxFile));
final OutputStream output = new FileOutputStream(dest);
ExampleBinaryCodec.convertToBinaryTest(reader, output);
}
/**
* Convenience method that creates an ExampleBinaryCodec file from another feature file.
*
* For testing purposes really
*
* @throws IOException
*/
public static <FEATURE_TYPE extends Feature> void convertToBinaryTest(final FeatureReader<FEATURE_TYPE> reader, final OutputStream out) throws IOException {
DataOutputStream dos = new DataOutputStream(out);
dos.writeBytes(HEADER_LINE + "\n");
Iterator<FEATURE_TYPE> it = reader.iterator();
while ( it.hasNext() ) {
final Feature f = it.next();
dos.writeUTF(f.getChr());
dos.writeInt(f.getStart());
dos.writeInt(f.getEnd());
}
dos.close();
reader.close();
}
}