htsjdk.samtools.cram.encoding.writer.DataWriterFactory Maven / Gradle / Ivy
/**
* ****************************************************************************
* Copyright 2013 EMBL-EBI
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* ****************************************************************************
*/
package htsjdk.samtools.cram.encoding.writer;
import htsjdk.samtools.cram.encoding.BitCodec;
import htsjdk.samtools.cram.encoding.DataSeries;
import htsjdk.samtools.cram.encoding.DataSeriesMap;
import htsjdk.samtools.cram.encoding.DataSeriesType;
import htsjdk.samtools.cram.encoding.Encoding;
import htsjdk.samtools.cram.encoding.EncodingFactory;
import htsjdk.samtools.cram.io.BitOutputStream;
import htsjdk.samtools.cram.io.ExposedByteArrayOutputStream;
import htsjdk.samtools.cram.structure.CompressionHeader;
import htsjdk.samtools.cram.structure.EncodingKey;
import htsjdk.samtools.cram.structure.EncodingParams;
import java.io.IOException;
import java.lang.reflect.Field;
import java.util.HashMap;
import java.util.Map;
public class DataWriterFactory {
public Writer buildWriter(final BitOutputStream bitOutputStream,
final Map outputMap,
final CompressionHeader h, final int refId) throws IllegalArgumentException,
IllegalAccessException {
final Writer writer = new Writer();
writer.setCaptureReadNames(h.readNamesIncluded);
writer.refId = refId;
writer.substitutionMatrix = h.substitutionMatrix;
writer.AP_delta = h.APDelta;
for (final Field f : writer.getClass().getFields()) {
if (f.isAnnotationPresent(DataSeries.class)) {
final DataSeries ds = f.getAnnotation(DataSeries.class);
final EncodingKey key = ds.key();
final DataSeriesType type = ds.type();
f.set(writer,
createWriter(type, h.encodingMap.get(key), bitOutputStream, outputMap));
}
if (f.isAnnotationPresent(DataSeriesMap.class)) {
final DataSeriesMap dsm = f.getAnnotation(DataSeriesMap.class);
final String name = dsm.name();
if ("TAG".equals(name)) {
final Map> map = new HashMap>();
for (final Integer key : h.tMap.keySet()) {
final EncodingParams params = h.tMap.get(key);
final DataWriter tagWriter = createWriter(
DataSeriesType.BYTE_ARRAY, params, bitOutputStream,
outputMap);
map.put(key, tagWriter);
}
f.set(writer, map);
}
}
}
return writer;
}
private DataWriter createWriter(final DataSeriesType valueType,
final EncodingParams params, final BitOutputStream bitOutputStream,
final Map outputMap) {
final EncodingFactory f = new EncodingFactory();
final Encoding encoding = f.createEncoding(valueType, params.id);
if (encoding == null)
throw new RuntimeException("Encoding not found: value type="
+ valueType.name() + ", encoding id=" + params.id.name());
encoding.fromByteArray(params.params);
return new DefaultDataWriter(encoding.buildCodec(null, outputMap),
bitOutputStream);
}
private static class DefaultDataWriter implements DataWriter {
private final BitCodec codec;
private final BitOutputStream bitOutputStream;
public DefaultDataWriter(final BitCodec codec, final BitOutputStream bitOutputStream) {
this.codec = codec;
this.bitOutputStream = bitOutputStream;
}
@Override
public long writeData(final T value) throws IOException {
return codec.write(bitOutputStream, value);
}
}
}