htsjdk.samtools.cram.encoding.SubexponentialIntegerEncoding Maven / Gradle / Ivy

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/**
 * ****************************************************************************
 * 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;

import htsjdk.samtools.cram.io.ExposedByteArrayOutputStream;
import htsjdk.samtools.cram.io.ITF8;
import htsjdk.samtools.cram.structure.EncodingID;
import htsjdk.samtools.cram.structure.EncodingParams;

import java.io.InputStream;
import java.nio.ByteBuffer;
import java.util.Map;

public class SubexponentialIntegerEncoding implements Encoding {
    private static final EncodingID ENCODING_ID = EncodingID.SUBEXPONENTIAL;
    private int offset;
    private int k;

    public SubexponentialIntegerEncoding() {
    }

    public SubexponentialIntegerEncoding(final int offset, final int k) {
        this.offset = offset;
        this.k = k;
    }

    @Override
    public EncodingID id() {
        return ENCODING_ID;
    }

    public static EncodingParams toParam(final int offset, final int k) {
        final SubexponentialIntegerEncoding subexponentialIntegerEncoding = new SubexponentialIntegerEncoding();
        subexponentialIntegerEncoding.offset = offset;
        subexponentialIntegerEncoding.k = k;
        return new EncodingParams(ENCODING_ID, subexponentialIntegerEncoding.toByteArray());
    }

    @Override
    public byte[] toByteArray() {
        final ByteBuffer buffer = ByteBuffer.allocate(10);
        ITF8.writeUnsignedITF8(offset, buffer);
        ITF8.writeUnsignedITF8(k, buffer);
        buffer.flip();
        final byte[] bytes = new byte[buffer.limit()];
        buffer.get(bytes);
        return bytes;
    }

    @Override
    public void fromByteArray(final byte[] data) {
        final ByteBuffer buffer = ByteBuffer.wrap(data);
        offset = ITF8.readUnsignedITF8(buffer);
        k = ITF8.readUnsignedITF8(buffer);
    }

    @Override
    public BitCodec buildCodec(final Map inputMap,
                                        final Map outputMap) {
        return new SubexponentialIntegerCodec(offset, k);
    }

}