Java tutorial
/* * Copyright (C) 2015 iychoi * * 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 2 * 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, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package kogiri.common.hadoop.io.datatypes; import java.io.DataInput; import java.io.DataOutput; import java.io.IOException; import kogiri.common.helpers.SequenceHelper; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.hadoop.io.BinaryComparable; import org.apache.hadoop.io.WritableComparable; import org.apache.hadoop.io.WritableComparator; /** * * @author iychoi */ public class CompressedSequenceWritable extends BinaryComparable implements WritableComparable<BinaryComparable> { private static final Log LOG = LogFactory.getLog(CompressedSequenceWritable.class); private byte[] compressedSequence; private int seqLength; private static final int LENGTH_BYTES = 1; public CompressedSequenceWritable() { } public CompressedSequenceWritable(String sequence) throws IOException { set(sequence); } public CompressedSequenceWritable(byte[] compressedSequence, int seqLength) { set(compressedSequence, seqLength); } /** * Set the value. */ public void set(byte[] compressedSequence, int seqLength) { this.compressedSequence = compressedSequence; this.seqLength = seqLength; } public void set(String sequence) throws IOException { this.compressedSequence = SequenceHelper.compress(sequence); this.seqLength = sequence.length(); } public void set(CompressedSequenceWritable that) throws IOException { this.compressedSequence = that.compressedSequence; this.seqLength = that.seqLength; } public void setEmpty() { this.compressedSequence = null; this.seqLength = 0; } public boolean isEmpty() { if (this.compressedSequence == null || this.seqLength == 0) { return true; } return false; } /** * Return the value. */ public byte[] getCompressedSequence() { return this.compressedSequence; } public String getSequence() { return SequenceHelper.decompress(this.compressedSequence, this.seqLength); } public int getSequenceLength() { return this.seqLength; } @Override public void readFields(DataInput in) throws IOException { this.seqLength = in.readByte(); int byteLen = SequenceHelper.getCompressedSize(this.seqLength); this.compressedSequence = new byte[byteLen]; in.readFully(this.compressedSequence, 0, byteLen); } @Override public void write(DataOutput out) throws IOException { out.writeByte(this.seqLength); out.write(this.compressedSequence); } /** * Returns true iff */ @Override public boolean equals(Object o) { if (o instanceof CompressedSequenceWritable) { return super.equals(o); } return false; } @Override public int hashCode() { return super.hashCode(); } @Override public String toString() { return SequenceHelper.decompress(this.compressedSequence, this.seqLength); } @Override public int getLength() { return this.compressedSequence.length; } @Override public byte[] getBytes() { return this.compressedSequence; } /** A Comparator optimized for CompressedFastaSequenceWritable. */ public static class Comparator extends WritableComparator { public Comparator() { super(CompressedSequenceWritable.class); } /** * Compare the buffers in serialized form. */ public int compare(byte[] b1, int s1, int l1, byte[] b2, int s2, int l2) { return compareBytes(b1, s1 + LENGTH_BYTES, l1 - LENGTH_BYTES, b2, s2 + LENGTH_BYTES, l2 - LENGTH_BYTES); } } static { // register this comparator WritableComparator.define(CompressedSequenceWritable.class, new Comparator()); } }