kogiri.common.hadoop.io.reader.fasta.FastaTextReadReader.java Source code

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Here is the source code for kogiri.common.hadoop.io.reader.fasta.FastaTextReadReader.java

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/*
 * 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.reader.fasta;

import java.io.IOException;
import kogiri.common.fasta.FastaRawRead;

import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.InputSplit;
import org.apache.hadoop.mapreduce.RecordReader;
import org.apache.hadoop.mapreduce.TaskAttemptContext;

/**
 *
 * @author iychoi
 */
public class FastaTextReadReader extends RecordReader<Text, Text> {

    private FastaRawReadReader rawReadReader = new FastaRawReadReader();

    private Text key;
    private Text value;

    @Override
    public Text getCurrentKey() throws IOException, InterruptedException {
        return this.key;
    }

    @Override
    public Text getCurrentValue() throws IOException, InterruptedException {
        return this.value;
    }

    @Override
    public void initialize(InputSplit genericSplit, TaskAttemptContext context)
            throws IOException, InterruptedException {

        this.rawReadReader.initialize(genericSplit, context);

        this.key = null;
        this.value = null;
    }

    @Override
    public boolean nextKeyValue() throws IOException, InterruptedException {
        boolean retVal = this.rawReadReader.nextKeyValue();
        if (retVal) {
            FastaRawRead value = this.rawReadReader.getCurrentValue();
            if (value != null) {
                String description = value.getDescription();
                String pureSequence = new String();
                for (int i = 0; i < value.getRawSequence().length; i++) {
                    pureSequence += value.getRawSequence()[i].getLine();
                }

                this.key = new Text(description);
                this.value = new Text(pureSequence);
            } else {
                this.key = null;
                this.value = null;
            }
        } else {
            this.key = null;
            this.value = null;
        }

        return retVal;
    }

    @Override
    public float getProgress() throws IOException {
        return this.rawReadReader.getProgress();
    }

    @Override
    public void close() throws IOException {
        this.rawReadReader.close();
    }
}