edu.rit.flick.genetics.FastaFileInflator.java Source code

Introduction

Here is the source code for edu.rit.flick.genetics.FastaFileInflator.java

Source

/**
 *  COPYRIGHT (C) 2015 Alex Aiezza. All Rights Reserved.
 *
 *  See the LICENSE for the specific language governing permissions and
 *  limitations under the License provided with this project.
 */
package edu.rit.flick.genetics;

import static org.apache.commons.io.FileUtils.getFile;

import java.io.File;
import java.io.IOException;
import java.util.Scanner;
import java.util.StringTokenizer;

import edu.rit.flick.genetics.util.HexPrinter;

/**
 * @author Alex Aiezza
 *
 */
public class FastaFileInflator extends FastFileInflator implements FastaFileArchiver {
    // Input files
    protected Scanner tandemFile;

    // Tracking fields
    protected boolean useCustomSequenceLineSize;
    protected int fastaSequenceLineSize = DEFAULT_FASTA_SEQUENCE_LINE_SIZE;

    protected long tandemStart = -1, tandemEnd = -1;
    protected boolean inTandemRepeat = false;

    @Override
    protected void afterWriteNucleotide() {
        super.afterWriteNucleotide();
        try {
            if (seqDnaPosition.get() % fastaSequenceLineSize == 0 && fastOut.position() != headerPosition)
                writeNewline();
        } catch (final IOException e) {
            e.printStackTrace();
        }
    }

    @Override
    protected void close() throws IOException, InterruptedException {
        super.close();
        if (tandemFile != null)
            tandemFile.close();
    }

    @SuppressWarnings("resource")
    @Override
    protected void createOutputFiles(final String tempOutputDirectory, final File fastFile) throws IOException {
        useCustomSequenceLineSize = false;
        super.createOutputFiles(tempOutputDirectory, fastFile);

        tandemFile = new Scanner(getFile(tempOutputDirectory, TANDEM_REPEAT_FILE)).useDelimiter("\\" + PIPE);
    }

    @Override
    public int getFastaSequenceLineSize() {
        return fastaSequenceLineSize;
    }

    private void getNextTandemRepeatChunk() {
        inTandemRepeat = false;
        if (tandemFile.hasNext()) {
            final StringTokenizer tandems = new StringTokenizer(tandemFile.next(), RANGE);
            tandemStart = Long.parseLong(tandems.nextToken(), HexPrinter.RADIX);
            tandemEnd = Long.parseLong(tandems.nextToken(), HexPrinter.RADIX);
        }
    }

    @Override
    protected void initializeInflator() {
        super.initializeInflator();

        tandemStart = -1;
        tandemEnd = -1;
        inTandemRepeat = false;

        // Get first tandem repeat chunk
        getNextTandemRepeatChunk();
    }

    @Override
    protected void parseProperties() {
        super.parseProperties();
        fastaSequenceLineSize = useCustomSequenceLineSize ? fastaSequenceLineSize
                : Integer.parseInt((String) metafile.get(META_FASTA_SEQUENCE_LINE_LENGTH));
    }

    @Override
    protected void processSequence() {
        if (dnaPosition.longValue() == tandemStart)
            inTandemRepeat = true;

        // Wrap up a tandem repeat section
        if (dnaPosition.longValue() == tandemEnd) {
            inTandemRepeat = false;
            // Get next tandemRepeatSection
            getNextTandemRepeatChunk();
        }
        super.processSequence();
    }

    @Override
    public void setFastaSequenceLineSize(final int fastaSequenceLineSize) {
        useCustomSequenceLineSize = true;
        this.fastaSequenceLineSize = fastaSequenceLineSize;
    }

    @Override
    protected void writeNucleotide(final byte base) {
        byte nucleotide = (byte) (inTandemRepeat ? Character.toLowerCase(base) : base);
        nucleotide = isRNAData() && nucleotide == t ? u : nucleotide;
        super.writeNucleotide(nucleotide);
    }
}