edu.dfci.cccb.mev.deseq.domain.simple.FileBackedDESeq.java Source code

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Here is the source code for edu.dfci.cccb.mev.deseq.domain.simple.FileBackedDESeq.java

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/**
 * 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 3 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, see <http://www.gnu.org/licenses/>.
 */
package edu.dfci.cccb.mev.deseq.domain.simple;

import static edu.dfci.cccb.mev.deseq.domain.simple.StatelessScriptEngineFileBackedDESeqBuilder.OUTPUT_FILENAME;
import static java.lang.Double.parseDouble;

import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.Iterator;

import lombok.Getter;
import lombok.SneakyThrows;
import lombok.Synchronized;
import lombok.ToString;
import org.apache.commons.io.IOUtils;

import edu.dfci.cccb.mev.deseq.domain.prototype.AbstractDESeq;
import edu.dfci.cccb.mev.io.implementation.TemporaryFolder;

/**
 * @author levk
 * 
 */
@ToString
public class FileBackedDESeq extends AbstractDESeq implements AutoCloseable {

    private @Getter final File full;
    private @Getter final TemporaryFolder tempFolder;

    public FileBackedDESeq(TemporaryFolder tempFolder) {
        this.tempFolder = tempFolder;
        this.full = new File(this.tempFolder, OUTPUT_FILENAME);
    }

    @SneakyThrows
    public static FileBackedDESeq from(InputStream results) {
        FileBackedDESeq result = new FileBackedDESeq(new TemporaryFolder());
        try (OutputStream full = new BufferedOutputStream(new FileOutputStream(result.full));
                BufferedInputStream in = new BufferedInputStream(results)) {
            IOUtils.copy(in, full);
        }
        return result;
    }

    @SneakyThrows
    public void to(OutputStream out) {
        try (InputStream full = new BufferedInputStream(new FileInputStream(this.full));
                OutputStream o = new BufferedOutputStream(out)) {
            IOUtils.copy(full, o);
        }
    }

    /* (non-Javadoc)
     * @see edu.dfci.cccb.mev.deseq.domain.contract.DESeqResult#full() */
    @Override
    public Iterable<Entry> full() {
        return iterateEntries(full);
    }

    private Iterable<Entry> iterateEntries(final File file) {
        return new Iterable<Entry>() {

            /* (non-Javadoc)
             * @see java.lang.Iterable#iterator() */
            @Override
            @SneakyThrows(IOException.class)
            public Iterator<Entry> iterator() {
                return new Iterator<Entry>() {

                    private final BufferedReader reader = new BufferedReader(new FileReader(file));
                    private String current = null;

                    @Override
                    @Synchronized
                    @SneakyThrows(IOException.class)
                    public boolean hasNext() {
                        return current == null ? (current = reader.readLine()) != null : true;
                    }

                    @Override
                    @Synchronized
                    public Entry next() {
                        hasNext();
                        Entry result = parse(current);
                        current = null;
                        return result;
                    }

                    @Override
                    public void remove() {
                        throw new UnsupportedOperationException();
                    }
                };
            }
        };
    }

    private Entry parse(String line) {
        final String[] split = line.split("\t");
        return new SimpleEntry(string(0, split), number(5, split), number(2, split), number(3, split),
                number(6, split), number(7, split));
    }

    private String string(int index, String[] split) {
        return split[index];
    }

    private Double number(int index, String[] split) {
        String value = string(index, split);
        if ("Inf".equals(value))
            return Double.POSITIVE_INFINITY;
        else if ("-Inf".equals(value))
            return Double.NEGATIVE_INFINITY;
        else if ("NA".equals(value))
            return Double.NaN;
        else
            return parseDouble(value);
    }

    /* (non-Javadoc)
     * @see java.lang.Object#finalize() */
    @Override
    protected void finalize() throws Throwable {
        close();
    }

    /* (non-Javadoc)
     * @see java.lang.AutoCloseable#close() */
    @Override
    public void close() throws Exception {
        tempFolder.close();
    }
}