edu.dfci.cccb.mev.stats.domain.cli.CliRWilcoxonBuilder.java Source code

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Here is the source code for edu.dfci.cccb.mev.stats.domain.cli.CliRWilcoxonBuilder.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.stats.domain.cli;

import static java.lang.Boolean.valueOf;
import static org.apache.commons.io.IOUtils.copy;

import java.io.BufferedReader;
import java.io.ByteArrayOutputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintStream;
import java.util.AbstractList;
import java.util.Collections;
import java.util.List;

import javax.inject.Inject;
import javax.inject.Named;
import javax.script.ScriptEngine;
import javax.script.ScriptException;

import lombok.Getter;
import lombok.Setter;
import lombok.SneakyThrows;
import lombok.experimental.Accessors;
import ch.lambdaj.Lambda;
import edu.dfci.cccb.mev.dataset.domain.contract.DatasetException;
import edu.dfci.cccb.mev.dataset.domain.contract.Dimension.Type;
import edu.dfci.cccb.mev.dataset.domain.contract.InvalidDimensionTypeException;
import edu.dfci.cccb.mev.io.implementation.TemporaryFile;
import edu.dfci.cccb.mev.stats.domain.contract.Wilcoxon;
import edu.dfci.cccb.mev.stats.domain.prototype.AbstractWilcoxonBuilder;

/**
 * @author levk
 * 
 */
@Accessors(chain = true)
public class CliRWilcoxonBuilder extends AbstractWilcoxonBuilder {

    private @Getter @Setter @Inject @Named("R") ScriptEngine r;

    @SuppressWarnings("unchecked")
    private List<Double> column(final String column) {
        return column != null ? new AbstractList<Double>() {

            @Override
            @SneakyThrows(DatasetException.class)
            public Double get(int index) {
                return dataset().values().get(dataset().dimension(Type.ROW).keys().get(index), column);
            }

            @Override
            @SneakyThrows(InvalidDimensionTypeException.class)
            public int size() {
                return dataset().dimension(Type.ROW).keys().size();
            }
        } : ((List<Double>) Collections.EMPTY_LIST);
    }

    /* (non-Javadoc)
     * @see edu.dfci.cccb.mev.dataset.domain.contract.AnalysisBuilder#build() */
    @Override
    public Wilcoxon build() throws DatasetException {
        try (TemporaryFile sample1 = new TemporaryFile();
                TemporaryFile sample2 = new TemporaryFile();
                TemporaryFile wilcoxon = new TemporaryFile();
                ByteArrayOutputStream script = new ByteArrayOutputStream();
                PrintStream s = new PrintStream(script)) {

            try (PrintStream s1 = new PrintStream(new FileOutputStream(sample1));
                    PrintStream s2 = new PrintStream(new FileOutputStream(sample2))) {
                s1.println(Lambda.join(column(first()), "\t"));
                if (second() != null)
                    s2.println(Lambda.join(column(second()), "\t"));
            }

            s.println("SAMPLE1_FILE=\"" + sample1.getAbsolutePath() + "\"");
            s.println("SAMPLE2_FILE=" + (second() == null ? "NULL" : ("\"" + sample2.getAbsolutePath() + "\"")));
            s.println("ALT_HYPOTHESIS=\"" + hypothesis() + "\"");
            s.println("IS_PAIRED=" + valueOf(pair()).toString().toUpperCase());
            s.println("IS_CONF_INT=" + valueOf(confidentInterval()).toString().toUpperCase());
            s.println("WILCOX_OUT=\"" + wilcoxon.getAbsolutePath() + "\"");

            copy(getClass().getResourceAsStream("/wilcoxon.r"), s);

            r.eval(script.toString());

            try (BufferedReader reader = new BufferedReader(new FileReader(wilcoxon))) {
                reader.readLine();
                final double wStat = Double.parseDouble(reader.readLine().split("\t")[1]);
                final double pValue = Double.parseDouble(reader.readLine().split("\t")[1]);

                return new PojoWilcoxon(wStat, pValue).name(this.name()).type(type());
            }
        } catch (IOException | ScriptException e) {
            throw new DatasetException(e);
        }
    }
}