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

Introduction

Here is the source code for edu.dfci.cccb.mev.stats.domain.cli.CliRFisherBuilder.java

Source

/**
 * 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.FileReader;
import java.io.IOException;
import java.io.PrintStream;

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

import lombok.Getter;
import lombok.Setter;
import lombok.experimental.Accessors;
import edu.dfci.cccb.mev.dataset.domain.contract.DatasetException;
import edu.dfci.cccb.mev.io.implementation.TemporaryFile;
import edu.dfci.cccb.mev.stats.domain.contract.Fisher;
import edu.dfci.cccb.mev.stats.domain.prototype.AbstractFisherBuilder;

/**
 * @author levk
 * 
 */
@Accessors(chain = true)
public class CliRFisherBuilder extends AbstractFisherBuilder {

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

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

            s.println("M=" + m());
            s.println("N=" + n());
            s.println("S=" + s());
            s.println("T=" + t());
            s.println("ALT_HYPOTHESIS=\"" + hypothesis() + "\"");
            s.println("IS_SIMULATED=" + valueOf(simulate()).toString().toUpperCase());
            s.println("FISHER_OUT=\"" + fisher.getAbsolutePath() + "\"");

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

            r.eval(script.toString());

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

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