gov.nih.nci.caintegrator.application.arraydata.GeneLocationFileLoader.java Source code

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Here is the source code for gov.nih.nci.caintegrator.application.arraydata.GeneLocationFileLoader.java

Source

/**
 * Copyright 5AM Solutions Inc, ESAC, ScenPro & SAIC
 *
 * Distributed under the OSI-approved BSD 3-Clause License.
 * See http://ncip.github.com/caintegrator/LICENSE.txt for details.
 */
package gov.nih.nci.caintegrator.application.arraydata;

import gov.nih.nci.caintegrator.application.study.ValidationException;
import gov.nih.nci.caintegrator.domain.genomic.ChromosomalLocation;
import gov.nih.nci.caintegrator.domain.genomic.GeneChromosomalLocation;
import gov.nih.nci.caintegrator.domain.genomic.GeneLocationConfiguration;

import java.io.File;
import java.io.FileReader;
import java.io.IOException;

import org.apache.commons.io.IOUtils;

import au.com.bytecode.opencsv.CSVReader;

/**
 * Loader for the Gene Location file, line format is the following:.
 * chromosomeNumber startPosition endPosition geneSymbol
 */
final class GeneLocationFileLoader {
    private static final char DELIMITER = ' ';

    private GeneLocationFileLoader() {
    }

    static void loadFile(GeneLocationConfiguration geneLocationConfiguration, File geneLocationFile)
            throws ValidationException, IOException {
        CSVReader geneFileReader = new CSVReader(new FileReader(geneLocationFile), DELIMITER);
        try {
            loadFile(geneLocationConfiguration, geneFileReader);
        } finally {
            IOUtils.closeQuietly(geneFileReader);
        }
    }

    private static void loadFile(GeneLocationConfiguration geneLocationConfiguration, CSVReader geneFileReader)
            throws IOException, ValidationException {
        String[] fields;
        while ((fields = geneFileReader.readNext()) != null) {
            if (fields.length != 4) {
                throw new ValidationException("A line in the Gene Location File has '" + fields.length
                        + "' fields, expected number is 4");
            }
            GeneChromosomalLocation gcl = new GeneChromosomalLocation();
            ChromosomalLocation cl = new ChromosomalLocation();
            cl.setChromosome(fields[0]);
            cl.setStartPosition(Integer.valueOf(fields[1]));
            cl.setEndPosition(Integer.valueOf(fields[2]));
            gcl.setLocation(cl);
            gcl.setGeneSymbol(fields[3]);
            gcl.setGeneLocationConfiguration(geneLocationConfiguration);
            geneLocationConfiguration.getGeneLocations().add(gcl);
        }
    }

}