ubc.pavlab.aspiredb.server.CytobandFileLoaderImpl.java Source code

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Here is the source code for ubc.pavlab.aspiredb.server.CytobandFileLoaderImpl.java

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/*
 * The aspiredb project
 * 
 * Copyright (c) 2013 University of British Columbia
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *       http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */
package ubc.pavlab.aspiredb.server;

import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.HashMap;
import java.util.Map;

import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.stereotype.Component;

/**
 * Load chromosome info from a file.
 * 
 * @author: anton date: 19/02/13
 */
@Component("cytobandFileLoader")
public class CytobandFileLoaderImpl implements CytobandFileLoader {

    protected static Log log = LogFactory.getLog(CytobandFileLoaderImpl.class);

    private static class FileRow {
        String chromosome;
        Integer start;
        Integer end;
        String cytoband;
        String staining;
    }

    private Map<String, Chromosome> chromosomes = new HashMap<String, Chromosome>();

    @Override
    public Map<String, Chromosome> load() {

        try {
            // Get file name with coordinate mappings (downloaded from UCSC)
            // String filePath = ConfigUtils.getString("aspiredb.cytoband.path");
            final InputStream cytobandResourceStream = this.getClass().getResourceAsStream("/data/cytoBand.txt");
            BufferedReader reader = new BufferedReader(new InputStreamReader(cytobandResourceStream));

            String line;
            while ((line = reader.readLine()) != null) {
                FileRow row = parseFileRow(line);

                Chromosome chromosome = getOrCreateChromosome(row.chromosome);
                chromosome.addBand(row.start, row.end, row.cytoband, row.staining);
            }

        } catch (FileNotFoundException e) {
            log.error(e);
        } catch (IOException e) {
            log.error(e);
        }

        return chromosomes;
    }

    private Chromosome getOrCreateChromosome(String name) {
        Chromosome chromosome = chromosomes.get(name);
        if (chromosome == null) {
            chromosome = new Chromosome(name);
            chromosomes.put(name, chromosome);
        }
        return chromosome;
    }

    private FileRow parseFileRow(String row) {
        // Row format (tab delimited): chromosome, start, end, cytoband, staining agent
        final int CHROMOSOME = 0;
        final int START = 1;
        final int END = 2;
        final int CYTOBAND = 3;
        final int STAINING_AGENT = 4;

        row = StringUtils.strip(row);
        String[] fields = row.split("\t");

        FileRow parsedRow = new FileRow();
        parsedRow.chromosome = fields[CHROMOSOME].replaceAll("chr", ""); // trim 'chr' part
        parsedRow.start = Integer.parseInt(fields[START]);
        parsedRow.end = Integer.parseInt(fields[END]);
        parsedRow.cytoband = fields[CYTOBAND];
        parsedRow.staining = fields[STAINING_AGENT];

        return parsedRow;
    }

}