ubic.gemma.loader.pazar.PazarParser.java Source code

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Here is the source code for ubic.gemma.loader.pazar.PazarParser.java

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/*
 * The Gemma project
 * 
 * Copyright (c) 2010 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 ubic.gemma.loader.pazar;

import java.util.Collection;
import java.util.HashSet;

import org.apache.commons.lang.StringUtils;

import ubic.gemma.loader.pazar.model.PazarRecord;
import ubic.gemma.loader.util.parser.BasicLineParser;

/**
 * ssTODO Document Me
 * 
 * @author paul
 * @version $Id: PazarParser.java,v 1.2 2011/10/31 13:07:10 paul Exp $
 */
public class PazarParser extends BasicLineParser<PazarRecord> {

    Collection<PazarRecord> results = new HashSet<PazarRecord>();

    @Override
    protected void addResult(PazarRecord obj) {
        results.add(obj);
    }

    @Override
    public Collection<PazarRecord> getResults() {
        return results;
    }

    @Override
    public PazarRecord parseOneLine(String line) {
        if (line == null || line.isEmpty())
            return null;

        if (line.startsWith("TF_PAZAR_ID"))
            return null;

        String[] fields = StringUtils.splitPreserveAllTokens(line, '\t');
        if (fields.length < 2)
            return null;

        PazarRecord r = new PazarRecord();

        r.setPazarTfId(StringUtils.strip(fields[0]));
        r.setTfAcc(fields[1]);
        r.setSpecies(fields[2]);
        r.setPazarTargetGeneId(fields[3]);
        r.setTargetGeneAcc(fields[4]);
        r.setProject(fields[6]);
        r.setPubMedId(fields[7]);
        // r.setMethod(fields[8);

        return r;

    }

}