edu.monash.merc.wsclient.biomart.CSVProbGeneCreator.java Source code

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Here is the source code for edu.monash.merc.wsclient.biomart.CSVProbGeneCreator.java

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/*
 * Copyright (c) 2011-2013, Monash e-Research Centre
 * (Monash University, Australia)
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *    * Redistributions of source code must retain the above copyright
 *      notice, this list of conditions and the following disclaimer.
 *    * Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in the
 *      documentation and/or other materials provided with the distribution.
 *    * Neither the name of the Monash University nor the names of its
 *      contributors may be used to endorse or promote products derived from
 *      this software without specific prior written permission.
 *
 * 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 Affero General Public License for more details.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
 * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY
 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * You should have received a copy of the GNU Affero General Public License along with
 * this program. If not, see <http://www.gnu.org/licenses/>.
 */

package edu.monash.merc.wsclient.biomart;

import edu.monash.merc.dto.ProbeGeneBean;
import org.apache.commons.lang.StringUtils;

import java.util.ArrayList;
import java.util.List;

/**
 * @author Simon Yu
 *         <p/>
 *         Email: xiaoming.yu@monash.edu
 * @version 1.0
 * @since 1.0
 *        <p/>
 *        Date: 2/07/13 11:48 AM
 */
public class CSVProbGeneCreator {

    private List<CSVColumn> columns = new ArrayList<CSVColumn>();

    public List<CSVColumn> getColumns() {
        return columns;
    }

    public void setColumns(List<CSVColumn> columns) {
        this.columns = columns;
    }

    public ProbeGeneBean createProbeGeneBean() {
        ProbeGeneBean probeGeneBean = new ProbeGeneBean();

        for (CSVColumn csvColumn : columns) {
            String columnName = csvColumn.getColumnName();
            String columnValue = csvColumn.getColumnValue();
            if (StringUtils.equalsIgnoreCase(columnName, ProbeConsts.ENSG_ACCESSION)) {
                if (StringUtils.isNotBlank(columnValue) && !StringUtils.equals("\t", columnValue)) {
                    probeGeneBean.setEnsgAccession(columnValue);
                }
            } else {
                if (StringUtils.isNotBlank(columnValue) && !StringUtils.equals("\t", columnValue)) {
                    probeGeneBean.setProbeId(columnValue);
                }
            }
        }
        return probeGeneBean;
    }
}