ubic.gemma.loader.expression.arrayDesign.ArrayDesignParser.java Source code

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Here is the source code for ubic.gemma.loader.expression.arrayDesign.ArrayDesignParser.java

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/*
 * The Gemma project
 * 
 * Copyright (c) 2006 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.expression.arrayDesign;

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

import org.apache.commons.lang.StringUtils;

import ubic.gemma.loader.util.parser.BasicLineParser;
import ubic.gemma.model.common.auditAndSecurity.Contact;
import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
import ubic.gemma.model.genome.Taxon;

/**
 * Parse ArrayDesigns from a flat file. This is used to seed the system from our legacy data. (probably not used)
 * <p>
 * Format:
 * <ol>
 * <li>Murine Genome U74A Array --- platform name
 * <li>Affymetrix -- Manufacturer name
 * <li>MG-U74A --- short name
 * <li>MOUSE --- taxon
 * <li>10044 --- advertised number of design elements
 * <li>(Masked) Affymetrix GeneChip expression probe array... --- Description
 * </ol>
 * 
 * @author keshav
 * @version $Id: ArrayDesignParser.java,v 1.11 2012/05/27 02:58:11 paul Exp $
 * @deprecated
 */
@Deprecated
public class ArrayDesignParser extends BasicLineParser<ArrayDesign> {

    private Collection<ArrayDesign> results = new HashSet<ArrayDesign>();

    @Override
    public ArrayDesign parseOneLine(String line) {
        ArrayDesign ad = ArrayDesign.Factory.newInstance();
        String[] fields = StringUtils.splitPreserveAllTokens(line, '\t');
        ad.setName(fields[0]);
        ad.setDescription(fields[5]);

        Taxon t = Taxon.Factory.newInstance();
        t.setCommonName(fields[4].toLowerCase());
        t.setIsSpecies(true); // assumption.
        t.setIsGenesUsable(true); // assumption
        ad.setPrimaryTaxon(t);

        Contact manufacturer = Contact.Factory.newInstance();
        manufacturer.setName(fields[1]);
        ad.setDesignProvider(manufacturer);

        ad.setAdvertisedNumberOfDesignElements(Integer.parseInt(fields[4]));
        return ad;
    }

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

    }

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

}