ubic.gemma.core.loader.genome.taxon.TaxonParser.java Source code

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Here is the source code for ubic.gemma.core.loader.genome.taxon.TaxonParser.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.core.loader.genome.taxon;

import org.apache.commons.lang3.StringUtils;
import ubic.gemma.core.loader.util.parser.BasicLineMapParser;
import ubic.gemma.model.genome.Taxon;

import java.util.Collection;
import java.util.HashMap;
import java.util.Map;

/**
 * Parse the "names.dmp" file from NCBI, ftp://ftp.ncbi.nih.gov/pub/taxonomy/.
 *
 * @author pavlidis
 */
public class TaxonParser extends BasicLineMapParser<Integer, Taxon> {

    private final Map<Integer, Taxon> results = new HashMap<>();

    @Override
    public boolean containsKey(Integer key) {
        return results.containsKey(key);
    }

    @Override
    public Taxon get(Integer key) {
        return results.get(key);
    }

    @Override
    public Collection<Integer> getKeySet() {
        return results.keySet();
    }

    @Override
    public Collection<Taxon> getResults() {
        return results.values();
    }

    @Override
    public Taxon parseOneLine(String line) {
        String[] fields = StringUtils.splitPreserveAllTokens(line, '|');

        int ncbiid = Integer.parseInt(StringUtils.strip(fields[0]));

        if (!results.containsKey(ncbiid)) {
            Taxon t = Taxon.Factory.newInstance();
            t.setNcbiId(ncbiid);
            t.setIsGenesUsable(false);
            results.put(ncbiid, t);
        }

        String tag = StringUtils.strip(fields[3]);
        if (tag.equals("scientific name")) {
            results.get(ncbiid).setScientificName(StringUtils.strip(fields[1]));
        } else if (tag.equals("genbank common name")) {
            results.get(ncbiid).setCommonName(fields[1]);
        }

        return results.get(ncbiid);

    }

    @Override
    protected Integer getKey(Taxon newItem) {
        return newItem.getNcbiId();
    }

    @Override
    protected void put(Integer key, Taxon value) {
        results.put(key, value);
    }

}