org.genemania.data.classification.lucene.LuceneGeneClassifier.java Source code

Introduction

Here is the source code for org.genemania.data.classification.lucene.LuceneGeneClassifier.java

Source

/**
 * This file is part of GeneMANIA.
 * Copyright (C) 2010 University of Toronto.
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 *
 * This library 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
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with this library; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 */

package org.genemania.data.classification.lucene;

import java.io.IOException;
import java.io.StringReader;

import org.apache.log4j.Logger;
import org.apache.lucene.analysis.Analyzer;
import org.apache.lucene.analysis.TokenStream;
import org.apache.lucene.analysis.tokenattributes.TermAttribute;
import org.apache.lucene.document.Document;
import org.apache.lucene.index.Term;
import org.apache.lucene.search.PhraseQuery;
import org.apache.lucene.search.Searcher;
import org.genemania.data.classification.IGeneClassificationHandler;
import org.genemania.data.classification.IGeneClassifier;
import org.genemania.exception.ApplicationException;
import org.genemania.mediator.lucene.AbstractCollector;
import org.genemania.mediator.lucene.LuceneMediator;

public class LuceneGeneClassifier implements IGeneClassifier {
    private Searcher searcher;
    private Analyzer analyzer;

    public LuceneGeneClassifier(Searcher searcher, Analyzer analyzer) {
        this.searcher = searcher;
        this.analyzer = analyzer;
    }

    public void classify(final String symbol, final IGeneClassificationHandler handler)
            throws ApplicationException {
        try {
            TokenStream tokens = analyze(symbol);
            PhraseQuery query = new PhraseQuery();
            tokens.reset();
            while (tokens.incrementToken()) {
                TermAttribute term = tokens.getAttribute(TermAttribute.class);
                query.add(new Term(LuceneMediator.GENE_SYMBOL, term.term()));
            }
            tokens.end();
            tokens.close();

            searcher.search(query, new AbstractCollector() {
                @Override
                public void handleHit(int doc) {
                    try {
                        Document document = searcher.doc(doc);
                        long organismId = Long.parseLong(document.get(LuceneMediator.GENE_ORGANISM_ID));
                        handler.handleClassification(symbol, organismId);
                    } catch (IOException e) {
                        log(e);
                    }
                }
            });
        } catch (IOException e) {
            throw new ApplicationException(e);
        }
    }

    void log(Throwable t) {
        Logger logger = Logger.getLogger(LuceneGeneClassifier.class);
        logger.error(t.getMessage(), t);
    }

    TokenStream analyze(String text) throws IOException {
        return analyzer.reusableTokenStream(LuceneMediator.GENE_SYMBOL, new StringReader(text));
    }
}