org.genemania.data.normalizer.GeneCompletionProvider2.java Source code

Introduction

Here is the source code for org.genemania.data.normalizer.GeneCompletionProvider2.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.normalizer;

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

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.BooleanQuery;
import org.apache.lucene.search.PrefixQuery;
import org.apache.lucene.search.Searcher;
import org.apache.lucene.search.TermQuery;
import org.apache.lucene.search.BooleanClause.Occur;
import org.apache.lucene.search.BooleanQuery.TooManyClauses;
import org.genemania.completion.CompletionConsumer;
import org.genemania.completion.CompletionProvider;
import org.genemania.domain.Gene;
import org.genemania.domain.Organism;
import org.genemania.mediator.lucene.AbstractCollector;
import org.genemania.mediator.lucene.LuceneGeneMediator;
import org.genemania.mediator.lucene.LuceneMediator;

public class GeneCompletionProvider2 implements CompletionProvider {
    private Organism organism;
    private LuceneGeneMediator mediator;
    private Searcher searcher;
    private Analyzer analyzer;

    public GeneCompletionProvider2(Searcher searcher, Analyzer analyzer, Organism organism) {
        this.organism = organism;
        this.searcher = searcher;
        this.mediator = new LuceneGeneMediator(searcher, analyzer);
        this.analyzer = analyzer;
    }

    public void close() {
    }

    public void computeProposals(final CompletionConsumer consumer, String queryString) {
        try {
            if (queryString.length() == 0) {
                return;
            }

            TokenStream stream = analyzer.tokenStream(LuceneGeneMediator.GENE_SYMBOL,
                    new StringReader(queryString));
            TermAttribute term = stream.getAttribute(TermAttribute.class);
            if (!stream.incrementToken()) {
                return;
            }

            BooleanQuery query = new BooleanQuery();
            query.add(new TermQuery(new Term(LuceneMediator.GENE_ORGANISM_ID, String.valueOf(organism.getId()))),
                    Occur.MUST);
            query.add(new PrefixQuery(new Term(LuceneMediator.GENE_SYMBOL, term.term())), Occur.MUST);
            searcher.search(query, new AbstractCollector() {
                @Override
                public void handleHit(int id) {
                    try {
                        Document document = searcher.doc(id);
                        consumer.consume(document.get(LuceneMediator.GENE_SYMBOL));
                    } catch (IOException e) {
                        log(e);
                    }
                }
            });
        } catch (IOException e) {
            log(e);
        } catch (TooManyClauses e) {
            consumer.tooManyCompletions();
        } finally {
            consumer.finish();
        }
    }

    public String getCanonicalForm(String proposal) {
        return mediator.getCanonicalSymbol(organism.getId(), proposal);
    }

    public boolean isValid(String proposal) {
        return mediator.isValid(organism.getId(), proposal);
    }

    public Gene getGene(String symbol) {
        return mediator.getGeneForSymbol(organism, symbol);
    }

    public Long getNodeId(String symbol) {
        return mediator.getNodeId(organism.getId(), symbol);
    }

    private void log(IOException e) {
        e.printStackTrace();
    }
}