ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperService.java Source code

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Here is the source code for ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperService.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.analysis.service;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import ubic.gemma.core.genome.gene.service.GeneService;
import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
import ubic.gemma.model.expression.designElement.CompositeSequence;
import ubic.gemma.model.genome.Gene;

import java.util.Collection;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.Set;

/**
 * @author keshav
 */
@SuppressWarnings({ "WeakerAccess", "unused" }) // Possible external use
@Component
public class CompositeSequenceGeneMapperService {
    private final Log log = LogFactory.getLog(this.getClass());
    @Autowired
    private GeneService geneService;

    /**
     * @param arrayDesigns    to look in
     * @param officialSymbols official symbols
     * @return map of gene to composite sequences
     */
    public LinkedHashMap<Gene, Collection<CompositeSequence>> getGene2ProbeMapByOfficialSymbols(
            Collection<String> officialSymbols, Collection<ArrayDesign> arrayDesigns) {

        LinkedHashMap<String, Collection<Gene>> genesMap = this.findGenesByOfficialSymbols(officialSymbols);

        Set<String> geneOfficialSymbolKeySet = genesMap.keySet();

        LinkedHashMap<Gene, Collection<CompositeSequence>> compositeSequencesForGeneMap = new LinkedHashMap<>();

        for (String officialSymbol : geneOfficialSymbolKeySet) {
            log.debug("official symbol: " + officialSymbol);
            Collection<Gene> genes = genesMap.get(officialSymbol);
            for (Gene g : genes) {
                Collection<CompositeSequence> compositeSequences = geneService.getCompositeSequencesById(g.getId());
                for (CompositeSequence sequence : compositeSequences) {
                    if (arrayDesigns.contains(sequence.getArrayDesign())) {
                        if (compositeSequencesForGeneMap.get(g) == null) {
                            compositeSequencesForGeneMap.put(g, new HashSet<CompositeSequence>());
                        }
                        compositeSequencesForGeneMap.get(g).add(sequence);
                    }
                }
            }
        }
        return compositeSequencesForGeneMap;
    }

    /**
     * @param geneService The geneService to set.
     */
    public void setGeneService(GeneService geneService) {
        this.geneService = geneService;
    }

    /**
     * Returns a map of gene collections, each keyed by a gene official symbol.
     *
     * @param officialSymbols official symbols
     * @return map of genes
     */
    private LinkedHashMap<String, Collection<Gene>> findGenesByOfficialSymbols(Collection<String> officialSymbols) {

        LinkedHashMap<String, Collection<Gene>> geneMap = new LinkedHashMap<>();
        for (String officialSymbol : officialSymbols) {
            Collection<Gene> genes = geneService.findByOfficialSymbol(officialSymbol);
            if (genes == null || genes.isEmpty()) {
                log.warn("Gene with official symbol " + officialSymbol + " does not exist.  Discarding ... ");
                continue;
            }
            geneMap.put(officialSymbol, genes);
        }

        return geneMap;
    }

}