edu.vt.vbi.patric.common.FASTAHelper.java Source code

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Here is the source code for edu.vt.vbi.patric.common.FASTAHelper.java

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/*******************************************************************************
 * Copyright 2014 Virginia Polytechnic Institute and State University
 * 
 * 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 edu.vt.vbi.patric.common;

import edu.vt.vbi.patric.beans.GenomeFeature;
import org.apache.commons.lang.StringUtils;
import org.apache.solr.client.solrj.SolrQuery;
import org.codehaus.jackson.map.ObjectMapper;
import org.codehaus.jackson.map.ObjectReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.portlet.PortletRequest;
import java.io.IOException;
import java.util.List;
import java.util.Map;

public class FASTAHelper {

    private static final Logger LOGGER = LoggerFactory.getLogger(FASTAHelper.class);

    private static ObjectReader jsonReader = (new ObjectMapper()).reader(Map.class);

    public static String getFASTASequence(PortletRequest request, List<String> featureIds, String type)
            throws IOException {
        StringBuilder fasta = new StringBuilder();

        SolrQuery query = new SolrQuery("feature_id:(" + StringUtils.join(featureIds, " OR ") + ")");
        query.setFields(
                "feature_id,patric_id,alt_locus_tag,refseq_locus_tag,annotation,gi,product,genome_id,genome_name,na_sequence,aa_sequence");
        query.setRows(featureIds.size());

        DataApiHandler dataApi = new DataApiHandler(request);
        LOGGER.trace("getFASTASequence: [{}] {}", SolrCore.FEATURE.getSolrCoreName(), query);
        String apiResponse = dataApi.solrQuery(SolrCore.FEATURE, query);
        Map resp = jsonReader.readValue(apiResponse);
        Map respBody = (Map) resp.get("response");

        List<GenomeFeature> features = dataApi.bindDocuments((List<Map>) respBody.get("docs"), GenomeFeature.class);

        for (GenomeFeature feature : features) {

            if (type.equals("dna") || type.equals("both")) {
                fasta.append(">");
                if (feature.getAnnotation().equals("PATRIC")) {
                    if (feature.hasPatricId()) {
                        fasta.append(feature.getPatricId()).append("|");
                    }
                } else if (feature.getAnnotation().equals("RefSeq")) {
                    if (feature.getGi() > 0) {
                        fasta.append("gi|").append(feature.getGi()).append("|");
                    }
                }

                if (feature.hasRefseqLocusTag()) {
                    fasta.append(feature.getRefseqLocusTag()).append("|");
                }
                if (feature.hasAltLocusTag()) {
                    fasta.append(feature.getAltLocusTag()).append("|");
                }
                if (feature.hasProduct()) {
                    fasta.append("   ").append(feature.getProduct());
                }
                fasta.append("   [").append(feature.getGenomeName()).append(" | ").append(feature.getGenomeId())
                        .append("]");

                fasta.append("\n");
                if (feature.hasNaSequence()) {
                    fasta.append(StringHelper.chunk_split(feature.getNaSequence(), 60, "\n"));
                }
            }

            if (type.equals("protein") || type.equals("both")) {
                fasta.append(">");
                if (feature.getAnnotation().equals("PATRIC")) {
                    if (feature.hasPatricId()) {
                        fasta.append(feature.getPatricId()).append("|");
                    }
                } else if (feature.getAnnotation().equals("RefSeq")) {
                    if (feature.getGi() > 0) {
                        fasta.append("gi|").append(feature.getGi()).append("|");
                    }
                }

                if (feature.hasRefseqLocusTag()) {
                    fasta.append(feature.getRefseqLocusTag()).append("|");
                }
                if (feature.hasAltLocusTag()) {
                    fasta.append(feature.getAltLocusTag()).append("|");
                }
                if (feature.hasProduct()) {
                    fasta.append("   ").append(feature.getProduct());
                }
                fasta.append("   [").append(feature.getGenomeName()).append(" | ").append(feature.getGenomeId())
                        .append("]");

                fasta.append("\n");
                if (feature.hasAaSequence()) {
                    fasta.append(StringHelper.chunk_split(feature.getAaSequence(), 60, "\n"));
                }
            }
        }

        return fasta.toString();
    }
}