edu.scripps.fl.pubchem.promiscuity.OverallListsAndMapsFactory.java Source code

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Here is the source code for edu.scripps.fl.pubchem.promiscuity.OverallListsAndMapsFactory.java

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/*               
 * Copyright 2011 The Scripps Research Institute               
 *               
 * 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.scripps.fl.pubchem.promiscuity;

import java.io.InputStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;

import org.apache.commons.collections.map.MultiValueMap;
import org.apache.commons.lang.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import edu.scripps.fl.pubchem.promiscuity.model.Protein;
import edu.scripps.fl.pubchem.web.ELinkResult;
import edu.scripps.fl.pubchem.web.entrez.EUtilsFactory;

public class OverallListsAndMapsFactory {

    private static final Logger log = LoggerFactory.getLogger(OverallListsAndMapsFactory.class);

    public List<Long> aidListEsearch(List<Long> ids, String searchTerm, String db) throws Exception {
        List<Long> newAids = new ArrayList<Long>();
        EUtilsFactory factory = new EUtilsFactory();
        StringBuffer query = new StringBuffer();
        query.append("(" + StringUtils.join(ids, "[" + db + "IdTested] OR "));
        query.append("[" + db + "IdTested]) AND " + searchTerm);
        newAids = factory.getIds(query.toString(), "pcassay");
        return newAids;
    }

    public List<Long> aidtoAIDListEsearch(List<Long> aids, String searchTerm) throws Exception {
        List<Long> newAids = new ArrayList<Long>();
        EUtilsFactory factory = new EUtilsFactory();
        StringBuffer query = new StringBuffer();
        query.append("(" + StringUtils.join(aids, "[uid] OR "));
        query.append("[uid]) AND " + searchTerm);
        newAids = factory.getIds(query.toString(), "pcassay");
        return newAids;
    }

    public Set<Protein> allProteinSet(Map<Long, List<Protein>> aidProteinMap) {
        Set<Protein> allProteinSet = new HashSet<Protein>();
        for (Long ll : aidProteinMap.keySet()) {
            List<Protein> proteins = aidProteinMap.get(ll);
            if (proteins.size() > 0)
                allProteinSet.addAll(proteins);
        }
        return allProteinSet;
    }

    public Map<Long, List<Protein>> getAIDProteinMap(List<Long> aids) throws Exception {
        log.info("Number of aids in eSummary request: " + aids.size());
        log.info("Memory usage before getting aid eSummary document: " + memUsage());
        SAXParserFactory factory = SAXParserFactory.newInstance();
        SAXParser saxParser = factory.newSAXParser();
        AssayESummaryHandler handler = new AssayESummaryHandler();
        InputStream is = EUtilsFactory.getInstance().getSummaries(aids, "pcassay");
        saxParser.parse(is, handler);
        log.info("Memory usage after getting aid eSummary document: " + memUsage());
        return handler.getMap();
    }

    public MultiValueMap getSummaryToAIDsMap(Map<Long, List<ELinkResult>> aidToSummaryMap) {
        MultiValueMap map = new MultiValueMap();
        log.info("Memory used before summary to aids map: " + memUsage());
        log.info("Setting up summary to AID map");
        for (Long ll : aidToSummaryMap.keySet()) {
            ELinkResult result = (ELinkResult) aidToSummaryMap.get(ll);
            if (result == null)
                continue;
            List<Long> summaries = result.getIds("pcassay", "pcassay_pcassay_neighbor_list");
            if (summaries != null) {
                for (Long summary : summaries) {
                    map.put(summary, ll);
                }
            }
        }
        log.info("Finished setting up summary to AID map");
        log.info("Memory used after summary to aids map: " + memUsage());
        return map;
    }

    private long memUsage() {
        long mem = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
        return mem / 1024 / 1024;
    }

    public Map<Protein, List<Long>> proteinAIDMap(Map<Long, List<Protein>> aidProteinMap,
            Set<Protein> allProteins) {
        Map<Protein, List<Long>> proteinAIDMap = new HashMap<Protein, List<Long>>();
        for (Protein protein : allProteins) {
            List<Long> aids = new ArrayList<Long>();
            for (Long aid : aidProteinMap.keySet()) {
                List<Protein> aidProteins = aidProteinMap.get(aid);
                if (aidProteins != null) {
                    if (aidProteins.contains(protein))
                        aids.add(aid);
                }
            }
            proteinAIDMap.put(protein, aids);
        }
        return proteinAIDMap;
    }

}