ubic.pubmedgate.interactions.focusedAnalysis.SplitConnectionsBySpecies.java Source code

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Here is the source code for ubic.pubmedgate.interactions.focusedAnalysis.SplitConnectionsBySpecies.java

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/*
 * The WhiteText project
 * 
 * Copyright (c) 2012 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.pubmedgate.interactions.focusedAnalysis;

import java.io.File;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import ubic.basecode.dataStructure.CountingMap;
import ubic.basecode.dataStructure.StringToStringSetMap;
import ubic.basecode.dataStructure.params.ParamKeeper;
import ubic.pubmedgate.Config;
import ubic.pubmedgate.ConnectionsDocument;
import ubic.pubmedgate.GateInterface;
import ubic.pubmedgate.interactions.AirolaXMLReader;
import ubic.pubmedgate.interactions.NormalizePairs;
import ubic.pubmedgate.interactions.NormalizeResult;
import ubic.pubmedgate.interactions.SLOutputReader;
import ubic.pubmedgate.interactions.evaluation.AllCuratorsCombined;
import ubic.pubmedgate.interactions.evaluation.LoadInteractionSpreadsheet;
import ubic.pubmedgate.interactions.evaluation.NormalizedConnection;
import ubic.pubmedgate.organism.SpeciesUtil;

public class SplitConnectionsBySpecies {
    protected static Log log = LogFactory.getLog(SplitConnectionsBySpecies.class);

    public static void getCounts() throws Exception {
        // String testSet = "Annotated";
        // String annotationSet = "Suzanne";
        //
        // String baseFolder = Config.config.getString( "whitetext.iteractions.ppiBaseFolder" )
        // + "Saved Results/SL/CV/WhiteTextNegFixFull/predict/WhiteTextNegFixFull";
        // String filename = Config.config.getString( "whitetext.iteractions.ppiBaseFolder" )
        // + "Corpora/Original-Modified/WhiteTextNegFixFull.xml";
        //
        // GateInterface p2g = new GateInterface();
        // p2g.setUnSeenCorpNull();
        //
        // AirolaXMLReader XMLReader = new AirolaXMLReader( filename, p2g, annotationSet );
        // SLOutputReader SLReader = new SLOutputReader( new File( baseFolder ) );
        String trainingSet = "WhiteTextNegFixFull";
        String testSet = "WhiteTextUnseen";
        String annotationSet = "Mallet";

        String baseFolder = Config.config.getString("whitetext.iteractions.ppiBaseFolder")
                + "Saved Results/SL/CC/NegFixFullOnUnseen/";
        String filename = Config.config.getString("whitetext.iteractions.ppiBaseFolder")
                + "Corpora/Original-Modified/WhiteTextUnseen.orig.xml";

        GateInterface p2g = new GateInterface();

        AirolaXMLReader XMLReader = new AirolaXMLReader(filename, p2g, annotationSet);
        SLOutputReader SLReader = new SLOutputReader(trainingSet, testSet, baseFolder);

        Map<String, String> pairIDtoPMID = XMLReader.getPairIDToPMID();

        List<String> posPredictions = SLReader.getPositivePredictions();

        CountingMap<String> speciesConCount = new CountingMap<String>();
        CountingMap<String> final2000Rows = new CountingMap<String>();
        CountingMap<String> final2000Accepts = new CountingMap<String>();

        LoadInteractionSpreadsheet final2000 = AllCuratorsCombined.getFinal2000Results();

        for (String pairID : posPredictions) {
            String PMID = pairIDtoPMID.get(pairID);
            ConnectionsDocument doc = p2g.getByPMID(PMID);
            Set<String> species = doc.getLinnaeusSpecies();
            speciesConCount.incrementAll(species);

            int final2000RowCount = final2000.getPairIDRowCount(pairID);
            int final2000AcceptCount = final2000.getPairIDAcceptCount(pairID);

            // ugly, but makes sense, increment the number of rows seen
            for (String spec : species) {
                for (int i = 0; i < final2000RowCount; i++) {
                    final2000Rows.increment(spec);
                }
                for (int i = 0; i < final2000AcceptCount; i++) {
                    final2000Accepts.increment(spec);
                }
            }
        }
        log.info("Pos predictions:" + posPredictions.size());

        log.info("speciesConCount:" + speciesConCount.size());

        StringToStringSetMap speciesStrings = SpeciesUtil.getSpeciesStrings(p2g, p2g.getUnseenCorp()).strings;
        ParamKeeper keeper = new ParamKeeper();
        for (String specieID : speciesConCount.keySet()) {
            Map<String, String> result = new HashMap<String, String>();
            result.put("speciesID", specieID);
            Set<String> speciesText = speciesStrings.get(specieID);
            if (speciesText == null)
                speciesText = new HashSet<String>();
            result.put("species text", speciesText.toString());
            result.put("connection count", "" + speciesConCount.get(specieID));
            result.put("final2000RowCount", "" + final2000Rows.get(specieID));
            result.put("final2000AcceptCount", "" + final2000Accepts.get(specieID));

            keeper.addParamInstance(result);
        }
        keeper.writeExcel(
                Config.config.getString("whitetext.iteractions.results.folder") + "connectionsBySpecies.xls");
        log.info(Config.config.getString("whitetext.iteractions.results.folder") + "connectionsBySpecies.xls");
        // p2g.get

    }

    /**
     * @param args
     */
    public static void main(String[] args) throws Exception {
        getCounts();
    }

}