001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021package org.biojava.nbio.survival.cox.comparators;
022
023import org.biojava.nbio.survival.cox.CoxInfo;
024import org.biojava.nbio.survival.cox.CoxVariables;
025
026import java.io.Serializable;
027import java.util.Comparator;
028
029/**
030 *
031 * @author Scooter Willis <willishf at gmail dot com>
032 */
033public class CoxVariablesOverallModelFitComparator implements Comparator<CoxVariables>, Serializable {
034        private static final long serialVersionUID = 1;
035
036        String variables = "";
037
038        /**
039         * Variables are stored as a string representation of an ArrayList
040         * [META_GENE] or [trtg, META_GENE] add variables used in cox regression to an array and then do toString.
041         * @param variables
042         */
043        public CoxVariablesOverallModelFitComparator(String variables) {
044                this.variables = variables;
045        }
046
047        @Override
048        public int compare(CoxVariables coxVariables1, CoxVariables coxVariables2) {
049                CoxInfo ci1 = coxVariables1.getCoxInfo(variables);
050                CoxInfo ci2 = coxVariables2.getCoxInfo(variables);
051
052                if (ci1.getWaldTestInfo().getPvalue() < ci2.getWaldTestInfo().getPvalue()) {
053                        return -1;
054                } else if (ci1.getWaldTestInfo().getPvalue() > ci2.getWaldTestInfo().getPvalue()) {
055                        return 1;
056                } else {
057                        return 0;
058                }
059                //ascending order
060                // return coxVariables1.compareTo(coxVariables2);
061        }
062}