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.structure.domain.pdp;
022
023import java.util.List;
024
025
026public class ShortSegmentRemover {
027
028        public static void cleanup(List<Domain> domains) {
029
030                int ndom = domains.size();
031
032                for(int j=0;j<ndom;j++) {
033
034                        int n=0;
035                        boolean allshort=true;
036                        // count the length of segments for this domain.
037                        for (int i=0;i<domains.get(j).nseg;i++) {
038                                int seglen=(domains.get(j).getSegmentAtPos(i).getTo()-domains.get(j).getSegmentAtPos(i).getFrom()+1);
039                                if(seglen>=30) allshort = false;
040                                n+=seglen;
041                        }
042
043                        if(n<PDPParameters.MIN_DOMAIN_LENGTH||allshort) {
044                                ndom--;
045                                domains.remove(j);
046                                j--;
047
048                        }
049                }
050        }
051}