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}