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 * created at May 28, 2008
021 */
022package org.biojava.nbio.structure.gui.util;
023
024public class AlignedPosition {
025        int pos1;
026        int pos2;
027        int equivalent;
028
029        /** flag if this position is equivalent
030         *
031         */
032        public static final int EQUIVALENT  = 1;
033
034        /** they can be shown in the same column (for a compact display)
035         * , but they are not structurally equivalent
036         *
037         */
038        public static final int NOT_ALIGNED = 0;
039
040        public AlignedPosition(){
041                pos1 = -1;
042                pos2 = -1;
043                equivalent = NOT_ALIGNED;
044        }
045
046        public int getPos(int position){
047                if (position == 1)
048                        return pos1;
049                else
050                        return pos2;
051        }
052        public void setPos(int position, int pos){
053                if (position == 1)
054                        pos1 = pos;
055                else
056                        pos2 = pos;
057        }
058
059
060
061
062        @Override
063        public  String toString(){
064                String t = " AlignedPosition pos1: " + pos1 + " pos2: "+ pos2 ;
065                if ( equivalent == EQUIVALENT)
066                        t+= " EQR";
067
068                return t;
069        }
070
071        public int getPos1() {
072                return pos1;
073        }
074
075        public void setPos1(int pos1) {
076                this.pos1 = pos1;
077        }
078
079        public int getPos2() {
080                return pos2;
081        }
082
083        public void setPos2(int pos2) {
084                this.pos2 = pos2;
085        }
086
087        public int getEquivalent() {
088                return equivalent;
089        }
090
091        public void setEquivalent(int equivalent) {
092                this.equivalent = equivalent;
093        }
094
095
096}