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.aaproperties.profeat.convertor;
022
023public class Convert2Charge extends Convertor{
024        /**
025         * Class for the conversion of protein sequence into charge
026         */
027
028        @Override
029        public char convert(char c){
030                switch(c){
031                case 'K':case 'R':
032                        return group1;//Positive
033                case 'A':case 'N':case 'C':case 'Q':case 'G':case 'H':case 'I':case 'L':case 'M':case 'F':case 'P':case 'S':case 'T':case 'W':case 'Y':case 'V':
034                        return group2;//Neutral
035                case 'D':case 'E':
036                        return group3;//Negative
037                default:
038                        return unknownGroup;//Non-standard AA
039                }
040        }
041
042        private static String[] subCategory = {"Positive", "Neutral", "Negative"};
043        @Override
044        public String[] getGrouping(){return Convert2Charge.subCategory;}
045        @Override
046        public String getAttribute(){return "Charge";}
047}