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 Convert2SolventAccessibility extends Convertor{
024        /**
025         * Class for the conversion of protein sequence into solvent accessibility
026         */
027        @Override
028        public char convert(char c){
029                switch(c){
030                case 'A':case 'L':case 'F':case 'C':case 'G':case 'I':case 'V':case 'W':
031                        return group1;//Buried
032                case 'R':case 'K':case 'Q':case 'E':case 'N':case 'D':
033                        return group2;//Exposed
034                case 'M':case 'P':case 'S':case 'T':case 'H':case 'Y':
035                        return group3;//Intermediate
036                default:
037                        return unknownGroup;//Non-standard AA
038                }
039        }
040
041        private static String[] subCategory = {"Buried", "Exposed", "Intermediate"};
042        @Override
043        public String[] getGrouping(){return subCategory;}
044        @Override
045        public String getAttribute(){return "Solvent Accessibility";}
046}