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.genome.parsers.gff;
022
023import org.biojava.nbio.core.sequence.DNASequence;
024
025import java.util.Collection;
026
027/**
028 *
029 * @author Scooter Willis <willishf at gmail dot com>
030 */
031public class GCStats {
032
033        public static double getGCStats(Collection<DNASequence> sequences) {
034                double gcCount = 0;
035                double total = 0;
036
037                for (DNASequence sequence : sequences) {
038                        char[] dna = sequence.toString().toCharArray();
039                        for (char d : dna) {
040                                if (d == 'G' || d == 'C' || d == 'g' || d == 'c') {
041                                        gcCount++;
042                                }
043                                total++;
044                        }
045                }
046
047                return (gcCount / total) * 100.0;
048        }
049
050        public static double getGCStatsString(Collection<String> sequences) {
051                double gcCount = 0;
052                double total = 0;
053
054                for (String sequence : sequences) {
055                        char[] dna = sequence.toCharArray();
056                        for (char d : dna) {
057                                if (d == 'G' || d == 'C' || d == 'g' || d == 'c') {
058                                        gcCount++;
059                                }
060                                total++;
061                        }
062                }
063
064                return (gcCount / total) * 100.0;
065        }
066}