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.biojavax.bio.phylo.io.nexus;
022
023import java.io.IOException;
024import java.io.Writer;
025import java.util.ArrayList;
026import java.util.Iterator;
027import java.util.List;
028
029/**
030 * Represents a Nexus comment, possibly nested.
031 * 
032 * @author Richard Holland
033 * @author Tobias Thierer
034 * @author Jim Balhoff
035 * @since 1.6
036 */
037public class NexusComment implements NexusObject {
038
039        private List components = new ArrayList();
040
041        private NexusComment nestedComment = null;
042
043        public void openSubComment() {
044                if (this.hasOpenSubComment())
045                        this.nestedComment.openSubComment();
046                else {
047                        this.nestedComment = new NexusComment();
048                        this.components.add(this.nestedComment);
049                }
050        }
051
052        public boolean hasOpenSubComment() {
053                return this.nestedComment != null;
054        }
055
056        public void closeSubComment() {
057                if (this.hasOpenSubComment() && this.nestedComment.hasOpenSubComment())
058                        this.nestedComment.closeSubComment();
059                else
060                        this.nestedComment = null;
061        }
062
063        public void addCommentText(final String text) {
064                if (this.hasOpenSubComment())
065                        this.nestedComment.addCommentText(text);
066                else
067                        this.components.add(text);
068        }
069
070        /**
071         * This iterator iterates over all parts of the comment. Each item returned
072         * is either a String or a NexusComment.
073         * 
074         * @return an iterator over the comment components.
075         */
076        public Iterator commentIterator() {
077                return this.components.iterator();
078        }
079
080        public void writeObject(final Writer writer) throws IOException {
081                writer.write('[');
082                for (final Iterator i = this.components.iterator(); i.hasNext();) {
083                        final Object obj = (Object) i.next();
084                        if (obj instanceof NexusComment)
085                                ((NexusComment) obj).writeObject(writer);
086                        else {
087                                String text = (String) obj;
088                                text = text.replaceAll("'", "''");
089                                if (text.indexOf('[') >= 0 || text.indexOf(']') >= 0)
090                                        text = "'" + text + "'";
091                                writer.write(text);
092                        }
093                }
094                writer.write(']');
095        }
096
097}