org.biojavax.bio.phylo.io.nexus.NexusComment Maven / Gradle / Ivy
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojavax.bio.phylo.io.nexus;
import java.io.IOException;
import java.io.Writer;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
* Represents a Nexus comment, possibly nested.
*
* @author Richard Holland
* @author Tobias Thierer
* @author Jim Balhoff
* @since 1.6
*/
public class NexusComment implements NexusObject {
private List components = new ArrayList();
private NexusComment nestedComment = null;
public void openSubComment() {
if (this.hasOpenSubComment())
this.nestedComment.openSubComment();
else {
this.nestedComment = new NexusComment();
this.components.add(this.nestedComment);
}
}
public boolean hasOpenSubComment() {
return this.nestedComment != null;
}
public void closeSubComment() {
if (this.hasOpenSubComment() && this.nestedComment.hasOpenSubComment())
this.nestedComment.closeSubComment();
else
this.nestedComment = null;
}
public void addCommentText(final String text) {
if (this.hasOpenSubComment())
this.nestedComment.addCommentText(text);
else
this.components.add(text);
}
/**
* This iterator iterates over all parts of the comment. Each item returned
* is either a String or a NexusComment.
*
* @return an iterator over the comment components.
*/
public Iterator commentIterator() {
return this.components.iterator();
}
public void writeObject(final Writer writer) throws IOException {
writer.write('[');
for (final Iterator i = this.components.iterator(); i.hasNext();) {
final Object obj = (Object) i.next();
if (obj instanceof NexusComment)
((NexusComment) obj).writeObject(writer);
else {
String text = (String) obj;
text = text.replaceAll("'", "''");
if (text.indexOf('[') >= 0 || text.indexOf(']') >= 0)
text = "'" + text + "'";
writer.write(text);
}
}
writer.write(']');
}
}