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 org.biojava.bio.seq.io.ParseException;
024
025/**
026 * Listens to events that represent Nexus distances blocks.
027 * 
028 * @author Richard Holland
029 * @author Tobias Thierer
030 * @author Jim Balhoff
031 * @since 1.6
032 */
033public interface DistancesBlockListener extends NexusBlockListener {
034
035        /**
036         * Set the NTAX value.
037         * 
038         * @param dimensionsNTax
039         *            the NTAX value.
040         */
041        public void setDimensionsNTax(int dimensionsNTax);
042
043        /**
044         * Set the NCHAR value.
045         * 
046         * @param dimensionsNChar
047         *            the NCHAR value.
048         */
049        public void setDimensionsNChar(int dimensionsNChar);
050
051        public void setTriangle(final String triangle);
052
053        public void setDiagonal(final boolean diagonal);
054
055        public void setLabels(final boolean labels);
056
057        public void setMissing(final String missing);
058
059        public void setInterleaved(final boolean interleaved);
060
061        /**
062         * Add a TAXLABEL. If it already exists, or is a number that refers to an
063         * index position that already exists, an exception is thrown.
064         * 
065         * @param taxLabel
066         *            the label to add.
067         * @throws ParseException
068         *             if the label cannot be added.
069         */
070        public void addTaxLabel(final String taxLabel) throws ParseException;
071
072        public void addMatrixEntry(final String taxa);
073
074        public void appendMatrixData(final String taxa, final Object data);
075}