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.util.List;
024
025import org.biojava.bio.seq.io.ParseException;
026
027/**
028 * Listens to events that represent Nexus characters blocks.
029 * 
030 * @author Richard Holland
031 * @author Tobias Thierer
032 * @author Jim Balhoff
033 * @since 1.6
034 */
035public interface CharactersBlockListener extends NexusBlockListener {
036
037        /**
038         * Set the NTAX value.
039         * 
040         * @param dimensionsNTax
041         *            the NTAX value.
042         */
043        public void setDimensionsNTax(int dimensionsNTax);
044
045        /**
046         * Set the NCHAR value.
047         * 
048         * @param dimensionsNChar
049         *            the NCHAR value.
050         */
051        public void setDimensionsNChar(int dimensionsNChar);
052
053        public void setDataType(final String dataType);
054
055        public void setRespectCase(final boolean respectCase);
056
057        public void setMissing(final String missing);
058
059        public void setGap(final String gap);
060
061        public void addSymbol(final String symbol);
062
063        public void addEquate(final String symbol, final List symbols);
064
065        public void setMatchChar(final String matchChar);
066
067        public void setLabels(final boolean labels);
068
069        public void setTransposed(final boolean transposed);
070
071        public void setInterleaved(final boolean interleaved);
072
073        public void addItem(final String item);
074
075        public void setStatesFormat(final String statesFormat);
076
077        public void setTokens(final boolean tokens);
078
079        public void setEliminateStart(final int eliminateStart);
080
081        public void setEliminateEnd(final int eliminateEnd);
082
083        /**
084         * Add a TAXLABEL. If it already exists, or is a number that refers to an
085         * index position that already exists, an exception is thrown.
086         * 
087         * @param taxLabel
088         *            the label to add.
089         * @throws ParseException
090         *             if the label cannot be added.
091         */
092        public void addTaxLabel(final String taxLabel) throws ParseException;
093
094        public void addCharState(final String charState);
095
096        public void setCharStateLabel(final String charState, final String label);
097
098        public void addCharStateKeyword(final String charState, final String keyword);
099
100        public void addCharLabel(final String charLabel);
101
102        public void addState(final String state);
103
104        public void addStateLabel(final String state, final String label);
105
106        public void addMatrixEntry(final String taxa);
107
108        public void appendMatrixData(final String taxa, final Object data);
109}