/*
 *                    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.Collection;
import java.util.Collections;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;

import org.biojava.bio.seq.io.ParseException;

/**
 * Represents Nexus distances blocks.
 * 
 * @author Richard Holland
 * @author Tobias Thierer
 * @author Jim Balhoff
 * @since 1.6
 */
public class DistancesBlock extends NexusBlock.Abstract {

        /**
         * A constant representing the name of Distances blocks.
         */
        public static final String DISTANCES_BLOCK = "DISTANCES";

        private int dimensionsNTax = 0;

        private int dimensionsNChar = 0;

        private String triangle = "LOWER";

        private boolean diagonal = true;

        private boolean labels = true;

        private String missing = "?";

        private boolean interleaved = false;

        private List taxLabels = new ArrayList();

        // values are lists, containing strings and nulls which are gaps
        private Map matrix = new LinkedHashMap();

        private List comments = new ArrayList();

        /**
         * Delegates to NexusBlock.Abstract constructor using
         * DistancesBlock.DISTANCES_BLOCK as the name.
         */
        public DistancesBlock() {
                super(DistancesBlock.DISTANCES_BLOCK);
        }

        /**
         * Set the NTAX value.
         * 
         * @param dimensionsNTax
         *            the NTAX value.
         */
        public void setDimensionsNTax(int dimensionsNTax) {
                this.dimensionsNTax = dimensionsNTax;
        }

        /**
         * Get the NTAX value.
         * 
         * @return the NTAX value.
         */
        public int getDimensionsNTax() {
                return this.dimensionsNTax;
        }

        /**
         * Set the NCHAR value.
         * 
         * @param dimensionsNChar
         *            the NCHAR value.
         */
        public void setDimensionsNChar(int dimensionsNChar) {
                this.dimensionsNChar = dimensionsNChar;
        }

        /**
         * Get the NCHAR value.
         * 
         * @return the NCHAR value.
         */
        public int getDimensionsNChar() {
                return this.dimensionsNChar;
        }

        public void setTriangle(final String triangle) {
                this.triangle = triangle;
        }

        public void setDiagonal(final boolean diagonal) {
                this.diagonal = diagonal;
        }

        public boolean isDiagonal() {
                return this.diagonal;
        }

        public void setLabels(final boolean labels) {
                this.labels = labels;
        }

        public boolean isLabels() {
                return this.labels;
        }

        public void setMissing(final String missing) {
                this.missing = missing;
        }

        public String getMissing() {
                return this.missing;
        }

        public void setInterleaved(final boolean interleaved) {
                this.interleaved = interleaved;
        }

        public boolean isInterleaved() {
                return this.interleaved;
        }

        /**
         * Add a TAXLABEL. If it already exists, or is a number that refers to an
         * index position that already exists, an exception is thrown.
         * 
         * @param taxLabel
         *            the label to add.
         * @throws ParseException
         *             if the label cannot be added.
         */
        public void addTaxLabel(final String taxLabel) throws ParseException {
                if (this.taxLabels.contains(taxLabel))
                        throw new ParseException("Duplicate taxa label: " + taxLabel);
                else
                        try {
                                // Try it as a number to see if it refers to
                                // position we already have.
                                final int i = Integer.parseInt(taxLabel);
                                if (i <= this.taxLabels.size() + 1)
                                        throw new ParseException("Taxa label " + i
                                                        + " refers to already extant taxa position");
                        } catch (NumberFormatException e) {
                                // It is not a number, so ignore.
                        } catch (ParseException e) {
                                // Throw it.
                                throw e;
                        }
                this.taxLabels.add(taxLabel);
        }

        /**
         * Removes the given TAXLABEL.
         * 
         * @param taxLabel
         *            the label to remove.
         */
        public void removeTaxLabel(final String taxLabel) {
                this.taxLabels.remove(taxLabel);
        }

        /**
         * Checks to see if we contain the given TAXLABEL.
         * 
         * @param taxLabel
         *            the label to check for.
         * @return <tt>true</tt> if we already contain it.
         */
        public boolean containsTaxLabel(final String taxLabel) {
                if (this.taxLabels.contains(taxLabel))
                        return true;
                else
                        try {
                                // Try it as a number to see if it refers to
                                // position we already have.
                                final int i = Integer.parseInt(taxLabel);
                                if (i <= this.taxLabels.size() + 1)
                                        return true;
                        } catch (NumberFormatException e) {
                                // It is not a number, so ignore.
                        }
                return false;
        }

        /**
         * Get the TAXLABEL values added so far.
         * 
         * @return this labels so far.
         */
        public List getTaxLabels() {
                return this.taxLabels;
        }

        public void addMatrixEntry(final String taxa) {
                if (!this.matrix.containsKey(taxa))
                        this.matrix.put(taxa, new ArrayList());
        }

        public void appendMatrixData(final String taxa, final Object data) {
                ((List) this.matrix.get(taxa)).add(data);
        }

        public List getMatrixData(final String taxa) {
                return (List) this.matrix.get(taxa);
        }
        
        public Collection getMatrixLabels() {
                return Collections.unmodifiableSet(this.matrix.keySet());
        }

        /**
         * Adds a comment.
         * 
         * @param comment
         *            the comment to add.
         */
        public void addComment(final NexusComment comment) {
                this.comments.add(comment);
        }

        /**
         * Removes a comment.
         * 
         * @param comment
         *            the comment to remove.
         */
        public void removeComment(final NexusComment comment) {
                this.comments.remove(comment);
        }

        /**
         * Returns all comments.
         * 
         * @return all the selected comments.
         */
        public List getComments() {
                return this.comments;
        }

        protected void writeBlockContents(Writer writer) throws IOException {
                for (final Iterator i = this.comments.iterator(); i.hasNext();) {
                        ((NexusComment) i.next()).writeObject(writer);
                        writer.write(NexusFileFormat.NEW_LINE);
                }
                writer.write(" DIMENSIONS ");
                if (!this.taxLabels.isEmpty())
                        writer.write("NEWTAXA ");
                if (this.dimensionsNTax > 0)
                        writer.write("NTAX=" + this.dimensionsNTax + " ");
                writer.write("NCHAR=" + this.dimensionsNChar + ";"
                                + NexusFileFormat.NEW_LINE);

                writer.write(" FORMAT TRIANGLE=");
                this.writeToken(writer, this.triangle);
                writer.write(this.diagonal ? " DIAGONAL" : " NODIAGONAL");
                writer.write(this.labels ? " LABELS" : " NOLABELS");
                writer.write(" MISSING=");
                this.writeToken(writer, this.missing);
                if (this.interleaved)
                        writer.write(" INTERLEAVED");
                writer.write(";" + NexusFileFormat.NEW_LINE);

                if (this.taxLabels.size() > 0) {
                        writer.write(" TAXLABELS");
                        for (final Iterator i = this.taxLabels.iterator(); i.hasNext();) {
                                writer.write(' ');
                                this.writeToken(writer, (String) i.next());
                        }
                        writer.write(";" + NexusFileFormat.NEW_LINE);
                }

                // if statesformat=statespresent and items=1, bracket only multi values,
                // otherwise bracket all values
                // only space tokens if reallyUseTokens=true
                writer.write(" MATRIX" + NexusFileFormat.NEW_LINE);
                for (final Iterator i = this.matrix.entrySet().iterator(); i.hasNext();) {
                        final Map.Entry entry = (Map.Entry) i.next();
                        writer.write('\t');
                        this.writeToken(writer, "" + entry.getKey());
                        writer.write('\t');
                        for (final Iterator j = ((List) entry.getValue()).iterator(); j
                                        .hasNext();) {
                                final Object obj = j.next();
                                if (obj instanceof String)
                                        this.writeToken(writer, (String) obj);
                                if (j.hasNext())
                                        writer.write('\t');
                        }
                        writer.write(NexusFileFormat.NEW_LINE);
                }
                writer.write(";" + NexusFileFormat.NEW_LINE);

        }
}