X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=dd2dbbf46dcd9c5ea053cfdde77462676daa4c09;hb=49685e6426d5ac136dce4907196751680c667670;hp=20d28f7e2fcbe49dd0deb690b65dc9d3de28260e;hpb=ddf4180014d2316824c4ecd4bcbbe20be4033d43;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 20d28f7..dd2dbbf 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,1208 +1,1295 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-package jalview.analysis;
-
-import jalview.datamodel.*;
-
-import jalview.io.NewickFile;
-
-import jalview.schemes.ResidueProperties;
-
-import jalview.util.*;
-
-import java.util.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class NJTree
-{
-    Vector cluster;
-    SequenceI[] sequence;
-
-    //SequenceData is a string representation of what the user
-    //sees. The display may contain hidden columns.
-    String [] sequenceString;
-
-    int[] done;
-    int noseqs;
-    int noClus;
-    float[][] distance;
-    int mini;
-    int minj;
-    float ri;
-    float rj;
-    Vector groups = new Vector();
-    SequenceNode maxdist;
-    SequenceNode top;
-    float maxDistValue;
-    float maxheight;
-    int ycount;
-    Vector node;
-    String type;
-    String pwtype;
-    Object found = null;
-    Object leaves = null;
-
-    boolean hasDistances = true; // normal case for jalview trees
-    boolean hasBootstrap = false; // normal case for jalview trees
-
-    private boolean hasRootDistance = true;
-
-
-    /**
-     * Creates a new NJTree object.
-     *
-     * @param seqs DOCUMENT ME!
-     * @param treefile DOCUMENT ME!
-     */
-    public NJTree(SequenceI[] seqs,  NewickFile treefile)
-    {
-        top = treefile.getTree();
-
-        if (sequenceString == null)
-        {
-          sequenceString = new String[sequence.length];
-          for (int i = 0; i < sequence.length; i++)
-          {
-            sequenceString[i] = sequence[i].getSequence();
-          }
-        }
-
-
-        hasDistances = treefile.HasDistances();
-        hasBootstrap = treefile.HasBootstrap();
-        hasRootDistance = treefile.HasRootDistance();
-
-        maxheight = findHeight(top);
-
-        SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
-
-        Vector leaves = new Vector();
-        findLeaves(top, leaves);
-
-        int i = 0;
-        int namesleft = seqs.length;
-
-        SequenceNode j;
-        SequenceI nam;
-        String realnam;
-
-        while (i < leaves.size())
-        {
-            j = (SequenceNode) leaves.elementAt(i++);
-            realnam = j.getName();
-            nam = null;
-
-            if (namesleft > -1)
-            {
-                nam = algnIds.findIdMatch(realnam);
-            }
-
-            if (nam != null)
-            {
-                j.setElement(nam);
-                namesleft--;
-            }
-            else
-            {
-                j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
-                j.setPlaceholder(true);
-            }
-        }
-    }
-
-    /**
-     * Creates a new NJTree object.
-     *
-     * @param sequence DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     * @param pwtype DOCUMENT ME!
-     * @param start DOCUMENT ME!
-     * @param end DOCUMENT ME!
-     */
-    public NJTree(SequenceI[] sequence,
-                  String [] sequenceString,
-                  String type,
-                  String pwtype,
-                  int start, int end)
-    {
-        this.sequence = sequence;
-        this.node = new Vector();
-        this.type = type;
-        this.pwtype = pwtype;
-
-        if (sequenceString == null)
-        {
-          this.sequenceString = new String[sequence.length];
-          for(int i=0; i<sequence.length; i++)
-          {
-            this.sequenceString[i] = sequence[i].getSequence(start, end);
-          }
-        }
-        else
-          this.sequenceString = sequenceString;
-
-
-        if (!(type.equals("NJ")))
-        {
-            type = "AV";
-        }
-
-        if (!(pwtype.equals("PID")))
-        {
-            type = "BL";
-        }
-
-        int i = 0;
-
-        done = new int[sequence.length];
-
-        while ((i < sequence.length) && (sequence[i] != null))
-        {
-            done[i] = 0;
-            i++;
-        }
-
-        noseqs = i++;
-
-        distance = findDistances();
-
-        makeLeaves();
-
-        noClus = cluster.size();
-
-        cluster();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String toString()
-    {
-        jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
-
-        return fout.print(false, true); // distances only
-    }
-
-    /**
-     *
-     * used when the alignment associated to a tree has changed.
-     *
-     * @param alignment Vector
-     */
-    public void UpdatePlaceHolders(Vector alignment)
-    {
-        Vector leaves = new Vector();
-        findLeaves(top, leaves);
-
-        int sz = leaves.size();
-        SequenceIdMatcher seqmatcher = null;
-        int i = 0;
-
-        while (i < sz)
-        {
-            SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
-
-            if (alignment.contains(leaf.element()))
-            {
-                leaf.setPlaceholder(false);
-            }
-            else
-            {
-                if (seqmatcher == null)
-                {
-                    // Only create this the first time we need it
-                    SequenceI[] seqs = new SequenceI[alignment.size()];
-
-                    for (int j = 0; j < seqs.length; j++)
-                        seqs[j] = (SequenceI) alignment.elementAt(j);
-
-                    seqmatcher = new SequenceIdMatcher(seqs);
-                }
-
-                SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
-
-                if (nam != null)
-                {
-                    leaf.setPlaceholder(false);
-                    leaf.setElement(nam);
-                }
-                else
-                {
-                    leaf.setPlaceholder(true);
-                }
-            }
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void cluster()
-    {
-        while (noClus > 2)
-        {
-            if (type.equals("NJ"))
-            {
-                findMinNJDistance();
-            }
-            else
-            {
-                findMinDistance();
-            }
-
-            Cluster c = joinClusters(mini, minj);
-
-            done[minj] = 1;
-
-            cluster.setElementAt(null, minj);
-            cluster.setElementAt(c, mini);
-
-            noClus--;
-        }
-
-        boolean onefound = false;
-
-        int one = -1;
-        int two = -1;
-
-        for (int i = 0; i < noseqs; i++)
-        {
-            if (done[i] != 1)
-            {
-                if (onefound == false)
-                {
-                    two = i;
-                    onefound = true;
-                }
-                else
-                {
-                    one = i;
-                }
-            }
-        }
-
-        joinClusters(one, two);
-        top = (SequenceNode) (node.elementAt(one));
-
-        reCount(top);
-        findHeight(top);
-        findMaxDist(top);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Cluster joinClusters(int i, int j)
-    {
-        float dist = distance[i][j];
-
-        int noi = ((Cluster) cluster.elementAt(i)).value.length;
-        int noj = ((Cluster) cluster.elementAt(j)).value.length;
-
-        int[] value = new int[noi + noj];
-
-        for (int ii = 0; ii < noi; ii++)
-        {
-            value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
-        }
-
-        for (int ii = noi; ii < (noi + noj); ii++)
-        {
-            value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
-        }
-
-        Cluster c = new Cluster(value);
-
-        ri = findr(i, j);
-        rj = findr(j, i);
-
-        if (type.equals("NJ"))
-        {
-            findClusterNJDistance(i, j);
-        }
-        else
-        {
-            findClusterDistance(i, j);
-        }
-
-        SequenceNode sn = new SequenceNode();
-
-        sn.setLeft((SequenceNode) (node.elementAt(i)));
-        sn.setRight((SequenceNode) (node.elementAt(j)));
-
-        SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
-        SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
-
-        if (type.equals("NJ"))
-        {
-            findNewNJDistances(tmpi, tmpj, dist);
-        }
-        else
-        {
-            findNewDistances(tmpi, tmpj, dist);
-        }
-
-        tmpi.setParent(sn);
-        tmpj.setParent(sn);
-
-        node.setElementAt(sn, i);
-
-        return c;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param tmpi DOCUMENT ME!
-     * @param tmpj DOCUMENT ME!
-     * @param dist DOCUMENT ME!
-     */
-    public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
-        float dist)
-    {
-
-        tmpi.dist = ((dist + ri) - rj) / 2;
-        tmpj.dist = (dist - tmpi.dist);
-
-        if (tmpi.dist < 0)
-        {
-            tmpi.dist = 0;
-        }
-
-        if (tmpj.dist < 0)
-        {
-            tmpj.dist = 0;
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param tmpi DOCUMENT ME!
-     * @param tmpj DOCUMENT ME!
-     * @param dist DOCUMENT ME!
-     */
-    public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
-        float dist)
-    {
-        float ih = 0;
-        float jh = 0;
-
-        SequenceNode sni = tmpi;
-        SequenceNode snj = tmpj;
-
-        while (sni != null)
-        {
-            ih = ih + sni.dist;
-            sni = (SequenceNode) sni.left();
-        }
-
-        while (snj != null)
-        {
-            jh = jh + snj.dist;
-            snj = (SequenceNode) snj.left();
-        }
-
-        tmpi.dist = ((dist / 2) - ih);
-        tmpj.dist = ((dist / 2) - jh);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     */
-    public void findClusterDistance(int i, int j)
-    {
-        int noi = ((Cluster) cluster.elementAt(i)).value.length;
-        int noj = ((Cluster) cluster.elementAt(j)).value.length;
-
-        // New distances from cluster to others
-        float[] newdist = new float[noseqs];
-
-        for (int l = 0; l < noseqs; l++)
-        {
-            if ((l != i) && (l != j))
-            {
-                newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +
-                    noj);
-            }
-            else
-            {
-                newdist[l] = 0;
-            }
-        }
-
-        for (int ii = 0; ii < noseqs; ii++)
-        {
-            distance[i][ii] = newdist[ii];
-            distance[ii][i] = newdist[ii];
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     */
-    public void findClusterNJDistance(int i, int j)
-    {
-
-        // New distances from cluster to others
-        float[] newdist = new float[noseqs];
-
-        for (int l = 0; l < noseqs; l++)
-        {
-            if ((l != i) && (l != j))
-            {
-                newdist[l] = ((distance[i][l] + distance[j][l]) -
-                    distance[i][j]) / 2;
-            }
-            else
-            {
-                newdist[l] = 0;
-            }
-        }
-
-        for (int ii = 0; ii < noseqs; ii++)
-        {
-            distance[i][ii] = newdist[ii];
-            distance[ii][i] = newdist[ii];
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float findr(int i, int j)
-    {
-        float tmp = 1;
-
-        for (int k = 0; k < noseqs; k++)
-        {
-            if ((k != i) && (k != j) && (done[k] != 1))
-            {
-                tmp = tmp + distance[i][k];
-            }
-        }
-
-        if (noClus > 2)
-        {
-            tmp = tmp / (noClus - 2);
-        }
-
-        return tmp;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float findMinNJDistance()
-    {
-        float min = 100000;
-
-        for (int i = 0; i < (noseqs - 1); i++)
-        {
-            for (int j = i + 1; j < noseqs; j++)
-            {
-                if ((done[i] != 1) && (done[j] != 1))
-                {
-                    float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
-
-                    if (tmp < min)
-                    {
-                        mini = i;
-                        minj = j;
-
-                        min = tmp;
-                    }
-                }
-            }
-        }
-
-        return min;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float findMinDistance()
-    {
-        float min = 100000;
-
-        for (int i = 0; i < (noseqs - 1); i++)
-        {
-            for (int j = i + 1; j < noseqs; j++)
-            {
-                if ((done[i] != 1) && (done[j] != 1))
-                {
-                    if (distance[i][j] < min)
-                    {
-                        mini = i;
-                        minj = j;
-
-                        min = distance[i][j];
-                    }
-                }
-            }
-        }
-
-        return min;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float[][] findDistances()
-    {
-        float[][] distance = new float[noseqs][noseqs];
-
-        if (pwtype.equals("PID"))
-        {
-            for (int i = 0; i < (noseqs - 1); i++)
-            {
-                for (int j = i; j < noseqs; j++)
-                {
-                    if (j == i)
-                    {
-                        distance[i][i] = 0;
-                    }
-                    else
-                    {
-                        distance[i][j] = 100 -
-                             Comparison.PID(sequenceString[i], sequenceString[j]);
-
-                        distance[j][i] = distance[i][j];
-                    }
-                }
-            }
-        }
-        else if (pwtype.equals("BL"))
-        {
-            int maxscore = 0;
-            int end = sequenceString[0].length();
-            for (int i = 0; i < (noseqs - 1); i++)
-            {
-                for (int j = i; j < noseqs; j++)
-                {
-                    int score = 0;
-
-                    for (int k = 0; k < end; k++)
-                    {
-                        try
-                        {
-                            score += ResidueProperties.getBLOSUM62(
-                              sequenceString[i].substring(k, k + 1),
-                              sequenceString[j].substring(k, k + 1));
-                        }
-                        catch (Exception ex)
-                        {
-                            System.err.println("err creating BLOSUM62 tree");
-                            ex.printStackTrace();
-                        }
-                    }
-
-                    distance[i][j] = (float) score;
-
-                    if (score > maxscore)
-                    {
-                        maxscore = score;
-                    }
-                }
-            }
-
-            for (int i = 0; i < (noseqs - 1); i++)
-            {
-                for (int j = i; j < noseqs; j++)
-                {
-                    distance[i][j] = (float) maxscore - distance[i][j];
-                    distance[j][i] = distance[i][j];
-                }
-            }
-        }
-      /*  else if (pwtype.equals("SW"))
-        {
-            float max = -1;
-
-            for (int i = 0; i < (noseqs - 1); i++)
-            {
-                for (int j = i; j < noseqs; j++)
-                {
-                    AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
-                    as.calcScoreMatrix();
-                    as.traceAlignment();
-                    as.printAlignment(System.out);
-                    distance[i][j] = (float) as.maxscore;
-
-                    if (max < distance[i][j])
-                    {
-                        max = distance[i][j];
-                    }
-                }
-            }
-
-            for (int i = 0; i < (noseqs - 1); i++)
-            {
-                for (int j = i; j < noseqs; j++)
-                {
-                    distance[i][j] = max - distance[i][j];
-                    distance[j][i] = distance[i][j];
-                }
-            }
-        }/*/
-
-        return distance;
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void makeLeaves()
-    {
-        cluster = new Vector();
-
-        for (int i = 0; i < noseqs; i++)
-        {
-            SequenceNode sn = new SequenceNode();
-
-            sn.setElement(sequence[i]);
-            sn.setName(sequence[i].getName());
-            node.addElement(sn);
-
-            int[] value = new int[1];
-            value[0] = i;
-
-            Cluster c = new Cluster(value);
-            cluster.addElement(c);
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     * @param leaves DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector findLeaves(SequenceNode node, Vector leaves)
-    {
-        if (node == null)
-        {
-            return leaves;
-        }
-
-        if ((node.left() == null) && (node.right() == null))
-        {
-            leaves.addElement(node);
-
-            return leaves;
-        }
-        else
-        {
-            findLeaves((SequenceNode) node.left(), leaves);
-            findLeaves((SequenceNode) node.right(), leaves);
-        }
-
-        return leaves;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     * @param count DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Object findLeaf(SequenceNode node, int count)
-    {
-        found = _findLeaf(node, count);
-
-        return found;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     * @param count DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Object _findLeaf(SequenceNode node, int count)
-    {
-        if (node == null)
-        {
-            return null;
-        }
-
-        if (node.ycount == count)
-        {
-            found = node.element();
-
-            return found;
-        }
-        else
-        {
-            _findLeaf((SequenceNode) node.left(), count);
-            _findLeaf((SequenceNode) node.right(), count);
-        }
-
-        return found;
-    }
-
-    /**
-     * printNode is mainly for debugging purposes.
-     *
-     * @param node SequenceNode
-     */
-    public void printNode(SequenceNode node)
-    {
-        if (node == null)
-        {
-            return;
-        }
-
-        if ((node.left() == null) && (node.right() == null))
-        {
-            System.out.println("Leaf = " +
-                ((SequenceI) node.element()).getName());
-            System.out.println("Dist " + ((SequenceNode) node).dist);
-            System.out.println("Boot " + node.getBootstrap());
-        }
-        else
-        {
-            System.out.println("Dist " + ((SequenceNode) node).dist);
-            printNode((SequenceNode) node.left());
-            printNode((SequenceNode) node.right());
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void findMaxDist(SequenceNode node)
-    {
-        if (node == null)
-        {
-            return;
-        }
-
-        if ((node.left() == null) && (node.right() == null))
-        {
-            float dist = ((SequenceNode) node).dist;
-
-            if (dist > maxDistValue)
-            {
-                maxdist = (SequenceNode) node;
-                maxDistValue = dist;
-            }
-        }
-        else
-        {
-            findMaxDist((SequenceNode) node.left());
-            findMaxDist((SequenceNode) node.right());
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getGroups()
-    {
-        return groups;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float getMaxHeight()
-    {
-        return maxheight;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     * @param threshold DOCUMENT ME!
-     */
-    public void groupNodes(SequenceNode node, float threshold)
-    {
-        if (node == null)
-        {
-            return;
-        }
-
-        if ((node.height / maxheight) > threshold)
-        {
-            groups.addElement(node);
-        }
-        else
-        {
-            groupNodes((SequenceNode) node.left(), threshold);
-            groupNodes((SequenceNode) node.right(), threshold);
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float findHeight(SequenceNode node)
-    {
-        if (node == null)
-        {
-            return maxheight;
-        }
-
-        if ((node.left() == null) && (node.right() == null))
-        {
-            node.height = ((SequenceNode) node.parent()).height + node.dist;
-
-            if (node.height > maxheight)
-            {
-                return node.height;
-            }
-            else
-            {
-                return maxheight;
-            }
-        }
-        else
-        {
-            if (node.parent() != null)
-            {
-                node.height = ((SequenceNode) node.parent()).height +
-                    node.dist;
-            }
-            else
-            {
-                maxheight = 0;
-                node.height = (float) 0.0;
-            }
-
-            maxheight = findHeight((SequenceNode) (node.left()));
-            maxheight = findHeight((SequenceNode) (node.right()));
-        }
-
-        return maxheight;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceNode reRoot()
-    {
-        if (maxdist != null)
-        {
-            ycount = 0;
-
-            float tmpdist = maxdist.dist;
-
-            // New top
-            SequenceNode sn = new SequenceNode();
-            sn.setParent(null);
-
-            // New right hand of top
-            SequenceNode snr = (SequenceNode) maxdist.parent();
-            changeDirection(snr, maxdist);
-            System.out.println("Printing reversed tree");
-            printN(snr);
-            snr.dist = tmpdist / 2;
-            maxdist.dist = tmpdist / 2;
-
-            snr.setParent(sn);
-            maxdist.setParent(sn);
-
-            sn.setRight(snr);
-            sn.setLeft(maxdist);
-
-            top = sn;
-
-            ycount = 0;
-            reCount(top);
-            findHeight(top);
-        }
-
-        return top;
-    }
-
-    public String printOriginalSequenceData()
-    {
-      StringBuffer sb = new StringBuffer();
-      for(int i=0; i<sequenceString.length; i++)
-      {
-        sb.append(new jalview.util.Format("%-" + 15 + "s").form(
-            sequence[i].getName()));
-        sb.append(" "+sequenceString[i]+"\n");
-      }
-      return sb.toString();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void printN(SequenceNode node)
-    {
-        if (node == null)
-        {
-            return;
-        }
-
-        if ((node.left() != null) && (node.right() != null))
-        {
-            printN((SequenceNode) node.left());
-            printN((SequenceNode) node.right());
-        }
-        else
-        {
-            System.out.println(" name = " +
-                ((SequenceI) node.element()).getName());
-        }
-
-        System.out.println(" dist = " + ((SequenceNode) node).dist + " " +
-            ((SequenceNode) node).count + " " + ((SequenceNode) node).height);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void reCount(SequenceNode node)
-    {
-        ycount = 0;
-        _reCount(node);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void _reCount(SequenceNode node)
-    {
-        if (node == null)
-        {
-            return;
-        }
-
-        if ((node.left() != null) && (node.right() != null))
-        {
-            _reCount((SequenceNode) node.left());
-            _reCount((SequenceNode) node.right());
-
-            SequenceNode l = (SequenceNode) node.left();
-            SequenceNode r = (SequenceNode) node.right();
-
-            ((SequenceNode) node).count = l.count + r.count;
-            ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
-        }
-        else
-        {
-            ((SequenceNode) node).count = 1;
-            ((SequenceNode) node).ycount = ycount++;
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void swapNodes(SequenceNode node)
-    {
-        if (node == null)
-        {
-            return;
-        }
-
-        SequenceNode tmp = (SequenceNode) node.left();
-
-        node.setLeft(node.right());
-        node.setRight(tmp);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     * @param dir DOCUMENT ME!
-     */
-    public void changeDirection(SequenceNode node, SequenceNode dir)
-    {
-        if (node == null)
-        {
-            return;
-        }
-
-        if (node.parent() != top)
-        {
-            changeDirection((SequenceNode) node.parent(), node);
-
-            SequenceNode tmp = (SequenceNode) node.parent();
-
-            if (dir == node.left())
-            {
-                node.setParent(dir);
-                node.setLeft(tmp);
-            }
-            else if (dir == node.right())
-            {
-                node.setParent(dir);
-                node.setRight(tmp);
-            }
-        }
-        else
-        {
-            if (dir == node.left())
-            {
-                node.setParent(node.left());
-
-                if (top.left() == node)
-                {
-                    node.setRight(top.right());
-                }
-                else
-                {
-                    node.setRight(top.left());
-                }
-            }
-            else
-            {
-                node.setParent(node.right());
-
-                if (top.left() == node)
-                {
-                    node.setLeft(top.right());
-                }
-                else
-                {
-                    node.setLeft(top.left());
-                }
-            }
-        }
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceNode getMaxDist()
-    {
-        return maxdist;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceNode getTopNode()
-    {
-        return top;
-    }
-    /**
-     *
-     * @return true if tree has real distances
-     */
-    public boolean isHasDistances() {
-      return hasDistances;
-    }
-
-    /**
-     *
-     * @return true if tree has real bootstrap values
-     */
-    public boolean isHasBootstrap() {
-      return hasBootstrap;
-    }
-
-  public boolean isHasRootDistance()
-  {
-    return hasRootDistance;
-  }
-
-}
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-class Cluster
-{
-    int[] value;
-
-    /**
-     * Creates a new Cluster object.
-     *
-     * @param value DOCUMENT ME!
-     */
-    public Cluster(int[] value)
-    {
-        this.value = value;
-    }
-}
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.analysis;
+
+import java.util.*;
+
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
+import jalview.util.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NJTree
+{
+  Vector cluster;
+  SequenceI[] sequence;
+
+  //SequenceData is a string representation of what the user
+  //sees. The display may contain hidden columns.
+  public AlignmentView seqData = null;
+
+  int[] done;
+  int noseqs;
+  int noClus;
+  float[][] distance;
+  int mini;
+  int minj;
+  float ri;
+  float rj;
+  Vector groups = new Vector();
+  SequenceNode maxdist;
+  SequenceNode top;
+  float maxDistValue;
+  float maxheight;
+  int ycount;
+  Vector node;
+  String type;
+  String pwtype;
+  Object found = null;
+  Object leaves = null;
+
+  boolean hasDistances = true; // normal case for jalview trees
+  boolean hasBootstrap = false; // normal case for jalview trees
+
+  private boolean hasRootDistance = true;
+
+  /**
+   * Create a new NJTree object with leaves associated with sequences in seqs,
+   * and original alignment data represented by Cigar strings.
+   * @param seqs SequenceI[]
+   * @param odata Cigar[]
+   * @param treefile NewickFile
+   */
+  public NJTree(SequenceI[] seqs, AlignmentView odata, NewickFile treefile)
+  {
+    this(seqs, treefile);
+    if (odata != null)
+    {
+      seqData = odata;
+    }
+    /*
+           sequenceString = new String[odata.length];
+           char gapChar = jalview.util.Comparison.GapChars.charAt(0);
+           for (int i = 0; i < odata.length; i++)
+           {
+      SequenceI oseq_aligned = odata[i].getSeq(gapChar);
+        sequenceString[i] = oseq_aligned.getSequence();
+           } */
+  }
+
+  /**
+   * Creates a new NJTree object from a tree from an external source
+   *
+   * @param seqs SequenceI which should be associated with leafs of treefile
+   * @param treefile A parsed tree
+   */
+  public NJTree(SequenceI[] seqs, NewickFile treefile)
+  {
+    this.sequence = seqs;
+    top = treefile.getTree();
+
+    /**
+     * There is no dependent alignment to be recovered from an
+     * imported tree.
+     *
+             if (sequenceString == null)
+             {
+      sequenceString = new String[seqs.length];
+      for (int i = 0; i < seqs.length; i++)
+      {
+        sequenceString[i] = seqs[i].getSequence();
+      }
+             }
+     */
+
+    hasDistances = treefile.HasDistances();
+    hasBootstrap = treefile.HasBootstrap();
+    hasRootDistance = treefile.HasRootDistance();
+
+    maxheight = findHeight(top);
+
+    SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
+
+    Vector leaves = new Vector();
+    findLeaves(top, leaves);
+
+    int i = 0;
+    int namesleft = seqs.length;
+
+    SequenceNode j;
+    SequenceI nam;
+    String realnam;
+    Vector one2many = new Vector();
+    int countOne2Many = 0;
+    while (i < leaves.size())
+    {
+      j = (SequenceNode) leaves.elementAt(i++);
+      realnam = j.getName();
+      nam = null;
+
+      if (namesleft > -1)
+      {
+        nam = algnIds.findIdMatch(realnam);
+      }
+
+      if (nam != null)
+      {
+        j.setElement(nam);
+        if (one2many.contains(nam))
+        {
+          countOne2Many++;
+          //  if (jalview.bin.Cache.log.isDebugEnabled())
+          //    jalview.bin.Cache.log.debug("One 2 many relationship for "+nam.getName());
+        }
+        else
+        {
+          one2many.addElement(nam);
+          namesleft--;
+        }
+      }
+      else
+      {
+        j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
+        j.setPlaceholder(true);
+      }
+    }
+    //  if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
+    //    jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment sequence ids (out of "+one2many.size()+" unique ids) linked to two or more leaves.");
+    //  }
+    //  one2many.clear();
+  }
+
+  /**
+   * Creates a new NJTree object.
+   *
+   * @param sequence DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   * @param pwtype DOCUMENT ME!
+   * @param start DOCUMENT ME!
+   * @param end DOCUMENT ME!
+   */
+  public NJTree(SequenceI[] sequence,
+                AlignmentView seqData,
+                String type,
+                String pwtype,
+                int start, int end)
+  {
+    this.sequence = sequence;
+    this.node = new Vector();
+    this.type = type;
+    this.pwtype = pwtype;
+    if (seqData != null)
+    {
+      this.seqData = seqData;
+    }
+    else
+    {
+      SeqCigar[] seqs = new SeqCigar[sequence.length];
+      for (int i = 0; i < sequence.length; i++)
+      {
+        seqs[i] = new SeqCigar(sequence[i], start, end);
+      }
+      CigarArray sdata = new CigarArray(seqs);
+      sdata.addOperation(CigarArray.M, end - start + 1);
+      this.seqData = new AlignmentView(sdata, start);
+    }
+
+    if (! (type.equals("NJ")))
+    {
+      type = "AV";
+    }
+
+    if (! (pwtype.equals("PID")))
+    {
+      if (ResidueProperties.getScoreMatrix(pwtype) == null)
+      {
+        type = "BLOSUM62";
+      }
+    }
+
+    int i = 0;
+
+    done = new int[sequence.length];
+
+    while ( (i < sequence.length) && (sequence[i] != null))
+    {
+      done[i] = 0;
+      i++;
+    }
+
+    noseqs = i++;
+
+    distance = findDistances(this.seqData.getSequenceStrings(Comparison.
+        GapChars.charAt(0)));
+
+    makeLeaves();
+
+    noClus = cluster.size();
+
+    cluster();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String toString()
+  {
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
+
+    return fout.print(false, true); // distances only
+  }
+
+  /**
+   *
+   * used when the alignment associated to a tree has changed.
+   *
+   * @param alignment Vector
+   */
+  public void UpdatePlaceHolders(Vector alignment)
+  {
+    Vector leaves = new Vector();
+    findLeaves(top, leaves);
+
+    int sz = leaves.size();
+    SequenceIdMatcher seqmatcher = null;
+    int i = 0;
+
+    while (i < sz)
+    {
+      SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
+
+      if (alignment.contains(leaf.element()))
+      {
+        leaf.setPlaceholder(false);
+      }
+      else
+      {
+        if (seqmatcher == null)
+        {
+          // Only create this the first time we need it
+          SequenceI[] seqs = new SequenceI[alignment.size()];
+
+          for (int j = 0; j < seqs.length; j++)
+          {
+            seqs[j] = (SequenceI) alignment.elementAt(j);
+          }
+
+          seqmatcher = new SequenceIdMatcher(seqs);
+        }
+
+        SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
+
+        if (nam != null)
+        {
+          if (!leaf.isPlaceholder())
+          {
+            // remapping the node to a new sequenceI - should remove any refs to old one.
+            // TODO - make many sequenceI to one leaf mappings possible! (JBPNote)
+          }
+          leaf.setPlaceholder(false);
+          leaf.setElement(nam);
+        }
+        else
+        {
+          if (!leaf.isPlaceholder())
+          {
+            // Construct a new placeholder sequence object for this leaf
+            leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
+          }
+          leaf.setPlaceholder(true);
+
+        }
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void cluster()
+  {
+    while (noClus > 2)
+    {
+      if (type.equals("NJ"))
+      {
+        findMinNJDistance();
+      }
+      else
+      {
+        findMinDistance();
+      }
+
+      Cluster c = joinClusters(mini, minj);
+
+      done[minj] = 1;
+
+      cluster.setElementAt(null, minj);
+      cluster.setElementAt(c, mini);
+
+      noClus--;
+    }
+
+    boolean onefound = false;
+
+    int one = -1;
+    int two = -1;
+
+    for (int i = 0; i < noseqs; i++)
+    {
+      if (done[i] != 1)
+      {
+        if (onefound == false)
+        {
+          two = i;
+          onefound = true;
+        }
+        else
+        {
+          one = i;
+        }
+      }
+    }
+
+    joinClusters(one, two);
+    top = (SequenceNode) (node.elementAt(one));
+
+    reCount(top);
+    findHeight(top);
+    findMaxDist(top);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Cluster joinClusters(int i, int j)
+  {
+    float dist = distance[i][j];
+
+    int noi = ( (Cluster) cluster.elementAt(i)).value.length;
+    int noj = ( (Cluster) cluster.elementAt(j)).value.length;
+
+    int[] value = new int[noi + noj];
+
+    for (int ii = 0; ii < noi; ii++)
+    {
+      value[ii] = ( (Cluster) cluster.elementAt(i)).value[ii];
+    }
+
+    for (int ii = noi; ii < (noi + noj); ii++)
+    {
+      value[ii] = ( (Cluster) cluster.elementAt(j)).value[ii - noi];
+    }
+
+    Cluster c = new Cluster(value);
+
+    ri = findr(i, j);
+    rj = findr(j, i);
+
+    if (type.equals("NJ"))
+    {
+      findClusterNJDistance(i, j);
+    }
+    else
+    {
+      findClusterDistance(i, j);
+    }
+
+    SequenceNode sn = new SequenceNode();
+
+    sn.setLeft( (SequenceNode) (node.elementAt(i)));
+    sn.setRight( (SequenceNode) (node.elementAt(j)));
+
+    SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
+    SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
+
+    if (type.equals("NJ"))
+    {
+      findNewNJDistances(tmpi, tmpj, dist);
+    }
+    else
+    {
+      findNewDistances(tmpi, tmpj, dist);
+    }
+
+    tmpi.setParent(sn);
+    tmpj.setParent(sn);
+
+    node.setElementAt(sn, i);
+
+    return c;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param tmpi DOCUMENT ME!
+   * @param tmpj DOCUMENT ME!
+   * @param dist DOCUMENT ME!
+   */
+  public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
+                                 float dist)
+  {
+
+    tmpi.dist = ( (dist + ri) - rj) / 2;
+    tmpj.dist = (dist - tmpi.dist);
+
+    if (tmpi.dist < 0)
+    {
+      tmpi.dist = 0;
+    }
+
+    if (tmpj.dist < 0)
+    {
+      tmpj.dist = 0;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param tmpi DOCUMENT ME!
+   * @param tmpj DOCUMENT ME!
+   * @param dist DOCUMENT ME!
+   */
+  public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
+                               float dist)
+  {
+    float ih = 0;
+    float jh = 0;
+
+    SequenceNode sni = tmpi;
+    SequenceNode snj = tmpj;
+
+    while (sni != null)
+    {
+      ih = ih + sni.dist;
+      sni = (SequenceNode) sni.left();
+    }
+
+    while (snj != null)
+    {
+      jh = jh + snj.dist;
+      snj = (SequenceNode) snj.left();
+    }
+
+    tmpi.dist = ( (dist / 2) - ih);
+    tmpj.dist = ( (dist / 2) - jh);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   */
+  public void findClusterDistance(int i, int j)
+  {
+    int noi = ( (Cluster) cluster.elementAt(i)).value.length;
+    int noj = ( (Cluster) cluster.elementAt(j)).value.length;
+
+    // New distances from cluster to others
+    float[] newdist = new float[noseqs];
+
+    for (int l = 0; l < noseqs; l++)
+    {
+      if ( (l != i) && (l != j))
+      {
+        newdist[l] = ( (distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +
+            noj);
+      }
+      else
+      {
+        newdist[l] = 0;
+      }
+    }
+
+    for (int ii = 0; ii < noseqs; ii++)
+    {
+      distance[i][ii] = newdist[ii];
+      distance[ii][i] = newdist[ii];
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   */
+  public void findClusterNJDistance(int i, int j)
+  {
+
+    // New distances from cluster to others
+    float[] newdist = new float[noseqs];
+
+    for (int l = 0; l < noseqs; l++)
+    {
+      if ( (l != i) && (l != j))
+      {
+        newdist[l] = ( (distance[i][l] + distance[j][l]) -
+                      distance[i][j]) / 2;
+      }
+      else
+      {
+        newdist[l] = 0;
+      }
+    }
+
+    for (int ii = 0; ii < noseqs; ii++)
+    {
+      distance[i][ii] = newdist[ii];
+      distance[ii][i] = newdist[ii];
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float findr(int i, int j)
+  {
+    float tmp = 1;
+
+    for (int k = 0; k < noseqs; k++)
+    {
+      if ( (k != i) && (k != j) && (done[k] != 1))
+      {
+        tmp = tmp + distance[i][k];
+      }
+    }
+
+    if (noClus > 2)
+    {
+      tmp = tmp / (noClus - 2);
+    }
+
+    return tmp;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float findMinNJDistance()
+  {
+    float min = 100000;
+
+    for (int i = 0; i < (noseqs - 1); i++)
+    {
+      for (int j = i + 1; j < noseqs; j++)
+      {
+        if ( (done[i] != 1) && (done[j] != 1))
+        {
+          float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
+
+          if (tmp < min)
+          {
+            mini = i;
+            minj = j;
+
+            min = tmp;
+          }
+        }
+      }
+    }
+
+    return min;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float findMinDistance()
+  {
+    float min = 100000;
+
+    for (int i = 0; i < (noseqs - 1); i++)
+    {
+      for (int j = i + 1; j < noseqs; j++)
+      {
+        if ( (done[i] != 1) && (done[j] != 1))
+        {
+          if (distance[i][j] < min)
+          {
+            mini = i;
+            minj = j;
+
+            min = distance[i][j];
+          }
+        }
+      }
+    }
+
+    return min;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float[][] findDistances(String[] sequenceString)
+  {
+    float[][] distance = new float[noseqs][noseqs];
+
+    if (pwtype.equals("PID"))
+    {
+      for (int i = 0; i < (noseqs - 1); i++)
+      {
+        for (int j = i; j < noseqs; j++)
+        {
+          if (j == i)
+          {
+            distance[i][i] = 0;
+          }
+          else
+          {
+            distance[i][j] = 100 -
+                Comparison.PID(sequenceString[i], sequenceString[j]);
+
+            distance[j][i] = distance[i][j];
+          }
+        }
+      }
+    }
+    else
+    {
+      // Pairwise substitution score (with no gap penalties)
+      ScoreMatrix pwmatrix = ResidueProperties.getScoreMatrix(pwtype);
+      if (pwmatrix == null)
+      {
+        pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
+      }
+      int maxscore = 0;
+      int end = sequenceString[0].length();
+      for (int i = 0; i < (noseqs - 1); i++)
+      {
+        for (int j = i; j < noseqs; j++)
+        {
+          int score = 0;
+
+          for (int k = 0; k < end; k++)
+          {
+            try
+            {
+              score += pwmatrix.getPairwiseScore(sequenceString[i].charAt(k),
+                                                 sequenceString[j].charAt(k));
+            }
+            catch (Exception ex)
+            {
+              System.err.println("err creating BLOSUM62 tree");
+              ex.printStackTrace();
+            }
+          }
+
+          distance[i][j] = (float) score;
+
+          if (score > maxscore)
+          {
+            maxscore = score;
+          }
+        }
+      }
+
+      for (int i = 0; i < (noseqs - 1); i++)
+      {
+        for (int j = i; j < noseqs; j++)
+        {
+          distance[i][j] = (float) maxscore - distance[i][j];
+          distance[j][i] = distance[i][j];
+        }
+      }
+
+    }
+    return distance;
+
+    //   else
+    /*  else if (pwtype.equals("SW"))
+      {
+          float max = -1;
+
+          for (int i = 0; i < (noseqs - 1); i++)
+          {
+              for (int j = i; j < noseqs; j++)
+              {
+                  AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
+                  as.calcScoreMatrix();
+                  as.traceAlignment();
+                  as.printAlignment(System.out);
+                  distance[i][j] = (float) as.maxscore;
+
+                  if (max < distance[i][j])
+                  {
+                      max = distance[i][j];
+                  }
+              }
+          }
+
+          for (int i = 0; i < (noseqs - 1); i++)
+          {
+              for (int j = i; j < noseqs; j++)
+              {
+                  distance[i][j] = max - distance[i][j];
+                  distance[j][i] = distance[i][j];
+              }
+          }
+      }/*/
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void makeLeaves()
+  {
+    cluster = new Vector();
+
+    for (int i = 0; i < noseqs; i++)
+    {
+      SequenceNode sn = new SequenceNode();
+
+      sn.setElement(sequence[i]);
+      sn.setName(sequence[i].getName());
+      node.addElement(sn);
+
+      int[] value = new int[1];
+      value[0] = i;
+
+      Cluster c = new Cluster(value);
+      cluster.addElement(c);
+    }
+  }
+
+  /**
+   * Search for leaf nodes.
+   *
+   * @param node root node to search from
+   * @param leaves Vector of leaves to add leaf node objects too.
+   *
+   * @return Vector of leaf nodes on binary tree
+   */
+  public Vector findLeaves(SequenceNode node, Vector leaves)
+  { 
+    if (node == null)
+    {
+      return leaves;
+    }
+
+    if ( (node.left() == null) && (node.right() == null)) // Interior node detection
+    {
+      leaves.addElement(node);
+
+      return leaves;
+    }
+    else
+    {
+/*  TODO: Identify internal nodes...    if (node.isSequenceLabel())
+      {
+        leaves.addElement(node);
+      }*/
+      findLeaves( (SequenceNode) node.left(), leaves);
+      findLeaves( (SequenceNode) node.right(), leaves);
+    }
+
+    return leaves;
+  }
+
+  /**
+   * Find the leaf node with a particular ycount 
+   *
+   * @param node initial point on tree to search from
+   * @param count value to search for
+   *
+   * @return null or the node with ycound=count
+   */
+  public Object findLeaf(SequenceNode node, int count)
+  {
+    found = _findLeaf(node, count);
+
+    return found;
+  }
+
+  /*#see findLeaf(SequenceNode node, count)
+   *
+   */
+  public Object _findLeaf(SequenceNode node, int count)
+  {
+    if (node == null)
+    {
+      return null;
+    }
+
+    if (node.ycount == count)
+    {
+      found = node.element();
+
+      return found;
+    }
+    else
+    {
+      _findLeaf( (SequenceNode) node.left(), count);
+      _findLeaf( (SequenceNode) node.right(), count);
+    }
+
+    return found;
+  }
+
+  /**
+   * printNode is mainly for debugging purposes.
+   *
+   * @param node SequenceNode
+   */
+  public void printNode(SequenceNode node)
+  {
+    if (node == null)
+    {
+      return;
+    }
+
+    if ( (node.left() == null) && (node.right() == null))
+    {
+      System.out.println("Leaf = " +
+                         ( (SequenceI) node.element()).getName());
+      System.out.println("Dist " + ( (SequenceNode) node).dist);
+      System.out.println("Boot " + node.getBootstrap());
+    }
+    else
+    {
+      System.out.println("Dist " + ( (SequenceNode) node).dist);
+      printNode( (SequenceNode) node.left());
+      printNode( (SequenceNode) node.right());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   */
+  public void findMaxDist(SequenceNode node)
+  {
+    if (node == null)
+    {
+      return;
+    }
+
+    if ( (node.left() == null) && (node.right() == null))
+    {
+      float dist = ( (SequenceNode) node).dist;
+
+      if (dist > maxDistValue)
+      {
+        maxdist = (SequenceNode) node;
+        maxDistValue = dist;
+      }
+    }
+    else
+    {
+      findMaxDist( (SequenceNode) node.left());
+      findMaxDist( (SequenceNode) node.right());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Vector getGroups()
+  {
+    return groups;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float getMaxHeight()
+  {
+    return maxheight;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   * @param threshold DOCUMENT ME!
+   */
+  public void groupNodes(SequenceNode node, float threshold)
+  {
+    if (node == null)
+    {
+      return;
+    }
+
+    if ( (node.height / maxheight) > threshold)
+    {
+      groups.addElement(node);
+    }
+    else
+    {
+      groupNodes( (SequenceNode) node.left(), threshold);
+      groupNodes( (SequenceNode) node.right(), threshold);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float findHeight(SequenceNode node)
+  {
+    if (node == null)
+    {
+      return maxheight;
+    }
+
+    if ( (node.left() == null) && (node.right() == null))
+    {
+      node.height = ( (SequenceNode) node.parent()).height + node.dist;
+
+      if (node.height > maxheight)
+      {
+        return node.height;
+      }
+      else
+      {
+        return maxheight;
+      }
+    }
+    else
+    {
+      if (node.parent() != null)
+      {
+        node.height = ( (SequenceNode) node.parent()).height +
+            node.dist;
+      }
+      else
+      {
+        maxheight = 0;
+        node.height = (float) 0.0;
+      }
+
+      maxheight = findHeight( (SequenceNode) (node.left()));
+      maxheight = findHeight( (SequenceNode) (node.right()));
+    }
+
+    return maxheight;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceNode reRoot()
+  {
+    if (maxdist != null)
+    {
+      ycount = 0;
+
+      float tmpdist = maxdist.dist;
+
+      // New top
+      SequenceNode sn = new SequenceNode();
+      sn.setParent(null);
+
+      // New right hand of top
+      SequenceNode snr = (SequenceNode) maxdist.parent();
+      changeDirection(snr, maxdist);
+      System.out.println("Printing reversed tree");
+      printN(snr);
+      snr.dist = tmpdist / 2;
+      maxdist.dist = tmpdist / 2;
+
+      snr.setParent(sn);
+      maxdist.setParent(sn);
+
+      sn.setRight(snr);
+      sn.setLeft(maxdist);
+
+      top = sn;
+
+      ycount = 0;
+      reCount(top);
+      findHeight(top);
+    }
+
+    return top;
+  }
+
+  /**
+   *
+   * @return true if original sequence data can be recovered
+   */
+  public boolean hasOriginalSequenceData()
+  {
+    return seqData != null;
+  }
+
+  /**
+   * Returns original alignment data used for calculation - or null where
+   * not available.
+   *
+   * @return null or cut'n'pasteable alignment
+   */
+  public String printOriginalSequenceData(char gapChar)
+  {
+    if (seqData == null)
+    {
+      return null;
+    }
+
+    StringBuffer sb = new StringBuffer();
+    String[] seqdatas = seqData.getSequenceStrings(gapChar);
+    for (int i = 0; i < seqdatas.length; i++)
+    {
+      sb.append(new jalview.util.Format("%-" + 15 + "s").form(
+          sequence[i].getName()));
+      sb.append(" " + seqdatas[i] + "\n");
+    }
+    return sb.toString();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   */
+  public void printN(SequenceNode node)
+  {
+    if (node == null)
+    {
+      return;
+    }
+
+    if ( (node.left() != null) && (node.right() != null))
+    {
+      printN( (SequenceNode) node.left());
+      printN( (SequenceNode) node.right());
+    }
+    else
+    {
+      System.out.println(" name = " +
+                         ( (SequenceI) node.element()).getName());
+    }
+
+    System.out.println(" dist = " + ( (SequenceNode) node).dist + " " +
+                       ( (SequenceNode) node).count + " " +
+                       ( (SequenceNode) node).height);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   */
+  public void reCount(SequenceNode node)
+  {
+    ycount = 0;
+    _reCount(node);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   */
+  public void _reCount(SequenceNode node)
+  {
+    if (node == null)
+    {
+      return;
+    }
+
+    if ( (node.left() != null) && (node.right() != null))
+    {
+      _reCount( (SequenceNode) node.left());
+      _reCount( (SequenceNode) node.right());
+
+      SequenceNode l = (SequenceNode) node.left();
+      SequenceNode r = (SequenceNode) node.right();
+
+      ( (SequenceNode) node).count = l.count + r.count;
+      ( (SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
+    }
+    else
+    {
+      ( (SequenceNode) node).count = 1;
+      ( (SequenceNode) node).ycount = ycount++;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   */
+  public void swapNodes(SequenceNode node)
+  {
+    if (node == null)
+    {
+      return;
+    }
+
+    SequenceNode tmp = (SequenceNode) node.left();
+
+    node.setLeft(node.right());
+    node.setRight(tmp);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   * @param dir DOCUMENT ME!
+   */
+  public void changeDirection(SequenceNode node, SequenceNode dir)
+  {
+    if (node == null)
+    {
+      return;
+    }
+
+    if (node.parent() != top)
+    {
+      changeDirection( (SequenceNode) node.parent(), node);
+
+      SequenceNode tmp = (SequenceNode) node.parent();
+
+      if (dir == node.left())
+      {
+        node.setParent(dir);
+        node.setLeft(tmp);
+      }
+      else if (dir == node.right())
+      {
+        node.setParent(dir);
+        node.setRight(tmp);
+      }
+    }
+    else
+    {
+      if (dir == node.left())
+      {
+        node.setParent(node.left());
+
+        if (top.left() == node)
+        {
+          node.setRight(top.right());
+        }
+        else
+        {
+          node.setRight(top.left());
+        }
+      }
+      else
+      {
+        node.setParent(node.right());
+
+        if (top.left() == node)
+        {
+          node.setLeft(top.right());
+        }
+        else
+        {
+          node.setLeft(top.left());
+        }
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceNode getMaxDist()
+  {
+    return maxdist;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceNode getTopNode()
+  {
+    return top;
+  }
+
+  /**
+   *
+   * @return true if tree has real distances
+   */
+  public boolean isHasDistances()
+  {
+    return hasDistances;
+  }
+
+  /**
+   *
+   * @return true if tree has real bootstrap values
+   */
+  public boolean isHasBootstrap()
+  {
+    return hasBootstrap;
+  }
+
+  public boolean isHasRootDistance()
+  {
+    return hasRootDistance;
+  }
+
+}
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+class Cluster
+{
+  int[] value;
+
+  /**
+   * Creates a new Cluster object.
+   *
+   * @param value DOCUMENT ME!
+   */
+  public Cluster(int[] value)
+  {
+    this.value = value;
+  }
+}