X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=98916e36a36b1c6996aadcdfc96b89c47e625415;hb=e33cdacd2ac2836504375c538574a0f1cafec7e3;hp=75d36c18018ec156aabbcc2d01c61724c60bc3a7;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 75d36c1..98916e3 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -16,750 +16,1233 @@
 * 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.util.*;
-import jalview.schemes.ResidueProperties;
-import java.util.*;
 
 import jalview.io.NewickFile;
 
-public class NJTree {
+import jalview.schemes.ResidueProperties;
 
-  Vector cluster;
-  SequenceI[] sequence;
+import jalview.util.*;
 
-  int done[];
-  int noseqs;
-  int noClus;
+import java.util.*;
 
-  float distance[][];
 
-  int mini;
-  int minj;
-  float ri;
-  float rj;
+/**
+ * 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.
+    CigarArray 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, CigarArray 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();
+      } */
+    }
 
-  Vector groups = new Vector();
-  SequenceNode maxdist;
-  SequenceNode top;
+    /**
+     * 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;
+
+        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);
+            }
+        }
+    }
 
-  float maxDistValue;
-  float maxheight;
+    /**
+     * 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,
+                  CigarArray 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);
+            }
+            this.seqData = new CigarArray(seqs);
+            this.seqData.addOperation(CigarArray.M, end-start+1);
+        }
 
-  int ycount;
+        if (!(type.equals("NJ")))
+        {
+            type = "AV";
+        }
 
-  Vector node;
+        if (!(pwtype.equals("PID")))
+        {
+            type = "BL";
+        }
 
-  String type;
-  String pwtype;
+        int i = 0;
 
-  Object found = null;
-  Object leaves = null;
+        done = new int[sequence.length];
 
-  int start;
-  int end;
+        while ((i < sequence.length) && (sequence[i] != null))
+        {
+            done[i] = 0;
+            i++;
+        }
 
-  public NJTree(SequenceNode node) {
-    top = node;
-    maxheight = findHeight(top);
-  }
+        noseqs = i++;
 
-  public String toString()
-  {
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
-    return fout.print(false,true); // distances only
-  }
+        distance = findDistances(this.seqData.getSequenceStrings(Comparison.GapChars.charAt(0)));
 
-  public NJTree(SequenceI[] seqs, NewickFile treefile) {
-    top = treefile.getTree();
-    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);
+        makeLeaves();
 
-      }
-    }
-  }
+        noClus = cluster.size();
 
-  /**
-   *
-   * 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);
-        }
-      }
+        cluster();
     }
-  }
-
-  public NJTree(SequenceI[] sequence,int start, int end) {
-    this(sequence,"NJ","BL",start,end);
-  }
 
-  public NJTree(SequenceI[] sequence,String type,String pwtype,int start, int end ) {
-
-    this.sequence = sequence;
-    this.node     = new Vector();
-    this.type     = type;
-    this.pwtype   = pwtype;
-    this.start    = start;
-    this.end      = end;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String toString()
+    {
+        jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
 
-    if (!(type.equals("NJ"))) {
-      type = "AV";
+        return fout.print(false, true); // distances only
     }
 
-    if (!(pwtype.equals("PID"))) {
-      type = "BL";
+    /**
+     *
+     * 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);
+                }
+            }
+        }
     }
 
-    int i=0;
-
-    done = new int[sequence.length];
+    /**
+     * DOCUMENT ME!
+     */
+    public void cluster()
+    {
+        while (noClus > 2)
+        {
+            if (type.equals("NJ"))
+            {
+                findMinNJDistance();
+            }
+            else
+            {
+                findMinDistance();
+            }
 
+            Cluster c = joinClusters(mini, minj);
 
-    while (i < sequence.length  && sequence[i] != null) {
-      done[i] = 0;
-      i++;
-    }
+            done[minj] = 1;
 
-    noseqs = i++;
+            cluster.setElementAt(null, minj);
+            cluster.setElementAt(c, mini);
 
-    distance = findDistances();
+            noClus--;
+        }
 
-    makeLeaves();
+        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;
+                }
+            }
+        }
 
-    noClus = cluster.size();
+        joinClusters(one, two);
+        top = (SequenceNode) (node.elementAt(one));
 
-    cluster();
+        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;
 
-  public void cluster() {
+        int[] value = new int[noi + noj];
 
-    while (noClus > 2) {
-      if (type.equals("NJ")) {
-        float mind = findMinNJDistance();
-      } else {
-        float mind = findMinDistance();
-      }
+        for (int ii = 0; ii < noi; ii++)
+        {
+            value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
+        }
 
-      Cluster c = joinClusters(mini,minj);
+        for (int ii = noi; ii < (noi + noj); ii++)
+        {
+            value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
+        }
 
+        Cluster c = new Cluster(value);
 
-      done[minj] = 1;
+        ri = findr(i, j);
+        rj = findr(j, i);
 
-      cluster.setElementAt(null,minj);
-      cluster.setElementAt(c,mini);
+        if (type.equals("NJ"))
+        {
+            findClusterNJDistance(i, j);
+        }
+        else
+        {
+            findClusterDistance(i, j);
+        }
 
-      noClus--;
-    }
+        SequenceNode sn = new SequenceNode();
 
-    boolean onefound = false;
+        sn.setLeft((SequenceNode) (node.elementAt(i)));
+        sn.setRight((SequenceNode) (node.elementAt(j)));
 
-    int one = -1;
-    int two = -1;
+        SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
+        SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
 
-    for (int i=0; i < noseqs; i++) {
-      if (done[i] != 1) {
-        if (onefound == false) {
-          two = i;
-          onefound = true;
-        } else {
-          one = i;
+        if (type.equals("NJ"))
+        {
+            findNewNJDistances(tmpi, tmpj, dist);
+        }
+        else
+        {
+            findNewDistances(tmpi, tmpj, dist);
         }
-      }
-    }
-
-    Cluster c = joinClusters(one,two);
-    top = (SequenceNode)(node.elementAt(one));
 
-    reCount(top);
-    findHeight(top);
-    findMaxDist(top);
+        tmpi.setParent(sn);
+        tmpj.setParent(sn);
 
-  }
+        node.setElementAt(sn, i);
 
-  public Cluster joinClusters(int i, int j) {
-
-    float dist = distance[i][j];
+        return c;
+    }
 
-    int noi = ((Cluster)cluster.elementAt(i)).value.length;
-    int noj = ((Cluster)cluster.elementAt(j)).value.length;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param tmpi DOCUMENT ME!
+     * @param tmpj DOCUMENT ME!
+     * @param dist DOCUMENT ME!
+     */
+    public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
+        float dist)
+    {
 
-    int[] value = new int[noi + noj];
+        tmpi.dist = ((dist + ri) - rj) / 2;
+        tmpj.dist = (dist - tmpi.dist);
 
-    for (int ii = 0; ii < noi;ii++) {
-      value[ii] =  ((Cluster)cluster.elementAt(i)).value[ii];
-    }
+        if (tmpi.dist < 0)
+        {
+            tmpi.dist = 0;
+        }
 
-    for (int ii = noi; ii < noi+ noj;ii++) {
-      value[ii] =  ((Cluster)cluster.elementAt(j)).value[ii-noi];
+        if (tmpj.dist < 0)
+        {
+            tmpj.dist = 0;
+        }
     }
 
-    Cluster c = new Cluster(value);
+    /**
+     * 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;
 
-    ri = findr(i,j);
-    rj = findr(j,i);
+        SequenceNode sni = tmpi;
+        SequenceNode snj = tmpj;
 
-    if (type.equals("NJ")) {
-      findClusterNJDistance(i,j);
-    } else {
-      findClusterDistance(i,j);
-    }
+        while (sni != null)
+        {
+            ih = ih + sni.dist;
+            sni = (SequenceNode) sni.left();
+        }
 
-    SequenceNode sn = new SequenceNode();
+        while (snj != null)
+        {
+            jh = jh + snj.dist;
+            snj = (SequenceNode) snj.left();
+        }
 
-    sn.setLeft((SequenceNode)(node.elementAt(i)));
-    sn.setRight((SequenceNode)(node.elementAt(j)));
+        tmpi.dist = ((dist / 2) - ih);
+        tmpj.dist = ((dist / 2) - jh);
+    }
 
-    SequenceNode tmpi = (SequenceNode)(node.elementAt(i));
-    SequenceNode tmpj = (SequenceNode)(node.elementAt(j));
+    /**
+     * 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;
+            }
+        }
 
-    if (type.equals("NJ")) {
-      findNewNJDistances(tmpi,tmpj,dist);
-    } else {
-      findNewDistances(tmpi,tmpj,dist);
+        for (int ii = 0; ii < noseqs; ii++)
+        {
+            distance[i][ii] = newdist[ii];
+            distance[ii][i] = newdist[ii];
+        }
     }
 
-    tmpi.setParent(sn);
-    tmpj.setParent(sn);
-
-    node.setElementAt(sn,i);
-    return c;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     */
+    public void findClusterNJDistance(int i, int j)
+    {
 
-  public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj, float dist) {
+        // 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;
+            }
+        }
 
-    float ih = 0;
-    float jh = 0;
+        for (int ii = 0; ii < noseqs; ii++)
+        {
+            distance[i][ii] = newdist[ii];
+            distance[ii][i] = newdist[ii];
+        }
+    }
 
-    SequenceNode sni = tmpi;
-    SequenceNode snj = tmpj;
+    /**
+     * 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];
+            }
+        }
 
-    tmpi.dist = (dist + ri - rj)/2;
-    tmpj.dist = (dist - tmpi.dist);
+        if (noClus > 2)
+        {
+            tmp = tmp / (noClus - 2);
+        }
 
-    if (tmpi.dist < 0) {
-      tmpi.dist = 0;
+        return tmp;
     }
-    if (tmpj.dist < 0) {
-      tmpj.dist = 0;
-    }
-  }
 
-  public void findNewDistances(SequenceNode tmpi,SequenceNode tmpj,float dist) {
+    /**
+     * 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;
+                    }
+                }
+            }
+        }
 
-    float ih = 0;
-    float jh = 0;
+        return min;
+    }
 
-    SequenceNode sni = tmpi;
-    SequenceNode snj = tmpj;
+    /**
+     * 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];
+                    }
+                }
+            }
+        }
 
-    while (sni != null) {
-      ih = ih + sni.dist;
-      sni = (SequenceNode)sni.left();
+        return min;
     }
 
-    while (snj != null) {
-      jh = jh + snj.dist;
-      snj = (SequenceNode)snj.left();
+    /**
+     * 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 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;
     }
 
-    tmpi.dist = (dist/2 - ih);
-    tmpj.dist = (dist/2 - jh);
-  }
-
-
+    /**
+     * DOCUMENT ME!
+     */
+    public void makeLeaves()
+    {
+        cluster = new Vector();
 
-  public void findClusterDistance(int i, int j) {
+        for (int i = 0; i < noseqs; i++)
+        {
+            SequenceNode sn = new SequenceNode();
 
-    int noi = ((Cluster)cluster.elementAt(i)).value.length;
-    int noj = ((Cluster)cluster.elementAt(j)).value.length;
+            sn.setElement(sequence[i]);
+            sn.setName(sequence[i].getName());
+            node.addElement(sn);
 
-    // New distances from cluster to others
-    float[] newdist = new float[noseqs];
+            int[] value = new int[1];
+            value[0] = i;
 
-    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];
+            Cluster c = new Cluster(value);
+            cluster.addElement(c);
+        }
     }
-  }
 
-  public void findClusterNJDistance(int i, int j) {
-
-    int noi = ((Cluster)cluster.elementAt(i)).value.length;
-    int noj = ((Cluster)cluster.elementAt(j)).value.length;
+    /**
+     * 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;
+        }
 
-    // New distances from cluster to others
-    float[] newdist = new float[noseqs];
+        if ((node.left() == null) && (node.right() == null))
+        {
+            leaves.addElement(node);
 
-    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;
-      }
-    }
+            return leaves;
+        }
+        else
+        {
+            findLeaves((SequenceNode) node.left(), leaves);
+            findLeaves((SequenceNode) node.right(), leaves);
+        }
 
-    for (int ii=0; ii < noseqs;ii++) {
-      distance[i][ii] = newdist[ii];
-      distance[ii][i] = newdist[ii];
+        return leaves;
     }
-  }
 
-  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];
-      }
-    }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     * @param count DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Object findLeaf(SequenceNode node, int count)
+    {
+        found = _findLeaf(node, count);
 
-    if (noClus > 2) {
-      tmp = tmp/(noClus - 2);
+        return found;
     }
 
-    return tmp;
-  }
-
-  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;
-
-          }
+    /**
+     * 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;
         }
-      }
-    }
-    return min;
-  }
-
-  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;
+        if (node.ycount == count)
+        {
+            found = node.element();
 
-            min = distance[i][j];
-          }
+            return found;
         }
-      }
+        else
+        {
+            _findLeaf((SequenceNode) node.left(), count);
+            _findLeaf((SequenceNode) node.right(), count);
+        }
+
+        return found;
     }
-    return min;
-  }
 
-  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(sequence[i], sequence[j], start, end);
-            distance[j][i] = distance[i][j];
-          }
-        }
-      }
-    } else if (pwtype.equals("BL")) {
-      int   maxscore = 0;
-
-      for (int i = 0; i < noseqs-1; i++) {
-        for (int j = i; j < noseqs; j++) {
-          int score = 0;
-          for (int k=start; k < end; k++) {
-            try{
-              score +=
-                  ResidueProperties.getBLOSUM62(sequence[i].getSequence(k,
-                  k + 1),
-                                                sequence[j].getSequence(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];
+    /**
+     * printNode is mainly for debugging purposes.
+     *
+     * @param node SequenceNode
+     */
+    public void printNode(SequenceNode node)
+    {
+        if (node == null)
+        {
+            return;
         }
-      }
-    } 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();
-          distance[i][j] = (float)as.maxscore;
-          if (max < distance[i][j]) {
-            max = distance[i][j];
-          }
+
+        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());
         }
-      }
-      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];
+        else
+        {
+            System.out.println("Dist " + ((SequenceNode) node).dist);
+            printNode((SequenceNode) node.left());
+            printNode((SequenceNode) node.right());
         }
-      }
     }
 
-    return distance;
-  }
-
-  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);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public void findMaxDist(SequenceNode node)
+    {
+        if (node == null)
+        {
+            return;
+        }
 
-      int[] value = new int[1];
-      value[0] = i;
+        if ((node.left() == null) && (node.right() == null))
+        {
+            float dist = ((SequenceNode) node).dist;
 
-      Cluster c = new Cluster(value);
-      cluster.addElement(c);
+            if (dist > maxDistValue)
+            {
+                maxdist = (SequenceNode) node;
+                maxDistValue = dist;
+            }
+        }
+        else
+        {
+            findMaxDist((SequenceNode) node.left());
+            findMaxDist((SequenceNode) node.right());
+        }
     }
-  }
 
-  public Vector findLeaves(SequenceNode node, Vector leaves) {
-    if (node == null) {
-      return leaves;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getGroups()
+    {
+        return groups;
     }
 
-    if (node.left() == null && node.right() == null) {
-      leaves.addElement(node);
-      return leaves;
-    } else {
-      findLeaves((SequenceNode)node.left(),leaves);
-      findLeaves((SequenceNode)node.right(),leaves);
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public float getMaxHeight()
+    {
+        return maxheight;
     }
-    return leaves;
-  }
 
-  public Object findLeaf(SequenceNode node, int count) {
-    found = _findLeaf(node,count);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     * @param threshold DOCUMENT ME!
+     */
+    public void groupNodes(SequenceNode node, float threshold)
+    {
+        if (node == null)
+        {
+            return;
+        }
 
-    return found;
-  }
-  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);
+        if ((node.height / maxheight) > threshold)
+        {
+            groups.addElement(node);
+        }
+        else
+        {
+            groupNodes((SequenceNode) node.left(), threshold);
+            groupNodes((SequenceNode) node.right(), threshold);
+        }
     }
 
-    return found;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public float findHeight(SequenceNode node)
+    {
+        if (node == null)
+        {
+            return maxheight;
+        }
 
-  /**
-   * 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());
-    }
-  }
-  public void findMaxDist(SequenceNode node) {
-    if (node == null) {
-      return;
-    }
-    if (node.left() == null && node.right() == null) {
+        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()));
+        }
 
-      float dist = ((SequenceNode)node).dist;
-      if (dist > maxDistValue) {
-          maxdist      = (SequenceNode)node;
-          maxDistValue = dist;
-      }
-    } else {
-      findMaxDist((SequenceNode)node.left());
-      findMaxDist((SequenceNode)node.right());
-    }
-  }
-    public Vector getGroups() {
-        return groups;
-    }
-    public float getMaxHeight() {
         return maxheight;
     }
-  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);
-    }
-  }
-
-  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;
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceNode reRoot()
+    {
+        if (maxdist != null)
+        {
+            ycount = 0;
 
-      maxheight = findHeight((SequenceNode)(node.left()));
-      maxheight = findHeight((SequenceNode)(node.right()));
-    }
-    return maxheight;
-  }
-  public SequenceNode reRoot() {
-    if (maxdist != null) {
-      ycount = 0;
-      float tmpdist = maxdist.dist;
+            float tmpdist = maxdist.dist;
 
-      // New top
-      SequenceNode sn = new SequenceNode();
-      sn.setParent(null);
+            // 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;
+            // 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);
+            snr.setParent(sn);
+            maxdist.setParent(sn);
 
-      sn.setRight(snr);
-      sn.setLeft(maxdist);
+            sn.setRight(snr);
+            sn.setLeft(maxdist);
 
-      top = sn;
+            top = sn;
 
-      ycount = 0;
-      reCount(top);
-      findHeight(top);
+            ycount = 0;
+            reCount(top);
+            findHeight(top);
+        }
 
+        return top;
     }
-    return top;
-  }
-  public static void printN(SequenceNode node) {
-    if (node == null) {
-      return;
+    /**
+     *
+     * @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()
+    {
+      if (seqData==null)
+        return null;
+//      return seqData.getSequenceString(Comparison.GapChars[0]);
+      StringBuffer sb = new StringBuffer();
+      String[] seqdatas = seqData.getSequenceStrings(Comparison.GapChars.charAt(0));
+      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();
     }
 
-    if (node.left() != null && node.right() != null) {
-      printN((SequenceNode)node.left());
-      printN((SequenceNode)node.right());
-    } else {
-      System.out.println(" name = " + ((SequenceI)node.element()).getName());
+    /**
+     * 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);
     }
-    System.out.println(" dist = " + ((SequenceNode)node).dist + " " + ((SequenceNode)node).count + " " + ((SequenceNode)node).height);
-  }
 
-    public void reCount(SequenceNode node) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public void reCount(SequenceNode node)
+    {
         ycount = 0;
         _reCount(node);
     }
-  public void _reCount(SequenceNode node) {
-    if (node == null) {
-      return;
-    }
 
-    if (node.left() != null && node.right() != null) {
-      _reCount((SequenceNode)node.left());
-      _reCount((SequenceNode)node.right());
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public void _reCount(SequenceNode node)
+    {
+        if (node == null)
+        {
+            return;
+        }
 
-      SequenceNode l = (SequenceNode)node.left();
-      SequenceNode r = (SequenceNode)node.right();
+        if ((node.left() != null) && (node.right() != null))
+        {
+            _reCount((SequenceNode) node.left());
+            _reCount((SequenceNode) node.right());
 
-      ((SequenceNode)node).count  = l.count + r.count;
-      ((SequenceNode)node).ycount = (l.ycount + r.ycount)/2;
+            SequenceNode l = (SequenceNode) node.left();
+            SequenceNode r = (SequenceNode) node.right();
 
-    } else {
-      ((SequenceNode)node).count = 1;
-      ((SequenceNode)node).ycount = ycount++;
+            ((SequenceNode) node).count = l.count + r.count;
+            ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
+        }
+        else
+        {
+            ((SequenceNode) node).count = 1;
+            ((SequenceNode) node).ycount = ycount++;
+        }
     }
 
-  }
-    public void swapNodes(SequenceNode node) {
-        if (node == null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public void swapNodes(SequenceNode node)
+    {
+        if (node == null)
+        {
             return;
         }
-        SequenceNode tmp = (SequenceNode)node.left();
+
+        SequenceNode tmp = (SequenceNode) node.left();
 
         node.setLeft(node.right());
         node.setRight(tmp);
     }
-  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());
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     * @param dir DOCUMENT ME!
+     */
+    public void changeDirection(SequenceNode node, SequenceNode dir)
+    {
+        if (node == null)
+        {
+            return;
         }
-      } else {
-        node.setParent(node.right());
 
-        if (top.left() == node) {
-          node.setLeft(top.right());
-        } else {
-          node.setLeft(top.left());
+        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());
+                }
+            }
         }
-      }
-    }
-  }
-    public void setMaxDist(SequenceNode node) {
-        this.maxdist = maxdist;
     }
-    public SequenceNode getMaxDist() {
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceNode getMaxDist()
+    {
         return maxdist;
     }
-    public SequenceNode getTopNode() {
+
+    /**
+     * 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;
+    }
 
-class Cluster {
+  public boolean isHasRootDistance()
+  {
+    return hasRootDistance;
+  }
 
-  int[] value;
+}
 
-  public Cluster(int[] value) {
-    this.value = value;
-  }
 
+/**
+ * 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;
+    }
 }