X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=6c239be1de8a3c2311e99ca0c59a2c0dc95a8ee2;hb=83193bc5c3e150dc7331b5b27a67cb5f9efb477c;hp=6daee9bae6f033e7b364691632d64333676f308a;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 6daee9b..6c239be 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -29,7 +29,14 @@ import jalview.util.*;
 import java.util.*;
 
 
-public class NJTree {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NJTree
+{
     Vector cluster;
     SequenceI[] sequence;
     int[] done;
@@ -54,12 +61,25 @@ public class NJTree {
     int start;
     int end;
 
-    public NJTree(SequenceNode node) {
+    /**
+     * Creates a new NJTree object.
+     *
+     * @param node DOCUMENT ME!
+     */
+    public NJTree(SequenceNode node)
+    {
         top = node;
         maxheight = findHeight(top);
     }
 
-    public NJTree(SequenceI[] seqs, NewickFile treefile) {
+    /**
+     * Creates a new NJTree object.
+     *
+     * @param seqs DOCUMENT ME!
+     * @param treefile DOCUMENT ME!
+     */
+    public NJTree(SequenceI[] seqs, NewickFile treefile)
+    {
         top = treefile.getTree();
         maxheight = findHeight(top);
 
@@ -75,31 +95,54 @@ public class NJTree {
         SequenceI nam;
         String realnam;
 
-        while (i < leaves.size()) {
+        while (i < leaves.size())
+        {
             j = (SequenceNode) leaves.elementAt(i++);
             realnam = j.getName();
             nam = null;
 
-            if (namesleft > -1) {
+            if (namesleft > -1)
+            {
                 nam = algnIds.findIdMatch(realnam);
             }
 
-            if (nam != null) {
+            if (nam != null)
+            {
                 j.setElement(nam);
                 namesleft--;
-            } else {
+            }
+            else
+            {
                 j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
                 j.setPlaceholder(true);
             }
         }
     }
 
-    public NJTree(SequenceI[] sequence, int start, int end) {
+    /**
+     * Creates a new NJTree object.
+     *
+     * @param sequence DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
+    public NJTree(SequenceI[] sequence, int start, int end)
+    {
         this(sequence, "NJ", "BL", start, end);
     }
 
+    /**
+     * 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 type, String pwtype, int start,
-        int end) {
+        int end)
+    {
         this.sequence = sequence;
         this.node = new Vector();
         this.type = type;
@@ -107,11 +150,13 @@ public class NJTree {
         this.start = start;
         this.end = end;
 
-        if (!(type.equals("NJ"))) {
+        if (!(type.equals("NJ")))
+        {
             type = "AV";
         }
 
-        if (!(pwtype.equals("PID"))) {
+        if (!(pwtype.equals("PID")))
+        {
             type = "BL";
         }
 
@@ -119,7 +164,8 @@ public class NJTree {
 
         done = new int[sequence.length];
 
-        while ((i < sequence.length) && (sequence[i] != null)) {
+        while ((i < sequence.length) && (sequence[i] != null))
+        {
             done[i] = 0;
             i++;
         }
@@ -135,7 +181,13 @@ public class NJTree {
         cluster();
     }
 
-    public String toString() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String toString()
+    {
         jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
 
         return fout.print(false, true); // distances only
@@ -147,7 +199,8 @@ public class NJTree {
      *
      * @param alignment Vector
      */
-    public void UpdatePlaceHolders(Vector alignment) {
+    public void UpdatePlaceHolders(Vector alignment)
+    {
         Vector leaves = new Vector();
         findLeaves(top, leaves);
 
@@ -155,13 +208,18 @@ public class NJTree {
         SequenceIdMatcher seqmatcher = null;
         int i = 0;
 
-        while (i < sz) {
+        while (i < sz)
+        {
             SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
 
-            if (alignment.contains(leaf.element())) {
+            if (alignment.contains(leaf.element()))
+            {
                 leaf.setPlaceholder(false);
-            } else {
-                if (seqmatcher == null) {
+            }
+            else
+            {
+                if (seqmatcher == null)
+                {
                     // Only create this the first time we need it
                     SequenceI[] seqs = new SequenceI[alignment.size()];
 
@@ -173,21 +231,32 @@ public class NJTree {
 
                 SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
 
-                if (nam != null) {
+                if (nam != null)
+                {
                     leaf.setPlaceholder(false);
                     leaf.setElement(nam);
-                } else {
+                }
+                else
+                {
                     leaf.setPlaceholder(true);
                 }
             }
         }
     }
 
-    public void cluster() {
-        while (noClus > 2) {
-            if (type.equals("NJ")) {
+    /**
+     * DOCUMENT ME!
+     */
+    public void cluster()
+    {
+        while (noClus > 2)
+        {
+            if (type.equals("NJ"))
+            {
                 float mind = findMinNJDistance();
-            } else {
+            }
+            else
+            {
                 float mind = findMinDistance();
             }
 
@@ -206,12 +275,17 @@ public class NJTree {
         int one = -1;
         int two = -1;
 
-        for (int i = 0; i < noseqs; i++) {
-            if (done[i] != 1) {
-                if (onefound == false) {
+        for (int i = 0; i < noseqs; i++)
+        {
+            if (done[i] != 1)
+            {
+                if (onefound == false)
+                {
                     two = i;
                     onefound = true;
-                } else {
+                }
+                else
+                {
                     one = i;
                 }
             }
@@ -225,7 +299,16 @@ public class NJTree {
         findMaxDist(top);
     }
 
-    public Cluster joinClusters(int i, int j) {
+    /**
+     * 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;
@@ -233,11 +316,13 @@ public class NJTree {
 
         int[] value = new int[noi + noj];
 
-        for (int ii = 0; ii < noi; ii++) {
+        for (int ii = 0; ii < noi; ii++)
+        {
             value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
         }
 
-        for (int ii = noi; ii < (noi + noj); ii++) {
+        for (int ii = noi; ii < (noi + noj); ii++)
+        {
             value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
         }
 
@@ -246,9 +331,12 @@ public class NJTree {
         ri = findr(i, j);
         rj = findr(j, i);
 
-        if (type.equals("NJ")) {
+        if (type.equals("NJ"))
+        {
             findClusterNJDistance(i, j);
-        } else {
+        }
+        else
+        {
             findClusterDistance(i, j);
         }
 
@@ -260,9 +348,12 @@ public class NJTree {
         SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
         SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
 
-        if (type.equals("NJ")) {
+        if (type.equals("NJ"))
+        {
             findNewNJDistances(tmpi, tmpj, dist);
-        } else {
+        }
+        else
+        {
             findNewDistances(tmpi, tmpj, dist);
         }
 
@@ -274,8 +365,16 @@ public class NJTree {
         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) {
+        float dist)
+    {
         float ih = 0;
         float jh = 0;
 
@@ -285,29 +384,41 @@ public class NJTree {
         tmpi.dist = ((dist + ri) - rj) / 2;
         tmpj.dist = (dist - tmpi.dist);
 
-        if (tmpi.dist < 0) {
+        if (tmpi.dist < 0)
+        {
             tmpi.dist = 0;
         }
 
-        if (tmpj.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 dist)
+    {
         float ih = 0;
         float jh = 0;
 
         SequenceNode sni = tmpi;
         SequenceNode snj = tmpj;
 
-        while (sni != null) {
+        while (sni != null)
+        {
             ih = ih + sni.dist;
             sni = (SequenceNode) sni.left();
         }
 
-        while (snj != null) {
+        while (snj != null)
+        {
             jh = jh + snj.dist;
             snj = (SequenceNode) snj.left();
         }
@@ -316,75 +427,121 @@ public class NJTree {
         tmpj.dist = ((dist / 2) - jh);
     }
 
-    public void findClusterDistance(int i, int 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)) {
+        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 {
+            }
+            else
+            {
                 newdist[l] = 0;
             }
         }
 
-        for (int ii = 0; ii < noseqs; ii++) {
+        for (int ii = 0; ii < noseqs; ii++)
+        {
             distance[i][ii] = newdist[ii];
             distance[ii][i] = newdist[ii];
         }
     }
 
-    public void findClusterNJDistance(int i, int j) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     */
+    public void findClusterNJDistance(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)) {
+        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 {
+            }
+            else
+            {
                 newdist[l] = 0;
             }
         }
 
-        for (int ii = 0; ii < noseqs; ii++) {
+        for (int ii = 0; ii < noseqs; ii++)
+        {
             distance[i][ii] = newdist[ii];
             distance[ii][i] = newdist[ii];
         }
     }
 
-    public float findr(int i, int j) {
+    /**
+     * 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)) {
+        for (int k = 0; k < noseqs; k++)
+        {
+            if ((k != i) && (k != j) && (done[k] != 1))
+            {
                 tmp = tmp + distance[i][k];
             }
         }
 
-        if (noClus > 2) {
+        if (noClus > 2)
+        {
             tmp = tmp / (noClus - 2);
         }
 
         return tmp;
     }
 
-    public float findMinNJDistance() {
+    /**
+     * 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)) {
+        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) {
+                    if (tmp < min)
+                    {
                         mini = i;
                         minj = j;
 
@@ -397,13 +554,23 @@ public class NJTree {
         return min;
     }
 
-    public float findMinDistance() {
+    /**
+     * 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) {
+        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;
 
@@ -416,34 +583,54 @@ public class NJTree {
         return min;
     }
 
-    public float[][] findDistances() {
+    /**
+     * 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) {
+        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 {
+                    }
+                    else
+                    {
                         distance[i][j] = 100 -
                             Comparison.PID(sequence[i], sequence[j], start, end);
                         distance[j][i] = distance[i][j];
                     }
                 }
             }
-        } else if (pwtype.equals("BL")) {
+        }
+        else if (pwtype.equals("BL"))
+        {
             int maxscore = 0;
 
-            for (int i = 0; i < (noseqs - 1); i++) {
-                for (int j = i; j < noseqs; j++) {
+            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 {
+                    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) {
+                        }
+                        catch (Exception ex)
+                        {
                             System.err.println("err creating BLOSUM62 tree");
                             ex.printStackTrace();
                         }
@@ -451,37 +638,47 @@ public class NJTree {
 
                     distance[i][j] = (float) score;
 
-                    if (score > maxscore) {
+                    if (score > maxscore)
+                    {
                         maxscore = score;
                     }
                 }
             }
 
-            for (int i = 0; i < (noseqs - 1); i++) {
-                for (int j = i; j < noseqs; j++) {
+            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")) {
+        }
+        else if (pwtype.equals("SW"))
+        {
             float max = -1;
 
-            for (int i = 0; i < (noseqs - 1); i++) {
-                for (int j = i; j < noseqs; j++) {
+            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]) {
+                    if (max < distance[i][j])
+                    {
                         max = distance[i][j];
                     }
                 }
             }
 
-            for (int i = 0; i < (noseqs - 1); i++) {
-                for (int j = i; j < noseqs; 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];
                 }
@@ -491,10 +688,15 @@ public class NJTree {
         return distance;
     }
 
-    public void makeLeaves() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void makeLeaves()
+    {
         cluster = new Vector();
 
-        for (int i = 0; i < noseqs; i++) {
+        for (int i = 0; i < noseqs; i++)
+        {
             SequenceNode sn = new SequenceNode();
 
             sn.setElement(sequence[i]);
@@ -509,16 +711,29 @@ public class NJTree {
         }
     }
 
-    public Vector findLeaves(SequenceNode node, Vector leaves) {
-        if (node == null) {
+    /**
+     * 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)) {
+        if ((node.left() == null) && (node.right() == null))
+        {
             leaves.addElement(node);
 
             return leaves;
-        } else {
+        }
+        else
+        {
             findLeaves((SequenceNode) node.left(), leaves);
             findLeaves((SequenceNode) node.right(), leaves);
         }
@@ -526,22 +741,44 @@ public class NJTree {
         return leaves;
     }
 
-    public Object findLeaf(SequenceNode node, int count) {
+    /**
+     * 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;
     }
 
-    public Object _findLeaf(SequenceNode node, int count) {
-        if (node == null) {
+    /**
+     * 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) {
+        if (node.ycount == count)
+        {
             found = node.element();
 
             return found;
-        } else {
+        }
+        else
+        {
             _findLeaf((SequenceNode) node.left(), count);
             _findLeaf((SequenceNode) node.right(), count);
         }
@@ -554,80 +791,137 @@ public class NJTree {
      *
      * @param node SequenceNode
      */
-    public void printNode(SequenceNode node) {
-        if (node == null) {
+    public void printNode(SequenceNode node)
+    {
+        if (node == null)
+        {
             return;
         }
 
-        if ((node.left() == null) && (node.right() == null)) {
+        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 {
+        }
+        else
+        {
             System.out.println("Dist " + ((SequenceNode) node).dist);
             printNode((SequenceNode) node.left());
             printNode((SequenceNode) node.right());
         }
     }
 
-    public void findMaxDist(SequenceNode node) {
-        if (node == null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public void findMaxDist(SequenceNode node)
+    {
+        if (node == null)
+        {
             return;
         }
 
-        if ((node.left() == null) && (node.right() == null)) {
+        if ((node.left() == null) && (node.right() == null))
+        {
             float dist = ((SequenceNode) node).dist;
 
-            if (dist > maxDistValue) {
+            if (dist > maxDistValue)
+            {
                 maxdist = (SequenceNode) node;
                 maxDistValue = dist;
             }
-        } else {
+        }
+        else
+        {
             findMaxDist((SequenceNode) node.left());
             findMaxDist((SequenceNode) node.right());
         }
     }
 
-    public Vector getGroups() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getGroups()
+    {
         return groups;
     }
 
-    public float getMaxHeight() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public float getMaxHeight()
+    {
         return maxheight;
     }
 
-    public void groupNodes(SequenceNode node, float threshold) {
-        if (node == null) {
+    /**
+     * 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) {
+        if ((node.height / maxheight) > threshold)
+        {
             groups.addElement(node);
-        } else {
+        }
+        else
+        {
             groupNodes((SequenceNode) node.left(), threshold);
             groupNodes((SequenceNode) node.right(), threshold);
         }
     }
 
-    public float findHeight(SequenceNode node) {
-        if (node == null) {
+    /**
+     * 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)) {
+        if ((node.left() == null) && (node.right() == null))
+        {
             node.height = ((SequenceNode) node.parent()).height + node.dist;
 
-            if (node.height > maxheight) {
+            if (node.height > maxheight)
+            {
                 return node.height;
-            } else {
+            }
+            else
+            {
                 return maxheight;
             }
-        } else {
-            if (node.parent() != null) {
+        }
+        else
+        {
+            if (node.parent() != null)
+            {
                 node.height = ((SequenceNode) node.parent()).height +
                     node.dist;
-            } else {
+            }
+            else
+            {
                 maxheight = 0;
                 node.height = (float) 0.0;
             }
@@ -639,8 +933,15 @@ public class NJTree {
         return maxheight;
     }
 
-    public SequenceNode reRoot() {
-        if (maxdist != null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceNode reRoot()
+    {
+        if (maxdist != null)
+        {
             ycount = 0;
 
             float tmpdist = maxdist.dist;
@@ -673,15 +974,25 @@ public class NJTree {
         return top;
     }
 
-    public static void printN(SequenceNode node) {
-        if (node == null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public static void printN(SequenceNode node)
+    {
+        if (node == null)
+        {
             return;
         }
 
-        if ((node.left() != null) && (node.right() != null)) {
+        if ((node.left() != null) && (node.right() != null))
+        {
             printN((SequenceNode) node.left());
             printN((SequenceNode) node.right());
-        } else {
+        }
+        else
+        {
             System.out.println(" name = " +
                 ((SequenceI) node.element()).getName());
         }
@@ -690,17 +1001,31 @@ public class NJTree {
             ((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) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public void _reCount(SequenceNode node)
+    {
+        if (node == null)
+        {
             return;
         }
 
-        if ((node.left() != null) && (node.right() != null)) {
+        if ((node.left() != null) && (node.right() != null))
+        {
             _reCount((SequenceNode) node.left());
             _reCount((SequenceNode) node.right());
 
@@ -709,14 +1034,23 @@ public class NJTree {
 
             ((SequenceNode) node).count = l.count + r.count;
             ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
-        } else {
+        }
+        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;
         }
 
@@ -726,62 +1060,117 @@ public class NJTree {
         node.setRight(tmp);
     }
 
-    public void changeDirection(SequenceNode node, SequenceNode dir) {
-        if (node == null) {
+    /**
+     * 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) {
+        if (node.parent() != top)
+        {
             changeDirection((SequenceNode) node.parent(), node);
 
             SequenceNode tmp = (SequenceNode) node.parent();
 
-            if (dir == node.left()) {
+            if (dir == node.left())
+            {
                 node.setParent(dir);
                 node.setLeft(tmp);
-            } else if (dir == node.right()) {
+            }
+            else if (dir == node.right())
+            {
                 node.setParent(dir);
                 node.setRight(tmp);
             }
-        } else {
-            if (dir == node.left()) {
+        }
+        else
+        {
+            if (dir == node.left())
+            {
                 node.setParent(node.left());
 
-                if (top.left() == node) {
+                if (top.left() == node)
+                {
                     node.setRight(top.right());
-                } else {
+                }
+                else
+                {
                     node.setRight(top.left());
                 }
-            } else {
+            }
+            else
+            {
                 node.setParent(node.right());
 
-                if (top.left() == node) {
+                if (top.left() == node)
+                {
                     node.setLeft(top.right());
-                } else {
+                }
+                else
+                {
                     node.setLeft(top.left());
                 }
             }
         }
     }
 
-    public void setMaxDist(SequenceNode node) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    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;
     }
 }
 
 
-class Cluster {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+class Cluster
+{
     int[] value;
 
-    public Cluster(int[] value) {
+    /**
+     * Creates a new Cluster object.
+     *
+     * @param value DOCUMENT ME!
+     */
+    public Cluster(int[] value)
+    {
         this.value = value;
     }
 }
+