X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=40dfc9b105c39ee234b6e1a54cd5edb796bc782f;hb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;hp=97b8519e561ce14412ee5a02cd1e645d8e1f271a;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 97b8519..40dfc9b 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -60,6 +60,10 @@ public class NJTree
     Object leaves = null;
     int start;
     int end;
+    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.
@@ -81,6 +85,11 @@ public class NJTree
     public NJTree(SequenceI[] seqs, NewickFile treefile)
     {
         top = treefile.getTree();
+
+        hasDistances = treefile.HasDistances();
+        hasBootstrap = treefile.HasBootstrap();
+        hasRootDistance = treefile.HasRootDistance();
+
         maxheight = findHeight(top);
 
         SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
@@ -251,14 +260,14 @@ public class NJTree
     {
         while (noClus > 2)
         {
-           /* if (type.equals("NJ"))
+            if (type.equals("NJ"))
             {
-                float mind = findMinNJDistance();
+                findMinNJDistance();
             }
             else
             {
-                float mind = findMinDistance();
-            }*/
+                findMinDistance();
+            }
 
             Cluster c = joinClusters(mini, minj);
 
@@ -273,7 +282,7 @@ public class NJTree
         boolean onefound = false;
 
         int one = -1;
-        //int two = -1;
+        int two = -1;
 
         for (int i = 0; i < noseqs; i++)
         {
@@ -281,7 +290,7 @@ public class NJTree
             {
                 if (onefound == false)
                 {
-                    //two = i;
+                    two = i;
                     onefound = true;
                 }
                 else
@@ -291,7 +300,7 @@ public class NJTree
             }
         }
 
-       // Cluster c = joinClusters(one, two);
+        joinClusters(one, two);
         top = (SequenceNode) (node.elementAt(one));
 
         reCount(top);
@@ -375,11 +384,6 @@ public class NJTree
     public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
         float dist)
     {
-        //float ih = 0;
-       // float jh = 0;
-
-        //SequenceNode sni = tmpi;
-        //SequenceNode snj = tmpj;
 
         tmpi.dist = ((dist + ri) - rj) / 2;
         tmpj.dist = (dist - tmpi.dist);
@@ -469,8 +473,6 @@ public class NJTree
      */
     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];
@@ -665,7 +667,7 @@ public class NJTree
                     AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
                     as.calcScoreMatrix();
                     as.traceAlignment();
-                    as.printAlignment();
+                    as.printAlignment(System.out);
                     distance[i][j] = (float) as.maxscore;
 
                     if (max < distance[i][j])
@@ -1141,6 +1143,27 @@ public class NJTree
     {
         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;
+  }
+
 }
 
 
@@ -1164,3 +1187,4 @@ class Cluster
         this.value = value;
     }
 }
+