X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=40dfc9b105c39ee234b6e1a54cd5edb796bc782f;hb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;hp=71d67379aa5203d6928b5103441e87672c5e704f;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 71d6737..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);
@@ -253,11 +262,11 @@ public class NJTree
         {
             if (type.equals("NJ"))
             {
-                float mind = findMinNJDistance();
+                findMinNJDistance();
             }
             else
             {
-                float mind = findMinDistance();
+                findMinDistance();
             }
 
             Cluster c = joinClusters(mini, minj);
@@ -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])
@@ -1121,15 +1123,6 @@ public class NJTree
         }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void setMaxDist(SequenceNode node)
-    {
-        this.maxdist = maxdist;
-    }
 
     /**
      * DOCUMENT ME!
@@ -1150,6 +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;
+  }
+
 }
 
 
@@ -1173,3 +1187,4 @@ class Cluster
         this.value = value;
     }
 }
+