X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=40dfc9b105c39ee234b6e1a54cd5edb796bc782f;hb=2959d102cb701ba58489e7222cd101d0eb02ead6;hp=46a2ced5a3314098e258ca951919cd40841ff793;hpb=2493af6c253a5a33cf783b9beb76caaaf1c777ec;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 46a2ced..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);
@@ -375,7 +384,7 @@ public class NJTree
     public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
         float dist)
     {
-     
+
         tmpi.dist = ((dist + ri) - rj) / 2;
         tmpj.dist = (dist - tmpi.dist);
 
@@ -658,7 +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])
@@ -1134,6 +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;
+  }
+
 }