X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=e9e1cd77f0e0de79270d96f5dee251fa5803d64f;hb=29cfe164a6c90fbaaf7ef7ed1f2ad4ef50940bfc;hp=6976dc365662c9038ceb6576e763d04d781ccfbd;hpb=95114daeda16764e98a2d8eb0b47acbeeeba5bcf;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
old mode 100755
new mode 100644
index 6976dc3..e9e1cd7
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -237,7 +237,7 @@ public class NJTree
     {
       if (ResidueProperties.getScoreMatrix(pwtype) == null)
       {
-        type = "BLOSUM62";
+        pwtype = "BLOSUM62";
       }
     }
 
@@ -267,15 +267,16 @@ public class NJTree
   }
 
   /**
-   * DOCUMENT ME!
+   * Generate a string representation of the Tree
    * 
-   * @return DOCUMENT ME!
+   * @return Newick File with all tree data available
    */
   public String toString()
   {
     jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
 
-    return fout.print(false, true); // distances only
+    return fout.print(isHasBootstrap(),
+    isHasDistances(), isHasRootDistance()); // output all data available for tree
   }
 
   /**