added default ClustalWS or MuscleWS to remove gaps.

[jalview.git] / src / jalview / analysis / NJTree.java

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index f44f990..d56464c 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -430,7 +430,7 @@ public class NJTree {
                   k + 1),\r
                                                 sequence[j].getSequence(k,\r
                   k + 1));\r
-            }catch(Exception ex){System.out.println("err creating BLOSUM62 tree");}\r
+            }catch(Exception ex){System.err.println("err creating BLOSUM62 tree");ex.printStackTrace();}\r
           }\r
           distance[i][j] = (float)score;\r
           if (score > maxscore) {\r
@@ -522,6 +522,11 @@ public class NJTree {
     return found;\r
   }\r
 \r
+  /**\r
+   * printNode is mainly for debugging purposes.\r
+   *\r
+   * @param node SequenceNode\r
+   */\r
   public void printNode(SequenceNode node) {\r
     if (node == null) {\r
       return;\r