findByShortName

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

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 46a2ced..0683265 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -375,7 +375,7 @@ public class NJTree
     public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,\r
         float dist)\r
     {\r
-     \r
+\r
         tmpi.dist = ((dist + ri) - rj) / 2;\r
         tmpj.dist = (dist - tmpi.dist);\r
 \r
@@ -658,7 +658,7 @@ public class NJTree
                     AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");\r
                     as.calcScoreMatrix();\r
                     as.traceAlignment();\r
-                    as.printAlignment();\r
+                    as.printAlignment(System.out);\r
                     distance[i][j] = (float) as.maxscore;\r
 \r
                     if (max < distance[i][j])\r