Alignment compression on middle mouse button

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

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 99592f2..40dfc9b 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -18,13 +18,16 @@
 */\r
 package jalview.analysis;\r
 \r
-import java.util.*;\r
-\r
 import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
+\r
+import jalview.io.NewickFile;\r
+\r
+import jalview.schemes.ResidueProperties;\r
+\r
 import jalview.util.*;\r
 \r
+import java.util.*;\r
+\r
 \r
 /**\r
  * DOCUMENT ME!\r
@@ -58,9 +61,9 @@ public class NJTree
     int start;\r
     int end;\r
     boolean hasDistances = true; // normal case for jalview trees\r
-    boolean hasBootstrap = false; // normal case for jalview trees\r
+       boolean hasBootstrap = false; // normal case for jalview trees\r
 \r
-  private boolean hasRootDistance = true;\r
+    private boolean hasRootDistance = true;\r
 \r
     /**\r
      * Creates a new NJTree object.\r
@@ -664,7 +667,7 @@ 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