X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=40dfc9b105c39ee234b6e1a54cd5edb796bc782f;hb=ce957421712f63416c9da127f1d4695f6e64c15a;hp=99592f2c0d16eb93d392448f87235529d3221b78;hpb=ba048bdd71d38ad45b484e7ff4c3f8b65d34c6ee;p=jalview.git

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