From 6cfa5983e39db21e566e8662722d231f5391e057 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 21 Aug 2009 11:09:22 +0000
Subject: [PATCH] commented debug lines indicating calculation progress

---
 src/jalview/analysis/NJTree.java |   20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 915f161..2fe8597 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -228,7 +228,7 @@ public class NJTree
       sdata.addOperation(CigarArray.M, end - start + 1);
       this.seqData = new AlignmentView(sdata, start);
     }
-
+//    System.err.println("Made seqData");// dbg
     if (!(type.equals("NJ")))
     {
       type = "AV";
@@ -256,12 +256,15 @@ public class NJTree
 
     distance = findDistances(this.seqData
             .getSequenceStrings(Comparison.GapChars.charAt(0)));
-
+//    System.err.println("Made distances");// dbg
     makeLeaves();
-
+//    System.err.println("Made leaves");// dbg
+    
     noClus = cluster.size();
 
     cluster();
+//    System.err.println("Made clusters");// dbg
+    
   }
 
   /**
@@ -1150,9 +1153,11 @@ public class NJTree
   public void reCount(SequenceNode node)
   {
     ycount = 0;
+    _lycount=0;
+//    _lylimit = this.node.size();
     _reCount(node);
   }
-
+  private long _lycount=0,_lylimit=0;
   /**
    * DOCUMENT ME!
    * 
@@ -1161,13 +1166,19 @@ public class NJTree
    */
   public void _reCount(SequenceNode node)
   {
+//    if (_lycount<_lylimit)
+//    {
+//      System.err.println("Warning: depth of _recount greater than number of nodes.");
+//    }
     if (node == null)
     {
       return;
     }
+    _lycount++;
 
     if ((node.left() != null) && (node.right() != null))
     {
+      
       _reCount((SequenceNode) node.left());
       _reCount((SequenceNode) node.right());
 
@@ -1182,6 +1193,7 @@ public class NJTree
       ((SequenceNode) node).count = 1;
       ((SequenceNode) node).ycount = ycount++;
     }
+    _lycount--;
   }
 
   /**
-- 
1.7.10.2