JAL-34 - quick hack to see how we can do alignment comparison for splitframes linking...

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

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index 90fe089..1068042 100644 (file)
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -353,7 +353,9 @@ public class TreeModel
 
     if ((nd.left() == null) && (nd.right() == null))
     {
-      jalview.bin.Console.outPrintln("Leaf = " + ((SequenceI) nd.element()).getName());
+      // TODO FIX FOR COLUMN TREES
+      jalview.bin.Console
+              .outPrintln("Leaf = " + ((SequenceI) nd.element()).getName());
       jalview.bin.Console.outPrintln("Dist " + nd.dist);
       jalview.bin.Console.outPrintln("Boot " + nd.getBootstrap());
     }
@@ -430,7 +432,7 @@ public class TreeModel
 
     if ((nd.left() == null) && (nd.right() == null))
     {
-      nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
+      nd.height = nd.parent().height + nd.dist;
 
       if (nd.height > maxheight)
       {
@@ -445,7 +447,7 @@ public class TreeModel
     {
       if (nd.parent() != null)
       {
-        nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
+        nd.height = nd.parent().height + nd.dist;
       }
       else
       {
@@ -480,7 +482,8 @@ public class TreeModel
     }
     else
     {
-      jalview.bin.Console.outPrintln(" name = " + ((SequenceI) nd.element()).getName());
+      jalview.bin.Console.outPrintln(
+              " name = " + ((SequenceI) nd.element()).getName());
     }
 
     jalview.bin.Console.outPrintln(
@@ -513,7 +516,8 @@ public class TreeModel
   {
     // if (_lycount<_lylimit)
     // {
-    // jalview.bin.Console.errPrintln("Warning: depth of _recount greater than number of
+    // jalview.bin.Console.errPrintln("Warning: depth of _recount greater than
+    // number of
     // nodes.");
     // }
     if (nd == null)