Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index dd56424..90fe089 100644 (file)
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -80,7 +80,7 @@ public class TreeModel
   public TreeModel(SequenceI[] seqs, AlignmentView odata,
           NewickFile treefile)
   {
-    this(seqs,  treefile.getTree(), treefile.HasDistances(),
+    this(seqs, treefile.getTree(), treefile.HasDistances(),
             treefile.HasBootstrap(), treefile.HasRootDistance());
     seqData = odata;
 
@@ -94,7 +94,7 @@ public class TreeModel
    */
   public TreeModel(TreeBuilder tree)
   {
-    this(tree.getSequences(),  tree.getTopNode(), tree.hasDistances(),
+    this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
             tree.hasBootstrap(), tree.hasRootDistance());
     seqData = tree.getOriginalData();
   }
@@ -141,7 +141,7 @@ public class TreeModel
     while (i < leaves.size())
     {
       // TODO - decide if we get rid of the polymorphism here ?
-      j = (SequenceNode)leaves.elementAt(i++);
+      j = (SequenceNode) leaves.elementAt(i++);
       realnam = j.getName();
       nam = null;
 
@@ -311,8 +311,7 @@ public class TreeModel
    * 
    * @return Vector of leaf nodes on binary tree
    */
-  Vector<BinaryNode> findLeaves(BinaryNode nd,
-          Vector<BinaryNode> leaves)
+  Vector<BinaryNode> findLeaves(BinaryNode nd, Vector<BinaryNode> leaves)
   {
     if (nd == null)
     {
@@ -354,13 +353,13 @@ public class TreeModel
 
     if ((nd.left() == null) && (nd.right() == null))
     {
-      System.out.println("Leaf = " + ((SequenceI) nd.element()).getName());
-      System.out.println("Dist " + nd.dist);
-      System.out.println("Boot " + nd.getBootstrap());
+      jalview.bin.Console.outPrintln("Leaf = " + ((SequenceI) nd.element()).getName());
+      jalview.bin.Console.outPrintln("Dist " + nd.dist);
+      jalview.bin.Console.outPrintln("Boot " + nd.getBootstrap());
     }
     else
     {
-      System.out.println("Dist " + nd.dist);
+      jalview.bin.Console.outPrintln("Dist " + nd.dist);
       printNode((BinaryNode) nd.left());
       printNode((BinaryNode) nd.right());
     }
@@ -409,8 +408,8 @@ public class TreeModel
     }
     else
     {
-      _groupNodes(groups, (SequenceNode) nd.left(), threshold);
-      _groupNodes(groups, (SequenceNode) nd.right(), threshold);
+      _groupNodes(groups, nd.left(), threshold);
+      _groupNodes(groups, nd.right(), threshold);
     }
   }
 
@@ -481,10 +480,10 @@ public class TreeModel
     }
     else
     {
-      System.out.println(" name = " + ((SequenceI) nd.element()).getName());
+      jalview.bin.Console.outPrintln(" name = " + ((SequenceI) nd.element()).getName());
     }
 
-    System.out.println(
+    jalview.bin.Console.outPrintln(
             " dist = " + nd.dist + " " + nd.count + " " + nd.height);
   }
 
@@ -514,7 +513,7 @@ public class TreeModel
   {
     // if (_lycount<_lylimit)
     // {
-    // System.err.println("Warning: depth of _recount greater than number of
+    // jalview.bin.Console.errPrintln("Warning: depth of _recount greater than number of
     // nodes.");
     // }
     if (nd == null)