X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FTreeModel.java;h=106804206cb0de2419fddac6bade5339bf50281b;hb=85299bc2db43c8b108169661ebc1c4d9b2d3d2e5;hp=1725adc7ed4f709eec82a26a8bc90befe637677a;hpb=8fbc01654883e68f8843ad6632efaabfaf21692e;p=jalview.git

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index 1725adc..1068042 100644
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -20,7 +20,6 @@
  */
 package jalview.analysis;
 
-import jalview.bin.Cache;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.BinaryNode;
 import jalview.datamodel.NodeTransformI;
@@ -81,7 +80,7 @@ public class TreeModel
   public TreeModel(SequenceI[] seqs, AlignmentView odata,
           NewickFile treefile)
   {
-    this(seqs, (SequenceNode) treefile.getTree(), treefile.HasDistances(),
+    this(seqs, treefile.getTree(), treefile.HasDistances(),
             treefile.HasBootstrap(), treefile.HasRootDistance());
     seqData = odata;
 
@@ -95,7 +94,7 @@ public class TreeModel
    */
   public TreeModel(TreeBuilder tree)
   {
-    this(tree.getSequences(), (SequenceNode) tree.getTopNode(), tree.hasDistances(),
+    this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
             tree.hasBootstrap(), tree.hasRootDistance());
     seqData = tree.getOriginalData();
   }
@@ -109,7 +108,7 @@ public class TreeModel
    * @param hasBoot
    * @param hasRootDist
    */
-  public TreeModel(SequenceI[] seqs, SequenceNode root, boolean hasDist,
+  public TreeModel(SequenceI[] seqs, BinaryNode root, boolean hasDist,
           boolean hasBoot, boolean hasRootDist)
   {
     this.sequences = seqs;
@@ -142,7 +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;
 
@@ -312,8 +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)
     {
@@ -333,8 +331,8 @@ public class TreeModel
        * TODO: Identify internal nodes... if (node.isSequenceLabel()) {
        * leaves.addElement(node); }
        */
-      findLeaves((SequenceNode) nd.left(), leaves);
-      findLeaves((SequenceNode) nd.right(), leaves);
+      findLeaves(nd.left(), leaves);
+      findLeaves(nd.right(), leaves);
     }
 
     return leaves;
@@ -355,13 +353,15 @@ 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());
+      // 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());
     }
     else
     {
-      System.out.println("Dist " + nd.dist);
+      jalview.bin.Console.outPrintln("Dist " + nd.dist);
       printNode((BinaryNode) nd.left());
       printNode((BinaryNode) nd.right());
     }
@@ -410,8 +410,8 @@ 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);
     }
   }
 
@@ -432,7 +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)
       {
@@ -447,7 +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
       {
@@ -482,10 +482,11 @@ 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);
   }
 
@@ -515,7 +516,8 @@ 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)