JAL-4134 - brutal hack to build a tree clustering columns of PAE Matrix

[jalview.git] / src / jalview / io / NewickFile.java

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 879b7d4..269ffb3 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -79,7 +79,7 @@ import com.stevesoft.pat.Regex;
  */
 public class NewickFile extends FileParse
 {
-  SequenceNode root;
+  BinaryNode root;
 
   private boolean HasBootstrap = false;
 
@@ -146,7 +146,7 @@ public class NewickFile extends FileParse
    * @param newtree
    *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree)
+  public NewickFile(BinaryNode newtree)
   {
     root = newtree;
   }
@@ -175,7 +175,7 @@ public class NewickFile extends FileParse
    * @param distances
    *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree, boolean bootstrap,
+  public NewickFile(BinaryNode newtree, boolean bootstrap,
           boolean distances)
   {
     root = newtree;
@@ -195,7 +195,7 @@ public class NewickFile extends FileParse
    * @param rootdistance
    *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree, boolean bootstrap,
+  public NewickFile(BinaryNode newtree, boolean bootstrap,
           boolean distances, boolean rootdistance)
   {
     root = newtree;
@@ -679,7 +679,7 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  public SequenceNode getTree()
+  public BinaryNode getTree()
   {
     return root;
   }
@@ -865,7 +865,7 @@ public class NewickFile extends FileParse
   }
 
   // Non recursive call deals with root node properties
-  public void print(StringBuffer tf, SequenceNode root)
+  public void print(StringBuffer tf, BinaryNode root)
   {
     if (root != null)
     {
@@ -877,20 +877,20 @@ public class NewickFile extends FileParse
       {
         if (root.isDummy())
         {
-          _print(tf, (SequenceNode) root.right());
-          _print(tf, (SequenceNode) root.left());
+          _print(tf,  root.right());
+          _print(tf,  root.left());
         }
         else
         {
           tf.append("(");
-          _print(tf, (SequenceNode) root.right());
+          _print(tf,  root.right());
 
           if (root.left() != null)
           {
             tf.append(",");
           }
 
-          _print(tf, (SequenceNode) root.left());
+          _print(tf,  root.left());
           tf.append(")" + printRootField(root));
         }
       }
@@ -898,7 +898,7 @@ public class NewickFile extends FileParse
   }
 
   // Recursive call for non-root nodes
-  public void _print(StringBuffer tf, SequenceNode c)
+  public void _print(StringBuffer tf, BinaryNode c)
   {
     if (c != null)
     {
@@ -910,24 +910,24 @@ public class NewickFile extends FileParse
       {
         if (c.isDummy())
         {
-          _print(tf, (SequenceNode) c.left());
+          _print(tf,  c.left());
           if (c.left() != null)
           {
             tf.append(",");
           }
-          _print(tf, (SequenceNode) c.right());
+          _print(tf,  c.right());
         }
         else
         {
           tf.append("(");
-          _print(tf, (SequenceNode) c.right());
+          _print(tf,  c.right());
 
           if (c.left() != null)
           {
             tf.append(",");
           }
 
-          _print(tf, (SequenceNode) c.left());
+          _print(tf,  c.left());
           tf.append(")" + printNodeField(c));
         }
       }