JAL-4134 - refactor tree calculation code to work with binaryNode base type.

[jalview.git] / src / jalview / datamodel / SequenceNode.java

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 0a694c2..30179f5 100755 (executable)
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -20,8 +20,6 @@
  */
 package jalview.datamodel;
 
-import java.awt.Color;
-
 /**
  * DOCUMENT ME!
  * 
@@ -30,24 +28,6 @@ import java.awt.Color;
  */
 public class SequenceNode extends BinaryNode
 {
-  /** DOCUMENT ME!! */
-  public double dist;
-
-  /** DOCUMENT ME!! */
-  public int count;
-
-  /** DOCUMENT ME!! */
-  public double height;
-
-  /** DOCUMENT ME!! */
-  public float ycount;
-
-  /** DOCUMENT ME!! */
-  public Color color = Color.black;
-
-  /** DOCUMENT ME!! */
-  public boolean dummy = false;
-
   private boolean placeholder = false;
 
   /**
@@ -70,7 +50,7 @@ public class SequenceNode extends BinaryNode
    * @param name
    *          DOCUMENT ME!
    */
-  public SequenceNode(Object val, SequenceNode parent, double dist,
+  public SequenceNode(Object val, BinaryNode parent, double dist,
           String name)
   {
     super(val, parent, name);
@@ -93,7 +73,7 @@ public class SequenceNode extends BinaryNode
    * @param dummy
    *          DOCUMENT ME!
    */
-  public SequenceNode(Object val, SequenceNode parent, String name,
+  public SequenceNode(Object val, BinaryNode parent, String name,
           double dist, int bootstrap, boolean dummy)
   {
     super(val, parent, name);
@@ -148,23 +128,6 @@ public class SequenceNode extends BinaryNode
   }
 
   /**
-   * ascends the tree but doesn't stop until a non-dummy node is discovered.
-   * This will probably break if the tree is a mixture of BinaryNodes and
-   * SequenceNodes.
-   */
-  public SequenceNode AscendTree()
-  {
-    SequenceNode c = this;
-
-    do
-    {
-      c = (SequenceNode) c.parent();
-    } while ((c != null) && c.dummy);
-
-    return c;
-  }
-
-  /**
    * test if this node has a name that might be a label rather than a bootstrap
    * value
    *