From 6ae908d9a0e2fb6daee16f88cf862525ede5b7cf Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 23 Feb 2023 12:24:39 +0000
Subject: [PATCH] JAL-4134 tidied up refactoring and fix compilation errrors

---
 src/jalview/datamodel/BinaryNode.java   |   51 ++++++++++++++++++++---
 src/jalview/datamodel/SequenceNode.java |   69 ++++---------------------------
 2 files changed, 55 insertions(+), 65 deletions(-)

diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index 6d392d4..5b55594 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -40,7 +40,7 @@ public class BinaryNode
 
   BinaryNode parent;
 
-  /** DOCUMENT ME!! */
+  /** Bootstrap value */
   public int bootstrap;
 
   /** DOCUMENT ME!! */
@@ -68,6 +68,7 @@ public class BinaryNode
   {
     left = right = parent = null;
     bootstrap = 0;
+    dist = 0;
   }
 
   /**
@@ -80,13 +81,28 @@ public class BinaryNode
    * @param name
    *          DOCUMENT ME!
    */
-  public BinaryNode(Object element, BinaryNode parent, String name)
+  public BinaryNode(Object element, BinaryNode parent, String name,
+          double dist)
   {
+    this();
     this.element = element;
     this.parent = parent;
     this.name = name;
+    this.dist = dist;
+  }
+
+  public BinaryNode(Object element, BinaryNode parent, String name,
+          double dist, int bootstrap)
+  {
+    this(element, parent, name, dist);
+    this.bootstrap = bootstrap;
+  }
 
-    left = right = null;
+  public BinaryNode(Object val, BinaryNode parent, String name, double dist,
+          int bootstrap, boolean dummy)
+  {
+    this(val, parent, name, dist, bootstrap);
+    this.dummy = dummy;
   }
 
   /**
@@ -322,18 +338,43 @@ public class BinaryNode
   }
 
   /**
+   * @param dummy
+   *          true if node is created for the representation of polytomous trees
+   */
+  public boolean isDummy()
+  {
+    return dummy;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param newstate
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean setDummy(boolean newstate)
+  {
+    boolean oldstate = dummy;
+    dummy = newstate;
+
+    return oldstate;
+  }
+
+  /**
    * ascends the tree but doesn't stop until a non-dummy node is discovered.
    * 
    */
   public BinaryNode AscendTree()
   {
     BinaryNode c = this;
-  
+
     do
     {
       c = c.parent();
     } while ((c != null) && c.dummy);
-  
+
     return c;
   }
 }
diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 30179f5..010d4aa 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -38,57 +38,22 @@ public class SequenceNode extends BinaryNode
     super();
   }
 
-  /**
-   * Creates a new SequenceNode object.
-   * 
-   * @param val
-   *          DOCUMENT ME!
-   * @param parent
-   *          DOCUMENT ME!
-   * @param dist
-   *          DOCUMENT ME!
-   * @param name
-   *          DOCUMENT ME!
-   */
-  public SequenceNode(Object val, BinaryNode parent, double dist,
-          String name)
+  public SequenceNode(SequenceI val, BinaryNode parent, String name,
+          double dist, int bootstrap, boolean dummy)
   {
-    super(val, parent, name);
-    this.dist = dist;
+    super(val, parent, name, dist, bootstrap, dummy);
   }
 
-  /**
-   * Creates a new SequenceNode object.
-   * 
-   * @param val
-   *          DOCUMENT ME!
-   * @param parent
-   *          DOCUMENT ME!
-   * @param name
-   *          DOCUMENT ME!
-   * @param dist
-   *          DOCUMENT ME!
-   * @param bootstrap
-   *          DOCUMENT ME!
-   * @param dummy
-   *          DOCUMENT ME!
-   */
-  public SequenceNode(Object val, BinaryNode parent, String name,
-          double dist, int bootstrap, boolean dummy)
+  public SequenceNode(SequenceI element, BinaryNode parent, String name,
+          double dist, int bootstrap)
   {
-    super(val, parent, name);
-    this.dist = dist;
-    this.bootstrap = bootstrap;
-    this.dummy = dummy;
+    super(element, parent, name, dist, bootstrap);
   }
 
-  /**
-   * @param dummy
-   *          true if node is created for the representation of polytomous trees
-   */
-  public boolean isDummy()
+  public SequenceNode(SequenceI element, BinaryNode parent, String name,
+          double dist)
   {
-    return dummy;
+    super(element, parent, name, dist);
   }
 
   /*
@@ -103,22 +68,6 @@ public class SequenceNode extends BinaryNode
   /**
    * DOCUMENT ME!
    * 
-   * @param newstate
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public boolean setDummy(boolean newstate)
-  {
-    boolean oldstate = dummy;
-    dummy = newstate;
-
-    return oldstate;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param Placeholder
    *          DOCUMENT ME!
    */
-- 
1.7.10.2