From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 18 May 2023 11:29:25 +0000 (+0100)
Subject: JAL-4134 properly specify BinaryNode as a typed generic container
X-Git-Tag: Release_2_11_3_0~14^2~3^2^2~26
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1475dd24b86e27e83ad077c10ad8ad024175337d;p=jalview.git

JAL-4134 properly specify BinaryNode as a typed generic container
---

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index dd56424..ad3e88c 100644
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -409,8 +409,8 @@ 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);
     }
   }
 
diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index 5b55594..0ab69ea 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -23,22 +23,22 @@ package jalview.datamodel;
 import java.awt.Color;
 
 /**
- * DOCUMENT ME!
+ * Represent a node in a binary tree
  * 
- * @author $author$
+ * @author $mclamp (probably!)$
  * @version $Revision$
  */
-public class BinaryNode
+public class BinaryNode<T>
 {
-  Object element;
+  T element;
 
   String name;
 
-  BinaryNode left;
+  BinaryNode<T> left;
 
-  BinaryNode right;
+  BinaryNode<T> right;
 
-  BinaryNode parent;
+  BinaryNode<T> parent;
 
   /** Bootstrap value */
   public int bootstrap;
@@ -58,7 +58,7 @@ public class BinaryNode
   /** DOCUMENT ME!! */
   public Color color = Color.black;
 
-  /** DOCUMENT ME!! */
+  /** if true, node is created to simulate polytomy between parent and its 3 or more children */
   public boolean dummy = false;
 
   /**
@@ -81,7 +81,7 @@ public class BinaryNode
    * @param name
    *          DOCUMENT ME!
    */
-  public BinaryNode(Object element, BinaryNode parent, String name,
+  public BinaryNode(T element, BinaryNode<T> parent, String name,
           double dist)
   {
     this();
@@ -91,14 +91,14 @@ public class BinaryNode
     this.dist = dist;
   }
 
-  public BinaryNode(Object element, BinaryNode parent, String name,
+  public BinaryNode(T element, BinaryNode<T> parent, String name,
           double dist, int bootstrap)
   {
     this(element, parent, name, dist);
     this.bootstrap = bootstrap;
   }
 
-  public BinaryNode(Object val, BinaryNode parent, String name, double dist,
+  public BinaryNode(T val, BinaryNode<T> parent, String name, double dist,
           int bootstrap, boolean dummy)
   {
     this(val, parent, name, dist, bootstrap);
@@ -110,7 +110,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public Object element()
+  public T element()
   {
     return element;
   }
@@ -123,7 +123,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public Object setElement(Object v)
+  public T setElement(T v)
   {
     return element = v;
   }
@@ -133,7 +133,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode left()
+  public BinaryNode<T> left()
   {
     return left;
   }
@@ -146,7 +146,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode setLeft(BinaryNode n)
+  public BinaryNode<T> setLeft(BinaryNode<T> n)
   {
     return left = n;
   }
@@ -156,7 +156,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode right()
+  public BinaryNode<T> right()
   {
     return right;
   }
@@ -169,7 +169,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode setRight(BinaryNode n)
+  public BinaryNode<T> setRight(BinaryNode<T> n)
   {
     return right = n;
   }
@@ -179,7 +179,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode parent()
+  public BinaryNode<T> parent()
   {
     return parent;
   }
@@ -192,7 +192,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode setParent(BinaryNode n)
+  public BinaryNode<T> setParent(BinaryNode<T> n)
   {
     return parent = n;
   }
@@ -214,7 +214,7 @@ public class BinaryNode
    * setChild(null), or detach() for this.
    * 
    */
-  public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
+  public void SetChildren(BinaryNode<T> leftchild, BinaryNode<T> rightchild)
   {
     if (leftchild != null)
     {
@@ -236,7 +236,7 @@ public class BinaryNode
    * 
    * @return BinaryNode The detached node.
    */
-  public BinaryNode detach()
+  public BinaryNode<T> detach()
   {
     if (this.parent != null)
     {
@@ -264,9 +264,9 @@ public class BinaryNode
    * 
    * @return BinaryNode
    */
-  public BinaryNode ascendLeft()
+  public BinaryNode<T> ascendLeft()
   {
-    BinaryNode c = this;
+    BinaryNode<T> c = this;
 
     do
     {
@@ -283,9 +283,9 @@ public class BinaryNode
    * 
    * @return BinaryNode
    */
-  public BinaryNode ascendRight()
+  public BinaryNode<T> ascendRight()
   {
-    BinaryNode c = this;
+    BinaryNode<T> c = this;
 
     do
     {
@@ -366,9 +366,9 @@ public class BinaryNode
    * ascends the tree but doesn't stop until a non-dummy node is discovered.
    * 
    */
-  public BinaryNode AscendTree()
+  public BinaryNode<T> AscendTree()
   {
-    BinaryNode c = this;
+    BinaryNode<T> c = this;
 
     do
     {
diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 010d4aa..89a6cb4 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -26,7 +26,7 @@ package jalview.datamodel;
  * @author $author$
  * @version $Revision$
  */
-public class SequenceNode extends BinaryNode
+public class SequenceNode extends BinaryNode<SequenceI>
 {
   private boolean placeholder = false;
 
@@ -38,19 +38,19 @@ public class SequenceNode extends BinaryNode
     super();
   }
 
-  public SequenceNode(SequenceI val, BinaryNode parent, String name,
+  public SequenceNode(SequenceI val, BinaryNode<SequenceI> parent, String name,
           double dist, int bootstrap, boolean dummy)
   {
     super(val, parent, name, dist, bootstrap, dummy);
   }
 
-  public SequenceNode(SequenceI element, BinaryNode parent, String name,
+  public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent, String name,
           double dist, int bootstrap)
   {
     super(element, parent, name, dist, bootstrap);
   }
 
-  public SequenceNode(SequenceI element, BinaryNode parent, String name,
+  public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent, String name,
           double dist)
   {
     super(element, parent, name, dist);
diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index c0d1774..2ad3573 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -358,7 +358,7 @@ public class Tree extends DatastoreItem
         }
         if (jvseq instanceof SequenceI)
         {
-          leaf.setElement(jvseq);
+          leaf.setElement((SequenceI)jvseq);
           leaf.setPlaceholder(false);
         }
         else