JAL-1953 -External from all interfaces names

[jalview.git] / src / jalview / ext / archaeopteryx / TreeNode.java

diff --git a/src/jalview/ext/archaeopteryx/TreeNode.java b/src/jalview/ext/archaeopteryx/TreeNode.java
index e37f89d..07c8d95 100644 (file)
--- a/src/jalview/ext/archaeopteryx/TreeNode.java
+++ b/src/jalview/ext/archaeopteryx/TreeNode.java
@@ -1,7 +1,7 @@
 package jalview.ext.archaeopteryx;
 
 import jalview.datamodel.SequenceI;
-import jalview.ext.treeviewer.ExternalTreeNodeI;
+import jalview.ext.treeviewer.TreeNodeI;
 
 import java.awt.Color;
 import java.util.ArrayList;
@@ -13,16 +13,16 @@ import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.BranchColor;
 
-public class TreeNode implements ExternalTreeNodeI
+public class TreeNode implements TreeNodeI
 {
   private final PhylogenyNode node;
 
   private SequenceI nodeSeq;
 
-  private static Map<PhylogenyNode, ExternalTreeNodeI> originalNodes = new HashMap<>(
+  private static Map<PhylogenyNode, TreeNodeI> originalNodes = new HashMap<>(
           500); // prolly make this size dynamic
 
-  private static Map<ExternalTreeNodeI, PhylogenyNode> wrappedNodes = new HashMap<>(
+  private static Map<TreeNodeI, PhylogenyNode> wrappedNodes = new HashMap<>(
           500);
 
   private TreeNode(PhylogenyNode aptxNode)
@@ -42,7 +42,7 @@ public class TreeNode implements ExternalTreeNodeI
 
 
   @Override
-  public List<ExternalTreeNodeI> getAllDescendants()
+  public List<TreeNodeI> getAllDescendants()
   {
 
     List<PhylogenyNode> descNodes = PhylogenyMethods
@@ -53,7 +53,7 @@ public class TreeNode implements ExternalTreeNodeI
   }
 
   @Override
-  public List<ExternalTreeNodeI> getExternalDescendants()
+  public List<TreeNodeI> getExternalDescendants()
   {
     List<PhylogenyNode> extDescNodes = node.getAllExternalDescendants();
     return getUniqueWrappers(extDescNodes);
@@ -61,7 +61,7 @@ public class TreeNode implements ExternalTreeNodeI
 
 
   @Override
-  public List<ExternalTreeNodeI> getDirectChildren()
+  public List<TreeNodeI> getDirectChildren()
   {
     List<PhylogenyNode> childNodes = node.getDescendants();
     return getUniqueWrappers(childNodes);
@@ -89,7 +89,7 @@ public class TreeNode implements ExternalTreeNodeI
   }
 
   @Override
-  public void addAsChild(ExternalTreeNodeI childNode)
+  public void addAsChild(TreeNodeI childNode)
   {
     PhylogenyNode aptxNode = unwrapNode(childNode);
 
@@ -122,10 +122,10 @@ public class TreeNode implements ExternalTreeNodeI
     return node.isInternal();
   }
 
-  public static List<ExternalTreeNodeI> getUniqueWrappers(
+  public static List<TreeNodeI> getUniqueWrappers(
           List<PhylogenyNode> aptxNodes)
   {
-    List<ExternalTreeNodeI> wrappedNodes = new ArrayList<>(
+    List<TreeNodeI> wrappedNodes = new ArrayList<>(
             aptxNodes.size());
 
     for (PhylogenyNode aptxNode : aptxNodes)
@@ -143,14 +143,14 @@ public class TreeNode implements ExternalTreeNodeI
    * @param aptxNode
    * @return
    */
-  public static ExternalTreeNodeI getUniqueWrapper(
+  public static TreeNodeI getUniqueWrapper(
           PhylogenyNode aptxNode)
   {
     if (aptxNode == null)
     {
       return null;
     }
-    ExternalTreeNodeI wrappedNode = originalNodes.get(aptxNode);
+    TreeNodeI wrappedNode = originalNodes.get(aptxNode);
     if (wrappedNode == null)
     {
       wrappedNode = new TreeNode(aptxNode);
@@ -168,7 +168,7 @@ public class TreeNode implements ExternalTreeNodeI
    * @param wrappedNode
    * @return
    */
-  protected static PhylogenyNode unwrapNode(ExternalTreeNodeI wrappedNode)
+  protected static PhylogenyNode unwrapNode(TreeNodeI wrappedNode)
   {
     if (wrappedNode == null)
     {