JAL-1953 -External from all interfaces names

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

diff --git a/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
index c6f7898..9dff141 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
@@ -3,9 +3,9 @@ package jalview.ext.archaeopteryx;
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
 import jalview.ext.forester.ForesterMatrix;
-import jalview.ext.treeviewer.ExternalTreeBuilderI;
-import jalview.ext.treeviewer.ExternalTreeI;
-import jalview.ext.treeviewer.ExternalTreeNodeI;
+import jalview.ext.treeviewer.TreeBuilderI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 
@@ -27,7 +27,7 @@ import org.forester.phylogeny.PhylogenyNode;
  *
  */
 public class AptxTreeBuilder
-        implements ExternalTreeBuilderI
+        implements TreeBuilderI
 {
   protected final SequenceI[] sequences;
 
@@ -37,13 +37,13 @@ public class AptxTreeBuilder
   
   public String treeTitle;
 
-  private final ExternalTreeI aptxTree;
+  private final TreeI aptxTree;
 
-  private ExternalTreeNodeI rootNode;
+  private TreeNodeI rootNode;
 
-  private final Map<SequenceI, ExternalTreeNodeI> alignmentWithNodes;
+  private final Map<SequenceI, TreeNodeI> alignmentWithNodes;
 
-  private final Map<ExternalTreeNodeI, SequenceI> nodesWithAlignment;
+  private final Map<TreeNodeI, SequenceI> nodesWithAlignment;
 
   public AptxTreeBuilder(final TreeBuilder calculatedTree)
   {
@@ -63,7 +63,7 @@ public class AptxTreeBuilder
   }
 
   @Override
-  public ExternalTreeI buildTree(final ExternalTreeNodeI treeRoot)
+  public TreeI buildTree(final TreeNodeI treeRoot)
   {
 
     if (treeRoot != null)
@@ -79,13 +79,13 @@ public class AptxTreeBuilder
 
 
   @Override
-  public ExternalTreeI buildTree()
+  public TreeI buildTree()
   {
 
     for (SequenceI sequence : sequences)
     {
 
-      ExternalTreeNodeI sequenceNode = TreeNode
+      TreeNodeI sequenceNode = TreeNode
               .getUniqueWrapper(
               new PhylogenyNode(sequence.getName()));
 
@@ -109,13 +109,13 @@ public class AptxTreeBuilder
   }
 
   @Override
-  public Map<SequenceI, ExternalTreeNodeI> getAlignmentBoundNodes()
+  public Map<SequenceI, TreeNodeI> getAlignmentBoundNodes()
   {
     return alignmentWithNodes;
   }
 
   @Override
-  public Map<ExternalTreeNodeI, SequenceI> getNodesBoundAlignment()
+  public Map<TreeNodeI, SequenceI> getNodesBoundAlignment()
   {
     return nodesWithAlignment;
   }