JAL-2805 loads of file reorganizing, interfaces expanded

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

diff --git a/src/jalview/ext/archaeopteryx/AptxBinding.java b/src/jalview/ext/archaeopteryx/JalviewBinding.java
similarity index 96%
rename from src/jalview/ext/archaeopteryx/AptxBinding.java
rename to src/jalview/ext/archaeopteryx/JalviewBinding.java
index d82f660..19a66f8 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxBinding.java
+++ b/src/jalview/ext/archaeopteryx/JalviewBinding.java
@@ -4,6 +4,7 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
 import jalview.gui.PaintRefresher;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
@@ -28,7 +29,7 @@ import org.forester.phylogeny.PhylogenyNode;
  * @author kjvanderheide
  *
  */
-public final class AptxBinding
+public final class JalviewBinding
         implements ExternalTreeViewerBindingI<PhylogenyNode>
 {
   private org.forester.archaeopteryx.TreePanel treeView;
@@ -56,7 +57,7 @@ public final class AptxBinding
    *          map with tree nodes and matching sequences used to calculate the
    *          tree as key, value pair respectively.
    */
-  public AptxBinding(final MainFrame archaeopteryx,
+  public JalviewBinding(final MainFrame archaeopteryx,
           final AlignmentViewport jalviewAlignmentViewport,
           final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
           final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
@@ -179,6 +180,7 @@ public final class AptxBinding
   {
     final List<PhylogenyNode> childNodes = PhylogenyMethods
             .getAllDescendants(parentNode);
+    // final BranchColor branchColor = new BranchColor();
 
     for (PhylogenyNode childNode : childNodes)
     {
@@ -186,6 +188,7 @@ public final class AptxBinding
       if (matchingSequence != null)
       {
         treeSelectionChanged(matchingSequence);
+
       }
     }