From 8b86c7788d83dff23b86e83462a076fb778d49fe Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Wed, 17 Jan 2018 16:51:57 +0000
Subject: [PATCH] JAL-2794 tree viewer frame now has its binding object
 properly set

---
 src/jalview/ext/archaeopteryx/JalviewBinding.java |   28 ++++++++++-----------
 1 file changed, 13 insertions(+), 15 deletions(-)

diff --git a/src/jalview/ext/archaeopteryx/JalviewBinding.java b/src/jalview/ext/archaeopteryx/JalviewBinding.java
index f7a5bfc..822f749 100644
--- a/src/jalview/ext/archaeopteryx/JalviewBinding.java
+++ b/src/jalview/ext/archaeopteryx/JalviewBinding.java
@@ -116,6 +116,7 @@ public final class JalviewBinding
     treeView = archaeopteryx.getTreePanel();
     ssm = parentAvport.getStructureSelectionManager();
     
+    aptxFrame.setViewBinding(this);
     ssm.addSelectionListener(this);
     treeView.addMouseListener(this);
     treeView.registerWithPaintRefresher(
@@ -174,22 +175,21 @@ public final class JalviewBinding
 
     if (treeView.showingSubTree())
     {
-    LoadedTreeSequenceAssociation bindAptxNodes = new LoadedTreeSequenceAssociation(
-            parentAvport.getAlignment().getSequencesArray(),
+      LoadedTreeSequenceAssociation bindAptxNodes = new LoadedTreeSequenceAssociation(
+              parentAvport.getAlignment().getSequencesArray(),
               treeView.getTree());
-    bindAptxNodes.associateLeavesToSequences();
-    sequencesBoundToNodes = bindAptxNodes.getAlignmentWithNodes();
-    nodesBoundToSequences = bindAptxNodes.getNodesWithAlignment();
-    TreeViewerUtils.associateNodesWithJalviewSequences(aptxFrame, parentAvport,
-            sequencesBoundToNodes, nodesBoundToSequences);
+      bindAptxNodes.associateLeavesToSequences();
+      sequencesBoundToNodes = bindAptxNodes.getAlignmentWithNodes();
+      nodesBoundToSequences = bindAptxNodes.getNodesWithAlignment();
+      TreeViewerUtils.associateNodesWithJalviewSequences(aptxFrame,
+              parentAvport, sequencesBoundToNodes, nodesBoundToSequences);
 
-
-    for (SequenceI seq : parentAvport.getAlignment().getSequencesArray())
-    {
-      if (!sequencesBoundToNodes.containsKey(seq))
+      for (SequenceI seq : parentAvport.getAlignment().getSequencesArray())
       {
-        parentAvport.hideSequence(new SequenceI[] { seq });
-      }
+        if (!sequencesBoundToNodes.containsKey(seq))
+        {
+          parentAvport.hideSequence(new SequenceI[] { seq });
+        }
       }
     }
 
@@ -680,8 +680,6 @@ public final class JalviewBinding
   @Override
   public CommandI sortAlignmentIn(AlignmentPanel ap)
   {
-    // TODO: move to alignment view controller
-
     AlignmentViewport viewport = ap.av;
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     try
-- 
1.7.10.2