From 62f2ed464010270830afcfe954647a51dfb5114b Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Fri, 24 Nov 2017 18:00:50 +0000
Subject: [PATCH] JAL-2799 all tabs now get mouse listeners and Jalview
 switches tree view

---
 src/jalview/ext/archaeopteryx/JalviewBinding.java |   56 ++++++++++++++-------
 1 file changed, 37 insertions(+), 19 deletions(-)

diff --git a/src/jalview/ext/archaeopteryx/JalviewBinding.java b/src/jalview/ext/archaeopteryx/JalviewBinding.java
index dae01f1..7a0668d 100644
--- a/src/jalview/ext/archaeopteryx/JalviewBinding.java
+++ b/src/jalview/ext/archaeopteryx/JalviewBinding.java
@@ -39,9 +39,11 @@ import org.forester.phylogeny.PhylogenyNode;
 public final class JalviewBinding
         implements ExternalTreeViewerBindingI<PhylogenyNode>
 {
-  private org.forester.archaeopteryx.TreePanel treeView;
+  private final MainFrame aptxFrame;
 
-  private AlignmentViewport parentAvport;
+  private org.forester.archaeopteryx.TreePanel currentTreeView;
+
+  private final AlignmentViewport parentAvport;
 
   private JTabbedPane treeTabs;
 
@@ -72,19 +74,30 @@ public final class JalviewBinding
           final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
   {
     // deal with/prohibit null values here as that will cause problems
+    aptxFrame = archaeopteryx;
     parentAvport = jalviewAlignmentViewport;
     sequencesBoundToNodes = alignMappedToNodes;
     nodesBoundToSequences = nodesMappedToAlign;
 
-    treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
-    treeTabs = archaeopteryx.getMainPanel().getTabbedPane();
+    treeTabs = aptxFrame.getMainPanel().getTabbedPane();
     ssm = parentAvport.getStructureSelectionManager();
 
     // archaeopteryx.getMainPanel().getControlPanel().setColorBranches(true);
     
     ssm.addSelectionListener(this);
-    treeView.addMouseListener(this);
-    PaintRefresher.Register(treeView, parentAvport.getSequenceSetId());
+
+    int tabCount = treeTabs.getTabCount();
+
+    for (int i = 0; i < tabCount; i++)
+    {
+      // roundabout way to select each tree because getComponentAt(i) requires
+      // casting to TreePanel which doesn't work
+      treeTabs.setSelectedIndex(i);
+      currentTreeView = aptxFrame.getMainPanel().getCurrentTreePanel();
+      currentTreeView.addMouseListener(this);
+      PaintRefresher.Register(currentTreeView,
+              parentAvport.getSequenceSetId());
+    }
 
 
     treeTabs.addChangeListener(new ChangeListener()
@@ -106,9 +119,9 @@ public final class JalviewBinding
            */
           public void run()
           {
+            currentTreeView = aptxFrame.getMainPanel()
+                    .getCurrentTreePanel();
             parentAvport.sendSelection();
-            // PaintRefresher.Refresh(treeView,
-            // parentAvport.getSequenceSetId());
 
           }
         });
@@ -135,13 +148,16 @@ public final class JalviewBinding
        */
       public void run()
       {
-        final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
+
+        final PhylogenyNode node = currentTreeView.findNode(e.getX(),
+                e.getY());
         if (node != null)
         {
           if ((e.getModifiers() & InputEvent.SHIFT_MASK) == 0) // clear previous
           // selection if shift
           // IS NOT pressed
           {
+
             parentAvport.setSelectionGroup(null);
 
           }
@@ -189,7 +205,7 @@ public final class JalviewBinding
     if (source == parentAvport) // check if source is alignment from where the
     // tree originates
     {
-      treeView.setFoundNodes0(
+      currentTreeView.setFoundNodes0(
               new HashSet<Long>(seqsel.getSequences().size()));
 
       for (SequenceI selectedSequence : seqsel.getSequences())
@@ -197,11 +213,11 @@ public final class JalviewBinding
         PhylogenyNode matchingNode = sequencesBoundToNodes.get(selectedSequence);
         if (matchingNode != null)
         {
-          treeView.getFoundNodes0().add(matchingNode.getId());
+          currentTreeView.getFoundNodes0().add(matchingNode.getId());
         }
 
       }
-      treeView.repaint();
+      aptxFrame.repaint();
 
     }
 
@@ -214,16 +230,16 @@ public final class JalviewBinding
   public void partitionTree(final MouseEvent e)
   {
     int x = e.getX();
-    int lineLength = treeView.getHeight();
+    int lineLength = currentTreeView.getHeight();
 
-    Phylogeny tree = treeView.getPhylogeny();
+    Phylogeny tree = currentTreeView.getPhylogeny();
     double treeHeight = tree.calculateHeight(true);
 
 
 
     if (treeHeight != 0)
     {
-      int viewWidth = treeView.getWidth();
+      int viewWidth = currentTreeView.getWidth();
 
       // treeView.validate();
 
@@ -267,7 +283,7 @@ public final class JalviewBinding
     if (matchingSequence != null)
     {
       long nodeId = nodeToMatch.getId();
-      addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
+      addOrRemoveInSet(currentTreeView.getFoundNodes0(), nodeId);
       treeSelectionChanged(matchingSequence);
       parentAvport.sendSelection();
 
@@ -289,7 +305,7 @@ public final class JalviewBinding
       if (matchingSequence != null)
       {
         long nodeId = childNode.getId();
-        addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
+        addOrRemoveInSet(currentTreeView.getFoundNodes0(), nodeId);
 
         treeSelectionChanged(matchingSequence);
 
@@ -424,11 +440,13 @@ public final class JalviewBinding
     return parentAvport;
   }
 
-  public void setParentAvport(final AlignmentViewport parentAvport)
+  public org.forester.archaeopteryx.TreePanel getTreeView()
   {
-    this.parentAvport = parentAvport;
+    return currentTreeView;
   }
+
 }
 
 
 
+
-- 
1.7.10.2