JAL-2794 binding now exclusively supports single tab Aptx views

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 138ed2c..67af027 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -387,6 +387,7 @@ label.not_enough_sequences = Not enough sequences
 label.selected_region_to_tree_may_only_contain_residues_or_gaps =  The selected region to create a tree may\nonly contain residues or gaps.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services.
 label.sequences_selection_not_aligned = Sequences in selection are not aligned
 label.problem_reading_tree_file =  Problem reading tree file
+label.tabs_detected_archaeopteryx = Warning, multiple trees detected in a single tree viewer instance. This will cause problems!
 label.possible_problem_with_tree_file = Possible problem with tree file
 label.tree_url_example = Please enter a complete URL, for example \"http://www.jalview.org/examples/ferredoxin.nw\"
 label.from_database = From Database...

diff --git a/src/jalview/ext/archaeopteryx/JalviewBinding.java b/src/jalview/ext/archaeopteryx/JalviewBinding.java
index dae01f1..f59bdd9 100644 (file)
--- a/src/jalview/ext/archaeopteryx/JalviewBinding.java
+++ b/src/jalview/ext/archaeopteryx/JalviewBinding.java
@@ -5,9 +5,12 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
 import jalview.gui.PaintRefresher;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.event.ActionEvent;
@@ -18,10 +21,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import javax.swing.JTabbedPane;
 import javax.swing.SwingUtilities;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
 
 import org.forester.archaeopteryx.MainFrame;
 import org.forester.phylogeny.Phylogeny;
@@ -43,7 +43,6 @@ public final class JalviewBinding
 
   private AlignmentViewport parentAvport;
 
-  private JTabbedPane treeTabs;
 
   private final StructureSelectionManager ssm;
 
@@ -71,15 +70,25 @@ public final class JalviewBinding
           final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
           final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
   {
+
+    if (archaeopteryx.getMainPanel().getTabbedPane().getTabCount() > 1)
+    {
+      JvOptionPane.showMessageDialog(Desktop.desktop,
+              MessageManager.getString("label.tabs_detected_archaeopteryx"),
+              MessageManager.getString("label.problem_reading_tree_file"),
+              JvOptionPane.WARNING_MESSAGE);
+      ;
+    }
+
     // deal with/prohibit null values here as that will cause problems
     parentAvport = jalviewAlignmentViewport;
     sequencesBoundToNodes = alignMappedToNodes;
     nodesBoundToSequences = nodesMappedToAlign;
 
     treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
-    treeTabs = archaeopteryx.getMainPanel().getTabbedPane();
     ssm = parentAvport.getStructureSelectionManager();
 
+
     // archaeopteryx.getMainPanel().getControlPanel().setColorBranches(true);
     
     ssm.addSelectionListener(this);
@@ -87,35 +96,36 @@ public final class JalviewBinding
     PaintRefresher.Register(treeView, parentAvport.getSequenceSetId());
 
 
-    treeTabs.addChangeListener(new ChangeListener()
-    {
-
-      @Override
-      public void stateChanged(ChangeEvent e)
-      {
-
-        SwingUtilities.invokeLater(new Runnable()
-        {
-
-          @Override
-          /**
-           * Resend the selection to the tree view when tabs get switched, this
-           * has to be buried in invokeLater as Forester first resets the tree
-           * view on switching tabs, without invokeLater this would get called
-           * before Forester resets which would nullify the selection.
-           */
-          public void run()
-          {
-            parentAvport.sendSelection();
-            // PaintRefresher.Refresh(treeView,
-            // parentAvport.getSequenceSetId());
-
-          }
-        });
-
-      }
-      
-    });
+    // treeTabs.addChangeListener(new ChangeListener()
+    // {
+    //
+    // @Override
+    // public void stateChanged(ChangeEvent e)
+    // {
+    //
+    // SwingUtilities.invokeLater(new Runnable()
+    // {
+    //
+    // @Override
+    // /**
+    // * Resend the selection to the tree view when tabs get switched, this
+    // * has to be buried in invokeLater as Forester first resets the tree
+    // * view on switching tabs, without invokeLater this would get called
+    // * before Forester resets which would nullify the selection.
+    // */
+    // public void run()
+    // {
+    // treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
+    // parentAvport.sendSelection();
+    // // PaintRefresher.Refresh(treeView,
+    // // parentAvport.getSequenceSetId());
+    //
+    // }
+    // });
+    //
+    // }
+    //
+    // });
 
   }
 
@@ -239,7 +249,10 @@ public final class JalviewBinding
   }
   
 
-
+  /**
+   * may or may not need an extra repaint on the alignment view (check what kira
+   * does)
+   */
   @Override
   public void showNodeSelectionOnAlign(final PhylogenyNode node)
   {
@@ -254,6 +267,7 @@ public final class JalviewBinding
         showMatchingSequence(node);
       }
 
+    PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
     }