JAL-2838 Aptx frames now appear in the alignment sorting menu

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index b9a7ae2..d76214e 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -15,6 +15,7 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
+import java.util.HashMap;
 import java.util.Map;
 
 import org.forester.archaeopteryx.AptxUtil;
@@ -65,6 +66,8 @@ public final class AptxInit
   private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG
           .getTaxonomyExtraction();
 
+  private static Map<MainFrame, JalviewBinding> activeAptx = new HashMap<>();
+
 
 
   public static MainFrame createInstanceFromCalculation(
@@ -131,7 +134,7 @@ public final class AptxInit
 //    }
     Phylogeny[] trees = PhylogenyMethods.readPhylogenies(parser, treeFile);
     MainFrame[] aptxFrames = new MainFrame[trees.length];
-    String treeTitle = treeFile.getName();
+
 
     for (int i = 0; i < trees.length; i++)
       {
@@ -141,6 +144,8 @@ public final class AptxInit
       {
         PhylogenyMethods.transferInternalNodeNamesToConfidence(tree, "");
       }
+      String treeTitle = treeFile.getName() + "[" + i + "]";
+      tree.setName(treeTitle);
       aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
 
     }
@@ -496,8 +501,11 @@ public final class AptxInit
           final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
           final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
   {
-    return new JalviewBinding(aptxApp, jalviewAlignViewport,
+    JalviewBinding treeBinding = new JalviewBinding(aptxApp,
+            jalviewAlignViewport,
             alignMappedToNodes, nodesMappedToAlign);
+    activeAptx.put(aptxApp, treeBinding);
+    return treeBinding;
   }
 
 
@@ -517,6 +525,10 @@ public final class AptxInit
 
   }
 
+  public static Map<MainFrame, JalviewBinding> getAllAptxFrames()
+  {
+    return activeAptx;
+  }
 
 
 }

diff --git a/src/jalview/ext/archaeopteryx/JalviewBinding.java b/src/jalview/ext/archaeopteryx/JalviewBinding.java
index 84f4347..61171b3 100644 (file)
--- a/src/jalview/ext/archaeopteryx/JalviewBinding.java
+++ b/src/jalview/ext/archaeopteryx/JalviewBinding.java
@@ -35,6 +35,8 @@ import javax.swing.JTabbedPane;
 import javax.swing.SwingUtilities;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
 
 import org.forester.archaeopteryx.MainFrame;
 import org.forester.phylogeny.Phylogeny;
@@ -73,6 +75,8 @@ public final class JalviewBinding
 
   private int nrTreeGroups = 0;
 
+  private boolean applyToAllViews = false;
+
   /**
    * 
    * @param archaeopteryx
@@ -115,10 +119,19 @@ public final class JalviewBinding
     ssm.addSelectionListener(this);
     treeView.addMouseListener(this);
     PaintRefresher.Register(treeView, parentAvport.getSequenceSetId());
-
     associatedPanels = PaintRefresher
             .getAssociatedPanels(parentAvport.getSequenceSetId());
 
+    archaeopteryx.addInternalFrameListener(new InternalFrameAdapter()
+    {
+
+      @Override
+      public void internalFrameClosed(InternalFrameEvent e)
+      {
+        AptxInit.getAllAptxFrames().remove(archaeopteryx);
+      }
+
+    });
 
     treeTabs.addChangeListener(new ChangeListener()
     {
@@ -280,9 +293,6 @@ public final class JalviewBinding
                                                        // of tree
       {
 
-        // int panelHeight = treeView.getHeight();
-        // g.drawLine(x, 0, x, panelHeight);
-
         float threshold = (x - rootX) / (furthestNodeX - rootX);
         List<PhylogenyNode> foundNodes = getNodesAboveThreshold(threshold,
                 tree.getRoot());

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5f26925..afe7ce5 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -61,6 +61,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.ext.archaeopteryx.AptxInit;
+import jalview.ext.archaeopteryx.JalviewBinding;
 import jalview.ext.forester.io.SupportedTreeFileFilter;
 import jalview.ext.forester.io.TreeParser;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
@@ -137,6 +138,7 @@ import java.util.Deque;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -152,6 +154,8 @@ import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.SwingUtilities;
 
+import org.forester.archaeopteryx.MainFrame;
+
 /**
  * DOCUMENT ME!
  * 
@@ -3739,6 +3743,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+
   /**
    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
@@ -3754,15 +3759,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     List<Component> comps = PaintRefresher.components
             .get(viewport.getSequenceSetId());
     List<TreePanel> treePanels = new ArrayList<>();
+
+    Map<MainFrame, JalviewBinding> aptxFrames = AptxInit.getAllAptxFrames();
+
     for (Component comp : comps)
     {
+      // old treepanels
       if (comp instanceof TreePanel)
       {
         treePanels.add((TreePanel) comp);
       }
+
     }
 
-    if (treePanels.size() < 1)
+    if (treePanels.isEmpty() && aptxFrames.isEmpty())
     {
       sortByTreeMenu.setVisible(false);
       return;
@@ -3770,6 +3780,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     sortByTreeMenu.setVisible(true);
 
+    for (Map.Entry<MainFrame, JalviewBinding> aptxFrameWithBinding : aptxFrames
+            .entrySet())
+    {
+      MainFrame aptxFrame = aptxFrameWithBinding.getKey();
+      JalviewBinding binding = aptxFrameWithBinding.getValue();
+
+      // future support for multiple tabs
+      // for (org.forester.archaeopteryx.TreePanel aptxTree : aptxFrame
+      // .getMainPanel().getTreePanels())
+      {
+        final JMenuItem item = new JMenuItem(
+                aptxFrame.getMainPanel().getCurrentTreePanel()
+                        .getPhylogeny().getName());
+
+          item.addActionListener(new ActionListener()
+          {
+
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              // tp.sortByTree_actionPerformed();
+              // addHistoryItem(tp.sortAlignmentIn(alignPanel));
+            }
+
+          });
+        sortByTreeMenu.add(item);
+      }
+
+
+
+      }
+       
+
+           
+
+
+    // old treepanels
     for (final TreePanel tp : treePanels)
     {
       final JMenuItem item = new JMenuItem(tp.getTitle());
@@ -3778,7 +3825,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         @Override
         public void actionPerformed(ActionEvent e)
         {
-          // adapt to Aptx
           tp.sortByTree_actionPerformed();
           addHistoryItem(tp.sortAlignmentIn(alignPanel));