JAL-1473 menu entries for different score models available for NJ/UPGMA tree building...

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4a06fdd..5160a3a 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -25,6 +25,7 @@ import jalview.analysis.CrossRef;
 import jalview.analysis.NJTree;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
@@ -71,6 +72,7 @@ import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
 import jalview.schemes.RNAHelicesColourChooser;
 import jalview.schemes.ResidueProperties;
+import jalview.schemes.ScoreMatrix;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.schemes.TaylorColourScheme;
@@ -136,7 +138,7 @@ import javax.swing.SwingUtilities;
  * @version $Revision$
  */
 public class AlignFrame extends GAlignFrame implements DropTargetListener,
-        IProgressIndicator
+        IProgressIndicator, AlignViewControllerGuiI
 {
 
   /** DOCUMENT ME!! */
@@ -294,7 +296,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void init()
   {
-    avc = new jalview.controller.AlignViewController(viewport, alignPanel);
+    avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
     {
       BLOSUM62Colour.setEnabled(false);
@@ -326,6 +328,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     setMenusFromViewport(viewport);
     buildSortByAnnotationScoresMenu();
+    buildTreeMenu();
     if (viewport.wrapAlignment)
     {
       wrapMenuItem_actionPerformed(null);
@@ -564,7 +567,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
   {
     ap.alignFrame = this;
-    avc = new jalview.controller.AlignViewController(viewport, alignPanel);
+    avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
 
     alignPanels.addElement(ap);
 
@@ -848,6 +851,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return false;
   }
 
+  @Override
+  public void setStatus(String text) {
+    statusBar.setText(text);
+  };
   /*
    * Added so Castor Mapping file can obtain Jalview Version
    */
@@ -3883,6 +3890,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void buildTreeMenu()
   {
+    calculateTree.removeAll();
+    // build the calculate menu
+    for (final String type:new String[] {"NJ", "AV"})
+    {
+      for (final Object pwtype: ResidueProperties.scoreMatrices.keySet())
+      {
+        JMenuItem tm = new JMenuItem();
+        ScoreMatrix sm = (ScoreMatrix) ResidueProperties.scoreMatrices.get(pwtype);
+        final String title="Calculate "+type+" using "+sm.getName();
+        tm.setText(title);// MessageManager.getString("label.neighbour_blosum62"));
+        tm
+                .addActionListener(new java.awt.event.ActionListener()
+                {
+                  public void actionPerformed(ActionEvent e)
+                  {
+                    NewTreePanel(type, (String) pwtype, title);
+                  }
+                });
+        calculateTree.add(tm);
+
+      }
+    }
     sortByTreeMenu.removeAll();
 
     Vector comps = (Vector) PaintRefresher.components.get(viewport
@@ -5297,7 +5326,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   ++i;
                   if (++icomp >= mcomp || i == (otherdb.size()))
                   {
-                    ifetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{imname,sname}));
+                    ifetch.setText(MessageManager.formatMessage("label.source_to_target",imname,sname));
                     dfetch.add(ifetch);
                     ifetch = new JMenu();
                     imname = null;
@@ -5309,7 +5338,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               ++dbi;
               if (comp >= mcomp || dbi >= (dbclasses.length))
               {
-                dfetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{mname,dbclass}));
+                dfetch.setText(MessageManager.formatMessage("label.source_to_target",mname,dbclass));
                 rfetch.add(dfetch);
                 dfetch = new JMenu();
                 mname = null;