develop merge

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index cb769bb..44d1d94 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -119,6 +119,8 @@ import java.awt.dnd.DropTargetEvent;
 import java.awt.dnd.DropTargetListener;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.KeyAdapter;
@@ -129,6 +131,7 @@ import java.awt.print.PageFormat;
 import java.awt.print.PrinterJob;
 import java.beans.PropertyChangeEvent;
 import java.io.File;
+import java.lang.reflect.Method;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -466,6 +469,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       formatMenu.add(vsel);
     }
+    addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusGained(FocusEvent e)
+      {
+        Desktop.setCurrentAlignFrame(AlignFrame.this);
+      }
+    });
 
   }
 
@@ -911,10 +922,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 
     showProducts.setEnabled(canShowProducts());
+    setGroovyEnabled(Desktop.getGroovyConsole() != null);
 
     updateEditMenuBar();
   }
 
+  /**
+   * Set the enabled state of the 'Run Groovy' option in the Calculate menu
+   * 
+   * @param b
+   */
+  public void setGroovyEnabled(boolean b)
+  {
+    runGroovy.setEnabled(b);
+  }
+
   private IProgressIndicator progressBar;
 
   /*
@@ -3619,8 +3641,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           @Override
           public void mousePressed(MouseEvent evt)
           {
-            if (evt.isControlDown()
-                    || SwingUtilities.isRightMouseButton(evt))
+            if (evt.isPopupTrigger())
             {
               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
@@ -4124,7 +4145,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         JMenuItem tm = new JMenuItem();
         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
-        if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
+        if (sm.isDNA() == viewport.getAlignment().isNucleotide()
+                || sm.isProtein() == !viewport.getAlignment()
+                        .isNucleotide())
         {
           String smn = MessageManager.getStringOrReturn(
                   "label.score_model_", sm.getName());
@@ -5371,7 +5394,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void tabbedPane_mousePressed(MouseEvent e)
   {
-    if (SwingUtilities.isRightMouseButton(e))
+    if (e.isPopupTrigger())
     {
       String msg = MessageManager.getString("label.enter_view_name");
       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
@@ -6088,6 +6111,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
   }
+
+  /**
+   * Try to run a script in the Groovy console, having first ensured that this
+   * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
+   * be targeted at this alignment.
+   */
+  @Override
+  protected void runGroovy_actionPerformed()
+  {
+    Desktop.setCurrentAlignFrame(this);
+    Object console = Desktop.instance.getGroovyConsole();
+    if (console != null)
+    {
+      /*
+       * use reflection here to avoid compile-time dependency
+       * on Groovy libraries
+       */
+      try
+      {
+        Class<?> gcClass = getClass().getClassLoader().loadClass(
+                "groovy.ui.Console");
+        Method runScript = gcClass.getMethod("runScript");
+        runScript.invoke(console);
+      } catch (Exception ex)
+      {
+        System.err.println((ex.toString()));
+        JOptionPane
+                .showInternalMessageDialog(Desktop.desktop, MessageManager
+                        .getString("label.couldnt_run_groovy_script"),
+                        MessageManager
+                                .getString("label.groovy_support_failed"),
+                        JOptionPane.ERROR_MESSAGE);
+      }
+    }
+    else
+    {
+      System.err.println("Can't run Groovy script as console not found");
+    }
+  }
 }
 
 class PrintThread extends Thread