X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=b2eb094295c7f40329c362973afce745c750203a;hb=566041d3e8ca1d8783b4572a695e83784c0b6bc7;hp=73d34c2ba0be3fb6eb7a8d970c2b54f9c75c7e85;hpb=384e43c561fbc2446923dd2ed227e2931a8ac406;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 73d34c2..b2eb094 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -55,7 +55,6 @@ import javax.swing.JPanel;
 import javax.swing.JRadioButtonMenuItem;
 import javax.swing.JTabbedPane;
 import javax.swing.KeyStroke;
-import javax.swing.SwingUtilities;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
@@ -173,8 +172,14 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem showTranslation = new JMenuItem();
 
+  protected JMenuItem showReverse = new JMenuItem();
+
+  protected JMenuItem showReverseComplement = new JMenuItem();
+
   protected JMenu showProducts = new JMenu();
 
+  protected JMenuItem runGroovy = new JMenuItem();
+
   protected JMenuItem rnahelicesColour = new JMenuItem();
 
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
@@ -289,8 +294,7 @@ public class GAlignFrame extends JInternalFrame
           @Override
           public void mousePressed(MouseEvent evt)
           {
-            if (evt.isControlDown()
-                    || SwingUtilities.isRightMouseButton(evt))
+            if (evt.isPopupTrigger())
             {
               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
@@ -1686,6 +1690,25 @@ public class GAlignFrame extends JInternalFrame
         showTranslation_actionPerformed(e);
       }
     });
+    showReverse.setText(MessageManager.getString("label.reverse"));
+    showReverse.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showReverse_actionPerformed(false);
+      }
+    });
+    showReverseComplement.setText(MessageManager
+            .getString("label.reverse_complement"));
+    showReverseComplement.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showReverse_actionPerformed(true);
+      }
+    });
 
     JMenuItem extractScores = new JMenuItem(
             MessageManager.getString("label.extract_scores"));
@@ -1703,6 +1726,17 @@ public class GAlignFrame extends JInternalFrame
     // for show products actions see AlignFrame.canShowProducts
     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
 
+    runGroovy.setText(MessageManager.getString("label.run_groovy"));
+    runGroovy.setToolTipText(MessageManager.getString("label.run_groovy_tip"));
+    runGroovy.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        runGroovy_actionPerformed();
+      }
+    });
+
     JMenuItem openFeatureSettings = new JMenuItem(
             MessageManager.getString("action.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
@@ -2137,6 +2171,7 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
+
     fileMenu.add(fetchSequence);
     fileMenu.add(addSequenceMenu);
     fileMenu.add(reload);
@@ -2155,6 +2190,9 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(associatedData);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
+
+    pasteMenu.add(pasteNew);
+    pasteMenu.add(pasteThis);
     editMenu.add(undoMenuItem);
     editMenu.add(redoMenuItem);
     editMenu.add(cut);
@@ -2175,6 +2213,13 @@ public class GAlignFrame extends JInternalFrame
     // editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
 
+    showMenu.add(showAllColumns);
+    showMenu.add(showAllSeqs);
+    showMenu.add(showAllhidden);
+    hideMenu.add(hideSelColumns);
+    hideMenu.add(hideSelSequences);
+    hideMenu.add(hideAllSelection);
+    hideMenu.add(hideAllButSelection);
     viewMenu.add(newView);
     viewMenu.add(expandViews);
     viewMenu.add(gatherViews);
@@ -2245,6 +2290,12 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(modifyPID);
     colourMenu.add(annotationColour);
     colourMenu.add(rnahelicesColour);
+
+    sort.add(sortIDMenuItem);
+    sort.add(sortLengthMenuItem);
+    sort.add(sortGroupMenuItem);
+    sort.add(sortPairwiseMenuItem);
+    sort.add(sortByTreeMenu);
     calculateMenu.add(sort);
     calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
@@ -2252,21 +2303,20 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
+    calculateMenu.add(showReverse);
+    calculateMenu.add(showReverseComplement);
     calculateMenu.add(showProducts);
     calculateMenu.add(autoCalculate);
     calculateMenu.add(sortByTree);
     calculateMenu.addSeparator();
+    calculateMenu.add(expandAlignment);
     calculateMenu.add(extractScores);
+    calculateMenu.addSeparator();
+    calculateMenu.add(runGroovy);
+
     webServiceNoServices = new JMenuItem(
             MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
-    pasteMenu.add(pasteNew);
-    pasteMenu.add(pasteThis);
-    sort.add(sortIDMenuItem);
-    sort.add(sortLengthMenuItem);
-    sort.add(sortGroupMenuItem);
-    sort.add(sortPairwiseMenuItem);
-    sort.add(sortByTreeMenu);
     exportImageMenu.add(htmlMenuItem);
     exportImageMenu.add(epsFile);
     exportImageMenu.add(createPNG);
@@ -2278,13 +2328,6 @@ public class GAlignFrame extends JInternalFrame
     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
     statusPanel.add(statusBar, null);
     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
-    showMenu.add(showAllColumns);
-    showMenu.add(showAllSeqs);
-    showMenu.add(showAllhidden);
-    hideMenu.add(hideSelColumns);
-    hideMenu.add(hideSelSequences);
-    hideMenu.add(hideAllSelection);
-    hideMenu.add(hideAllButSelection);
 
     formatMenu.add(font);
     formatMenu.addSeparator();
@@ -2312,7 +2355,6 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(grpsFromSelection);
     selectMenu.add(deleteGroups);
     selectMenu.add(annotationColumn);
-    calculateMenu.add(expandAlignment);
     // TODO - determine if the listenToViewSelections button is needed : see bug
     // JAL-574
     // selectMenu.addSeparator();
@@ -2320,6 +2362,24 @@ public class GAlignFrame extends JInternalFrame
   }
 
   /**
+   * Generate the reverse sequence (or reverse complement if the flag is true)
+   * and add it to the alignment
+   * 
+   * @param complement
+   */
+  protected void showReverse_actionPerformed(boolean complement)
+  {
+  }
+
+  /**
+   * Try to run script in a Groovy console, having first ensured that this
+   * alignframe is set as currentAlignFrame in Desktop
+   */
+  protected void runGroovy_actionPerformed()
+  {
+
+  }
+  /**
    * Adds the given action listener and key accelerator to the given menu item.
    * Also saves in a lookup table to support lookup of action by key stroke.
    * 
@@ -3107,7 +3167,7 @@ public class GAlignFrame extends JInternalFrame
     return this.splitFrame;
   }
 
-  protected void showComplement_actionPerformed(boolean state)
+  protected void showComplement_actionPerformed(boolean complement)
   {
   }
 }