X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=18731adda63651610e5e5385519f320cb9f22d39;hb=3da878124135ff033f42d19d8733891b09e953cd;hp=2b056fcebd60bf23385da81c242d9c74571327e9;hpb=96026e673c3629afa54a0d03be4b0022c7b42869;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 2b056fc..18731ad 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -21,12 +21,14 @@
 package jalview.jbgui;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.GeneticCodeI;
+import jalview.analysis.GeneticCodes;
 import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
-import jalview.bin.Jalview;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
 import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
@@ -76,7 +78,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu sortByAnnotScore = new JMenu();
 
-  public JLabel statusBar = new JLabel();
+  protected JLabel statusBar = new JLabel();
 
   protected JMenu outputTextboxMenu = new JMenu();
 
@@ -124,7 +126,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem modifyPID;
 
-  protected JMenuItem annotationColour;
+  protected JRadioButtonMenuItem annotationColour;
 
   protected JMenu sortByTreeMenu = new JMenu();
 
@@ -138,7 +140,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 
-  protected JMenuItem showTranslation = new JMenuItem();
+  protected JMenu showTranslation = new JMenu();
 
   protected JMenuItem showReverse = new JMenuItem();
 
@@ -204,7 +206,7 @@ public class GAlignFrame extends JInternalFrame
 
   private boolean showAutoCalculatedAbove = false;
 
-  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 
   private SplitContainerI splitFrame;
 
@@ -236,7 +238,7 @@ public class GAlignFrame extends JInternalFrame
       System.err.println(e.toString());
     }
 
-    if (Platform.isWin()) // was "not mac and not JS"
+    if (Platform.allowMnemonics()) // was "not mac and not JS"
     {
       closeMenuItem.setMnemonic('C');
       outputTextboxMenu.setMnemonic('T');
@@ -970,7 +972,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        copy_actionPerformed(e);
+        copy_actionPerformed();
       }
     };
     addMenuActionAndAccelerator(keyStroke, copy, al);
@@ -983,7 +985,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        cut_actionPerformed(e);
+        cut_actionPerformed();
       }
     };
     addMenuActionAndAccelerator(keyStroke, cut, al);
@@ -995,7 +997,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        delete_actionPerformed(e);
+        delete_actionPerformed();
       }
     });
 
@@ -1224,16 +1226,33 @@ public class GAlignFrame extends JInternalFrame
         vamsasStore_actionPerformed(e);
       }
     });
-    showTranslation
-            .setText(MessageManager.getString("label.translate_cDNA"));
-    showTranslation.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
+
+    /*
+     * Translate as cDNA with sub-menu of translation tables
+     */
+    showTranslation.setText(MessageManager
+            .getString("label.translate_cDNA"));
+    boolean first = true;
+    for (final GeneticCodeI table : GeneticCodes.getInstance()
+            .getCodeTables())
+    {
+      JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
+      showTranslation.add(item);
+      item.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          showTranslation_actionPerformed(table);
+        }
+      });
+      if (first)
       {
-        showTranslation_actionPerformed(e);
+        showTranslation.addSeparator();
       }
-    });
+      first = false;
+    }
+
     showReverse.setText(MessageManager.getString("label.reverse"));
     showReverse.addActionListener(new ActionListener()
     {
@@ -1711,7 +1730,7 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(formatMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       alignFrameMenuBar.add(webService);
     }
@@ -1732,7 +1751,7 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(loadTreeMenuItem);
     fileMenu.add(associatedData);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       fileMenu.add(loadVcf);
     }
@@ -1830,7 +1849,7 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.addSeparator();
     calculateMenu.add(expandAlignment);
     calculateMenu.add(extractScores);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       calculateMenu.addSeparator();
       calculateMenu.add(runGroovy);
@@ -1839,15 +1858,15 @@ public class GAlignFrame extends JInternalFrame
     webServiceNoServices = new JMenuItem(
             MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       exportImageMenu.add(htmlMenuItem);
     }
     exportImageMenu.add(epsFile);
     exportImageMenu.add(createPNG);
-    exportImageMenu.add(createBioJS);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
+      exportImageMenu.add(createBioJS);
       exportImageMenu.add(createSVG);
     }
     addSequenceMenu.add(addFromFile);
@@ -1965,8 +1984,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    annotationColour = new JMenuItem(
+    annotationColour = new JRadioButtonMenuItem(
             MessageManager.getString("action.by_annotation"));
+    annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
     annotationColour.addActionListener(new ActionListener()
     {
       @Override
@@ -2352,15 +2372,15 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void copy_actionPerformed(ActionEvent e)
+  protected void copy_actionPerformed()
   {
   }
 
-  protected void cut_actionPerformed(ActionEvent e)
+  protected void cut_actionPerformed()
   {
   }
 
-  protected void delete_actionPerformed(ActionEvent e)
+  protected void delete_actionPerformed()
   {
   }
 
@@ -2462,7 +2482,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void showTranslation_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(GeneticCodeI codeTable)
   {
 
   }