FileFormatI further tweaks, clean compile

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 3504ea4..73d1b3c 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -25,6 +25,7 @@ import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
+import jalview.io.FileFormat;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
 
@@ -55,7 +56,6 @@ 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;
@@ -137,8 +137,6 @@ public class GAlignFrame extends JInternalFrame
 
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 
-  public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
-
   JMenuItem copy = new JMenuItem();
 
   JMenuItem cut = new JMenuItem();
@@ -173,8 +171,14 @@ 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();
@@ -241,10 +245,9 @@ public class GAlignFrame extends JInternalFrame
       setJMenuBar(alignFrameMenuBar);
 
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+      for (String ff : FileFormat.getWritableFormats())
       {
-        JMenuItem item = new JMenuItem(
-                jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+        JMenuItem item = new JMenuItem(ff);
 
         item.addActionListener(new ActionListener()
         {
@@ -289,8 +292,7 @@ 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]);
 
@@ -491,8 +493,7 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("action.calculate"));
     webService.setText(MessageManager.getString("action.web_service"));
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
-            MessageManager
-            .getString("action.select_all"));
+            MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -703,8 +704,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    JMenuItem removeRedundancyMenuItem = new JMenuItem(MessageManager
-.getString("action.remove_redundancy"));
+    JMenuItem removeRedundancyMenuItem = new JMenuItem(
+            MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1296,8 +1297,10 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("label.show_last"));
     buttonGroup.add(showAutoFirst);
     buttonGroup.add(showAutoLast);
-    showAutoFirst.setSelected(Cache.getDefault(
-            Preferences.SHOW_AUTOCALC_ABOVE, false));
+    final boolean autoFirst = Cache.getDefault(
+            Preferences.SHOW_AUTOCALC_ABOVE, false);
+    showAutoFirst.setSelected(autoFirst);
+    setShowAutoCalculatedAbove(autoFirst);
     showAutoFirst.addActionListener(new ActionListener()
     {
       @Override
@@ -1586,7 +1589,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem modifyPID = new JMenuItem(
-            MessageManager.getString("label.modify_identity_thereshold"));
+            MessageManager.getString("label.modify_identity_threshold"));
     modifyPID.addActionListener(new ActionListener()
     {
       @Override
@@ -1596,7 +1599,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     modifyConservation.setText(MessageManager
-            .getString("label.modify_conservation_thereshold"));
+            .getString("label.modify_conservation_threshold"));
     modifyConservation.addActionListener(new ActionListener()
     {
       @Override
@@ -1685,6 +1688,25 @@ 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"));
@@ -1702,6 +1724,17 @@ 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()
@@ -1959,8 +1992,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask()
             | KeyEvent.ALT_MASK, false);
     al = new ActionListener()
     {
@@ -2136,6 +2169,7 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
+
     fileMenu.add(fetchSequence);
     fileMenu.add(addSequenceMenu);
     fileMenu.add(reload);
@@ -2154,6 +2188,9 @@ 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);
@@ -2174,6 +2211,13 @@ 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);
@@ -2244,6 +2288,12 @@ 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();
@@ -2251,21 +2301,20 @@ 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);
@@ -2277,13 +2326,6 @@ 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();
@@ -2311,7 +2353,6 @@ 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();
@@ -2319,6 +2360,24 @@ 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.
    * 
@@ -2459,13 +2518,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  protected void showSeqFeaturesHeight_actionPerformed(
-          ActionEvent actionEvent)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub
@@ -2803,6 +2855,7 @@ public class GAlignFrame extends JInternalFrame
   {
 
   }
+
   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {
 
@@ -3057,7 +3110,8 @@ public class GAlignFrame extends JInternalFrame
     return annotationSortOrder;
   }
 
-  protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
+  protected void setAnnotationSortOrder(
+          SequenceAnnotationOrder annotationSortOrder)
   {
     this.annotationSortOrder = annotationSortOrder;
   }
@@ -3104,7 +3158,7 @@ public class GAlignFrame extends JInternalFrame
     return this.splitFrame;
   }
 
-  protected void showComplement_actionPerformed(boolean state)
+  protected void showComplement_actionPerformed(boolean complement)
   {
   }
 }