accelerators, save menu item
[jalview.git] / src / jalview / jbgui / GAlignFrame.java
index 8c29d96..304134c 100755 (executable)
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -21,8 +21,13 @@ package jalview.jbgui;
 import java.awt.*;\r
 import java.awt.event.*;\r
 import javax.swing.*;\r
+import javax.swing.event.*;\r
 \r
 import jalview.schemes.*;\r
+import java.awt.BorderLayout;\r
+\r
+\r
+\r
 \r
 public class GAlignFrame\r
     extends JInternalFrame\r
@@ -56,7 +61,7 @@ public class GAlignFrame
   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
   BorderLayout borderLayout1 = new BorderLayout();\r
   public JLabel statusBar = new JLabel();\r
-  protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
+  protected JMenuItem saveAs = new JMenuItem();\r
   protected JMenu outputTextboxMenu = new JMenu();\r
   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
@@ -86,7 +91,7 @@ public class GAlignFrame
   JMenuItem findMenuItem = new JMenuItem();\r
   JMenu searchMenu = new JMenu();\r
   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
-  public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
+  public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
   JMenuItem deleteGroups = new JMenuItem();\r
   JMenuItem delete = new JMenuItem();\r
@@ -110,31 +115,46 @@ public class GAlignFrame
   protected JMenu sort = new JMenu();\r
   JMenu calculate = new JMenu();\r
   JMenu jMenu2 = new JMenu();\r
-  JMenuItem padGapsMenuitem = new JMenuItem();\r
+  protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
   protected ButtonGroup colours = new ButtonGroup();\r
   JMenuItem vamsasStore = new JMenuItem();\r
-  protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
-  //protected JTabbedPane tabbedPane = new JTabbedPane();\r
+  protected JMenuItem showTranslation = new JMenuItem();\r
   public JMenuItem featureSettings = new JMenuItem();\r
   JMenuItem fetchSequence = new JMenuItem();\r
   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
   JMenuItem annotationColour = new JMenuItem();\r
-\r
+  JMenuItem associatedData = new JMenuItem();\r
+  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
+  JMenu addSequenceMenu = new JMenu();\r
+  JMenuItem addFromFile = new JMenuItem();\r
+  JMenuItem addFromText = new JMenuItem();\r
+  JMenuItem addFromURL = new JMenuItem();\r
+  JMenuItem exportAnnotations = new JMenuItem();\r
+  JMenuItem exportFeatures = new JMenuItem();\r
+  protected JPanel statusPanel = new JPanel();\r
+  GridLayout gridLayout1 = new GridLayout();\r
+  JMenu jMenu3 = new JMenu();\r
+  JMenuItem showAllSeqs = new JMenuItem();\r
+  JMenuItem showAllColumns = new JMenuItem();\r
+  JMenu hideMenu = new JMenu();\r
+  JMenuItem hideSelSequences = new JMenuItem();\r
+  JMenuItem hideSelColumns = new JMenuItem();\r
+  protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
+  JMenuItem invertColSel = new JMenuItem();\r
+  protected JTabbedPane tabbedPane = new JTabbedPane();\r
+  JMenuItem save = new JMenuItem();\r
   public GAlignFrame()\r
   {\r
-\r
-\r
     try\r
     {\r
       jbInit();\r
       setJMenuBar(alignFrameMenuBar);\r
 \r
       // dynamically fill save as menu with available formats\r
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
+      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
       {\r
-        JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
-                             elementAt(\r
-                                 i));\r
+        JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
+\r
         item.addActionListener(new java.awt.event.ActionListener()\r
         {\r
           public void actionPerformed(ActionEvent e)\r
@@ -297,21 +317,21 @@ public class GAlignFrame
   private void jbInit()\r
       throws Exception\r
   {\r
-    fileMenu.setMnemonic('F');\r
     fileMenu.setText("File");\r
-    saveAlignmentMenu.setMnemonic('L');\r
-    saveAlignmentMenu.setText("Save As");\r
-    saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
-        awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
-    saveAlignmentMenu.addActionListener(new ActionListener()\r
+    saveAs.setText("Save As ...");\r
+    saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+        KeyEvent.VK_S, java.awt.event.KeyEvent.ALT_MASK, false));\r
+    saveAs.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        saveAlignmentMenu_actionPerformed(e);\r
+        saveAs_actionPerformed(e);\r
       }\r
     });\r
     closeMenuItem.setMnemonic('C');\r
     closeMenuItem.setText("Close");\r
+    closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_W, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -348,7 +368,10 @@ public class GAlignFrame
         deselectAllSequenceMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    invertSequenceMenuItem.setText("Invert Selection");\r
+    invertSequenceMenuItem.setText("Invert Sequence Selection");\r
+    invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+        java.awt.event.KeyEvent.VK_I,\r
+        java.awt.event.KeyEvent.SHIFT_MASK, false));\r
     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -357,6 +380,8 @@ public class GAlignFrame
       }\r
     });\r
     remove2LeftMenuItem.setText("Remove Left");\r
+    remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
+        awt.event.KeyEvent.VK_L, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -365,6 +390,8 @@ public class GAlignFrame
       }\r
     });\r
     remove2RightMenuItem.setText("Remove Right");\r
+    remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
+        awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -373,6 +400,9 @@ public class GAlignFrame
       }\r
     });\r
     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
+    removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.\r
+                                              getKeyStroke(java.awt.event.\r
+        KeyEvent.VK_E, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
                                                  ActionListener()\r
     {\r
@@ -382,6 +412,8 @@ public class GAlignFrame
       }\r
     });\r
     removeAllGapsMenuItem.setText("Remove All Gaps");\r
+    removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+        java.awt.event.KeyEvent.VK_G, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -432,6 +464,8 @@ public class GAlignFrame
       }\r
     });\r
     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
+    removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+        java.awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
                                                ActionListener()\r
     {\r
@@ -640,6 +674,8 @@ public class GAlignFrame
     redoMenuItem.setEnabled(false);\r
     redoMenuItem.setMnemonic('0');\r
     redoMenuItem.setText("Redo");\r
+    redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_Y, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -672,6 +708,8 @@ public class GAlignFrame
       }\r
     });\r
     printMenuItem.setText("Print");\r
+    printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_P, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -709,12 +747,12 @@ public class GAlignFrame
         abovePIDThreshold_actionPerformed(e);\r
       }\r
     });\r
-    sequenceFeatures.setText("Sequence Features");\r
-    sequenceFeatures.addActionListener(new ActionListener()\r
+    showSeqFeatures.setText("Show Sequence Features");\r
+    showSeqFeatures.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent actionEvent)\r
       {\r
-        sequenceFeatures_actionPerformed(actionEvent);\r
+        showSeqFeatures_actionPerformed(actionEvent);\r
       }\r
     });\r
     nucleotideColour.setText("Nucleotide");\r
@@ -726,6 +764,8 @@ public class GAlignFrame
       }\r
     });\r
     deleteGroups.setText("Undefine groups");\r
+    deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_U, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -788,7 +828,6 @@ public class GAlignFrame
       }\r
     });\r
     applyToAllGroups.setText("Apply Colour To All Groups");\r
-    applyToAllGroups.setState(true);\r
     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -889,8 +928,9 @@ public class GAlignFrame
     sort.setText("Sort");\r
     calculate.setText("Calculate Tree");\r
 \r
-    jMenu2.setText("Export");\r
+    jMenu2.setText("Export Image");\r
     padGapsMenuitem.setText("Pad Gaps");\r
+    padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
     padGapsMenuitem.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -916,15 +956,7 @@ public class GAlignFrame
       }\r
     });\r
 \r
-   /* tabbedPane.addChangeListener(new ChangeListener()\r
-        {\r
-          public void stateChanged(ChangeEvent ece)\r
-          {\r
 \r
-            tabSelected();\r
-          }\r
-        });*/\r
-    featureSettings.setEnabled(false);\r
     featureSettings.setText("Feature Settings...");\r
     featureSettings.addActionListener(new ActionListener()\r
     {\r
@@ -949,7 +981,7 @@ public class GAlignFrame
         smoothFont_actionPerformed(e);\r
       }\r
     });\r
-    smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
+\r
     annotationColour.setText("By Annotation...");\r
     annotationColour.addActionListener(new ActionListener()\r
     {\r
@@ -958,6 +990,151 @@ public class GAlignFrame
         annotationColour_actionPerformed(e);\r
       }\r
     });\r
+    associatedData.setText("Load Features / Annotations");\r
+    associatedData.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        associatedData_actionPerformed(e);\r
+      }\r
+    });\r
+    autoCalculate.setText("Autocalculate Consensus");\r
+    autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
+    autoCalculate.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        autoCalculate_actionPerformed(e);\r
+      }\r
+    });\r
+    addSequenceMenu.setText("Add Sequences");\r
+    addFromFile.setText("From File");\r
+    addFromFile.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        addFromFile_actionPerformed(e);\r
+      }\r
+    });\r
+    addFromText.setText("From Textbox");\r
+    addFromText.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        addFromText_actionPerformed(e);\r
+      }\r
+    });\r
+    addFromURL.setText("From URL");\r
+    addFromURL.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        addFromURL_actionPerformed(e);\r
+      }\r
+    });\r
+    exportFeatures.setText("Export Features...");\r
+    exportFeatures.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        exportFeatures_actionPerformed(e);\r
+      }\r
+    });\r
+    exportAnnotations.setText("Export Annotations...");\r
+    exportAnnotations.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        exportAnnotations_actionPerformed(e);\r
+      }\r
+    });\r
+    statusPanel.setLayout(gridLayout1);\r
+    jMenu3.setText("Show");\r
+    showAllSeqs.setText("All Sequences");\r
+    showAllSeqs.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        showAllSeqs_actionPerformed(e);\r
+      }\r
+    });\r
+    showAllColumns.setText("All Columns");\r
+    showAllColumns.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        showAllColumns_actionPerformed(e);\r
+      }\r
+    });\r
+    hideMenu.setText("Hide");\r
+    hideSelSequences.setText("Selected Sequences");\r
+    hideSelSequences.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        hideSelSequences_actionPerformed(e);\r
+      }\r
+    });\r
+    hideSelColumns.setText("Selected Columns");\r
+    hideSelColumns.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        hideSelColumns_actionPerformed(e);\r
+      }\r
+    });\r
+    hiddenMarkers.setText("Hidden Markers");\r
+    hiddenMarkers.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        hiddenMarkers_actionPerformed(e);\r
+      }\r
+    });\r
+    invertColSel.setText("Invert Column Selection");\r
+    invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_I, java.awt.event.KeyEvent.CTRL_MASK, false));\r
+    invertColSel.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        invertColSel_actionPerformed(e);\r
+      }\r
+    });\r
+    tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
+    {\r
+        public void stateChanged(ChangeEvent evt)\r
+        {\r
+            JTabbedPane pane = (JTabbedPane)evt.getSource();\r
+            int sel = pane.getSelectedIndex();\r
+            tabSelectionChanged(sel);\r
+        }\r
+    });\r
+    tabbedPane.addMouseListener(new MouseAdapter()\r
+    {\r
+      public void mousePressed(MouseEvent e)\r
+      {\r
+        tabbedPane_mousePressed(e);\r
+      }\r
+    });\r
+    tabbedPane.addFocusListener(new FocusAdapter()\r
+    {\r
+      public void focusGained(FocusEvent e)\r
+      {\r
+        tabbedPane_focusGained(e);\r
+      }\r
+    });\r
+    save.setText("Save");\r
+    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+        KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
+    save.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        save_actionPerformed(e);\r
+      }\r
+    });\r
+\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
@@ -965,14 +1142,20 @@ public class GAlignFrame
     alignFrameMenuBar.add(colourMenu);\r
     alignFrameMenuBar.add(calculateMenu);\r
     alignFrameMenuBar.add(webService);\r
+    fileMenu.add(addSequenceMenu);\r
     fileMenu.add(fetchSequence);\r
+    fileMenu.addSeparator();\r
     fileMenu.add(vamsasStore);\r
-    fileMenu.add(saveAlignmentMenu);\r
-    fileMenu.add(jMenu2);\r
+    fileMenu.add(save);\r
+    fileMenu.add(saveAs);\r
     fileMenu.add(outputTextboxMenu);\r
     fileMenu.add(printMenuItem);\r
     fileMenu.addSeparator();\r
+    fileMenu.add(jMenu2);\r
+    fileMenu.add(exportFeatures);\r
+    fileMenu.add(exportAnnotations);\r
     fileMenu.add(LoadtreeMenuItem);\r
+    fileMenu.add(associatedData);\r
     fileMenu.addSeparator();\r
     fileMenu.add(closeMenuItem);\r
     editMenu.add(undoMenuItem);\r
@@ -985,6 +1168,7 @@ public class GAlignFrame
     editMenu.add(selectAllSequenceMenuItem);\r
     editMenu.add(deselectAllSequenceMenuItem);\r
     editMenu.add(invertSequenceMenuItem);\r
+    editMenu.add(invertColSel);\r
     editMenu.add(deleteGroups);\r
     editMenu.addSeparator();\r
     editMenu.add(remove2LeftMenuItem);\r
@@ -998,6 +1182,10 @@ public class GAlignFrame
     viewMenu.add(font);\r
     viewMenu.add(smoothFont);\r
     viewMenu.addSeparator();\r
+    viewMenu.add(jMenu3);\r
+    viewMenu.add(hideMenu);\r
+    viewMenu.add(hiddenMarkers);\r
+    viewMenu.addSeparator();\r
     viewMenu.add(wrapMenuItem);\r
     viewMenu.add(seqLimits);\r
     viewMenu.add(scaleAbove);\r
@@ -1009,13 +1197,12 @@ public class GAlignFrame
     viewMenu.add(renderGapsMenuItem);\r
     viewMenu.add(annotationPanelMenuItem);\r
     viewMenu.addSeparator();\r
-    viewMenu.add(sequenceFeatures);\r
+    viewMenu.add(showSeqFeatures);\r
     viewMenu.add(featureSettings);\r
     viewMenu.addSeparator();\r
     viewMenu.add(overviewMenuItem);\r
     colourMenu.add(applyToAllGroups);\r
     colourMenu.addSeparator();\r
-    colourMenu.add(annotationColour);\r
     colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r
     colourMenu.add(BLOSUM62Colour);\r
@@ -1034,7 +1221,7 @@ public class GAlignFrame
     colourMenu.add(modifyConservation);\r
     colourMenu.add(abovePIDThreshold);\r
     colourMenu.add(modifyPID);\r
-    colourMenu.addSeparator();\r
+    colourMenu.add(annotationColour);\r
     calculateMenu.add(sort);\r
     calculateMenu.add(calculate);\r
     calculateMenu.addSeparator();\r
@@ -1042,11 +1229,9 @@ public class GAlignFrame
     calculateMenu.add(PCAMenuItem);\r
     calculateMenu.addSeparator();\r
     calculateMenu.add(showTranslation);\r
+    calculateMenu.add(autoCalculate);\r
     webServiceNoServices=new JMenuItem("<No Services>");\r
-    webService.add(webServiceNoServices);\r
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
-  //  this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
-    jMenu1.add(pasteNew);\r
+    webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
     jMenu1.add(pasteThis);\r
     sort.add(sortIDMenuItem);\r
     sort.add(sortGroupMenuItem);\r
@@ -1058,12 +1243,47 @@ public class GAlignFrame
     jMenu2.add(htmlMenuItem);\r
     jMenu2.add(epsFile);\r
     jMenu2.add(createPNG);\r
+    addSequenceMenu.add(addFromFile);\r
+    addSequenceMenu.add(addFromText);\r
+    addSequenceMenu.add(addFromURL);\r
+    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
+    statusPanel.add(statusBar, null);\r
+    this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
+    jMenu3.add(showAllColumns);\r
+    jMenu3.add(showAllSeqs);\r
+    hideMenu.add(hideSelColumns);\r
+    hideMenu.add(hideSelSequences);\r
   }\r
 \r
   protected void outputText_actionPerformed(ActionEvent e)\r
   {\r
   }\r
 \r
+  public void addFromFile_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void addFromText_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void addFromURL_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void exportFeatures_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void exportAnnotations_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
   {\r
   }\r
@@ -1240,7 +1460,7 @@ public class GAlignFrame
   {\r
   }\r
 \r
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
   {\r
   }\r
 \r
@@ -1328,7 +1548,7 @@ public class GAlignFrame
 \r
 \r
 \r
-  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+  protected void saveAs_actionPerformed(ActionEvent e)\r
   {\r
   }\r
 \r
@@ -1352,11 +1572,6 @@ public class GAlignFrame
 \r
   }\r
 \r
-  public void tabSelected()\r
-  {\r
-\r
-  }\r
-\r
   public void featureSettings_actionPerformed(ActionEvent e)\r
   {\r
 \r
@@ -1376,4 +1591,80 @@ public class GAlignFrame
   {\r
 \r
   }\r
+\r
+\r
+  public void associatedData_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void autoCalculate_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void showAllSeqs_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void showAllColumns_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void hideSelSequences_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void hideSelColumns_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void hiddenMarkers_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void findPdbId_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void enterPdbId_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void pdbFile_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void invertColSel_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void tabSelectionChanged(int sel)\r
+  {\r
+\r
+  }\r
+\r
+  public void tabbedPane_mousePressed(MouseEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void tabbedPane_focusGained(FocusEvent e)\r
+  {\r
+    requestFocus();\r
+  }\r
+\r
+  public void save_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
 }\r