X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=d5c8c01cb29a3b9e259b42847dd918319d58a6ae;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=c8aa94f9be11ef2c85df359786b02521dadbd0d8;hpb=06ce849ffedc7ab10a3c54cda96b9a7dec58c136;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index c8aa94f..d5c8c01 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -75,7 +75,7 @@ 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();
 
@@ -113,7 +113,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu colourMenu = new JMenu();
 
-  protected JRadioButtonMenuItem textColour;
+  protected JMenuItem textColour;
 
   protected JCheckBoxMenuItem conservationMenuItem;
 
@@ -129,7 +129,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu sort = new JMenu();
 
-  protected JMenu calculateTree = new JMenu();
+  protected JMenuItem calculateTree = new JMenuItem();
 
   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 
@@ -147,6 +147,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem runGroovy = new JMenuItem();
 
+  protected JMenuItem loadVcf;
+
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
@@ -199,7 +201,7 @@ 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;
 
@@ -260,14 +262,15 @@ public class GAlignFrame extends JInternalFrame
     };
 
     // FIXME getDefaultToolkit throws an exception in Headless mode
-    KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask()
-            | KeyEvent.SHIFT_MASK, false);
+    KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.SHIFT_MASK,
+            false);
     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 
     closeMenuItem.setText(MessageManager.getString("action.close"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -289,8 +292,8 @@ public class GAlignFrame extends JInternalFrame
     webService.setText(MessageManager.getString("action.web_service"));
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -316,8 +319,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem invertSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.invert_sequence_selection"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -340,8 +343,8 @@ public class GAlignFrame extends JInternalFrame
     });
     JMenuItem expandAlignment = new JMenuItem(
             MessageManager.getString("action.view_flanking_regions"));
-    expandAlignment.setToolTipText(MessageManager
-            .getString("label.view_flanking_regions"));
+    expandAlignment.setToolTipText(
+            MessageManager.getString("label.view_flanking_regions"));
     expandAlignment.addActionListener(new ActionListener()
     {
       @Override
@@ -352,8 +355,8 @@ public class GAlignFrame extends JInternalFrame
     });
     JMenuItem remove2LeftMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_left"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -366,8 +369,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -380,8 +383,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_empty_columns"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -394,9 +397,10 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem removeAllGapsMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_all_gaps"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask()
-            | KeyEvent.SHIFT_MASK, false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.SHIFT_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -447,8 +451,8 @@ public class GAlignFrame extends JInternalFrame
         viewTextMenuItem_actionPerformed(e);
       }
     });
-    showNonconservedMenuItem.setText(MessageManager
-            .getString("label.show_non_conserved"));
+    showNonconservedMenuItem
+            .setText(MessageManager.getString("label.show_non_conserved"));
     showNonconservedMenuItem.setState(false);
     showNonconservedMenuItem.addActionListener(new ActionListener()
     {
@@ -501,8 +505,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -523,36 +527,6 @@ public class GAlignFrame extends JInternalFrame
         pairwiseAlignmentMenuItem_actionPerformed(e);
       }
     });
-    JMenuItem PCAMenuItem = new JMenuItem(
-            MessageManager.getString("label.principal_component_analysis"));
-    PCAMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        PCAMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
-            MessageManager.getString("label.average_distance_identity"));
-    averageDistanceTreeMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        averageDistanceTreeMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem neighbourTreeMenuItem = new JMenuItem(
-            MessageManager.getString("label.neighbour_joining_identity"));
-    neighbourTreeMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        neighbourTreeMenuItem_actionPerformed(e);
-      }
-    });
 
     this.getContentPane().setLayout(new BorderLayout());
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
@@ -560,35 +534,14 @@ public class GAlignFrame extends JInternalFrame
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
     statusBar.setText(MessageManager.getString("label.status_bar"));
-    outputTextboxMenu.setText(MessageManager
-            .getString("label.out_to_textbox"));
-
+    outputTextboxMenu
+            .setText(MessageManager.getString("label.out_to_textbox"));
 
-    JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
-            MessageManager.getString("label.average_distance_blosum62"));
-    avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        avTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem njTreeBlosumMenuItem = new JMenuItem(
-            MessageManager.getString("label.neighbour_blosum62"));
-    njTreeBlosumMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        njTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
     annotationPanelMenuItem.setActionCommand("");
-    annotationPanelMenuItem.setText(MessageManager
-            .getString("label.show_annotations"));
-    annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
-            true));
+    annotationPanelMenuItem
+            .setText(MessageManager.getString("label.show_annotations"));
+    annotationPanelMenuItem
+            .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
     annotationPanelMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -597,8 +550,8 @@ public class GAlignFrame extends JInternalFrame
         annotationPanelMenuItem_actionPerformed(e);
       }
     });
-    showAllAlAnnotations.setText(MessageManager
-            .getString("label.show_all_al_annotations"));
+    showAllAlAnnotations.setText(
+            MessageManager.getString("label.show_all_al_annotations"));
     final boolean isAnnotationPanelShown = annotationPanelMenuItem
             .getState();
     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
@@ -610,8 +563,8 @@ public class GAlignFrame extends JInternalFrame
         showAllAnnotations_actionPerformed(false, true);
       }
     });
-    hideAllAlAnnotations.setText(MessageManager
-            .getString("label.hide_all_al_annotations"));
+    hideAllAlAnnotations.setText(
+            MessageManager.getString("label.hide_all_al_annotations"));
     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
     hideAllAlAnnotations.addActionListener(new ActionListener()
     {
@@ -621,8 +574,8 @@ public class GAlignFrame extends JInternalFrame
         hideAllAnnotations_actionPerformed(false, true);
       }
     });
-    showAllSeqAnnotations.setText(MessageManager
-            .getString("label.show_all_seq_annotations"));
+    showAllSeqAnnotations.setText(
+            MessageManager.getString("label.show_all_seq_annotations"));
     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
     showAllSeqAnnotations.addActionListener(new ActionListener()
     {
@@ -632,8 +585,8 @@ public class GAlignFrame extends JInternalFrame
         showAllAnnotations_actionPerformed(true, false);
       }
     });
-    hideAllSeqAnnotations.setText(MessageManager
-            .getString("label.hide_all_seq_annotations"));
+    hideAllSeqAnnotations.setText(
+            MessageManager.getString("label.hide_all_seq_annotations"));
     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
     hideAllSeqAnnotations.addActionListener(new ActionListener()
     {
@@ -651,8 +604,8 @@ public class GAlignFrame extends JInternalFrame
     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
             MessageManager.getString("label.sort_annotations_by_label"));
 
-    sortAnnBySequence
-            .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+    sortAnnBySequence.setSelected(
+            sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
     sortAnnBySequence.addActionListener(new ActionListener()
     {
       @Override
@@ -660,13 +613,14 @@ public class GAlignFrame extends JInternalFrame
       {
         boolean newState = sortAnnBySequence.getState();
         sortAnnByLabel.setSelected(false);
-        setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
-                : SequenceAnnotationOrder.NONE);
+        setAnnotationSortOrder(
+                newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+                        : SequenceAnnotationOrder.NONE);
         sortAnnotations_actionPerformed();
       }
     });
-    sortAnnByLabel
-            .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+    sortAnnByLabel.setSelected(
+            sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
     sortAnnByLabel.addActionListener(new ActionListener()
     {
       @Override
@@ -674,14 +628,14 @@ public class GAlignFrame extends JInternalFrame
       {
         boolean newState = sortAnnByLabel.getState();
         sortAnnBySequence.setSelected(false);
-        setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
-                : SequenceAnnotationOrder.NONE);
+        setAnnotationSortOrder(
+                newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+                        : SequenceAnnotationOrder.NONE);
         sortAnnotations_actionPerformed();
       }
     });
     colourTextMenuItem = new JCheckBoxMenuItem(
-            MessageManager
-            .getString("label.colour_text"));
+            MessageManager.getString("label.colour_text"));
     colourTextMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -726,8 +680,8 @@ public class GAlignFrame extends JInternalFrame
 
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -740,8 +694,8 @@ public class GAlignFrame extends JInternalFrame
 
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -752,17 +706,6 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 
-    conservationMenuItem.setText(MessageManager
-            .getString("action.by_conservation"));
-    conservationMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        conservationMenuItem_actionPerformed();
-      }
-    });
-
     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
     wrapMenuItem.addActionListener(new ActionListener()
     {
@@ -775,8 +718,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -801,8 +744,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.find_tip")));
     al = new ActionListener()
@@ -815,19 +758,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 
-    abovePIDThreshold.setText(MessageManager
-            .getString("label.above_identity_threshold"));
-    abovePIDThreshold.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        abovePIDThreshold_actionPerformed();
-      }
-    });
-
-    showSeqFeatures.setText(MessageManager
-            .getString("label.show_sequence_features"));
+    showSeqFeatures.setText(
+            MessageManager.getString("label.show_sequence_features"));
     showSeqFeatures.addActionListener(new ActionListener()
     {
       @Override
@@ -842,8 +774,8 @@ public class GAlignFrame extends JInternalFrame
      * void actionPerformed(ActionEvent actionEvent) {
      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
      */
-    showDbRefsMenuitem.setText(MessageManager
-            .getString("label.show_database_refs"));
+    showDbRefsMenuitem
+            .setText(MessageManager.getString("label.show_database_refs"));
     showDbRefsMenuitem.addActionListener(new ActionListener()
     {
 
@@ -854,8 +786,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    showNpFeatsMenuitem.setText(MessageManager
-            .getString("label.show_non_positional_features"));
+    showNpFeatsMenuitem.setText(
+            MessageManager.getString("label.show_non_positional_features"));
     showNpFeatsMenuitem.addActionListener(new ActionListener()
     {
 
@@ -866,8 +798,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    showGroupConservation.setText(MessageManager
-            .getString("label.group_conservation"));
+    showGroupConservation
+            .setText(MessageManager.getString("label.group_conservation"));
     showGroupConservation.addActionListener(new ActionListener()
     {
 
@@ -879,8 +811,8 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
-    showGroupConsensus.setText(MessageManager
-            .getString("label.group_consensus"));
+    showGroupConsensus
+            .setText(MessageManager.getString("label.group_consensus"));
     showGroupConsensus.addActionListener(new ActionListener()
     {
 
@@ -891,8 +823,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    showConsensusHistogram.setText(MessageManager
-            .getString("label.show_consensus_histogram"));
+    showConsensusHistogram.setText(
+            MessageManager.getString("label.show_consensus_histogram"));
     showConsensusHistogram.addActionListener(new ActionListener()
     {
 
@@ -903,8 +835,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    showSequenceLogo.setText(MessageManager
-            .getString("label.show_consensus_logo"));
+    showSequenceLogo
+            .setText(MessageManager.getString("label.show_consensus_logo"));
     showSequenceLogo.addActionListener(new ActionListener()
     {
 
@@ -915,8 +847,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    normaliseSequenceLogo.setText(MessageManager
-            .getString("label.norm_consensus_logo"));
+    normaliseSequenceLogo
+            .setText(MessageManager.getString("label.norm_consensus_logo"));
     normaliseSequenceLogo.addActionListener(new ActionListener()
     {
 
@@ -927,8 +859,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    applyAutoAnnotationSettings.setText(MessageManager
-            .getString("label.apply_all_groups"));
+    applyAutoAnnotationSettings
+            .setText(MessageManager.getString("label.apply_all_groups"));
     applyAutoAnnotationSettings.setState(false);
     applyAutoAnnotationSettings.setVisible(true);
     applyAutoAnnotationSettings.addActionListener(new ActionListener()
@@ -947,8 +879,8 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("label.show_last"));
     buttonGroup.add(showAutoFirst);
     buttonGroup.add(showAutoLast);
-    final boolean autoFirst = 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()
@@ -973,8 +905,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -997,9 +929,9 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem createGroup = new JMenuItem(
-            MessageManager.getString("action.create_groups"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            MessageManager.getString("action.create_group"));
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -1012,9 +944,10 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem unGroup = new JMenuItem(
             MessageManager.getString("action.remove_group"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask()
-            | KeyEvent.SHIFT_MASK, false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.SHIFT_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1026,8 +959,8 @@ public class GAlignFrame extends JInternalFrame
     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 
     copy.setText(MessageManager.getString("action.copy"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 
     al = new ActionListener()
     {
@@ -1040,8 +973,8 @@ public class GAlignFrame extends JInternalFrame
     addMenuActionAndAccelerator(keyStroke, copy, al);
 
     cut.setText(MessageManager.getString("action.cut"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -1066,9 +999,10 @@ public class GAlignFrame extends JInternalFrame
     pasteMenu.setText(MessageManager.getString("action.paste"));
     JMenuItem pasteNew = new JMenuItem(
             MessageManager.getString("label.to_new_alignment"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask()
-            | KeyEvent.SHIFT_MASK, false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.SHIFT_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1081,8 +1015,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem pasteThis = new JMenuItem(
             MessageManager.getString("label.to_this_alignment"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -1102,8 +1036,8 @@ public class GAlignFrame extends JInternalFrame
         createPNG(null);
       }
     });
-    createPNG.setActionCommand(MessageManager
-            .getString("label.save_png_image"));
+    createPNG.setActionCommand(
+            MessageManager.getString("label.save_png_image"));
 
     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
     font.addActionListener(new ActionListener()
@@ -1114,8 +1048,8 @@ public class GAlignFrame extends JInternalFrame
         font_actionPerformed(e);
       }
     });
-    seqLimits.setText(MessageManager
-            .getString("label.show_sequence_limits"));
+    seqLimits.setText(
+            MessageManager.getString("label.show_sequence_limits"));
     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
     seqLimits.addActionListener(new ActionListener()
     {
@@ -1147,8 +1081,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem loadTreeMenuItem = new JMenuItem(
             MessageManager.getString("label.load_associated_tree"));
-    loadTreeMenuItem.setActionCommand(MessageManager
-            .getString("label.load_tree_for_sequence_set"));
+    loadTreeMenuItem.setActionCommand(
+            MessageManager.getString("label.load_tree_for_sequence_set"));
     loadTreeMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1192,8 +1126,8 @@ public class GAlignFrame extends JInternalFrame
     });
     centreColumnLabelsMenuItem.setVisible(true);
     centreColumnLabelsMenuItem.setState(false);
-    centreColumnLabelsMenuItem.setText(MessageManager
-            .getString("label.centre_column_labels"));
+    centreColumnLabelsMenuItem.setText(
+            MessageManager.getString("label.centre_column_labels"));
     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1204,8 +1138,8 @@ public class GAlignFrame extends JInternalFrame
     });
     followHighlightMenuItem.setVisible(true);
     followHighlightMenuItem.setState(true);
-    followHighlightMenuItem.setText(MessageManager
-            .getString("label.automatic_scrolling"));
+    followHighlightMenuItem
+            .setText(MessageManager.getString("label.automatic_scrolling"));
     followHighlightMenuItem.addActionListener(new ActionListener()
     {
 
@@ -1217,27 +1151,6 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
-    modifyPID = new JMenuItem(
-            MessageManager.getString("label.modify_identity_threshold"));
-    modifyPID.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyPID_actionPerformed();
-      }
-    });
-    modifyConservation.setText(MessageManager
-            .getString("label.modify_conservation_threshold"));
-    modifyConservation.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyConservation_actionPerformed();
-      }
-    });
-
     sortByTreeMenu
             .setText(MessageManager.getString("action.by_tree_order"));
     sort.setText(MessageManager.getString("action.sort"));
@@ -1246,7 +1159,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void menuSelected(MenuEvent e)
       {
-        buildTreeMenu();
+        buildTreeSortMenu();
       }
 
       @Override
@@ -1259,8 +1172,8 @@ public class GAlignFrame extends JInternalFrame
       {
       }
     });
-    sortByAnnotScore.setText(MessageManager
-            .getString("label.sort_by_score"));
+    sortByAnnotScore
+            .setText(MessageManager.getString("label.sort_by_score"));
     sort.add(sortByAnnotScore);
     sort.addMenuListener(new javax.swing.event.MenuListener()
     {
@@ -1284,11 +1197,11 @@ public class GAlignFrame extends JInternalFrame
     sortByAnnotScore.setVisible(false);
 
     calculateTree
-            .setText(MessageManager.getString("action.calculate_tree"));
+            .setText(MessageManager.getString("action.calculate_tree_pca"));
 
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
-    padGapsMenuitem.setState(jalview.bin.Cache
-            .getDefault("PAD_GAPS", false));
+    padGapsMenuitem
+            .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
       @Override
@@ -1308,8 +1221,8 @@ public class GAlignFrame extends JInternalFrame
         vamsasStore_actionPerformed(e);
       }
     });
-    showTranslation.setText(MessageManager
-            .getString("label.translate_cDNA"));
+    showTranslation
+            .setText(MessageManager.getString("label.translate_cDNA"));
     showTranslation.addActionListener(new ActionListener()
     {
       @Override
@@ -1327,8 +1240,8 @@ public class GAlignFrame extends JInternalFrame
         showReverse_actionPerformed(false);
       }
     });
-    showReverseComplement.setText(MessageManager
-            .getString("label.reverse_complement"));
+    showReverseComplement
+            .setText(MessageManager.getString("label.reverse_complement"));
     showReverseComplement.addActionListener(new ActionListener()
     {
       @Override
@@ -1355,8 +1268,8 @@ public class GAlignFrame extends JInternalFrame
     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
 
     runGroovy.setText(MessageManager.getString("label.run_groovy"));
-    runGroovy.setToolTipText(MessageManager
-            .getString("label.run_groovy_tip"));
+    runGroovy.setToolTipText(
+            MessageManager.getString("label.run_groovy_tip"));
     runGroovy.addActionListener(new ActionListener()
     {
       @Override
@@ -1397,10 +1310,20 @@ public class GAlignFrame extends JInternalFrame
         associatedData_actionPerformed(e);
       }
     });
-    autoCalculate.setText(MessageManager
-            .getString("label.autocalculate_consensus"));
-    autoCalculate.setState(jalview.bin.Cache.getDefault(
-            "AUTO_CALC_CONSENSUS", true));
+    loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
+    loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
+    loadVcf.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        loadVcf_actionPerformed();
+      }
+    });
+    autoCalculate.setText(
+            MessageManager.getString("label.autocalculate_consensus"));
+    autoCalculate.setState(
+            jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
     {
       @Override
@@ -1409,12 +1332,10 @@ public class GAlignFrame extends JInternalFrame
         autoCalculate_actionPerformed(e);
       }
     });
-    sortByTree.setText(MessageManager
-            .getString("label.sort_alignment_new_tree"));
-    sortByTree
-            .setToolTipText("<html>"
-                    + MessageManager
-                            .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
+    sortByTree.setText(
+            MessageManager.getString("label.sort_alignment_new_tree"));
+    sortByTree.setToolTipText("<html>" + MessageManager.getString(
+            "label.enable_automatically_sort_alignment_when_open_new_tree"));
     sortByTree
             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
     sortByTree.addActionListener(new ActionListener()
@@ -1426,12 +1347,11 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    listenToViewSelections.setText(MessageManager
-            .getString("label.listen_for_selections"));
+    listenToViewSelections.setText(
+            MessageManager.getString("label.listen_for_selections"));
     listenToViewSelections
-            .setToolTipText("<html>"
-                    + MessageManager
-                            .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
+            .setToolTipText("<html>" + MessageManager.getString(
+                    "label.selections_mirror_selections_made_same_sequences_other_views"));
     listenToViewSelections.setState(false);
     listenToViewSelections.addActionListener(new ActionListener()
     {
@@ -1497,8 +1417,8 @@ public class GAlignFrame extends JInternalFrame
     statusPanel.setLayout(new GridLayout());
     JMenuItem showAllSeqs = new JMenuItem(
             MessageManager.getString("label.all_sequences"));
-    showAllSeqs.setToolTipText(MessageManager
-            .getString("label.toggle_sequence_visibility"));
+    showAllSeqs.setToolTipText(
+            MessageManager.getString("label.toggle_sequence_visibility"));
     showAllSeqs.addActionListener(new ActionListener()
     {
       @Override
@@ -1509,8 +1429,8 @@ public class GAlignFrame extends JInternalFrame
     });
     JMenuItem showAllColumns = new JMenuItem(
             MessageManager.getString("label.all_columns"));
-    showAllColumns.setToolTipText(MessageManager
-            .getString("label.toggle_columns_visibility"));
+    showAllColumns.setToolTipText(
+            MessageManager.getString("label.toggle_columns_visibility"));
     showAllColumns.addActionListener(new ActionListener()
     {
       @Override
@@ -1522,8 +1442,8 @@ public class GAlignFrame extends JInternalFrame
     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
     JMenuItem hideSelSequences = new JMenuItem(
             MessageManager.getString("label.selected_sequences"));
-    hideSelSequences.setToolTipText(MessageManager
-            .getString("label.toggle_sequence_visibility"));
+    hideSelSequences.setToolTipText(
+            MessageManager.getString("label.toggle_sequence_visibility"));
     hideSelSequences.addActionListener(new ActionListener()
     {
       @Override
@@ -1534,8 +1454,8 @@ public class GAlignFrame extends JInternalFrame
     });
     JMenuItem hideSelColumns = new JMenuItem(
             MessageManager.getString("label.selected_columns"));
-    hideSelColumns.setToolTipText(MessageManager
-            .getString("label.toggle_columns_visibility"));
+    hideSelColumns.setToolTipText(
+            MessageManager.getString("label.toggle_columns_visibility"));
     hideSelColumns.addActionListener(new ActionListener()
     {
       @Override
@@ -1577,8 +1497,8 @@ public class GAlignFrame extends JInternalFrame
         showAllhidden_actionPerformed(e);
       }
     });
-    hiddenMarkers.setText(MessageManager
-            .getString("action.show_hidden_markers"));
+    hiddenMarkers.setText(
+            MessageManager.getString("action.show_hidden_markers"));
     hiddenMarkers.addActionListener(new ActionListener()
     {
       @Override
@@ -1590,9 +1510,10 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask()
-            | KeyEvent.ALT_MASK, false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.ALT_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1653,8 +1574,8 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -1678,8 +1599,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -1696,8 +1617,9 @@ public class GAlignFrame extends JInternalFrame
 
     formatMenu.setText(MessageManager.getString("action.format"));
     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
-    idRightAlign.setText(MessageManager
-            .getString("label.right_align_sequence_id"));
+
+    idRightAlign.setText(
+            MessageManager.getString("label.right_align_sequence_id"));
     idRightAlign.addActionListener(new ActionListener()
     {
       @Override
@@ -1755,8 +1677,8 @@ public class GAlignFrame extends JInternalFrame
     });
     JMenuItem selectHighlighted = new JMenuItem(
             MessageManager.getString("action.select_highlighted_columns"));
-    selectHighlighted.setToolTipText(MessageManager
-            .getString("tooltip.select_highlighted_columns"));
+    selectHighlighted.setToolTipText(
+            MessageManager.getString("tooltip.select_highlighted_columns"));
     al = new ActionListener()
     {
       @Override
@@ -1800,6 +1722,7 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(loadTreeMenuItem);
     fileMenu.add(associatedData);
+    fileMenu.add(loadVcf);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
 
@@ -1875,7 +1798,6 @@ public class GAlignFrame extends JInternalFrame
     autoAnnMenu.add(showGroupConsensus);
     annotationsMenu.add(autoAnnMenu);
 
-
     sort.add(sortIDMenuItem);
     sort.add(sortLengthMenuItem);
     sort.add(sortGroupMenuItem);
@@ -1885,7 +1807,6 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
-    calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
     calculateMenu.add(showReverse);
@@ -1947,6 +1868,10 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
+  protected void loadVcf_actionPerformed()
+  {
+  }
+
   /**
    * Constructs the entries on the Colour menu (but does not add them to the
    * menu).
@@ -1960,12 +1885,12 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        applyToAllGroups_actionPerformed();
+        applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
       }
     });
 
-    textColour = new JRadioButtonMenuItem(
-            MessageManager.getString("action.set_text_colour"));
+    textColour = new JMenuItem(
+            MessageManager.getString("label.text_colour"));
     textColour.addActionListener(new ActionListener()
     {
       @Override
@@ -1982,7 +1907,8 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed();
+        conservationMenuItem_actionPerformed(
+                conservationMenuItem.isSelected());
       }
     });
 
@@ -1993,7 +1919,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDThreshold_actionPerformed();
+        abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
       }
     });
     modifyPID = new JMenuItem(
@@ -2006,8 +1932,7 @@ public class GAlignFrame extends JInternalFrame
         modifyPID_actionPerformed();
       }
     });
-    modifyConservation = new JMenuItem(
-            MessageManager
+    modifyConservation = new JMenuItem(MessageManager
             .getString("label.modify_conservation_threshold"));
     modifyConservation.addActionListener(new ActionListener()
     {
@@ -2365,27 +2290,11 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void PCAMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
   }
 
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void conservationMenuItem_actionPerformed()
+  protected void conservationMenuItem_actionPerformed(boolean selected)
   {
   }
 
@@ -2401,7 +2310,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void abovePIDThreshold_actionPerformed()
+  protected void abovePIDThreshold_actionPerformed(boolean selected)
   {
   }
 
@@ -2441,7 +2350,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void applyToAllGroups_actionPerformed()
+  protected void applyToAllGroups_actionPerformed(boolean selected)
   {
   }
 
@@ -2669,7 +2578,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void buildTreeMenu()
+  public void buildTreeSortMenu()
   {
 
   }