X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=507bbc8fb1589cfe93730298937174b2be687844;hb=16fb72caf8587ec0434c6413afdd956b3b111ec4;hp=a320a9c56a3beee37ad63f4b2fab7fa10935e6ad;hpb=ca0a70b02a67f842a195319414d241ffa336656b;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index a320a9c..507bbc8 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -25,6 +25,8 @@ import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
+import jalview.hmmer.HmmerCommand;
+import jalview.io.FileFormatException;
 import jalview.io.FileFormats;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -40,6 +42,7 @@ import java.awt.event.FocusEvent;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.io.IOException;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -65,10 +68,30 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem closeMenuItem = new JMenuItem();
 
-  protected JMenu colourMenu = new JMenu();
-
   protected JMenu webService = new JMenu();
 
+  protected JMenu hmmerMenu = new JMenu();
+
+  protected JMenu hmmAlign = new JMenu();
+
+  protected JMenuItem hmmAlignRun = new JMenuItem();
+
+  protected JMenuItem hmmAlignSettings = new JMenuItem();
+
+  protected JMenu hmmSearch = new JMenu();
+
+  protected JMenuItem hmmSearchRun = new JMenuItem();
+
+  protected JMenuItem hmmSearchSettings = new JMenuItem();
+
+  protected JMenuItem addDatabase = new JMenuItem();
+
+  protected JMenu hmmBuild = new JMenu();
+
+  protected JMenuItem hmmBuildRun = new JMenuItem();
+
+  protected JMenuItem hmmBuildSettings = new JMenuItem();
+
   protected JMenuItem webServiceNoServices;
 
   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
@@ -81,8 +104,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu outputTextboxMenu = new JMenu();
 
-  protected JRadioButtonMenuItem textColour;
-
   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
@@ -93,14 +114,10 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem redoMenuItem = new JMenuItem();
 
-  protected JCheckBoxMenuItem conservationMenuItem;
-
   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 
-  protected JCheckBoxMenuItem abovePIDThreshold;
-
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 
   JMenuItem copy = new JMenuItem();
@@ -109,8 +126,6 @@ public class GAlignFrame extends JInternalFrame
 
   JMenu pasteMenu = new JMenu();
 
-  protected JCheckBoxMenuItem applyToAllGroups;
-
   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
@@ -119,17 +134,27 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 
-  protected JMenuItem modifyPID;
+  protected JCheckBoxMenuItem applyToAllGroups;
+
+  protected JMenu colourMenu = new JMenu();
+
+  protected JMenuItem textColour;
+
+  protected JCheckBoxMenuItem conservationMenuItem;
 
   protected JMenuItem modifyConservation;
 
+  protected JCheckBoxMenuItem abovePIDThreshold;
+
+  protected JMenuItem modifyPID;
+
   protected JMenuItem annotationColour;
 
   protected JMenu sortByTreeMenu = new JMenu();
 
   protected JMenu sort = new JMenu();
 
-  protected JMenu calculateTree = new JMenu();
+  protected JMenuItem calculateTree = new JMenuItem();
 
   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 
@@ -147,6 +172,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem runGroovy = new JMenuItem();
 
+  protected JMenuItem loadVcf;
+
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
@@ -193,13 +220,19 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 
+  protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
+
   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 
   private SequenceAnnotationOrder annotationSortOrder;
 
   private boolean showAutoCalculatedAbove = false;
 
-  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 
   private SplitContainerI splitFrame;
 
@@ -247,7 +280,8 @@ public class GAlignFrame extends JInternalFrame
   private void jbInit() throws Exception
   {
     initColourMenu();
-
+    initHMMERMenu();
+  
     JMenuItem saveAs = new JMenuItem(
             MessageManager.getString("action.save_as"));
     ActionListener al = new ActionListener()
@@ -258,16 +292,17 @@ public class GAlignFrame extends JInternalFrame
         saveAs_actionPerformed(e);
       }
     };
-
+  
     // 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
@@ -277,7 +312,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
-
+  
     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
     JMenu annotationsMenu = new JMenu(
@@ -287,10 +322,24 @@ public class GAlignFrame extends JInternalFrame
     JMenu calculateMenu = new JMenu(
             MessageManager.getString("action.calculate"));
     webService.setText(MessageManager.getString("action.web_service"));
+    hmmerMenu.setText(MessageManager.getString("action.hmmer"));
+    hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+    hmmerMenu.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmerMenu_actionPerformed(e);
+      }
+    });
+    hmmerMenu.add(hmmBuild);
+    hmmerMenu.add(hmmAlign);
+    hmmerMenu.add(hmmSearch);
+
     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
@@ -300,7 +349,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
-
+  
     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.deselect_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
@@ -313,11 +362,11 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
-
+  
     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
@@ -327,7 +376,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
-
+  
     JMenuItem grpsFromSelection = new JMenuItem(
             MessageManager.getString("action.make_groups_selection"));
     grpsFromSelection.addActionListener(new ActionListener()
@@ -340,8 +389,8 @@ 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 +401,8 @@ 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
@@ -363,11 +412,11 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
-
+  
     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
@@ -377,11 +426,11 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
-
+  
     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
@@ -391,12 +440,13 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
-
+  
     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
@@ -406,7 +456,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
-
+  
     JMenuItem justifyLeftMenuItem = new JMenuItem(
             MessageManager.getString("action.left_justify_alignment"));
     justifyLeftMenuItem.addActionListener(new ActionListener()
@@ -447,8 +497,8 @@ 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()
     {
@@ -498,11 +548,11 @@ public class GAlignFrame extends JInternalFrame
         sortGroupMenuItem_actionPerformed(e);
       }
     });
-
+  
     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
@@ -512,7 +562,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
-
+  
     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
             MessageManager.getString("action.pairwise_alignment"));
     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
@@ -523,72 +573,23 @@ 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));
     statusBar.setBackground(Color.white);
     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 +598,8 @@ 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 +611,8 @@ 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 +622,8 @@ 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 +633,8 @@ 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 +652,9 @@ 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 +662,14 @@ 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 +677,14 @@ 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
@@ -690,7 +693,7 @@ public class GAlignFrame extends JInternalFrame
         colourTextMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem htmlMenuItem = new JMenuItem(
             MessageManager.getString("label.html"));
     htmlMenuItem.addActionListener(new ActionListener()
@@ -701,7 +704,7 @@ public class GAlignFrame extends JInternalFrame
         htmlMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem createBioJS = new JMenuItem(
             MessageManager.getString("label.biojs_html_export"));
     createBioJS.addActionListener(new java.awt.event.ActionListener()
@@ -712,7 +715,7 @@ public class GAlignFrame extends JInternalFrame
         bioJSMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem overviewMenuItem = new JMenuItem(
             MessageManager.getString("label.overview_window"));
     overviewMenuItem.addActionListener(new ActionListener()
@@ -723,11 +726,11 @@ public class GAlignFrame extends JInternalFrame
         overviewMenuItem_actionPerformed(e);
       }
     });
-
+  
     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
@@ -737,11 +740,11 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
-
+  
     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
@@ -751,7 +754,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
-
+  
     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
     wrapMenuItem.addActionListener(new ActionListener()
     {
@@ -761,11 +764,11 @@ public class GAlignFrame extends JInternalFrame
         wrapMenuItem_actionPerformed(e);
       }
     });
-
+  
     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
@@ -775,7 +778,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
-
+  
     renderGapsMenuItem
             .setText(MessageManager.getString("action.show_gaps"));
     renderGapsMenuItem.setState(true);
@@ -787,11 +790,11 @@ public class GAlignFrame extends JInternalFrame
         renderGapsMenuItem_actionPerformed(e);
       }
     });
-
+  
     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()
@@ -804,8 +807,9 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 
-    showSeqFeatures.setText(MessageManager
-            .getString("label.show_sequence_features"));
+    showSeqFeatures.setText(
+            MessageManager.getString("label.show_sequence_features"));
+
     showSeqFeatures.addActionListener(new ActionListener()
     {
       @Override
@@ -820,93 +824,93 @@ 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()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showDbRefs_actionPerformed(e);
       }
-
+  
     });
-    showNpFeatsMenuitem.setText(MessageManager
-            .getString("label.show_non_positional_features"));
+    showNpFeatsMenuitem.setText(
+            MessageManager.getString("label.show_non_positional_features"));
     showNpFeatsMenuitem.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showNpFeats_actionPerformed(e);
       }
-
+  
     });
-    showGroupConservation.setText(MessageManager
-            .getString("label.group_conservation"));
+    showGroupConservation
+            .setText(MessageManager.getString("label.group_conservation"));
     showGroupConservation.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showGroupConservation_actionPerformed(e);
       }
-
+  
     });
 
-    showGroupConsensus.setText(MessageManager
-            .getString("label.group_consensus"));
+    showGroupConsensus
+            .setText(MessageManager.getString("label.group_consensus"));
     showGroupConsensus.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showGroupConsensus_actionPerformed(e);
       }
-
+  
     });
-    showConsensusHistogram.setText(MessageManager
-            .getString("label.show_consensus_histogram"));
+    showConsensusHistogram.setText(
+            MessageManager.getString("label.show_consensus_histogram"));
     showConsensusHistogram.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showConsensusHistogram_actionPerformed(e);
       }
-
+  
     });
-    showSequenceLogo.setText(MessageManager
-            .getString("label.show_consensus_logo"));
+    showSequenceLogo
+            .setText(MessageManager.getString("label.show_consensus_logo"));
     showSequenceLogo.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showSequenceLogo_actionPerformed(e);
       }
-
+  
     });
-    normaliseSequenceLogo.setText(MessageManager
-            .getString("label.norm_consensus_logo"));
+    normaliseSequenceLogo
+            .setText(MessageManager.getString("label.norm_consensus_logo"));
     normaliseSequenceLogo.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         normaliseSequenceLogo_actionPerformed(e);
       }
-
+  
     });
-    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()
@@ -917,7 +921,7 @@ public class GAlignFrame extends JInternalFrame
         applyAutoAnnotationSettings_actionPerformed(e);
       }
     });
-
+  
     ButtonGroup buttonGroup = new ButtonGroup();
     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
             MessageManager.getString("label.show_first"));
@@ -925,8 +929,8 @@ 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()
@@ -948,11 +952,11 @@ public class GAlignFrame extends JInternalFrame
         sortAnnotations_actionPerformed();
       }
     });
-
+  
     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
@@ -962,7 +966,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
-
+  
     JMenuItem annotationColumn = new JMenuItem(
             MessageManager.getString("action.select_by_annotation"));
     annotationColumn.addActionListener(new ActionListener()
@@ -973,11 +977,11 @@ public class GAlignFrame extends JInternalFrame
         annotationColumn_actionPerformed(e);
       }
     });
-
+  
     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
@@ -987,12 +991,13 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, createGroup, al);
-
+  
     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
@@ -1002,10 +1007,10 @@ 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()
     {
@@ -1016,10 +1021,10 @@ 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
@@ -1029,7 +1034,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, cut, al);
-
+  
     JMenuItem delete = new JMenuItem(
             MessageManager.getString("action.delete"));
     delete.addActionListener(new ActionListener()
@@ -1040,37 +1045,52 @@ public class GAlignFrame extends JInternalFrame
         delete_actionPerformed(e);
       }
     });
-
+  
     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
       public void actionPerformed(ActionEvent e)
       {
-        pasteNew_actionPerformed(e);
+        try
+        {
+          pasteNew_actionPerformed(e);
+        } catch (IOException | InterruptedException e1)
+        {
+          // TODO Auto-generated catch block
+          e1.printStackTrace();
+        }
       }
     };
     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
-
+  
     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
       public void actionPerformed(ActionEvent e)
       {
-        pasteThis_actionPerformed(e);
+        try
+        {
+          pasteThis_actionPerformed(e);
+        } catch (IOException | InterruptedException e1)
+        {
+          // TODO Auto-generated catch block
+          e1.printStackTrace();
+        }
       }
     };
     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
-
+  
     JMenuItem createPNG = new JMenuItem("PNG");
     createPNG.addActionListener(new ActionListener()
     {
@@ -1080,9 +1100,8 @@ 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()
     {
@@ -1092,8 +1111,8 @@ 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()
     {
@@ -1112,7 +1131,7 @@ public class GAlignFrame extends JInternalFrame
         createEPS(null);
       }
     });
-
+  
     JMenuItem createSVG = new JMenuItem("SVG");
     createSVG.addActionListener(new ActionListener()
     {
@@ -1122,11 +1141,11 @@ public class GAlignFrame extends JInternalFrame
         createSVG(null);
       }
     });
-
+  
     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
@@ -1135,7 +1154,7 @@ public class GAlignFrame extends JInternalFrame
         loadTreeMenuItem_actionPerformed(e);
       }
     });
-
+  
     scaleAbove.setVisible(false);
     scaleAbove.setText(MessageManager.getString("action.scale_above"));
     scaleAbove.addActionListener(new ActionListener()
@@ -1170,8 +1189,8 @@ 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
@@ -1182,19 +1201,19 @@ 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()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         followHighlight_actionPerformed();
       }
-
+  
     });
-
+  
     sortByTreeMenu
             .setText(MessageManager.getString("action.by_tree_order"));
     sort.setText(MessageManager.getString("action.sort"));
@@ -1203,35 +1222,35 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void menuSelected(MenuEvent e)
       {
-        buildTreeMenu();
+        buildTreeSortMenu();
       }
-
+  
       @Override
       public void menuDeselected(MenuEvent e)
       {
       }
-
+  
       @Override
       public void menuCanceled(MenuEvent e)
       {
       }
     });
-    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()
     {
-
+  
       @Override
       public void menuCanceled(MenuEvent e)
       {
       }
-
+  
       @Override
       public void menuDeselected(MenuEvent e)
       {
       }
-
+  
       @Override
       public void menuSelected(MenuEvent e)
       {
@@ -1241,11 +1260,11 @@ 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
@@ -1265,8 +1284,8 @@ 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
@@ -1284,8 +1303,8 @@ 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
@@ -1294,7 +1313,7 @@ public class GAlignFrame extends JInternalFrame
         showReverse_actionPerformed(true);
       }
     });
-
+  
     JMenuItem extractScores = new JMenuItem(
             MessageManager.getString("label.extract_scores"));
     extractScores.addActionListener(new ActionListener()
@@ -1307,13 +1326,13 @@ public class GAlignFrame extends JInternalFrame
     });
     extractScores.setVisible(true);
     // JBPNote: TODO: make gui for regex based score extraction
-
+  
     // 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.setToolTipText(
+            MessageManager.getString("label.run_groovy_tip"));
     runGroovy.addActionListener(new ActionListener()
     {
       @Override
@@ -1322,7 +1341,7 @@ public class GAlignFrame extends JInternalFrame
         runGroovy_actionPerformed();
       }
     });
-
+  
     JMenuItem openFeatureSettings = new JMenuItem(
             MessageManager.getString("action.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
@@ -1343,7 +1362,7 @@ public class GAlignFrame extends JInternalFrame
         fetchSequence_actionPerformed(e);
       }
     });
-
+  
     JMenuItem associatedData = new JMenuItem(
             MessageManager.getString("label.load_features_annotations"));
     associatedData.addActionListener(new ActionListener()
@@ -1351,13 +1370,30 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        associatedData_actionPerformed(e);
+        try
+        {
+          associatedData_actionPerformed(e);
+        } catch (IOException | InterruptedException e1)
+        {
+          // TODO Auto-generated catch block
+          e1.printStackTrace();
+        }
       }
     });
-    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
@@ -1366,12 +1402,10 @@ 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()
@@ -1383,12 +1417,11 @@ 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()
     {
@@ -1398,7 +1431,7 @@ public class GAlignFrame extends JInternalFrame
         listenToViewSelections_actionPerformed(e);
       }
     });
-
+  
     JMenu addSequenceMenu = new JMenu(
             MessageManager.getString("label.add_sequences"));
     JMenuItem addFromFile = new JMenuItem(
@@ -1454,8 +1487,8 @@ 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
@@ -1466,8 +1499,8 @@ 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
@@ -1479,8 +1512,8 @@ 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
@@ -1491,8 +1524,8 @@ 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
@@ -1534,8 +1567,8 @@ 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
@@ -1544,12 +1577,13 @@ public class GAlignFrame extends JInternalFrame
         hiddenMarkers_actionPerformed(e);
       }
     });
-
+  
     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
@@ -1559,7 +1593,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
-
+  
     showComplementMenuItem.setVisible(false);
     showComplementMenuItem.addActionListener(new ActionListener()
     {
@@ -1569,7 +1603,7 @@ public class GAlignFrame extends JInternalFrame
         showComplement_actionPerformed(showComplementMenuItem.getState());
       }
     });
-
+  
     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
     {
       @Override
@@ -1590,7 +1624,7 @@ public class GAlignFrame extends JInternalFrame
           tabbedPane_mousePressed(e);
         }
       }
-
+  
       @Override
       public void mouseReleased(MouseEvent e)
       {
@@ -1608,10 +1642,10 @@ public class GAlignFrame extends JInternalFrame
         tabbedPane_focusGained(e);
       }
     });
-
+  
     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
@@ -1621,7 +1655,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, save, al);
-
+  
     reload.setEnabled(false);
     reload.setText(MessageManager.getString("action.reload"));
     reload.addActionListener(new ActionListener()
@@ -1632,11 +1666,11 @@ public class GAlignFrame extends JInternalFrame
         reload_actionPerformed(e);
       }
     });
-
+  
     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
@@ -1646,15 +1680,16 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, newView, al);
-
+  
     tabbedPane.setToolTipText("<html><i>"
             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
             + "</i></html>");
-
+  
     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
@@ -1663,7 +1698,7 @@ public class GAlignFrame extends JInternalFrame
         idRightAlign_actionPerformed(e);
       }
     });
-
+  
     gatherViews.setEnabled(false);
     gatherViews.setText(MessageManager.getString("action.gather_views"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
@@ -1676,7 +1711,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
-
+  
     expandViews.setEnabled(false);
     expandViews.setText(MessageManager.getString("action.expand_views"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
@@ -1689,7 +1724,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, expandViews, al);
-
+  
     JMenuItem pageSetup = new JMenuItem(
             MessageManager.getString("action.page_setup"));
     pageSetup.addActionListener(new ActionListener()
@@ -1712,8 +1747,8 @@ 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
@@ -1722,12 +1757,87 @@ public class GAlignFrame extends JInternalFrame
         selectHighlightedColumns_actionPerformed(actionEvent);
       }
     };
+    hmmBuildRun.setText(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmbuild"));
+    hmmBuildRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmBuildRun_actionPerformed();
+      }
+    });
+    hmmBuildSettings.setText(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmBuildSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmBuildSettings_actionPerformed();
+      }
+    });
+    hmmAlignRun.setText(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmalign"));
+    hmmAlignRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmAlignRun_actionPerformed();
+      }
+    });
+    hmmAlignSettings.setText(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmAlignSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmAlignSettings_actionPerformed();
+      }
+    });
+    hmmSearchRun.setText(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmsearch"));
+    hmmSearchRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmSearchRun_actionPerformed();
+      }
+    });
+    addDatabase.setText(MessageManager.getString("label.add_database"));
+    addDatabase.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          addDatabase_actionPerformed();
+        } catch (IOException e1)
+        {
+          e1.printStackTrace();
+        }
+      }
+    });
+    hmmSearchSettings.setText(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmSearchSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmSearchSettings_actionPerformed();
+      }
+    });
     selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
     JMenu autoAnnMenu = new JMenu(
             MessageManager.getString("label.autocalculated_annotation"));
-
+  
     JMenu exportImageMenu = new JMenu(
             MessageManager.getString("label.export_image"));
     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
@@ -1740,7 +1850,8 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
-
+    alignFrameMenuBar.add(hmmerMenu);
+  
     fileMenu.add(fetchSequence);
     fileMenu.add(addSequenceMenu);
     fileMenu.add(reload);
@@ -1757,9 +1868,10 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(loadTreeMenuItem);
     fileMenu.add(associatedData);
+    fileMenu.add(loadVcf);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
-
+  
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
     editMenu.add(undoMenuItem);
@@ -1781,7 +1893,7 @@ public class GAlignFrame extends JInternalFrame
     // editMenu.add(justifyRightMenuItem);
     // editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
-
+  
     showMenu.add(showAllColumns);
     showMenu.add(showAllSeqs);
     showMenu.add(showAllhidden);
@@ -1809,7 +1921,7 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(alignmentProperties);
     viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
-
+  
     annotationsMenu.add(annotationPanelMenuItem);
     annotationsMenu.addSeparator();
     annotationsMenu.add(showAllAlAnnotations);
@@ -1832,7 +1944,6 @@ public class GAlignFrame extends JInternalFrame
     autoAnnMenu.add(showGroupConsensus);
     annotationsMenu.add(autoAnnMenu);
 
-
     sort.add(sortIDMenuItem);
     sort.add(sortLengthMenuItem);
     sort.add(sortGroupMenuItem);
@@ -1842,7 +1953,6 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
-    calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
     calculateMenu.add(showReverse);
@@ -1855,7 +1965,7 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(extractScores);
     calculateMenu.addSeparator();
     calculateMenu.add(runGroovy);
-
+  
     webServiceNoServices = new JMenuItem(
             MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
@@ -1870,7 +1980,7 @@ 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);
-
+  
     formatMenu.add(font);
     formatMenu.addSeparator();
     formatMenu.add(wrapMenuItem);
@@ -1904,6 +2014,46 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
+  public void hmmerMenu_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  /**
+   * Constructs the entries on the HMMER menu (does not add them to the menu).
+   */
+  protected void initHMMERMenu()
+  {
+    hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
+    hmmAlignSettings = new JMenuItem(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmalign"));
+    hmmAlign.add(hmmAlignSettings);
+    hmmAlign.add(hmmAlignRun);
+    hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
+    hmmBuildSettings = new JMenuItem(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmbuild"));
+    hmmBuild.add(hmmBuildSettings);
+    hmmBuild.add(hmmBuildRun);
+    hmmSearch = new JMenu(MessageManager.getString("label.hmmsearch"));
+    hmmSearchSettings = new JMenuItem(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmsearch"));
+    addDatabase = new JMenuItem(
+            MessageManager.getString("label.add_database"));
+    hmmSearch.add(hmmSearchSettings);
+    hmmSearch.add(hmmSearchRun);
+    hmmSearch.add(addDatabase);
+  }
+
+  protected void loadVcf_actionPerformed()
+  {
+  }
+
   /**
    * Constructs the entries on the Colour menu (but does not add them to the
    * menu).
@@ -1917,12 +2067,12 @@ 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
@@ -1939,7 +2089,8 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed();
+        conservationMenuItem_actionPerformed(
+                conservationMenuItem.isSelected());
       }
     });
 
@@ -1950,7 +2101,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDThreshold_actionPerformed();
+        abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
       }
     });
     modifyPID = new JMenuItem(
@@ -1963,8 +2114,7 @@ public class GAlignFrame extends JInternalFrame
         modifyPID_actionPerformed();
       }
     });
-    modifyConservation = new JMenuItem(
-            MessageManager
+    modifyConservation = new JMenuItem(MessageManager
             .getString("label.modify_conservation_threshold"));
     modifyConservation.addActionListener(new ActionListener()
     {
@@ -2322,27 +2472,11 @@ 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)
   {
   }
 
@@ -2358,7 +2492,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void abovePIDThreshold_actionPerformed()
+  protected void abovePIDThreshold_actionPerformed(boolean selected)
   {
   }
 
@@ -2391,14 +2525,45 @@ public class GAlignFrame extends JInternalFrame
   }
 
   protected void pasteNew_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
   }
 
   protected void pasteThis_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
+  {
+  }
+
+  protected void applyToAllGroups_actionPerformed(boolean selected)
+  {
+  }
+
+  protected void hmmBuildRun_actionPerformed()
+  {
+  }
+
+  protected void hmmSearchRun_actionPerformed()
+  {
+  }
+
+  protected void addDatabase_actionPerformed()
+          throws FileFormatException, IOException
+  {
+  }
+
+  protected void hmmAlignRun_actionPerformed()
+  {
+  }
+
+  protected void hmmBuildSettings_actionPerformed()
+  {
+  }
+
+  protected void hmmSearchSettings_actionPerformed()
   {
   }
 
-  protected void applyToAllGroups_actionPerformed()
+  protected void hmmAlignSettings_actionPerformed()
   {
   }
 
@@ -2517,6 +2682,7 @@ public class GAlignFrame extends JInternalFrame
   }
 
   public void associatedData_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
 
   }
@@ -2626,7 +2792,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void buildTreeMenu()
+  public void buildTreeSortMenu()
   {
 
   }