X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=25db31aab3246021583926c1e9b1902cd7c4daaf;hb=586ade46bdcd05ff028a1cff82c3c527326d28ec;hp=6685c67c589abf56cf914af2d41a4089f1a0f1c9;hpb=17e4ea278bc9a5fb280db1252ce78b7a295215f5;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6685c67..25db31a 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -20,18 +20,6 @@
  */
 package jalview.jbgui;
 
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.GeneticCodeI;
-import jalview.analysis.GeneticCodes;
-import jalview.api.SplitContainerI;
-import jalview.bin.Cache;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.Preferences;
-import jalview.io.FileFormats;
-import jalview.schemes.ResidueColourScheme;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.GridLayout;
@@ -39,9 +27,11 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusAdapter;
 import java.awt.event.FocusEvent;
+import java.awt.event.InputEvent;
 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;
 
@@ -61,6 +51,21 @@ import javax.swing.event.ChangeEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.GeneticCodeI;
+import jalview.analysis.GeneticCodes;
+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.schemes.ResidueColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+
 @SuppressWarnings("serial")
 public class GAlignFrame extends JInternalFrame
 {
@@ -70,9 +75,11 @@ public class GAlignFrame extends JInternalFrame
 
   public JMenu webService = new JMenu();// BH 2019 was protected, but not
                                         // sufficient for AlignFrame thread run
+    // JBP - followed suite for these other service related GUI elements.
+    // TODO: check we really need these to be public
+  public JMenu hmmerMenu = new JMenu();
 
-  public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
-                                        // sufficient for AlignFrame thread run
+  public JMenuItem webServiceNoServices;
 
   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
 
@@ -202,6 +209,12 @@ 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();
 
   protected JMenuItem openFeatureSettings;
@@ -220,7 +233,8 @@ public class GAlignFrame extends JInternalFrame
     {
 
       // for Web-page embedding using id=align-frame-div
-      setName("jalview-alignment");
+      setName(Platform.getAppID("alignment"));
+
 
       jbInit();
       setJMenuBar(alignFrameMenuBar);
@@ -262,7 +276,7 @@ public class GAlignFrame extends JInternalFrame
   private void jbInit() throws Exception
   {
     initColourMenu();
-
+  
     JMenuItem saveAs = new JMenuItem(
             MessageManager.getString("action.save_as"));
     ActionListener al = new ActionListener()
@@ -273,17 +287,14 @@ public class GAlignFrame extends JInternalFrame
         saveAs_actionPerformed();
       }
     };
-
+  
     // FIXME getDefaultToolkit throws an exception in Headless mode
-    KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
-                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+    KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Platform.SHORTCUT_KEY_MASK | InputEvent.SHIFT_DOWN_MASK,
             false);
     addMenuActionAndAccelerator(keyStroke, saveAs, al);
-
+  
     closeMenuItem.setText(MessageManager.getString("action.close"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -293,7 +304,7 @@ 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(
@@ -303,10 +314,13 @@ public class GAlignFrame extends JInternalFrame
     JMenu calculateMenu = new JMenu(
             MessageManager.getString("action.calculate"));
     webService.setText(MessageManager.getString("action.web_service"));
+
+    initHMMERMenu();
+
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -316,7 +330,7 @@ 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);
@@ -329,11 +343,11 @@ 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,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -343,7 +357,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
-
+  
     JMenuItem grpsFromSelection = new JMenuItem(
             MessageManager.getString("action.make_groups_selection"));
     grpsFromSelection.addActionListener(new ActionListener()
@@ -369,7 +383,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2LeftMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_left"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -379,11 +393,11 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
-
+  
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -393,11 +407,11 @@ 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,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -407,12 +421,12 @@ 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,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
-                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+            Platform.SHORTCUT_KEY_MASK
+                    | InputEvent.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -423,7 +437,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
-
+  
     JMenuItem justifyLeftMenuItem = new JMenuItem(
             MessageManager.getString("action.left_justify_alignment"));
     justifyLeftMenuItem.addActionListener(new ActionListener()
@@ -515,11 +529,31 @@ public class GAlignFrame extends JInternalFrame
         sortGroupMenuItem_actionPerformed(e);
       }
     });
-
+    JMenuItem sortEValueMenuItem = new JMenuItem(
+            MessageManager.getString("action.by_evalue"));
+    sortEValueMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sortEValueMenuItem_actionPerformed(e);
+      }
+    });
+    JMenuItem sortBitScoreMenuItem = new JMenuItem(
+            MessageManager.getString("action.by_bit_score"));
+    sortBitScoreMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sortBitScoreMenuItem_actionPerformed(e);
+      }
+    });
+  
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -530,6 +564,30 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 
+    JMenuItem filterByEValue = new JMenuItem(
+            MessageManager.getString("action.filter_by_evalue"));
+    filterByEValue.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        filterByEValue_actionPerformed();
+      }
+
+    });
+
+    JMenuItem filterByScore = new JMenuItem(
+            MessageManager.getString("action.filter_by_score"));
+    filterByScore.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        filterByScore_actionPerformed();
+      }
+
+    });
+  
     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
             MessageManager.getString("action.pairwise_alignment"));
     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
@@ -540,16 +598,18 @@ public class GAlignFrame extends JInternalFrame
         pairwiseAlignmentMenuItem_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"));
 
+
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem
             .setText(MessageManager.getString("label.show_annotations"));
@@ -617,6 +677,7 @@ 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.addActionListener(new ActionListener()
@@ -657,7 +718,7 @@ public class GAlignFrame extends JInternalFrame
         colourTextMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem htmlMenuItem = new JMenuItem(
             MessageManager.getString("label.html"));
     htmlMenuItem.addActionListener(new ActionListener()
@@ -668,7 +729,7 @@ 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()
@@ -679,7 +740,7 @@ public class GAlignFrame extends JInternalFrame
         bioJSMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem overviewMenuItem = new JMenuItem(
             MessageManager.getString("label.overview_window"));
     overviewMenuItem.addActionListener(new ActionListener()
@@ -690,11 +751,11 @@ public class GAlignFrame extends JInternalFrame
         overviewMenuItem_actionPerformed(e);
       }
     });
-
+  
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -704,11 +765,11 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
-
+  
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -718,7 +779,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
-
+  
     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
     wrapMenuItem.addActionListener(new ActionListener()
     {
@@ -728,11 +789,11 @@ public class GAlignFrame extends JInternalFrame
         wrapMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -742,7 +803,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
-
+  
     renderGapsMenuItem
             .setText(MessageManager.getString("action.show_gaps"));
     renderGapsMenuItem.setState(true);
@@ -754,11 +815,11 @@ public class GAlignFrame extends JInternalFrame
         renderGapsMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.find_tip")));
     al = new ActionListener()
@@ -773,6 +834,7 @@ public class GAlignFrame extends JInternalFrame
 
     showSeqFeatures.setText(
             MessageManager.getString("label.show_sequence_features"));
+
     showSeqFeatures.addActionListener(new ActionListener()
     {
       @Override
@@ -791,86 +853,86 @@ public class GAlignFrame extends JInternalFrame
             .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.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showNpFeats_actionPerformed(e);
       }
-
+  
     });
     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.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showGroupConsensus_actionPerformed(e);
       }
-
+  
     });
     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.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showSequenceLogo_actionPerformed(e);
       }
-
+  
     });
     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"));
@@ -884,7 +946,7 @@ public class GAlignFrame extends JInternalFrame
         applyAutoAnnotationSettings_actionPerformed(e);
       }
     });
-
+  
     ButtonGroup buttonGroup = new ButtonGroup();
     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
             MessageManager.getString("label.show_first"));
@@ -915,11 +977,11 @@ public class GAlignFrame extends JInternalFrame
         sortAnnotations_actionPerformed();
       }
     });
-
+  
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -929,7 +991,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
-
+  
     JMenuItem annotationColumn = new JMenuItem(
             MessageManager.getString("action.select_by_annotation"));
     annotationColumn.addActionListener(new ActionListener()
@@ -940,11 +1002,11 @@ public class GAlignFrame extends JInternalFrame
         annotationColumn_actionPerformed(e);
       }
     });
-
+  
     JMenuItem createGroup = new JMenuItem(
             MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -954,12 +1016,12 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, createGroup, al);
-
+  
     JMenuItem unGroup = new JMenuItem(
             MessageManager.getString("action.remove_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
-                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+            Platform.SHORTCUT_KEY_MASK
+                    | InputEvent.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -970,10 +1032,10 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, unGroup, al);
-
+  
     copy.setText(MessageManager.getString("action.copy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
 
     al = new ActionListener()
     {
@@ -984,10 +1046,10 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, copy, al);
-
+  
     cut.setText(MessageManager.getString("action.cut"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -997,7 +1059,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, cut, al);
-
+  
     JMenuItem delete = new JMenuItem(
             MessageManager.getString("action.delete"));
     delete.addActionListener(new ActionListener()
@@ -1008,38 +1070,52 @@ public class GAlignFrame extends JInternalFrame
         delete_actionPerformed();
       }
     });
-
+  
     pasteMenu.setText(MessageManager.getString("action.paste"));
     JMenuItem pasteNew = new JMenuItem(
             MessageManager.getString("label.to_new_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
-                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+            Platform.SHORTCUT_KEY_MASK
+                    | InputEvent.SHIFT_DOWN_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,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, 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()
     {
@@ -1051,7 +1127,6 @@ public class GAlignFrame extends JInternalFrame
     });
     createPNG.setActionCommand(
             MessageManager.getString("label.save_png_image"));
-
     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
     font.addActionListener(new ActionListener()
     {
@@ -1081,7 +1156,7 @@ public class GAlignFrame extends JInternalFrame
         createEPS(null);
       }
     });
-
+  
     JMenuItem createSVG = new JMenuItem("SVG");
     createSVG.addActionListener(new ActionListener()
     {
@@ -1091,7 +1166,7 @@ public class GAlignFrame extends JInternalFrame
         createSVG(null);
       }
     });
-
+  
     JMenuItem loadTreeMenuItem = new JMenuItem(
             MessageManager.getString("label.load_associated_tree"));
     loadTreeMenuItem.setActionCommand(
@@ -1104,7 +1179,7 @@ public class GAlignFrame extends JInternalFrame
         loadTreeMenuItem_actionPerformed(e);
       }
     });
-
+  
     scaleAbove.setVisible(false);
     scaleAbove.setText(MessageManager.getString("action.scale_above"));
     scaleAbove.addActionListener(new ActionListener()
@@ -1155,15 +1230,15 @@ public class GAlignFrame extends JInternalFrame
             .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"));
@@ -1172,7 +1247,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void menuSelected(MenuEvent e)
       {
-        buildTreeSortMenu();
+        enableSortMenuOptions();
       }
 
       @Override
@@ -1185,22 +1260,40 @@ public class GAlignFrame extends JInternalFrame
       {
       }
     });
+    sortByTreeMenu.addMenuListener(new MenuListener()
+    {
+      @Override
+      public void menuSelected(MenuEvent e)
+      {
+        buildTreeSortMenu();
+      }
+  
+      @Override
+      public void menuDeselected(MenuEvent e)
+      {
+      }
+  
+      @Override
+      public void menuCanceled(MenuEvent e)
+      {
+      }
+    });
     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)
       {
@@ -1280,7 +1373,7 @@ public class GAlignFrame extends JInternalFrame
         showReverse_actionPerformed(true);
       }
     });
-
+  
     JMenuItem extractScores = new JMenuItem(
             MessageManager.getString("label.extract_scores"));
     extractScores.addActionListener(new ActionListener()
@@ -1293,10 +1386,10 @@ 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"));
@@ -1333,7 +1426,7 @@ public class GAlignFrame extends JInternalFrame
         fetchSequence_actionPerformed();
       }
     });
-
+  
     JMenuItem associatedData = new JMenuItem(
             MessageManager.getString("label.load_features_annotations"));
     associatedData.addActionListener(new ActionListener()
@@ -1341,7 +1434,14 @@ 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();
+        }
       }
     });
     loadVcf = new JMenuItem(
@@ -1396,7 +1496,7 @@ public class GAlignFrame extends JInternalFrame
         listenToViewSelections_actionPerformed(e);
       }
     });
-
+  
     JMenu addSequenceMenu = new JMenu(
             MessageManager.getString("label.add_sequences"));
     JMenuItem addFromFile = new JMenuItem(
@@ -1542,12 +1642,12 @@ public class GAlignFrame extends JInternalFrame
         hiddenMarkers_actionPerformed(e);
       }
     });
-
+  
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
-                    | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
+            Platform.SHORTCUT_KEY_MASK
+                    | InputEvent.ALT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1558,7 +1658,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
-
+  
     showComplementMenuItem.setVisible(false);
     showComplementMenuItem.addActionListener(new ActionListener()
     {
@@ -1568,7 +1668,7 @@ public class GAlignFrame extends JInternalFrame
         showComplement_actionPerformed(showComplementMenuItem.getState());
       }
     });
-
+  
     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
     {
       @Override
@@ -1589,7 +1689,7 @@ public class GAlignFrame extends JInternalFrame
           tabbedPane_mousePressed(e);
         }
       }
-
+  
       @Override
       public void mouseReleased(MouseEvent e)
       {
@@ -1607,10 +1707,10 @@ public class GAlignFrame extends JInternalFrame
         tabbedPane_focusGained(e);
       }
     });
-
+  
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -1620,7 +1720,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, save, al);
-
+  
     reload.setEnabled(false);
     reload.setText(MessageManager.getString("action.reload"));
     reload.addActionListener(new ActionListener()
@@ -1631,11 +1731,11 @@ public class GAlignFrame extends JInternalFrame
         reload_actionPerformed(e);
       }
     });
-
+  
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -1645,11 +1745,11 @@ 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"));
 
@@ -1663,7 +1763,7 @@ 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 +1776,7 @@ 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 +1789,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, expandViews, al);
-
+  
     JMenuItem pageSetup = new JMenuItem(
             MessageManager.getString("action.page_setup"));
     pageSetup.addActionListener(new ActionListener()
@@ -1712,6 +1812,18 @@ public class GAlignFrame extends JInternalFrame
     });
     JMenuItem selectHighlighted = new JMenuItem(
             MessageManager.getString("action.select_highlighted_columns"));
+    selectHighlighted.setToolTipText(JvSwingUtils.wrapTooltip(true, 
+            MessageManager.getString("tooltip.select_highlighted_columns")));
+    al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        selectHighlightedColumns_actionPerformed(actionEvent);
+      }
+    };
+    JMenuItem Filter = new JMenuItem(
+            MessageManager.getString("action.select_highlighted_columns"));
     selectHighlighted.setToolTipText(
             MessageManager.getString("tooltip.select_highlighted_columns"));
     al = new ActionListener()
@@ -1727,7 +1839,7 @@ public class GAlignFrame extends JInternalFrame
             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"));
@@ -1739,11 +1851,12 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(formatMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
+    alignFrameMenuBar.add(webService);
     if (!Platform.isJS())
     {
-      alignFrameMenuBar.add(webService);
+      alignFrameMenuBar.add(hmmerMenu);
     }
-
+  
     fileMenu.add(fetchSequence);
     fileMenu.add(addSequenceMenu);
     fileMenu.add(reload);
@@ -1766,7 +1879,7 @@ public class GAlignFrame extends JInternalFrame
     }
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
-
+  
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
     editMenu.add(undoMenuItem);
@@ -1788,7 +1901,10 @@ public class GAlignFrame extends JInternalFrame
     // editMenu.add(justifyRightMenuItem);
     // editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
-
+    editMenu.addSeparator();
+    editMenu.add(filterByEValue);
+    editMenu.add(filterByScore);
+  
     showMenu.add(showAllColumns);
     showMenu.add(showAllSeqs);
     showMenu.add(showAllhidden);
@@ -1816,7 +1932,7 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(alignmentProperties);
     viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
-
+  
     annotationsMenu.add(annotationPanelMenuItem);
     annotationsMenu.addSeparator();
     annotationsMenu.add(showAllAlAnnotations);
@@ -1843,6 +1959,8 @@ public class GAlignFrame extends JInternalFrame
     sort.add(sortLengthMenuItem);
     sort.add(sortGroupMenuItem);
     sort.add(sortPairwiseMenuItem);
+    sort.add(sortEValueMenuItem);
+    sort.add(sortBitScoreMenuItem);
     sort.add(sortByTreeMenu);
     calculateMenu.add(sort);
     calculateMenu.add(calculateTree);
@@ -1863,7 +1981,6 @@ public class GAlignFrame extends JInternalFrame
       calculateMenu.addSeparator();
       calculateMenu.add(runGroovy);
     }
-
     webServiceNoServices = new JMenuItem(
             MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
@@ -1884,7 +2001,7 @@ 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);
@@ -1918,6 +2035,174 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
+  /**
+   * Constructs the entries on the HMMER menu
+   */
+  protected void initHMMERMenu()
+  {
+    /*
+     * hmmbuild
+     */
+    JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
+    JMenuItem hmmBuildSettings = new JMenuItem(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmBuildSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmBuild_actionPerformed(false);
+      }
+    });
+    JMenuItem hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmbuild"));
+    hmmBuildRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmBuild_actionPerformed(true);
+      }
+    });
+    hmmBuild.add(hmmBuildRun);
+    hmmBuild.add(hmmBuildSettings);
+
+    /*
+     * hmmalign
+     */
+    JMenu hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
+    JMenuItem hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmalign"));
+    hmmAlignRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmAlign_actionPerformed(true);
+      }
+    });
+    JMenuItem hmmAlignSettings = new JMenuItem(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmAlignSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmAlign_actionPerformed(false);
+      }
+    });
+    hmmAlign.add(hmmAlignRun);
+    hmmAlign.add(hmmAlignSettings);
+
+    /*
+     * hmmsearch
+     */
+    JMenu hmmSearch = new JMenu(
+            MessageManager.getString("label.hmmsearch"));
+    JMenuItem hmmSearchSettings = new JMenuItem(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmSearchSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmSearch_actionPerformed(false);
+      }
+    });
+    JMenuItem hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmsearch"));
+    hmmSearchRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmSearch_actionPerformed(true);
+      }
+    });
+    JMenuItem addDatabase = new JMenuItem(
+            MessageManager.getString("label.add_database"));
+    addDatabase.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          addDatabase_actionPerformed();
+        } catch (IOException e1)
+        {
+          e1.printStackTrace();
+        }
+      }
+    });
+    hmmSearch.add(hmmSearchRun);
+    hmmSearch.add(hmmSearchSettings);
+    // hmmSearch.add(addDatabase);
+
+    /*
+     * jackhmmer
+     */
+    JMenu jackhmmer = new JMenu(
+            MessageManager.getString("label.jackhmmer"));
+    JMenuItem jackhmmerSettings = new JMenuItem(
+            MessageManager.getString("label.edit_settings_and_run"));
+    jackhmmerSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        jackhmmer_actionPerformed(false);
+      }
+    });
+    JMenuItem jackhmmerRun = new JMenuItem(MessageManager.formatMessage(
+            "label.action_with_default_settings", "jackhmmer"));
+    jackhmmerRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        jackhmmer_actionPerformed(true);
+      }
+
+    });
+    /*
+    JMenuItem addDatabase = new JMenuItem(
+            MessageManager.getString("label.add_database"));
+    addDatabase.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          addDatabase_actionPerformed();
+        } catch (IOException e1)
+        {
+          e1.printStackTrace();
+        }
+      }
+    });
+    */
+    jackhmmer.add(jackhmmerRun);
+    jackhmmer.add(jackhmmerSettings);
+    // hmmSearch.add(addDatabase);
+
+    /*
+     * top level menu
+     */
+    hmmerMenu.setText(MessageManager.getString("action.hmmer"));
+    hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+    hmmerMenu.add(hmmBuild);
+    hmmerMenu.add(hmmAlign);
+    hmmerMenu.add(hmmSearch);
+    hmmerMenu.add(jackhmmer);
+
+  }
+
+  protected void enableSortMenuOptions()
+  {
+  }
+  
   protected void loadVcf_actionPerformed()
   {
   }
@@ -2333,6 +2618,14 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void sortEValueMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
   }
@@ -2394,10 +2687,12 @@ public class GAlignFrame extends JInternalFrame
   }
 
   protected void pasteNew_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
   }
 
   protected void pasteThis_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
   }
 
@@ -2405,6 +2700,27 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void hmmBuild_actionPerformed(boolean withDefaults)
+  {
+  }
+
+  protected void hmmSearch_actionPerformed(boolean withDefaults)
+  {
+  }
+
+  protected void jackhmmer_actionPerformed(boolean b)
+  {
+  }
+
+  protected void addDatabase_actionPerformed()
+          throws FileFormatException, IOException
+  {
+  }
+
+  protected void hmmAlign_actionPerformed(boolean withDefaults)
+  {
+  }
+
   public void createPNG(java.io.File f)
   {
   }
@@ -2461,6 +2777,14 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void filterByEValue_actionPerformed()
+  {
+  }
+
+  protected void filterByScore_actionPerformed()
+  {
+  }
+
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
   }
@@ -2520,6 +2844,7 @@ public class GAlignFrame extends JInternalFrame
   }
 
   public void associatedData_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
 
   }
@@ -2716,4 +3041,6 @@ public class GAlignFrame extends JInternalFrame
   protected void showComplement_actionPerformed(boolean complement)
   {
   }
+  
+
 }