X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=62165cdef1a950763e4b4b8c9f5ffe14e278da48;hb=ed581b841fe9361bfe80bb006df190a29df264fb;hp=27d6c0e0038b29e072c7cc96d9971774b5d6819d;hpb=bd6ce8f5f9fc8e5bc8a6188d15987ce0ffd2c1ee;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 27d6c0e..62165cd 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -21,6 +21,8 @@
 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;
@@ -28,13 +30,13 @@ 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;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.GridLayout;
-import java.awt.Toolkit;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusAdapter;
@@ -72,26 +74,6 @@ public class GAlignFrame extends JInternalFrame
 
   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();
@@ -100,7 +82,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu sortByAnnotScore = new JMenu();
 
-  public JLabel statusBar = new JLabel();
+  protected JLabel statusBar = new JLabel();
 
   protected JMenu outputTextboxMenu = new JMenu();
 
@@ -148,7 +130,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem modifyPID;
 
-  protected JMenuItem annotationColour;
+  protected JRadioButtonMenuItem annotationColour;
 
   protected JMenu sortByTreeMenu = new JMenu();
 
@@ -162,7 +144,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 
-  protected JMenuItem showTranslation = new JMenuItem();
+  protected JMenu showTranslation = new JMenu();
 
   protected JMenuItem showReverse = new JMenuItem();
 
@@ -280,7 +262,6 @@ public class GAlignFrame extends JInternalFrame
   private void jbInit() throws Exception
   {
     initColourMenu();
-    initHMMERMenu();
   
     JMenuItem saveAs = new JMenuItem(
             MessageManager.getString("action.save_as"));
@@ -295,14 +276,14 @@ public class GAlignFrame extends JInternalFrame
   
     // FIXME getDefaultToolkit throws an exception in Headless mode
     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     addMenuActionAndAccelerator(keyStroke, saveAs, al);
   
     closeMenuItem.setText(MessageManager.getString("action.close"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -322,24 +303,13 @@ 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);
+
+    initHMMERMenu();
 
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -366,7 +336,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem invertSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.invert_sequence_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -402,7 +372,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2LeftMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_left"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -416,7 +386,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -430,7 +400,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_empty_columns"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -444,8 +414,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeAllGapsMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_all_gaps"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -552,7 +522,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -562,6 +532,30 @@ 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"));
@@ -730,7 +724,7 @@ public class GAlignFrame extends JInternalFrame
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -744,7 +738,7 @@ public class GAlignFrame extends JInternalFrame
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -768,7 +762,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -794,7 +788,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.find_tip")));
     al = new ActionListener()
@@ -956,7 +950,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -981,7 +975,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem createGroup = new JMenuItem(
             MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -995,8 +989,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem unGroup = new JMenuItem(
             MessageManager.getString("action.remove_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1010,7 +1004,7 @@ public class GAlignFrame extends JInternalFrame
   
     copy.setText(MessageManager.getString("action.copy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 
     al = new ActionListener()
     {
@@ -1024,7 +1018,7 @@ public class GAlignFrame extends JInternalFrame
   
     cut.setText(MessageManager.getString("action.cut"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1050,8 +1044,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem pasteNew = new JMenuItem(
             MessageManager.getString("label.to_new_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1073,7 +1067,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem pasteThis = new JMenuItem(
             MessageManager.getString("label.to_this_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1284,16 +1278,33 @@ public class GAlignFrame extends JInternalFrame
         vamsasStore_actionPerformed(e);
       }
     });
-    showTranslation
-            .setText(MessageManager.getString("label.translate_cDNA"));
-    showTranslation.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
+
+    /*
+     * Translate as cDNA with sub-menu of translation tables
+     */
+    showTranslation.setText(MessageManager
+            .getString("label.translate_cDNA"));
+    boolean first = true;
+    for (final GeneticCodeI table : GeneticCodes.getInstance()
+            .getCodeTables())
+    {
+      JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
+      showTranslation.add(item);
+      item.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          showTranslation_actionPerformed(table);
+        }
+      });
+      if (first)
       {
-        showTranslation_actionPerformed(e);
+        showTranslation.addSeparator();
       }
-    });
+      first = false;
+    }
+
     showReverse.setText(MessageManager.getString("label.reverse"));
     showReverse.addActionListener(new ActionListener()
     {
@@ -1581,8 +1592,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.ALT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1645,7 +1656,7 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1670,7 +1681,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1757,81 +1768,18 @@ 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()
+    JMenuItem Filter = new JMenuItem(
+            MessageManager.getString("action.select_highlighted_columns"));
+    selectHighlighted.setToolTipText(
+            MessageManager.getString("tooltip.select_highlighted_columns"));
+    al = new ActionListener()
     {
       @Override
-      public void actionPerformed(ActionEvent e)
+      public void actionPerformed(ActionEvent actionEvent)
       {
-        hmmSearchSettings_actionPerformed();
+        selectHighlightedColumns_actionPerformed(actionEvent);
       }
-    });
+    };
     selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
@@ -1893,6 +1841,9 @@ 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);
@@ -2014,40 +1965,168 @@ 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).
+   * Constructs the entries on the HMMER 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(
+    /*
+     * hmmbuild
+     */
+    JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
+    JMenuItem hmmBuildSettings = new JMenuItem(
             MessageManager.getString("label.edit_settings_and_run"));
-    hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
+    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"));
-    hmmBuild.add(hmmBuildSettings);
+    hmmBuildRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmBuild_actionPerformed(true);
+      }
+    });
     hmmBuild.add(hmmBuildRun);
-    hmmSearch = new JMenu(MessageManager.getString("label.hmmsearch"));
-    hmmSearchSettings = new JMenuItem(
+    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"));
-    hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
+    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"));
-    addDatabase = new JMenuItem(
+    hmmSearchRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmSearch_actionPerformed(true);
+      }
+    });
+    JMenuItem addDatabase = new JMenuItem(
             MessageManager.getString("label.add_database"));
-    hmmSearch.add(hmmSearchSettings);
+    addDatabase.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          addDatabase_actionPerformed();
+        } catch (IOException e1)
+        {
+          e1.printStackTrace();
+        }
+      }
+    });
     hmmSearch.add(hmmSearchRun);
-    hmmSearch.add(addDatabase);
+    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 loadVcf_actionPerformed()
@@ -2125,8 +2204,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    annotationColour = new JMenuItem(
+    annotationColour = new JRadioButtonMenuItem(
             MessageManager.getString("action.by_annotation"));
+    annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
     annotationColour.addActionListener(new ActionListener()
     {
       @Override
@@ -2538,32 +2618,24 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void hmmBuildRun_actionPerformed()
+  protected void hmmBuild_actionPerformed(boolean withDefaults)
   {
   }
 
-  protected void hmmSearchRun_actionPerformed()
-  {
-  }
-
-  protected void addDatabase_actionPerformed()
-          throws FileFormatException, IOException
+  protected void hmmSearch_actionPerformed(boolean withDefaults)
   {
   }
 
-  protected void hmmAlignRun_actionPerformed()
+  protected void jackhmmer_actionPerformed(boolean b)
   {
   }
 
-  protected void hmmBuildSettings_actionPerformed()
-  {
-  }
-
-  protected void hmmSearchSettings_actionPerformed()
+  protected void addDatabase_actionPerformed()
+          throws FileFormatException, IOException
   {
   }
 
-  protected void hmmAlignSettings_actionPerformed()
+  protected void hmmAlign_actionPerformed(boolean withDefaults)
   {
   }
 
@@ -2623,6 +2695,14 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void filterByEValue_actionPerformed()
+  {
+  }
+
+  protected void filterByScore_actionPerformed()
+  {
+  }
+
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
   }
@@ -2653,7 +2733,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void showTranslation_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(GeneticCodeI codeTable)
   {
 
   }
@@ -2879,20 +2959,4 @@ public class GAlignFrame extends JInternalFrame
   protected void showComplement_actionPerformed(boolean complement)
   {
   }
-
-  protected void showInformationHistogram_actionPerformed(ActionEvent e)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
-  {
-
-  }
 }