JAL-2629 add ability to add and select a DB for hmmsearch

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 518c51a..c2d19d7 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -25,6 +25,7 @@ import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
+import jalview.io.FileFormatException;
 import jalview.io.FileFormats;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -70,11 +71,25 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu hmmerMenu = new JMenu();
 
-  protected JMenuItem hmmAlign = new JMenuItem();
+  protected JMenu hmmAlign = new JMenu();
 
-  protected JMenuItem hmmSearch = new JMenuItem();
+  protected JMenuItem hmmAlignRun = new JMenuItem();
 
-  protected JMenuItem hmmBuild = new JCheckBoxMenuItem();
+  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;
 
@@ -276,14 +291,15 @@ public class GAlignFrame extends JInternalFrame
     };
   
     // FIXME getDefaultToolkit throws an exception in Headless mode
-    KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask()
-            | KeyEvent.SHIFT_MASK, false);
+    KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.SHIFT_MASK,
+            false);
     addMenuActionAndAccelerator(keyStroke, saveAs, al);
   
     closeMenuItem.setText(MessageManager.getString("action.close"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -323,8 +339,8 @@ public class GAlignFrame extends JInternalFrame
     });
     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
@@ -350,8 +366,8 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem invertSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.invert_sequence_selection"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -374,8 +390,8 @@ 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
@@ -386,8 +402,8 @@ 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
@@ -400,8 +416,8 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -414,8 +430,8 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_empty_columns"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -428,9 +444,10 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem removeAllGapsMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_all_gaps"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask()
-            | KeyEvent.SHIFT_MASK, false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.SHIFT_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -481,8 +498,8 @@ 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()
     {
@@ -535,8 +552,8 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -564,14 +581,16 @@ public class GAlignFrame extends JInternalFrame
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
     statusBar.setText(MessageManager.getString("label.status_bar"));
-    outputTextboxMenu.setText(MessageManager
-            .getString("label.out_to_textbox"));
-  
+
+    outputTextboxMenu
+            .setText(MessageManager.getString("label.out_to_textbox"));
+
+
     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
@@ -580,8 +599,8 @@ 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);
@@ -593,8 +612,8 @@ 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()
     {
@@ -604,8 +623,8 @@ 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()
     {
@@ -615,8 +634,8 @@ 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()
     {
@@ -633,9 +652,10 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("label.sort_annotations_by_sequence"));
     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
@@ -643,13 +663,14 @@ 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
@@ -657,14 +678,14 @@ 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
@@ -709,8 +730,8 @@ public class GAlignFrame extends JInternalFrame
   
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -723,8 +744,8 @@ public class GAlignFrame extends JInternalFrame
   
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -747,8 +768,8 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -773,8 +794,8 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.find_tip")));
     al = new ActionListener()
@@ -786,9 +807,10 @@ 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
@@ -803,8 +825,8 @@ public class GAlignFrame extends JInternalFrame
      * void actionPerformed(ActionEvent actionEvent) {
      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
      */
-    showDbRefsMenuitem.setText(MessageManager
-            .getString("label.show_database_refs"));
+    showDbRefsMenuitem
+            .setText(MessageManager.getString("label.show_database_refs"));
     showDbRefsMenuitem.addActionListener(new ActionListener()
     {
   
@@ -815,8 +837,8 @@ public class GAlignFrame extends JInternalFrame
       }
   
     });
-    showNpFeatsMenuitem.setText(MessageManager
-            .getString("label.show_non_positional_features"));
+    showNpFeatsMenuitem.setText(
+            MessageManager.getString("label.show_non_positional_features"));
     showNpFeatsMenuitem.addActionListener(new ActionListener()
     {
   
@@ -827,8 +849,8 @@ public class GAlignFrame extends JInternalFrame
       }
   
     });
-    showGroupConservation.setText(MessageManager
-            .getString("label.group_conservation"));
+    showGroupConservation
+            .setText(MessageManager.getString("label.group_conservation"));
     showGroupConservation.addActionListener(new ActionListener()
     {
   
@@ -839,9 +861,9 @@ public class GAlignFrame extends JInternalFrame
       }
   
     });
-  
-    showGroupConsensus.setText(MessageManager
-            .getString("label.group_consensus"));
+
+    showGroupConsensus
+            .setText(MessageManager.getString("label.group_consensus"));
     showGroupConsensus.addActionListener(new ActionListener()
     {
   
@@ -852,8 +874,8 @@ public class GAlignFrame extends JInternalFrame
       }
   
     });
-    showConsensusHistogram.setText(MessageManager
-            .getString("label.show_consensus_histogram"));
+    showConsensusHistogram.setText(
+            MessageManager.getString("label.show_consensus_histogram"));
     showConsensusHistogram.addActionListener(new ActionListener()
     {
   
@@ -864,8 +886,8 @@ public class GAlignFrame extends JInternalFrame
       }
   
     });
-    showSequenceLogo.setText(MessageManager
-            .getString("label.show_consensus_logo"));
+    showSequenceLogo
+            .setText(MessageManager.getString("label.show_consensus_logo"));
     showSequenceLogo.addActionListener(new ActionListener()
     {
   
@@ -876,8 +898,8 @@ public class GAlignFrame extends JInternalFrame
       }
   
     });
-    normaliseSequenceLogo.setText(MessageManager
-            .getString("label.norm_consensus_logo"));
+    normaliseSequenceLogo
+            .setText(MessageManager.getString("label.norm_consensus_logo"));
     normaliseSequenceLogo.addActionListener(new ActionListener()
     {
   
@@ -888,8 +910,8 @@ public class GAlignFrame extends JInternalFrame
       }
   
     });
-    applyAutoAnnotationSettings.setText(MessageManager
-            .getString("label.apply_all_groups"));
+    applyAutoAnnotationSettings
+            .setText(MessageManager.getString("label.apply_all_groups"));
     applyAutoAnnotationSettings.setState(false);
     applyAutoAnnotationSettings.setVisible(true);
     applyAutoAnnotationSettings.addActionListener(new ActionListener()
@@ -908,8 +930,8 @@ 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()
@@ -934,8 +956,8 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -959,8 +981,8 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem createGroup = new JMenuItem(
             MessageManager.getString("action.create_group"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -973,9 +995,10 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem unGroup = new JMenuItem(
             MessageManager.getString("action.remove_group"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask()
-            | KeyEvent.SHIFT_MASK, false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.SHIFT_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -987,9 +1010,9 @@ 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()
     {
       @Override
@@ -1001,8 +1024,8 @@ public class GAlignFrame extends JInternalFrame
     addMenuActionAndAccelerator(keyStroke, copy, al);
   
     cut.setText(MessageManager.getString("action.cut"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -1027,9 +1050,10 @@ public class GAlignFrame extends JInternalFrame
     pasteMenu.setText(MessageManager.getString("action.paste"));
     JMenuItem pasteNew = new JMenuItem(
             MessageManager.getString("label.to_new_alignment"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask()
-            | KeyEvent.SHIFT_MASK, false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.SHIFT_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1049,8 +1073,8 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem pasteThis = new JMenuItem(
             MessageManager.getString("label.to_this_alignment"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -1077,9 +1101,8 @@ 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()
     {
@@ -1089,8 +1112,8 @@ 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()
     {
@@ -1122,8 +1145,8 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem loadTreeMenuItem = new JMenuItem(
             MessageManager.getString("label.load_associated_tree"));
-    loadTreeMenuItem.setActionCommand(MessageManager
-            .getString("label.load_tree_for_sequence_set"));
+    loadTreeMenuItem.setActionCommand(
+            MessageManager.getString("label.load_tree_for_sequence_set"));
     loadTreeMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1167,8 +1190,8 @@ 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
@@ -1179,8 +1202,8 @@ public class GAlignFrame extends JInternalFrame
     });
     followHighlightMenuItem.setVisible(true);
     followHighlightMenuItem.setState(true);
-    followHighlightMenuItem.setText(MessageManager
-            .getString("label.automatic_scrolling"));
+    followHighlightMenuItem
+            .setText(MessageManager.getString("label.automatic_scrolling"));
     followHighlightMenuItem.addActionListener(new ActionListener()
     {
   
@@ -1213,8 +1236,8 @@ public class GAlignFrame extends JInternalFrame
       {
       }
     });
-    sortByAnnotScore.setText(MessageManager
-            .getString("label.sort_by_score"));
+    sortByAnnotScore
+            .setText(MessageManager.getString("label.sort_by_score"));
     sort.add(sortByAnnotScore);
     sort.addMenuListener(new javax.swing.event.MenuListener()
     {
@@ -1236,13 +1259,13 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     sortByAnnotScore.setVisible(false);
-  
-    calculateTree.setText(MessageManager
-            .getString("action.calculate_tree_pca"));
-  
+
+    calculateTree
+            .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
@@ -1262,8 +1285,8 @@ 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
@@ -1281,8 +1304,8 @@ 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
@@ -1309,8 +1332,8 @@ public class GAlignFrame extends JInternalFrame
     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
   
     runGroovy.setText(MessageManager.getString("label.run_groovy"));
-    runGroovy.setToolTipText(MessageManager
-            .getString("label.run_groovy_tip"));
+    runGroovy.setToolTipText(
+            MessageManager.getString("label.run_groovy_tip"));
     runGroovy.addActionListener(new ActionListener()
     {
       @Override
@@ -1358,10 +1381,10 @@ public class GAlignFrame extends JInternalFrame
         }
       }
     });
-    autoCalculate.setText(MessageManager
-            .getString("label.autocalculate_consensus"));
-    autoCalculate.setState(jalview.bin.Cache.getDefault(
-            "AUTO_CALC_CONSENSUS", true));
+    autoCalculate.setText(
+            MessageManager.getString("label.autocalculate_consensus"));
+    autoCalculate.setState(
+            jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
     {
       @Override
@@ -1370,12 +1393,10 @@ 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()
@@ -1386,13 +1407,12 @@ public class GAlignFrame extends JInternalFrame
         sortByTreeOption_actionPerformed(e);
       }
     });
-  
-    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()
     {
@@ -1458,8 +1478,8 @@ 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
@@ -1470,8 +1490,8 @@ 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
@@ -1483,8 +1503,8 @@ 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
@@ -1495,8 +1515,8 @@ 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
@@ -1538,8 +1558,8 @@ 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
@@ -1551,9 +1571,10 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask()
-            | KeyEvent.ALT_MASK, false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.ALT_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1614,8 +1635,8 @@ public class GAlignFrame extends JInternalFrame
     });
   
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -1639,8 +1660,8 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -1657,9 +1678,9 @@ public class GAlignFrame extends JInternalFrame
   
     formatMenu.setText(MessageManager.getString("action.format"));
     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
-  
-    idRightAlign.setText(MessageManager
-            .getString("label.right_align_sequence_id"));
+
+    idRightAlign.setText(
+            MessageManager.getString("label.right_align_sequence_id"));
     idRightAlign.addActionListener(new ActionListener()
     {
       @Override
@@ -1717,8 +1738,8 @@ 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
@@ -1727,49 +1748,123 @@ public class GAlignFrame extends JInternalFrame
         selectHighlightedColumns_actionPerformed(actionEvent);
       }
     };
-    hmmBuild.setText(MessageManager.getString("label.hmmbuild"));
-    hmmBuild.addActionListener(new ActionListener()
+    hmmBuildRun.setText(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmbuild"));
+    hmmBuildRun.addActionListener(new ActionListener()
     {
-  
+
       @Override
       public void actionPerformed(ActionEvent e)
       {
         try
         {
-          hmmBuild_actionPerformed(e);
-        } catch (IOException e1)
+          hmmBuildRun_actionPerformed(e);
+        } catch (IOException | InterruptedException e1)
         {
           // TODO Auto-generated catch block
           e1.printStackTrace();
-        } catch (InterruptedException e1)
+        }
+      }
+
+    });
+    hmmBuildSettings.setText(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmBuildSettings.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          hmmBuildSettings_actionPerformed(e);
+        } catch (IOException | InterruptedException e1)
         {
           // TODO Auto-generated catch block
           e1.printStackTrace();
         }
       }
-  
+
     });
-    hmmAlign.setText(MessageManager.getString("label.hmmalign"));
-    hmmAlign.addActionListener(new ActionListener()
+    hmmAlignRun.setText(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmalign"));
+    hmmAlignRun.addActionListener(new ActionListener()
     {
-  
+
       @Override
       public void actionPerformed(ActionEvent e)
       {
         try
         {
-          hmmAlign_actionPerformed(e);
-        } catch (IOException e1)
+          hmmAlignRun_actionPerformed(e);
+        } catch (IOException | InterruptedException e1)
+        {
+          // TODO Auto-generated catch block
+          e1.printStackTrace();
+        }
+      }
+
+    });
+    hmmAlignSettings.setText(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmAlignSettings.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          hmmAlignSettings_actionPerformed(e);
+        } catch (IOException | InterruptedException e1)
         {
           // TODO Auto-generated catch block
           e1.printStackTrace();
-        } catch (InterruptedException e1)
+        }
+      }
+
+    });
+    hmmSearchRun.setText(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmsearch"));
+    hmmSearchRun.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmSearchRun_actionPerformed(e);
+      }
+
+    });
+    addDatabase.setText(MessageManager.getString("label.add_database"));
+    addDatabase.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          addDatabase_actionPerformed(e);
+        } catch (IOException e1)
         {
           // TODO Auto-generated catch block
           e1.printStackTrace();
         }
       }
-  
+
+    });
+    hmmSearchSettings.setText(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmSearchSettings.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmSearchSettings_actionPerformed(e);
+      }
+
     });
     selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
@@ -1881,8 +1976,7 @@ public class GAlignFrame extends JInternalFrame
     autoAnnMenu.add(showGroupConservation);
     autoAnnMenu.add(showGroupConsensus);
     annotationsMenu.add(autoAnnMenu);
-  
-  
+
     sort.add(sortIDMenuItem);
     sort.add(sortLengthMenuItem);
     sort.add(sortGroupMenuItem);
@@ -1959,15 +2053,40 @@ public class GAlignFrame extends JInternalFrame
   }
 
   /**
-   * Constructs the entries on the Colour menu (but does not add them to the
-   * menu).
+   * Constructs the entries on the HMMER menu (does not add them to the menu).
    */
   protected void initHMMERMenu()
   {
-    hmmAlign = new JMenuItem(MessageManager.getString("label.hmmalign"));
-    hmmBuild = new JMenuItem(MessageManager.getString("label.hmmbuild"));
-    hmmSearch = new JMenuItem(MessageManager.getString("label.hmmsearch"));
+    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);
   }
+
+  /**
+   * Constructs the entries on the Colour menu (but does not add them to the
+   * menu).
+   */
   protected void initColourMenu()
   {
     applyToAllGroups = new JCheckBoxMenuItem(
@@ -1999,8 +2118,8 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed(conservationMenuItem
-                .isSelected());
+        conservationMenuItem_actionPerformed(
+                conservationMenuItem.isSelected());
       }
     });
 
@@ -2024,8 +2143,7 @@ public class GAlignFrame extends JInternalFrame
         modifyPID_actionPerformed();
       }
     });
-    modifyConservation = new JMenuItem(
-            MessageManager
+    modifyConservation = new JMenuItem(MessageManager
             .getString("label.modify_conservation_threshold"));
     modifyConservation.addActionListener(new ActionListener()
     {
@@ -2449,25 +2567,36 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void autoAlignSeqs_actionPerformed(boolean selected)
+  protected void hmmBuildRun_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
   }
 
-  protected void hmmAlign_actionPerformed(ActionEvent e)
-          throws IOException, InterruptedException
+  protected void hmmSearchRun_actionPerformed(ActionEvent e)
   {
   }
 
-  protected void changeHMMERLocation_actionPerformed(ActionEvent e)
+  protected void addDatabase_actionPerformed(ActionEvent e)
+          throws FileFormatException, IOException
   {
   }
 
-  protected void hmmBuild_actionPerformed(ActionEvent e)
+  protected void hmmAlignRun_actionPerformed(ActionEvent e)
           throws IOException, InterruptedException
   {
   }
 
-  protected void hmmSearch_actionPerformed(ActionEvent e)
+  protected void hmmBuildSettings_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
+  {
+  }
+
+  protected void hmmSearchSettings_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void hmmAlignSettings_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
   }
 
@@ -2792,13 +2921,11 @@ public class GAlignFrame extends JInternalFrame
 
   protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
   {
-    // TODO Auto-generated method stub
 
   }
 
   protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
   {
-    // TODO Auto-generated method stub
 
   }
 }