JAL-2629 the HMMER tab is now disabled when HMMER is not installed

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 807f88f..a03ab7f 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1342,4 +1342,5 @@ label.hmmsearch_not_found = The hmmsearch binary was not found.
 warn.hmmbuild_failed = hmmbuild was not found. 
 warn.align_failed = hmmalign was not found.
 label.invalid_folder = Invalid Folder
-label.folder_not_exists = HMMER not found. \n Please enter the path to HMMER (if installed).
\ No newline at end of file
+label.folder_not_exists = HMMER not found. \n Please enter the path to HMMER (if installed).
+label.hmmer_installed = HMMER installed
\ No newline at end of file

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c2a1b94..9c4a75c 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -5693,6 +5693,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       new CalculationChooser(AlignFrame.this);
     }
   }
+
+  public void updateHMMERStatus(boolean status)
+  {
+    hmmerMenu.setEnabled(status);
+  }
 }
 
 class PrintThread extends Thread

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index e11bdec..39023dc 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -204,6 +204,8 @@ public class Preferences extends GPreferences
      * Set HMMER tab defaults
      */
     trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+    isHMMERInstalled
+            .setSelected(Cache.getDefault("HMMER_INSTALLED", false));
     if (Cache.getDefault("USE_UNIPROT", false))
     {
       uniprot.setSelected(true);
@@ -214,6 +216,8 @@ public class Preferences extends GPreferences
     }
     numberOfSequencesToKeepField
             .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+    installationLocation.setEnabled(isHMMERInstalled.isSelected());
+    hmmerPath.setEnabled(isHMMERInstalled.isSelected());
     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
     hmmerPath.addActionListener(new ActionListener()
     {
@@ -674,6 +678,20 @@ public class Preferences extends GPreferences
             numberOfSequencesToKeepField.getText());
     Cache.applicationProperties.setProperty(HMMER_PATH,
             hmmerPath.getText());
+    boolean hmmerInstalled = isHMMERInstalled.isSelected();
+    Cache.applicationProperties.setProperty("HMMER_INSTALLED",
+            Boolean.toString(hmmerInstalled));
+    boolean hmmerFunctioning = validateHMMERPath(false);
+    Cache.applicationProperties.setProperty("HMMER_FUNCTIONING",
+            Boolean.toString(hmmerFunctioning));
+    AlignFrame[] frames = Desktop.getAlignFrames();
+    boolean hmmerStatus = hmmerFunctioning && hmmerInstalled ? true : false;
+    for (AlignFrame frame : frames)
+    {
+      frame.updateHMMERStatus(hmmerStatus);
+    }
+    
+    
     trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
     if (Cache.getDefault("USE_UNIPROT", false))
     {
@@ -844,10 +862,13 @@ public class Preferences extends GPreferences
       structureTab.requestFocusInWindow();
       return false;
     }
-    if (!validateHMMER())
+    if (isHMMERInstalled.isSelected())
     {
-      hmmerTab.requestFocusInWindow();
-      return false;
+      if (!validateHMMER())
+      {
+        hmmerTab.requestFocusInWindow();
+        return false;
+      }
     }
     return true;
   }
@@ -1158,27 +1179,26 @@ public class Preferences extends GPreferences
   }
   
   /**
-   * Returns true if hmmer path contains the necessary valid executables, else show an error
-   * dialog.
+   * Returns true if hmmer path contains the necessary valid executables, else
+   * show an error dialog (if showing dialog).
    */
-  private boolean validateHMMERPath()
+  private boolean validateHMMERPath(boolean showDialog)
   {
     int missing = 0;
     String message = "";
-    String path = hmmerPath.getText();
-    if (path.length() < 1)
-    {
-      return false;
-    }
-    else
+    String path = hmmerPath.getText().trim();
+    if (path.length() > 0)
     {
       File f = new File(path);
       if (!f.exists())
       {
-        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+        if (showDialog)
+        {
+          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.getString("label.folder_not_exists"),
                 MessageManager.getString("label.invalid_folder"),
                 JvOptionPane.ERROR_MESSAGE);
+        }
         return false;
       }
 
@@ -1216,17 +1236,24 @@ public class Preferences extends GPreferences
       {
         if (missing < 3)
         {
-          JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
+          if (showDialog)
+          {
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
                   MessageManager.getString("label.invalid_folder"),
                   JvOptionPane.ERROR_MESSAGE);
+          }
           return false;
         }
         else
         {
-          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+          if (showDialog)
+          {
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                   MessageManager.getString("label.no_binaries"),
                   MessageManager.getString("label.invalid_folder"),
                   JvOptionPane.ERROR_MESSAGE);
+          }
+
           return false;
         }
       }
@@ -1235,6 +1262,11 @@ public class Preferences extends GPreferences
     return true;
   }
 
+  private boolean validateHMMERPath()
+  {
+    return validateHMMERPath(true);
+  }
+
   /**
    * If Chimera is selected, check it can be found on default or user-specified
    * path, if not show a warning/help dialog.

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 74a3940..e9dd53b 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -263,7 +263,7 @@ public class GAlignFrame extends JInternalFrame
   {
     initColourMenu();
     initHMMERMenu();
-
+  
     JMenuItem saveAs = new JMenuItem(
             MessageManager.getString("action.save_as"));
     ActionListener al = new ActionListener()
@@ -274,13 +274,13 @@ public class GAlignFrame extends JInternalFrame
         saveAs_actionPerformed(e);
       }
     };
-
+  
     // FIXME getDefaultToolkit throws an exception in Headless mode
     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask()
             | KeyEvent.SHIFT_MASK, false);
     addMenuActionAndAccelerator(keyStroke, saveAs, al);
-
+  
     closeMenuItem.setText(MessageManager.getString("action.close"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
@@ -293,7 +293,7 @@ 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(
@@ -304,6 +304,16 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("action.calculate"));
     webService.setText(MessageManager.getString("action.web_service"));
     hmmerMenu.setText(MessageManager.getString("action.hmmer"));
+    String status = Cache.getProperty("HMMER_FUNCTIONING");
+    if ("false".equals(status) || status == null)
+    {
+      hmmerMenu.setEnabled(false);
+    }
+    else
+    {
+      hmmerMenu.setEnabled(true);
+    }
+
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
@@ -317,7 +327,7 @@ 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);
@@ -330,7 +340,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
-
+  
     JMenuItem invertSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.invert_sequence_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
@@ -344,7 +354,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
-
+  
     JMenuItem grpsFromSelection = new JMenuItem(
             MessageManager.getString("action.make_groups_selection"));
     grpsFromSelection.addActionListener(new ActionListener()
@@ -380,7 +390,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
-
+  
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
@@ -394,7 +404,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
-
+  
     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_empty_columns"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
@@ -408,7 +418,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
-
+  
     JMenuItem removeAllGapsMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_all_gaps"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
@@ -423,7 +433,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
-
+  
     JMenuItem justifyLeftMenuItem = new JMenuItem(
             MessageManager.getString("action.left_justify_alignment"));
     justifyLeftMenuItem.addActionListener(new ActionListener()
@@ -515,7 +525,7 @@ public class GAlignFrame extends JInternalFrame
         sortGroupMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
@@ -529,7 +539,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
-
+  
     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
             MessageManager.getString("action.pairwise_alignment"));
     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
@@ -540,7 +550,7 @@ 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);
@@ -549,7 +559,7 @@ public class GAlignFrame extends JInternalFrame
     statusBar.setText(MessageManager.getString("label.status_bar"));
     outputTextboxMenu.setText(MessageManager
             .getString("label.out_to_textbox"));
-
+  
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem.setText(MessageManager
             .getString("label.show_annotations"));
@@ -616,7 +626,7 @@ 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.addActionListener(new ActionListener()
@@ -656,7 +666,7 @@ public class GAlignFrame extends JInternalFrame
         colourTextMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem htmlMenuItem = new JMenuItem(
             MessageManager.getString("label.html"));
     htmlMenuItem.addActionListener(new ActionListener()
@@ -667,7 +677,7 @@ 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()
@@ -678,7 +688,7 @@ public class GAlignFrame extends JInternalFrame
         bioJSMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem overviewMenuItem = new JMenuItem(
             MessageManager.getString("label.overview_window"));
     overviewMenuItem.addActionListener(new ActionListener()
@@ -689,7 +699,7 @@ public class GAlignFrame extends JInternalFrame
         overviewMenuItem_actionPerformed(e);
       }
     });
-
+  
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
@@ -703,7 +713,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
-
+  
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
@@ -717,7 +727,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
-
+  
     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
     wrapMenuItem.addActionListener(new ActionListener()
     {
@@ -727,7 +737,7 @@ public class GAlignFrame extends JInternalFrame
         wrapMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
@@ -741,7 +751,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
-
+  
     renderGapsMenuItem
             .setText(MessageManager.getString("action.show_gaps"));
     renderGapsMenuItem.setState(true);
@@ -753,7 +763,7 @@ public class GAlignFrame extends JInternalFrame
         renderGapsMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
@@ -769,7 +779,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
-
+  
     showSeqFeatures.setText(MessageManager
             .getString("label.show_sequence_features"));
     showSeqFeatures.addActionListener(new ActionListener()
@@ -790,86 +800,86 @@ public class GAlignFrame extends JInternalFrame
             .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"));
@@ -883,7 +893,7 @@ public class GAlignFrame extends JInternalFrame
         applyAutoAnnotationSettings_actionPerformed(e);
       }
     });
-
+  
     ButtonGroup buttonGroup = new ButtonGroup();
     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
             MessageManager.getString("label.show_first"));
@@ -914,7 +924,7 @@ public class GAlignFrame extends JInternalFrame
         sortAnnotations_actionPerformed();
       }
     });
-
+  
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
@@ -928,7 +938,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
-
+  
     JMenuItem annotationColumn = new JMenuItem(
             MessageManager.getString("action.select_by_annotation"));
     annotationColumn.addActionListener(new ActionListener()
@@ -939,7 +949,7 @@ public class GAlignFrame extends JInternalFrame
         annotationColumn_actionPerformed(e);
       }
     });
-
+  
     JMenuItem createGroup = new JMenuItem(
             MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
@@ -953,7 +963,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, createGroup, al);
-
+  
     JMenuItem unGroup = new JMenuItem(
             MessageManager.getString("action.remove_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
@@ -968,11 +978,11 @@ 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);
-
+  
     al = new ActionListener()
     {
       @Override
@@ -982,7 +992,7 @@ 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);
@@ -995,7 +1005,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, cut, al);
-
+  
     JMenuItem delete = new JMenuItem(
             MessageManager.getString("action.delete"));
     delete.addActionListener(new ActionListener()
@@ -1006,7 +1016,7 @@ public class GAlignFrame extends JInternalFrame
         delete_actionPerformed(e);
       }
     });
-
+  
     pasteMenu.setText(MessageManager.getString("action.paste"));
     JMenuItem pasteNew = new JMenuItem(
             MessageManager.getString("label.to_new_alignment"));
@@ -1029,7 +1039,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
-
+  
     JMenuItem pasteThis = new JMenuItem(
             MessageManager.getString("label.to_this_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
@@ -1050,7 +1060,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
-
+  
     JMenuItem createPNG = new JMenuItem("PNG");
     createPNG.addActionListener(new ActionListener()
     {
@@ -1062,7 +1072,7 @@ 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()
     {
@@ -1092,7 +1102,7 @@ public class GAlignFrame extends JInternalFrame
         createEPS(null);
       }
     });
-
+  
     JMenuItem createSVG = new JMenuItem("SVG");
     createSVG.addActionListener(new ActionListener()
     {
@@ -1102,7 +1112,7 @@ public class GAlignFrame extends JInternalFrame
         createSVG(null);
       }
     });
-
+  
     JMenuItem loadTreeMenuItem = new JMenuItem(
             MessageManager.getString("label.load_associated_tree"));
     loadTreeMenuItem.setActionCommand(MessageManager
@@ -1115,7 +1125,7 @@ public class GAlignFrame extends JInternalFrame
         loadTreeMenuItem_actionPerformed(e);
       }
     });
-
+  
     scaleAbove.setVisible(false);
     scaleAbove.setText(MessageManager.getString("action.scale_above"));
     scaleAbove.addActionListener(new ActionListener()
@@ -1166,15 +1176,15 @@ public class GAlignFrame extends JInternalFrame
             .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"));
@@ -1185,12 +1195,12 @@ public class GAlignFrame extends JInternalFrame
       {
         buildTreeSortMenu();
       }
-
+  
       @Override
       public void menuDeselected(MenuEvent e)
       {
       }
-
+  
       @Override
       public void menuCanceled(MenuEvent e)
       {
@@ -1201,17 +1211,17 @@ public class GAlignFrame extends JInternalFrame
     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)
       {
@@ -1219,10 +1229,10 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     sortByAnnotScore.setVisible(false);
-
+  
     calculateTree.setText(MessageManager
             .getString("action.calculate_tree_pca"));
-
+  
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
     padGapsMenuitem.setState(jalview.bin.Cache
             .getDefault("PAD_GAPS", false));
@@ -1274,7 +1284,7 @@ public class GAlignFrame extends JInternalFrame
         showReverse_actionPerformed(true);
       }
     });
-
+  
     JMenuItem extractScores = new JMenuItem(
             MessageManager.getString("label.extract_scores"));
     extractScores.addActionListener(new ActionListener()
@@ -1287,10 +1297,10 @@ 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"));
@@ -1302,7 +1312,7 @@ public class GAlignFrame extends JInternalFrame
         runGroovy_actionPerformed();
       }
     });
-
+  
     JMenuItem openFeatureSettings = new JMenuItem(
             MessageManager.getString("action.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
@@ -1323,7 +1333,7 @@ public class GAlignFrame extends JInternalFrame
         fetchSequence_actionPerformed(e);
       }
     });
-
+  
     JMenuItem associatedData = new JMenuItem(
             MessageManager.getString("label.load_features_annotations"));
     associatedData.addActionListener(new ActionListener()
@@ -1369,7 +1379,7 @@ public class GAlignFrame extends JInternalFrame
         sortByTreeOption_actionPerformed(e);
       }
     });
-
+  
     listenToViewSelections.setText(MessageManager
             .getString("label.listen_for_selections"));
     listenToViewSelections
@@ -1385,7 +1395,7 @@ public class GAlignFrame extends JInternalFrame
         listenToViewSelections_actionPerformed(e);
       }
     });
-
+  
     JMenu addSequenceMenu = new JMenu(
             MessageManager.getString("label.add_sequences"));
     JMenuItem addFromFile = new JMenuItem(
@@ -1531,7 +1541,7 @@ public class GAlignFrame extends JInternalFrame
         hiddenMarkers_actionPerformed(e);
       }
     });
-
+  
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
@@ -1546,7 +1556,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
-
+  
     showComplementMenuItem.setVisible(false);
     showComplementMenuItem.addActionListener(new ActionListener()
     {
@@ -1556,7 +1566,7 @@ public class GAlignFrame extends JInternalFrame
         showComplement_actionPerformed(showComplementMenuItem.getState());
       }
     });
-
+  
     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
     {
       @Override
@@ -1577,7 +1587,7 @@ public class GAlignFrame extends JInternalFrame
           tabbedPane_mousePressed(e);
         }
       }
-
+  
       @Override
       public void mouseReleased(MouseEvent e)
       {
@@ -1595,7 +1605,7 @@ public class GAlignFrame extends JInternalFrame
         tabbedPane_focusGained(e);
       }
     });
-
+  
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
@@ -1608,7 +1618,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, save, al);
-
+  
     reload.setEnabled(false);
     reload.setText(MessageManager.getString("action.reload"));
     reload.addActionListener(new ActionListener()
@@ -1619,7 +1629,7 @@ public class GAlignFrame extends JInternalFrame
         reload_actionPerformed(e);
       }
     });
-
+  
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
@@ -1633,14 +1643,14 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, newView, al);
-
+  
     tabbedPane.setToolTipText("<html><i>"
             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
             + "</i></html>");
-
+  
     formatMenu.setText(MessageManager.getString("action.format"));
     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
-
+  
     idRightAlign.setText(MessageManager
             .getString("label.right_align_sequence_id"));
     idRightAlign.addActionListener(new ActionListener()
@@ -1651,7 +1661,7 @@ 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);
@@ -1664,7 +1674,7 @@ 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);
@@ -1677,7 +1687,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, expandViews, al);
-
+  
     JMenuItem pageSetup = new JMenuItem(
             MessageManager.getString("action.page_setup"));
     pageSetup.addActionListener(new ActionListener()
@@ -1713,7 +1723,7 @@ public class GAlignFrame extends JInternalFrame
     hmmBuild.setText(MessageManager.getString("label.hmmbuild"));
     hmmBuild.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
@@ -1730,12 +1740,12 @@ public class GAlignFrame extends JInternalFrame
           e1.printStackTrace();
         }
       }
-
+  
     });
     hmmAlign.setText(MessageManager.getString("label.hmmalign"));
     hmmAlign.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
@@ -1752,14 +1762,14 @@ public class GAlignFrame extends JInternalFrame
           e1.printStackTrace();
         }
       }
-
+  
     });
     selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
     JMenu autoAnnMenu = new JMenu(
             MessageManager.getString("label.autocalculated_annotation"));
-
+  
     JMenu exportImageMenu = new JMenu(
             MessageManager.getString("label.export_image"));
     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
@@ -1773,7 +1783,7 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
     alignFrameMenuBar.add(hmmerMenu);
-
+  
     fileMenu.add(fetchSequence);
     fileMenu.add(addSequenceMenu);
     fileMenu.add(reload);
@@ -1792,7 +1802,7 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(associatedData);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
-
+  
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
     editMenu.add(undoMenuItem);
@@ -1814,7 +1824,7 @@ public class GAlignFrame extends JInternalFrame
     // editMenu.add(justifyRightMenuItem);
     // editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
-
+  
     showMenu.add(showAllColumns);
     showMenu.add(showAllSeqs);
     showMenu.add(showAllhidden);
@@ -1842,7 +1852,7 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(alignmentProperties);
     viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
-
+  
     annotationsMenu.add(annotationPanelMenuItem);
     annotationsMenu.addSeparator();
     annotationsMenu.add(showAllAlAnnotations);
@@ -1864,8 +1874,8 @@ public class GAlignFrame extends JInternalFrame
     autoAnnMenu.add(showGroupConservation);
     autoAnnMenu.add(showGroupConsensus);
     annotationsMenu.add(autoAnnMenu);
-
-
+  
+  
     sort.add(sortIDMenuItem);
     sort.add(sortLengthMenuItem);
     sort.add(sortGroupMenuItem);
@@ -1887,7 +1897,7 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(extractScores);
     calculateMenu.addSeparator();
     calculateMenu.add(runGroovy);
-
+  
     webServiceNoServices = new JMenuItem(
             MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
@@ -1902,7 +1912,7 @@ 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);

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 25742b4..68dc27b 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -276,6 +276,8 @@ public class GPreferences extends JPanel
 
   protected JLabel installationLocation = new JLabel();
 
+  protected JCheckBox isHMMERInstalled = new JCheckBox();
+
   protected JTextField hmmerPath = new JTextField();
 
   protected JLabel hmmsearch = new JLabel();
@@ -377,7 +379,8 @@ public class GPreferences extends JPanel
           }
         }
         else if (lastTab == hmmerTab
-                && tabbedPane.getSelectedComponent() != hmmerTab)
+                && tabbedPane.getSelectedComponent() != hmmerTab
+                && isHMMERInstalled.isSelected())
         {
           if (!validateHMMER())
           {
@@ -427,7 +430,6 @@ public class GPreferences extends JPanel
    */
   private JPanel initHMMERTab()
   {
-    JPanel hmmerTab = new JPanel();
     hmmerTab.setLayout(null);
 
     hmmalign.setFont(LABEL_FONT);
@@ -448,6 +450,20 @@ public class GPreferences extends JPanel
     sequencesToKeep.setBounds(new Rectangle(250, 30, 125, 23));
     numberOfSequencesToKeepField.setBounds(new Rectangle(375, 30, 40, 23));
 
+    isHMMERInstalled.setFont(LABEL_FONT);
+    isHMMERInstalled.setText(
+            MessageManager.getString("label.hmmer_installed"));
+    isHMMERInstalled.setBounds(new Rectangle(22, 180, 200, 23));
+    isHMMERInstalled.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        boolean status = isHMMERInstalled.isSelected();
+        installationLocation.setEnabled(status);
+        hmmerPath.setEnabled(status);
+      }
+    });
     installationLocation.setFont(LABEL_FONT);
     installationLocation.setText(
             MessageManager.getString("label.change_hmmer_location"));
@@ -491,6 +507,8 @@ public class GPreferences extends JPanel
     hmmerTab.add(sequencesToKeep);
     hmmerTab.add(sequencesToKeep);
     hmmerTab.add(numberOfSequencesToKeepField);
+    hmmerTab.add(isHMMERInstalled);
+
     return hmmerTab;
   }