JAL-2629 refactoring of Hmmer preferences

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index c2d19d7..663f544 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.hmmer.HmmerCommand;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormats;
 import jalview.util.MessageManager;
@@ -320,15 +321,7 @@ 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);
-    }
+    hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
     hmmerMenu.addActionListener(new ActionListener()
     {
       @Override
@@ -337,6 +330,10 @@ public class GAlignFrame extends JInternalFrame
         hmmerMenu_actionPerformed(e);
       }
     });
+    hmmerMenu.add(hmmBuild);
+    hmmerMenu.add(hmmAlign);
+    hmmerMenu.add(hmmSearch);
+
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
@@ -1752,119 +1749,76 @@ public class GAlignFrame extends JInternalFrame
             "label.action_with_default_settings", "hmmbuild"));
     hmmBuildRun.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        try
-        {
-          hmmBuildRun_actionPerformed(e);
-        } catch (IOException | InterruptedException e1)
-        {
-          // TODO Auto-generated catch block
-          e1.printStackTrace();
-        }
+        hmmBuildRun_actionPerformed();
       }
-
     });
     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();
-        }
+        hmmBuildSettings_actionPerformed();
       }
-
     });
     hmmAlignRun.setText(MessageManager.formatMessage(
             "label.action_with_default_settings", "hmmalign"));
     hmmAlignRun.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        try
-        {
-          hmmAlignRun_actionPerformed(e);
-        } catch (IOException | InterruptedException e1)
-        {
-          // TODO Auto-generated catch block
-          e1.printStackTrace();
-        }
+        hmmAlignRun_actionPerformed();
       }
-
     });
     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();
-        }
+        hmmAlignSettings_actionPerformed();
       }
-
     });
     hmmSearchRun.setText(MessageManager.formatMessage(
             "label.action_with_default_settings", "hmmsearch"));
     hmmSearchRun.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        hmmSearchRun_actionPerformed(e);
+        hmmSearchRun_actionPerformed();
       }
-
     });
     addDatabase.setText(MessageManager.getString("label.add_database"));
     addDatabase.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent e)
       {
         try
         {
-          addDatabase_actionPerformed(e);
+          addDatabase_actionPerformed();
         } 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);
+        hmmSearchSettings_actionPerformed();
       }
-
     });
     selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
@@ -2567,36 +2521,32 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void hmmBuildRun_actionPerformed(ActionEvent e)
-          throws IOException, InterruptedException
+  protected void hmmBuildRun_actionPerformed()
   {
   }
 
-  protected void hmmSearchRun_actionPerformed(ActionEvent e)
+  protected void hmmSearchRun_actionPerformed()
   {
   }
 
-  protected void addDatabase_actionPerformed(ActionEvent e)
+  protected void addDatabase_actionPerformed()
           throws FileFormatException, IOException
   {
   }
 
-  protected void hmmAlignRun_actionPerformed(ActionEvent e)
-          throws IOException, InterruptedException
+  protected void hmmAlignRun_actionPerformed()
   {
   }
 
-  protected void hmmBuildSettings_actionPerformed(ActionEvent e)
-          throws IOException, InterruptedException
+  protected void hmmBuildSettings_actionPerformed()
   {
   }
 
-  protected void hmmSearchSettings_actionPerformed(ActionEvent e)
+  protected void hmmSearchSettings_actionPerformed()
   {
   }
 
-  protected void hmmAlignSettings_actionPerformed(ActionEvent e)
-          throws IOException, InterruptedException
+  protected void hmmAlignSettings_actionPerformed()
   {
   }