JAL-2629 add simple jackhmmer functionality

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index c228c90..f650707 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -2031,6 +2031,54 @@ public class GAlignFrame extends JInternalFrame
     // 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"));
@@ -2038,6 +2086,7 @@ public class GAlignFrame extends JInternalFrame
     hmmerMenu.add(hmmBuild);
     hmmerMenu.add(hmmAlign);
     hmmerMenu.add(hmmSearch);
+    hmmerMenu.add(jackhmmer);
 
   }
 
@@ -2538,6 +2587,10 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void jackhmmer_actionPerformed(boolean b)
+  {
+  }
+
   protected void addDatabase_actionPerformed()
           throws FileFormatException, IOException
   {