From 77641e9e184bf2566b1f930646e250917b753ac7 Mon Sep 17 00:00:00 2001
From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Mon, 14 Aug 2017 11:43:46 +0100
Subject: [PATCH] JAL-2629 remove redundant options from HMMER menu

---
 src/jalview/gui/AlignFrame.java    |    7 -------
 src/jalview/jbgui/GAlignFrame.java |   27 ---------------------------
 2 files changed, 34 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2694434..c2a1b94 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -499,16 +499,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     hmmerMenu.removeAll();
 
-    hmmerMenu.add(changeHMMERLocation);
-    hmmerMenu.addSeparator();
-
-    hmmerMenu.add(autoAlignSeqs);
-    hmmerMenu.addSeparator();
-
     hmmerMenu.add(hmmAlign);
     hmmerMenu.add(hmmBuild);
     hmmerMenu.add(hmmSearch);
-    
   }
 
   /**
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6e3c517..74a3940 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -70,10 +70,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu hmmerMenu = new JMenu();
 
-  protected JCheckBoxMenuItem autoAlignSeqs = new JCheckBoxMenuItem();
-
-  protected JMenuItem changeHMMERLocation = new JCheckBoxMenuItem();
-
   protected JMenuItem hmmAlign = new JMenuItem();
 
   protected JMenuItem hmmSearch = new JMenuItem();
@@ -1758,18 +1754,6 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    changeHMMERLocation.setText(
-            MessageManager.getString("label.change_hmmer_location"));
-    changeHMMERLocation.addActionListener(new ActionListener()
-    {
-
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        changeHMMERLocation_actionPerformed(e);
-      }
-
-    });
     selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
@@ -1958,20 +1942,9 @@ public class GAlignFrame extends JInternalFrame
    */
   protected void initHMMERMenu()
   {
-    autoAlignSeqs = new JCheckBoxMenuItem(
-            MessageManager.getString("label.auto_align_seqs"));
     hmmAlign = new JMenuItem(MessageManager.getString("label.hmmalign"));
     hmmBuild = new JMenuItem(MessageManager.getString("label.hmmbuild"));
     hmmSearch = new JMenuItem(MessageManager.getString("label.hmmsearch"));
-    autoAlignSeqs.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        autoAlignSeqs_actionPerformed(autoAlignSeqs.isSelected());
-      }
-    });
-
   }
   protected void initColourMenu()
   {
-- 
1.7.10.2