From 2afbc744f6769674e1af81918206526d90a93b12 Mon Sep 17 00:00:00 2001
From: hansonr <hansonr@stolaf.edu>
Date: Mon, 2 Jul 2018 17:55:00 +0100
Subject: [PATCH] JAL-3026  Java+JavaScript fix for GD#95

View...Features Settings... not disabled when there are no features.

Involves an anonymous subclassing of JMenu for viewMenu that checks that
there are features just before opening.

GAlignFrame, with a call into AlignFrame for checking the viewport.
---
 src/jalview/gui/AlignFrame.java    |   21 +++++++++++++++++++++
 src/jalview/jbgui/GAlignFrame.java |   23 +++++++++++++++++++++--
 2 files changed, 42 insertions(+), 2 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index aa0a1fe..ee2875a 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -333,6 +333,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     Desktop.getDesktop().propertyChange(evt);
   }
 
+  
+  /**
+   *  BH 2018
+   *   
+   * @return true if we have any features
+   */
+  @Override
+  protected boolean haveAlignmentFeatures() { 
+    AlignmentI alignment = getViewport().getAlignment();
+
+    for (int i = 0; i < alignment.getHeight(); i++)
+    {
+      SequenceI seq = alignment.getSequenceAt(i);
+      for (String group : seq.getFeatures().getFeatureGroups(true))
+      {
+        if (group != null)return true;
+      }
+    }
+    return  false; 
+  }
+  
   /**
    * initalise the alignframe from the underlying viewport data and the
    * configurations
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index a64030b..9fdc47c 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -196,6 +196,8 @@ public class GAlignFrame extends JInternalFrame
   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
+  
+  protected JMenuItem openFeatureSettings;
 
   private SequenceAnnotationOrder annotationSortOrder;
 
@@ -282,7 +284,17 @@ 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 viewMenu = new JMenu(MessageManager.getString("action.view")) {
+      
+      public void setPopupMenuVisible(boolean b) {
+        if (b) {
+          System.out.println("openFeatureSettings " + haveAlignmentFeatures());
+          openFeatureSettings.setEnabled(haveAlignmentFeatures());
+        }
+        super.setPopupMenuVisible(b);
+      }
+
+    };
     JMenu annotationsMenu = new JMenu(
             MessageManager.getString("action.annotations"));
     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
@@ -1279,8 +1291,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    JMenuItem openFeatureSettings = new JMenuItem(
+    openFeatureSettings = new JMenuItem(
             MessageManager.getString("action.feature_settings"));
+    openFeatureSettings.setEnabled(false);
     openFeatureSettings.addActionListener(new ActionListener()
     {
       @Override
@@ -1874,6 +1887,12 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
+  protected boolean haveAlignmentFeatures()
+  {
+    // because gAlignFrame is not an abstract class  -- see AlignFrame
+    return false;
+  }
+
   protected void loadVcf_actionPerformed()
   {
   }
-- 
1.7.10.2