From a91518f29f584c4e8276ca36b4aeede71803cf7c Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 31 Mar 2015 16:06:20 +0100
Subject: [PATCH] JAL-1264 reinstated 'show annotations' menu item (and set
 from params)

---
 src/jalview/appletgui/AlignFrame.java |   22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 3e919f6..93bd155 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -113,9 +113,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   public AlignViewport viewport;
 
-  int DEFAULT_WIDTH = 700;
+  // width and height may be overridden by applet parameters
+  int frameWidth = 700;
 
-  int DEFAULT_HEIGHT = 500;
+  int frameHeight = 500;
 
   String jalviewServletURL;
 
@@ -176,13 +177,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         if (param != null)
         {
           int width = Integer.parseInt(param);
-          DEFAULT_WIDTH = width;
+          frameWidth = width;
         }
         param = applet.getParameter("windowHeight");
         if (param != null)
         {
           int height = Integer.parseInt(param);
-          DEFAULT_HEIGHT = height;
+          frameHeight = height;
         }
       } catch (Exception ex)
       {
@@ -203,6 +204,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     showSequenceLogo.setState(viewport.isShowSequenceLogo());
     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
+    annotationPanelMenuItem.setState(viewport.isShowAnnotation());
     showAlignmentAnnotations.setState(viewport.isShowAnnotation());
     showSequenceAnnotations.setState(viewport.isShowAnnotation());
 
@@ -1964,8 +1966,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           }
         }
 
-        jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
-                DEFAULT_HEIGHT);
+        jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
+                frameHeight);
       }
       else
       {
@@ -3596,8 +3598,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     /*
      * Annotations menu
      */
-    // annotationsMenu.add(annotationPanelMenuItem);
-    // annotationsMenu.addSeparator();
+    annotationsMenu.add(annotationPanelMenuItem);
+    annotationsMenu.addSeparator();
     annotationsMenu.add(showAlignmentAnnotations);
     annotationsMenu.add(showSequenceAnnotations);
     annotationsMenu.add(sortAnnBySequence);
@@ -3771,8 +3773,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       add(alignPanel, BorderLayout.CENTER);
       // and register with the applet so it can pass external API calls to us
       jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
-              DEFAULT_WIDTH,
-              DEFAULT_HEIGHT);
+              frameWidth,
+              frameHeight);
     }
   }
 
-- 
1.7.10.2