From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 30 Aug 2013 11:32:07 +0000 (+0100)
Subject: JAL-1370 allow show unconserved to reflect differences from the current reference... 
X-Git-Tag: Jalview_2_9~108^2~27^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2b2a6b7291f378c5d3463db9ddbbd2df5f9879b1;p=jalview.git

JAL-1370 allow show unconserved to reflect differences from the current reference seqeunce
---

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index c71818e..1bfc0b3 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -113,6 +113,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   MenuItem selSeqDetails = new MenuItem("Sequence Details ...");
 
+  MenuItem makeReferenceSeq = new MenuItem();
+  
   Sequence seq;
 
   MenuItem revealAll = new MenuItem();
@@ -300,6 +302,12 @@ public class APopupMenu extends java.awt.PopupMenu implements
     if (seq != null)
     {
       seqMenu.setLabel(seq.getName());
+      if (seq == ap.av.getAlignment().getSeqrep())
+      {
+        makeReferenceSeq.setLabel("Unmark representative");
+      } else {
+        makeReferenceSeq.setLabel("Mark as representative");
+      }
       repGroup.setLabel("Represent Group with " + seq.getName());
     }
     else
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 14cccc9..9eb70bd 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -363,8 +363,7 @@ public class IdCanvas extends Panel
     Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
             .getSize());
 
-    if (av.getHiddenRepSequences() != null
-            && av.getHiddenRepSequences().containsKey(seq))
+    if (av.isHiddenRepSequence(seq))
     {
       gg.setFont(bold);
       return true;