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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index c71818e..1bfc0b3 100755 (executable)
--- 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 (executable)
--- 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;