X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=0ac4e55c6a935fef57c9513d2fbe0273aae150f3;hb=fd235cc7542d6e308e054a8a76580a6c511ae631;hp=a35be1510f36712603e585d1bd4ecd69cbc0d8b1;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index a35be15..0ac4e55 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
@@ -224,7 +227,7 @@ public class IdCanvas extends Panel
 
           SequenceI s = av.getAlignment().getSequenceAt(i);
           gg.setFont(italic);
-          if (av.hasHiddenRows())
+          if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
           {
             setHiddenFont(s);
           }
@@ -254,7 +257,7 @@ public class IdCanvas extends Panel
         }
         gg.setFont(italic);
         // boolean isrep=false;
-        if (av.hasHiddenRows())
+        if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
         {
           // isrep =
           setHiddenFont(seq);
@@ -363,8 +366,7 @@ 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;