Merge branch 'JAL-1372_referenceseq' into feature_29/JAL-1372_referenceseq

[jalview.git] / src / jalview / appletgui / IdCanvas.java

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 25aa315..0ac4e55 100755 (executable)
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -227,7 +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);
           }
@@ -257,7 +257,7 @@ public class IdCanvas extends Panel
         }
         gg.setFont(italic);
         // boolean isrep=false;
-        if (av.hasHiddenRows())
+        if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
         {
           // isrep =
           setHiddenFont(seq);
@@ -366,8 +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;