X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=168b50d5dd35b47ad384d4244e9c035acf77beab;hb=0452450533728e478ef8c893ea2cb3483c740fb3;hp=d1f130bffe41ff97b6d7750e745e0e8ee6b4f86c;hpb=dbcfef03ad3d2853eda62c727978a160fc347f58;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index d1f130b..168b50d 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -82,7 +82,7 @@ public class IdCanvas extends JPanel
             gg.setColor(Color.white);
         }
         else if ((av.getSelectionGroup() != null) &&
-                av.getSelectionGroup().getSequences(false).contains(s))
+                av.getSelectionGroup().getSequences(null).contains(s))
         {
             gg.setColor(Color.lightGray);
             gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
@@ -271,14 +271,14 @@ public class IdCanvas extends JPanel
             {
               for (int i = starty; i < alheight; i++)
               {
+                SequenceI s = av.alignment.getSequenceAt(i);
                 if (av.hasHiddenRows)
                 {
-                  setHiddenFont(i);
+                  setHiddenFont(s);
                 }
                 else
                   gg.setFont(italic);
 
-                SequenceI s = av.alignment.getSequenceAt(i);
                 drawIdString(gg, s, i, 0, ypos);
               }
 
@@ -310,7 +310,7 @@ public class IdCanvas extends JPanel
 
               if (av.hasHiddenRows)
               {
-                setHiddenFont(i);
+                setHiddenFont(sequence);
               }
 
                 // Selected sequence colours
@@ -321,7 +321,7 @@ public class IdCanvas extends JPanel
                   currentTextColor = Color.white;
                 }
                 else if ( (av.getSelectionGroup() != null) &&
-                         av.getSelectionGroup().getSequences(false).contains(
+                         av.getSelectionGroup().getSequences(null).contains(
                              sequence))
                 {
                   currentColor = Color.lightGray;
@@ -419,7 +419,7 @@ public class IdCanvas extends JPanel
         }
     }
 
-    void setHiddenFont(int i)
+    void setHiddenFont(SequenceI seq)
     {
       Font italic = new Font(av.getFont().getName(), Font.ITALIC,
                              av.getFont().getSize());
@@ -427,8 +427,8 @@ public class IdCanvas extends JPanel
                            av.getFont().getSize());
 
 
-      if (av.alignment.getSequenceAt(i)!=null
-          && av.alignment.getSequenceAt(i).getHiddenSequences() != null)
+      if (av.hiddenRepSequences!=null &&
+          av.hiddenRepSequences.containsKey(seq))
         gg.setFont(bold);
       else
         gg.setFont(italic);