X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=d3b56bea723690c97915ba89278711467ed02302;hb=4059c82f431d3f98931b290d9a72da2a54a0fc95;hp=1f91e26be49b5af5c4143b30e1c647b0c812abf1;hpb=f3bc67915e61855d87866b4a614fe7a953813408;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 1f91e26..d3b56be 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -331,12 +331,32 @@ public class IdCanvas extends JPanel
 
     void drawMarker(int i, int starty, int yoffset)
     {
-      int hiddenIndex = av.adjustForHiddenSeqs(i);
-      int lastIndex = av.adjustForHiddenSeqs(i - 1);
-      int nextIndex = av.adjustForHiddenSeqs(i + 1);
+
+      SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+      //Use this method here instead of calling hiddenSeq adjust
+      //3 times.
+      int hSize = hseqs.length;
+
+      int hiddenIndex = i;
+      int lastIndex = i - 1;
+      int nextIndex = i + 1;
+
+      for(int j=0; j<hSize; j++)
+      {
+        if (hseqs[j] != null)
+        {
+          if(j-1<hiddenIndex)
+            hiddenIndex++;
+          if(j-1<lastIndex)
+            lastIndex++;
+          if(j-1<nextIndex)
+            nextIndex++;
+        }
+      }
 
       boolean below = (hiddenIndex > lastIndex + 1);
-      boolean above = (nextIndex>hiddenIndex+1);
+      boolean above = (nextIndex > hiddenIndex+1);
+
 
         gg.setColor(Color.blue);
         if(below)
@@ -375,7 +395,9 @@ public class IdCanvas extends JPanel
       Font bold = new Font(av.getFont().getName(), Font.BOLD,
                            av.getFont().getSize());
 
-      if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)
+
+      if (av.alignment.getSequenceAt(i)!=null
+          && av.alignment.getSequenceAt(i).getHiddenSequences() != null)
         gg.setFont(bold);
       else
         gg.setFont(italic);