X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=dd057a347e4a3839445d9742282026c87d63874e;hb=14ead5d8009f9ac9a139ae93faf44e67a3998d46;hp=0f5aad9c53eb121e2dff6390b443c336bc35056a;hpb=5cd5b6e7864fe435ceb3f5c2f339a436ea0aac93;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 0f5aad9..dd057a3 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -295,12 +295,32 @@ public class IdCanvas
 
   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;
 
     boolean below = (hiddenIndex > lastIndex + 1);
-    boolean above = (nextIndex>hiddenIndex+1);
+    boolean above = (nextIndex > hiddenIndex + 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++;
+      }
+      }
 
       gg.setColor(Color.blue);
       if(below)