X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;fp=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=d3aa01af3aaacd2b668c9b5946e55d50f6357f6d;hb=7f4da0a2b0c10f158a03dbfce8878e67e90c4a68;hp=9c02f29b06f8dcab31b592ca1e5548ea02a84909;hpb=f20144e54bcecee1a25b94dddf6c9bf802012b38;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 9c02f29..d3aa01a 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -260,8 +260,14 @@ public class HiddenSequences
     }
     int index = 0;
     int hiddenSeqs = 0;
+    int diff = 0;
     if (hiddenSequences.length <= alignmentIndex)
     {
+      // if the alignmentIndex runs past the end of hidden sequences
+      // and therefore actually past the end of the alignment
+      // store the difference to add back on at the end, so that behaviour
+      // is consistent with hidden columns behaviour (used by overview panel)
+      diff = alignmentIndex - hiddenSequences.length + 1;
       alignmentIndex = hiddenSequences.length - 1;
     }
 
@@ -274,7 +280,7 @@ public class HiddenSequences
       index++;
     }
 
-    return (alignmentIndex - hiddenSeqs);
+    return (alignmentIndex - hiddenSeqs + diff);
   }
 
   /**