JAL-2437 Fixed reordering of sequences when hiding and revealing

[jalview.git] / src / jalview / datamodel / HiddenSequences.java

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 588e5ed..aca0be6 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -154,8 +154,8 @@ public class HiddenSequences
       hiddenSequences = new SequenceI[alignment.getHeight()];
     }
 
-    int alignmentIndex = alignment.findIndex(sequence);
-    alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
+    int absAlignmentIndex = alignment.findIndex(sequence);
+    int alignmentIndex = adjustForHiddenSeqs(absAlignmentIndex);
 
     if (hiddenSequences[alignmentIndex] != null)
     {
@@ -164,7 +164,7 @@ public class HiddenSequences
 
     hiddenSequences[alignmentIndex] = sequence;
 
-    alignment.deleteSequence(sequence);
+    alignment.deleteHiddenSequence(absAlignmentIndex);
   }
 
   public List<SequenceI> showAll(