X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;fp=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=32443d820f3aaccd57b076f5d5d78043b5a1d6f7;hb=4a9a2fc8a1b1a66b21e66429083f27a6fc8541b9;hp=ed07290992cd984f8d5f82784edf019e4aea9c8c;hpb=30f552046feaba47955d5ffdcec6d0fc67a7e13b;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index ed07290..32443d8 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -157,9 +157,10 @@ public class HiddenSequences
     int absAlignmentIndex = alignment.findIndex(sequence);
     int alignmentIndex = adjustForHiddenSeqs(absAlignmentIndex);
 
-    if (hiddenSequences[alignmentIndex] != null)
+    if (alignmentIndex < 0 || hiddenSequences[alignmentIndex] != null)
     {
       System.out.println("ERROR!!!!!!!!!!!");
+      return;
     }
 
     hiddenSequences[alignmentIndex] = sequence;
@@ -253,7 +254,8 @@ public class HiddenSequences
   }
 
   /**
-   * Convert absolute alignment index to visible alignment index
+   * Convert absolute alignment index to visible alignment index (or -1 if
+   * before the first visible sequence)
    * 
    * @param alignmentIndex
    * @return