X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=b5efeb49ef117305942c710669f9b2544959196f;hb=66270dda280788c15956c7a0485f0b9adf03c62a;hp=ed07290992cd984f8d5f82784edf019e4aea9c8c;hpb=4a3198610bf947684199326eeb41fefa0a74d9e4;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index ed07290..b5efeb4 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;
@@ -221,8 +222,8 @@ public class HiddenSequences
       end = hiddenSequences.length - 1;
     }
 
-    List<SequenceI> asequences;
-    synchronized (asequences = alignment.getSequences())
+    List<SequenceI> asequences = alignment.getSequences();
+    synchronized (asequences)
     {
       for (int index = end; index > start; index--)
       {
@@ -238,8 +239,8 @@ public class HiddenSequences
           }
           else
           {
-            System.out.println(seq.getName()
-                    + " has been deleted whilst hidden");
+            System.out.println(
+                    seq.getName() + " has been deleted whilst hidden");
           }
         }
       }
@@ -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