X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=31eda50520f39cb1b451f6258f8d26bdf23cf34c;hb=2d7deb9d3e1ddc98abae846c8ffbc62606b023be;hp=17a6c1128075a9601e08e7def8a40c4ecdf42335;hpb=4e488d7e3ee2b70b798fd91ae90546462c890212;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 17a6c11..31eda50 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -73,10 +73,13 @@ public class HiddenSequences
 
     for (int i = 0; i < hiddenSequences.length; i++)
     {
+      if(hiddenSequences[i]==null)
+        continue;
+
       if (i > deletionIndex)
         tmp[i-1] = hiddenSequences[i];
       else
-        tmp[i] = hiddenSequences[i];
+       tmp[i] = hiddenSequences[i];
     }
 
    hiddenSequences = tmp;
@@ -111,7 +114,7 @@ public class HiddenSequences
     alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
 
     if(hiddenSequences[alignmentIndex]!=null)
-    System.out.println("ERROR!!!!!!!!!!!");
+      System.out.println("ERROR!!!!!!!!!!!");
 
     hiddenSequences[alignmentIndex] = sequence;
 
@@ -158,12 +161,17 @@ public class HiddenSequences
 
       if(seq!=null)
       {
-        revealedSeqs.addElement(seq);
-        alignment.getSequences().insertElementAt(seq, alignmentIndex);
-        if(repSequence!=null)
-        {
-          repSequence.showHiddenSequence(seq);
-        }
+        if(seq.getLength()>0)
+         {
+           revealedSeqs.addElement(seq);
+           alignment.getSequences().insertElementAt(seq, alignmentIndex);
+         }
+         else
+           System.out.println(seq.getName()+" has been deleted");
+         if (repSequence != null)
+         {
+           repSequence.showHiddenSequence(seq);
+         }
       }
 
     }