X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=9d9fa81609aa1112b652cc45afa6d812e6ddae2b;hb=b0a90dcb797054f5e01a3b10969e782ef3aafa4a;hp=9a4e7c6d024d378284f32fcb0a7d59084405bebd;hpb=d1a58585358deed317674daeeac5fb5be66637ab;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 9a4e7c6..9d9fa81 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -73,9 +73,12 @@ 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 if(hiddenSequences[i]!=null)
+      else
        tmp[i] = hiddenSequences[i];
     }
 
@@ -158,12 +161,18 @@ 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 whilst hidden");
+
+         if (repSequence != null)
+         {
+           repSequence.showHiddenSequence(seq);
+         }
       }
 
     }