From 5cf622544aaa7453e5e1710186b53734334783d6 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 26 Oct 2006 09:39:01 +0000
Subject: [PATCH] Check if hiddenSequence has been deleted

---
 src/jalview/datamodel/HiddenSequences.java |   22 +++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 9a4e7c6..31eda50 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 +161,17 @@ 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);
+         }
       }
 
     }
-- 
1.7.10.2