From c97b0d0f8b52d2049f81b30df969a64a6d58240c Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 9 Aug 2006 16:20:41 +0000
Subject: [PATCH] alignment from seqCigars will correctly mark deleted
 residues as isolated insertions.

---
 src/jalview/datamodel/Alignment.java |    2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index d67592a..507102e 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -70,7 +70,7 @@ public class Alignment implements AlignmentI
      * @param seqs SeqCigar[]
      */
     public Alignment(SeqCigar[] alseqs) {
-      SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, gapCharacter, new ColumnSelection());
+      SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, gapCharacter, new ColumnSelection(), null);
       initAlignment(seqs);
     }
     /**
-- 
1.7.10.2