From: jprocter <Jim Procter>
Date: Wed, 9 Aug 2006 16:20:41 +0000 (+0000)
Subject: alignment from seqCigars will correctly mark deleted residues as
X-Git-Tag: Release_2_1~124
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c97b0d0f8b52d2049f81b30df969a64a6d58240c;p=jalview.git

alignment from seqCigars will correctly mark deleted residues as
isolated insertions.
---

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);
     }
     /**