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 (executable)
--- 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);
     }
     /**