X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=5fb16d6050add60b4ea8e80f6b3c6e743286c927;hb=e207348a53bcdda0dac93c574bf3ca1be1241929;hp=bdc48d00123a40896b36b3c37e75cd35b1ea106d;hpb=2a66892874abea357a5e5d9ef2f69919453c31d0;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index bdc48d0..5fb16d6 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -593,4 +593,19 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   public void setupJPredAlignment();
 
+  /**
+   * Add gaps into the sequences aligned to profileseq under the given
+   * AlignmentView
+   * 
+   * @param profileseq
+   *          sequence in al which sequences are aligned to
+   * @param input
+   *          alignment view where sequence corresponding to profileseq is first
+   *          entry
+   * @return new HiddenColumns for new alignment view, with insertions into
+   *         profileseq marked as hidden.
+   */
+  public HiddenColumns propagateInsertions(SequenceI profileseq,
+          AlignmentView input);
+
 }