X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;fp=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=396ef2dcdcf0c113a98dd3bb58236e3fa89bd4de;hb=49428d3a57e4f4863acbdeb3f77049ed95efd6c3;hp=de794880c09116107c838861ae269d082b49be84;hpb=d579f105e3feca4b77ac93c52bb45f8cc39c39cd;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index de79488..396ef2d 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -375,12 +375,12 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 
    * @return
    */
-  Set<AlignedCodonFrame> getCodonFrames();
+  List<AlignedCodonFrame> getCodonFrames();
 
   /**
-   * Set the codon frame mappings (replacing any existing set).
+   * Set the codon frame mappings (replacing any existing list).
    */
-  void setCodonFrames(Set<AlignedCodonFrame> acfs);
+  void setCodonFrames(List<AlignedCodonFrame> acfs);
 
   /**
    * get codon frames involving sequenceI
@@ -524,4 +524,23 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return
    */
   public boolean hasValidSequence();
+
+  /**
+   * Update any mappings to 'virtual' sequences to compatible real ones, if
+   * present in the added sequences. Returns a count of mappings updated.
+   * 
+   * @param seqs
+   * @return
+   */
+  int realiseMappings(List<SequenceI> seqs);
+
+  /**
+   * Returns the first AlignedCodonFrame that has a mapping between the given
+   * dataset sequences
+   * 
+   * @param mapFrom
+   * @param mapTo
+   * @return
+   */
+  AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 }