X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=c15bb99b84c393da6f4b0afacc731f3aa5c1f95c;hb=90ad4273c7105b7763247192e1c6739eed30ba4c;hp=4ae8ba29add38dc36920b878eeaaf90941ae97ba;hpb=0ebcd487f08f9873987d9a32edce7df47aa27927;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 4ae8ba2..c15bb99 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -305,7 +305,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return Alignment containing dataset sequences or null of this is a
    *         dataset.
    */
-  Alignment getDataset();
+  AlignmentI getDataset();
 
   /**
    * Set the associated dataset for the alignment, or create one.
@@ -313,7 +313,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @param dataset
    *          The dataset alignment or null to construct one.
    */
-  void setDataset(Alignment dataset);
+  void setDataset(AlignmentI dataset);
 
   /**
    * pads sequences with gaps (to ensure the set looks like an alignment)
@@ -363,14 +363,6 @@ public interface AlignmentI extends AnnotatedCollectionI
   void addCodonFrame(AlignedCodonFrame codons);
 
   /**
-   * add a set of aligned codons mappings for this alignment, apart from any
-   * duplicates which are ignored
-   * 
-   * @param codons
-   */
-  void addCodonFrames(Iterable<AlignedCodonFrame> codons);
-
-  /**
    * remove a particular codon frame reference from this alignment
    * 
    * @param codons