X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=558b38d69665439b4e5e65b7081f4d10664be707;hb=30bc1314d4206cafea412dcd9decdea7e318481f;hp=34a5ff2bb7c265f154541510160687b591e7f517;hpb=77b038f418aea84563953ad94f839592317ea500;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 34a5ff2..558b38d 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -267,4 +267,39 @@ public interface AlignmentI
    * @return hashtable of alignment properties (or null if none are defined)
    */
   public Hashtable getProperties();
+
+  /**
+   * add a reference to a frame of aligned codons for this alignment
+   * @param codons
+   */
+  public void addCodonFrame(AlignedCodonFrame codons);
+  /**
+   * remove a particular codon frame reference from this alignment
+   * @param codons
+   * @return true if codon frame was removed.
+   */
+  public boolean removeCodonFrame(AlignedCodonFrame codons);
+  /**
+   * get all codon frames associated with this alignment
+   * @return
+   */
+  public AlignedCodonFrame[] getCodonFrames();
+  /**
+   * get a particular codon frame
+   * @param index
+   * @return
+   */
+  public AlignedCodonFrame getCodonFrame(int index);
+  /**
+   * get codon frames involving sequenceI
+   */
+  public AlignedCodonFrame[] getCodonFrame(SequenceI seq);
+  /**
+   * find sequence with given name in alignment
+   * @param token name to find
+   * @param b true implies that case insensitive matching will <em>also</em> be tried 
+   * @return matched sequence or null
+   */
+  public SequenceI findName(String token, boolean b);
+  
 }