X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=f89602fcf79beaf9c994ab342a32ef264dbd2a90;hb=ed52d72ae281a74a5496a605e51159931caa925c;hp=2b210cc9eef479fc628f4585e0fb9c6fb0aa4ee8;hpb=6bbf32c80d96e3ee32d38b9eb1478cd9dd249734;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2b210cc..f89602f 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -181,11 +181,12 @@ public interface AlignmentI
* Deletes a specific AlignmentAnnotation from the alignment,
* and removes its reference from any SequenceI object's annotation
* if and only if aa is contained within the alignment's annotation
- * vector.
+ * vector. Otherwise, it will do nothing.
*
* @param aa the annotation to delete
+ * @return true if annotation was deleted from this alignment.
*/
- public void deleteAnnotation(AlignmentAnnotation aa);
+ public boolean deleteAnnotation(AlignmentAnnotation aa);
/**
* Get the annotation associated with this alignment
@@ -266,4 +267,47 @@ 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 also be tried
+ * @return matched sequence or null
+ */
+ public SequenceI findName(String token, boolean b);
+ /**
+ * find next sequence with given name in alignment starting after a given sequence
+ * @param startAfter the sequence after which the search will be started (usually the result of the last call to findName)
+ * @param token name to find
+ * @param b true implies that case insensitive matching will also be tried
+ * @return matched sequence or null
+ */
+ public SequenceI findName(SequenceI startAfter, String token, boolean b);
+
}