* - null or specific sequence reference
* @param groupRef
* - null or specific group reference
- * @param method
- * - CalcId for the annotation (must match)
*
* @return existing annotation matching the given attributes
*/
boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef);
/**
+ * like findOrCreateAnnotation - looks for an existing alignment annotation
+ * row with matching name, calcId, sequenceRef, groupRef and autoCalculated
+ * flag and updates it from the annotation. If none is found the annotation is
+ * added directly.
+ *
+ * @param ala
+ * @return ala or the annotation row that was updated.
+ */
+ AlignmentAnnotation updateFromOrCopyAnnotation(AlignmentAnnotation ala);
+
+ /**
* move the given group up or down in the alignment by the given number of
* rows. Implementor assumes given group is already present on alignment - no
* recalculations are triggered.
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
/**
- * Set the hidden columns collection on the alignment
+ * Set the hidden columns collection on the alignment. Answers true if the
+ * hidden column selection changed, else false.
*
* @param cols
+ * @return
*/
- public void setHiddenColumns(HiddenColumns cols);
+ public boolean setHiddenColumns(HiddenColumns cols);
+
+ /**
+ * Insert a sequence at a position in an alignment
+ *
+ * @param i
+ * The index of the position.
+ * @param snew
+ * The new sequence.
+ */
+ void insertSequenceAt(int i, SequenceI snew);
/**
* Set the first sequence as representative and hide its insertions. Typically
*/
public HiddenColumns propagateInsertions(SequenceI profileseq,
AlignmentView input);
-
}