+
+ /**
+ * search for or create a specific annotation row on the alignment
+ * @param name name for annotation (must match)
+ * @param calcId calcId for the annotation (null or must match)
+ * @param autoCalc - value of autocalc flag for the annotation
+ * @param seqRef - 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
+ */
+ public AlignmentAnnotation findOrCreateAnnotation(String name, String calcId,
+ boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef);
+
+ /**
+ * 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.
+ * @param sg
+ * @param map
+ * @param up
+ * @param i
+ */
+ public void moveSelectedSequencesByOne(SequenceGroup sg,
+ Map<SequenceI, SequenceCollectionI> map, boolean up);