*/
package jalview.api;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.datamodel.AlignmentAnnotation;
* - a group defined on sequences in the alignment held by the view
*/
void addSequenceGroup(SequenceGroup sequenceGroup);
+
+ /**
+ * Returns true if autocalculated annotations are shown above other
+ * annotations, false if below
+ *
+ * @return
+ */
+ boolean isShowAutocalculatedAbove();
+
+ /**
+ * Sets the flag for whether autocalculated annotations are shown above (true)
+ * or below (false) other annotations
+ *
+ * @param showAutocalculatedAbove
+ */
+ void setShowAutocalculatedAbove(boolean showAutocalculatedAbove);
+
+ /**
+ * Sets the sort order to apply to annotations
+ *
+ * @param sortAnnotationsBy
+ */
+ void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy);
}