+ /**
+ * create a new instance of the colourscheme configured to colour the given
+ * connection
+ *
+ * @param sg
+ * @param hiddenRepSequences
+ * @return copy of current scheme with any inherited settings transfered
+ */
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+