+ /**
+ * Returns the colour for the given character. For use when the colour depends
+ * only on the symbol.
+ *
+ * @param c
+ * @return
+ */
+ Color findColour(char c);
+
+ /**
+ * Returns the possibly context dependent colour for the given symbol at the
+ * aligned position in the given sequence. For example, the colour may depend
+ * on the symbol's relationship to the consensus residue for the column.
+ *
+ * @param symbol
+ * @param position
+ * @param seq
+ * @return
+ */
+ Color findColour(char symbol, int position, SequenceI seq);
+
+ /**
+ * Assigns the given consensus profile for the colourscheme
+ */
+ void setConsensus(ProfilesI hconsensus);
+
+ /**
+ * Assigns the given conservation to the colourscheme
+ *
+ * @param c
+ */
+ void setConservation(Conservation c);
+
+ /**
+ * Enable or disable conservation shading for this colourscheme
+ *
+ * @param conservationApplied
+ */
+ void setConservationApplied(boolean conservationApplied);
+
+ /**
+ * Answers true if conservation shading is enabled for this colourscheme
+ *
+ * @return
+ */
+ boolean conservationApplied();