import java.util.Map;
/**
- * A data bean that holds the information to determine the colour scheme of an
- * alignment (or subgroup), consisting of
+ * A class that computes the colouring of an alignment (or subgroup). Currently
+ * the factors that may influence residue colouring are
* <ul>
- * <li>the colour scheme that determines the colour of a residue</li>
+ * <li>the colour scheme that provides a colour for each aligned residue</li>
* <li>any threshold for colour, based on percentage identity with consensus</li>
- * <li>any graduation based on consensus</li>
- * <li>the consensus data</li>
+ * <li>any graduation based on conservation of physico-chemical properties</li>
* </ul>
*
* @author gmcarstairs