JAL-2360 JAL-2371 updates from review CR-JAL-1

[jalview.git] / src / jalview / schemes / CollectionColourScheme.java

diff --git a/src/jalview/schemes/CollectionColourScheme.java b/src/jalview/schemes/CollectionColourScheme.java
index a212795..ebff6e6 100644 (file)
--- a/src/jalview/schemes/CollectionColourScheme.java
+++ b/src/jalview/schemes/CollectionColourScheme.java
@@ -13,13 +13,12 @@ import java.awt.Color;
 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