JAL-2438 Javadoc updates

diff --git a/src/jalview/renderer/seqfeatures/FeatureColourFinder.java b/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
index 6f4d4de..761f418 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
+++ b/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
@@ -41,14 +41,16 @@ public class FeatureColourFinder
   /**
    * Answers the feature colour to show for the given sequence and column
    * position. This delegates to the FeatureRenderer to find the colour, which
-   * will depend on feature location, visibility, ordering, and whether or not
-   * transparency is applied. For feature rendering with transparency, this
-   * class provides a dummy 'offscreen' graphics context where multiple feature
-   * colours can be overlaid and the combined colour read back.
+   * will depend on feature location, visibility, ordering, colour scheme, and
+   * whether or not transparency is applied. For feature rendering with
+   * transparency, this class provides a dummy 'offscreen' graphics context
+   * where multiple feature colours can be overlaid and the combined colour read
+   * back.
    * 
    * @param defaultColour
    * @param seq
    * @param column
+   *          alignment column position (base zero)
    * @return
    */
   public Color findFeatureColour(Color defaultColour, SequenceI seq,

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 100b58f..84c9477 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -550,9 +550,10 @@ public abstract class FeatureRendererModel implements
   }
 
   /**
-   * Returns the configured colour for a specific feature using current feature
-   * settings. This does not include any consideration of feature visibility,
-   * colour transparency, graduated colour shading etc.
+   * Returns the configured colour for a particular feature instance. This
+   * includes calculation of 'colour by label', or of a graduated score colour,
+   * if applicable. It does not take into account feature visibility or colour
+   * transparency.
    * 
    * @param feature
    * @return