JAL-2438 clarify code and javadoc, reinstate updateFeatures() check

[jalview.git] / src / jalview / api / FeatureRenderer.java

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index b1813a6..7123b8c 100644 (file)
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -38,19 +38,32 @@ public interface FeatureRenderer
 {
 
   /**
-   * compute the perceived colour for a given column position in sequenceI,
-   * taking transparency and feature visibility into account.
-   * 
-   * @param col
-   *          - background colour (due to alignment/group shading schemes, etc).
-   * @param sequenceI
-   *          - sequence providing features
-   * @param r
-   *          - column position
+   * Computes the feature colour for a given sequence and column position,
+   * taking into account sequence feature locations, feature colour schemes,
+   * render ordering, feature and feature group visibility, and transparency.
+   * <p>
+   * The graphics argument should be provided if transparency is applied
+   * (getTransparency() < 1). With feature transparency, visible features are
+   * written to the graphics context and the composite colour may be read off
+   * from it. In this case, the returned feature colour is not the composite
+   * colour but that of the last feature drawn.
+   * <p>
+   * If no transparency applies, then the graphics argument may be null, and the
+   * returned colour is the one that would be drawn for the feature.
+   * <p>
+   * Returns null if there is no visible feature at the position.
+   * <p>
+   * This is provided to support rendering of feature colours other than on the
+   * sequence alignment, including by structure viewers and the overview window.
+   * Note this method takes no account of whether the sequence or column is
+   * hidden.
+   * 
+   * @param sequence
+   * @param column
    * @param g
    * @return
    */
-  Color findFeatureColour(Color col, SequenceI sequenceI, int r, Graphics g);
+  Color findFeatureColour(SequenceI sequence, int column, Graphics g);
 
   /**
    * trigger the feature discovery process for a newly created feature renderer.