JAL-3148 further bug fix to state of 'colourBy'

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

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index cf3c8da..dc9b9b9 100644 (file)
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -43,6 +43,11 @@ public interface FeatureRenderer
    * taking into account sequence feature locations, feature colour schemes,
    * render ordering, feature and feature group visibility, and transparency.
    * <p>
+   * Does not take into account global feature visibility (show features on or
+   * off). Test for this before calling this method if necessary. This allows,
+   * for example, feature colours to be computed for structures even if not 
+   * shown on the alignment.
+   * <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