X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=9d2d7f44fdc801a2c0e4ecd6133fa4b45ac80a19;hb=584c1b0136786968958e22e52b6ce51bd24511e5;hp=356548801f0a358b745f50c2612ed2fe4df8c862;hpb=a496dd6d71c9808c7a1c115ed5cf91ba4e246c21;p=jalview.git diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java index 3565488..9d2d7f4 100644 --- a/src/jalview/api/FeatureRenderer.java +++ b/src/jalview/api/FeatureRenderer.java @@ -38,17 +38,33 @@ public interface FeatureRenderer { /** - * compute the perceived colour for a given column position in sequenceI, - * taking transparency and feature visibility into account. + * 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. + *
+ * 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. + *
+ * 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. + *
+ * Returns null if there is no visible feature at the position. + *
+ * 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 sequenceI
- * - sequence providing features
- * @param r
- * - column position
+ * @param sequence
+ * @param column
+ * aligned column position (1..)
* @param g
* @return
*/
- Color findFeatureColour(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.
@@ -132,14 +148,27 @@ public interface FeatureRenderer
void setGroupVisibility(String group, boolean visible);
/**
- * Returns features at the specified position on the given sequence.
+ * Returns features at the specified aligned column on the given sequence.
+ * Non-positional features are not included. If the column has a gap, then
+ * enclosing features are included (but not contact features).
+ *
+ * @param sequence
+ * @param column
+ * aligned column position (1..)
+ * @return
+ */
+ List