X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=9d2d7f44fdc801a2c0e4ecd6133fa4b45ac80a19;hb=de27aab70330aed476328fd0eaf131581d7d352d;hp=839119ddeff232ff3a0e85383e9389d32b834742;hpb=846f3f1ad573cad309d41356af68887a4a3348eb;p=jalview.git diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java index 839119d..9d2d7f4 100644 --- a/src/jalview/api/FeatureRenderer.java +++ b/src/jalview/api/FeatureRenderer.java @@ -38,20 +38,29 @@ public interface FeatureRenderer { /** - * Returns the combined feature colour for a given sequence and column - * position, taking into account feature colour schemes, ordering, feature and - * feature group visibility, and transparency. Returns null if there is no - * visible feature at the 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. *
- * The Graphics argument is optional and may be null if no transparency is - * applied. With feature transparency, visible features are written to the - * graphics context and the composite colour can be read off. + * 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. *
- * This is provided for use by Structure Viewers and the Overview Window to - * get the feature colour of the rendered sequence. + * 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 sequence
* @param column
+ * aligned column position (1..)
* @param g
* @return
*/
@@ -139,14 +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