X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=8aa28581842e88b557b84de0232f8f269119c32b;hb=c7bc2d0abe568732fd9249c56b98370944a6e43f;hp=356548801f0a358b745f50c2612ed2fe4df8c862;hpb=a496dd6d71c9808c7a1c115ed5cf91ba4e246c21;p=jalview.git diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java index 3565488..8aa2858 100644 --- a/src/jalview/api/FeatureRenderer.java +++ b/src/jalview/api/FeatureRenderer.java @@ -20,8 +20,10 @@ */ package jalview.api; +import jalview.datamodel.MappedFeatures; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.FeatureMatcherSetI; import java.awt.Color; import java.awt.Graphics; @@ -38,17 +40,33 @@ 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.
@@ -116,7 +134,7 @@ public interface FeatureRenderer
List
+ * Returns null if
+ *
+ *
+ * This method does not check feature type visibility.
+ *
+ * @param feature
+ * @return
+ */
+ Color getColour(SequenceFeature feature);
+
+ /**
+ * Answers true if feature would be shown, else false. A feature is shown if
+ *
+ *
+ *
+ * @param feature
+ * @return
+ */
+ boolean isVisible(SequenceFeature feature);
+
+ /**
+ * Answers a bean containing a mapping, and a list of visible features in this
+ * alignment at a position (or range) which is mappable from the given sequence
+ * residue position in a mapped alignment. Features are returned in render order
+ * of feature type (on top last), with order within feature type undefined. If
+ * no features or mapping are found, answers null.
+ *
+ * @param sequence
+ * @param pos
+ * @return
+ */
+ MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence, int pos);
}