X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=7123b8ca896aa453de720c829122df5298bf4853;hb=b47e77607ffc252a8b85120126070ed00af53757;hp=21319fdf00fc1ac04c8a15e1139abca1b11f6a99;hpb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;p=jalview.git diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java index 21319fd..7123b8c 100644 --- a/src/jalview/api/FeatureRenderer.java +++ b/src/jalview/api/FeatureRenderer.java @@ -24,6 +24,7 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import java.awt.Color; +import java.awt.Graphics; import java.util.List; import java.util.Map; @@ -37,18 +38,32 @@ 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 col
- * - background colour (due to alignment/group shading schemes, etc).
- * @param sequenceI
- * - sequence providing features
- * @param r
- * - column position
+ * @param sequence
+ * @param column
+ * @param g
* @return
*/
- Color findFeatureColour(Color col, SequenceI sequenceI, int r);
+ Color findFeatureColour(SequenceI sequence, int column, Graphics g);
/**
* trigger the feature discovery process for a newly created feature renderer.
@@ -132,7 +147,8 @@ public interface FeatureRenderer
void setGroupVisibility(String group, boolean visible);
/**
- * locate features at a particular position on the given sequence
+ * Returns features at the specified position on the given sequence.
+ * Non-positional features are not included.
*
* @param sequence
* @param res
@@ -141,25 +157,19 @@ public interface FeatureRenderer
List