import jalview.datamodel.SequenceI;
import java.awt.Color;
+import java.awt.Graphics;
import java.util.List;
import java.util.Map;
{
/**
- * 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.
+ * <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
+ * from it. In this case, the returned feature colour is not the composite
+ * colour but that of the last feature drawn.
+ * <p>
+ * 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.
+ * <p>
+ * Returns null if there is no visible feature at the position.
+ * <p>
+ * 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.
*/
void setVisible(String featureType);
+ /**
+ * Sets the transparency value, between 0 (full transparency) and 1 (no
+ * transparency)
+ *
+ * @param value
+ */
+ void setTransparency(float value);
+
+ /**
+ * Returns the transparency value, between 0 (full transparency) and 1 (no
+ * transparency)
+ *
+ * @return
+ */
+ float getTransparency();
}