X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=9d2d7f44fdc801a2c0e4ecd6133fa4b45ac80a19;hb=d5a877fec053515bfd780d289ace37cbb85a357c;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.
+   * <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 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<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column);
+
+  /**
+   * Returns features at the specified residue position on the given sequence.
    * Non-positional features are not included.
    * 
    * @param sequence
-   * @param res
+   * @param resNo
+   *          residue position (start..)
    * @return
    */
-  List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res);
+  List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence, int resNo);
 
   /**
    * get current displayed types, in ordering of rendering (on top last)
@@ -150,9 +179,9 @@ public interface FeatureRenderer
   List<String> getDisplayedFeatureTypes();
 
   /**
-   * get current displayed groups
+   * Returns a (possibly empty) list of currently visible feature groups
    * 
-   * @return a (possibly empty) list of feature groups
+   * @return
    */
   List<String> getDisplayedFeatureGroups();
 
@@ -185,4 +214,5 @@ public interface FeatureRenderer
    * @return
    */
   float getTransparency();
+
 }