JAL-2438 unit test, fixes, Javadoc updates

[jalview.git] / src / jalview / api / FeatureRenderer.java

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 0d0adaa..839119d 100644 (file)
--- 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 +38,24 @@ public interface FeatureRenderer
 {
 
   /**
-   * compute the perceived colour for a given column position in sequenceI,
-   * taking transparency and feature visibility into account.
+   * 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.
+   * <p>
+   * 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.
+   * <p>
+   * This is provided for use by Structure Viewers and the Overview Window to
+   * get the feature colour of the rendered sequence.
    * 
-   * @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.
@@ -60,17 +67,15 @@ public interface FeatureRenderer
    * @param ft
    * @return display style for a feature
    */
-  Object getFeatureStyle(String ft);
+  FeatureColourI getFeatureStyle(String ft);
 
   /**
    * update the feature style for a particular feature
    * 
    * @param ft
    * @param ggc
-   *          - currently allows java.awt.Color and
-   *          jalview.schemes.GraduatedColor
    */
-  void setColour(String ft, Object ggc);
+  void setColour(String ft, FeatureColourI ggc);
 
   AlignViewportI getViewport();
 
@@ -85,7 +90,7 @@ public interface FeatureRenderer
    * 
    * @return
    */
-  Map<String, Object> getFeatureColours();
+  Map<String, FeatureColourI> getFeatureColours();
 
   /**
    * query the alignment view to find all features
@@ -100,7 +105,7 @@ public interface FeatureRenderer
    * 
    * @return
    */
-  Map<String, Object> getDisplayedFeatureCols();
+  Map<String, FeatureColourI> getDisplayedFeatureCols();
 
   /**
    * get all registered groups
@@ -134,7 +139,8 @@ 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
@@ -143,25 +149,19 @@ public interface FeatureRenderer
   List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res);
 
   /**
+   * get current displayed types, in ordering of rendering (on top last)
    * 
-   * @return true if the rendering platform supports transparency
-   */
-  boolean isTransparencyAvailable();
-
-  /**
-   * get current displayed types
-   * 
-   * @return
+   * @return a (possibly empty) list of feature types
    */
 
-  String[] getDisplayedFeatureTypes();
+  List<String> getDisplayedFeatureTypes();
 
   /**
    * get current displayed groups
    * 
-   * @return
+   * @return a (possibly empty) list of feature groups
    */
-  String[] getDisplayedFeatureGroups();
+  List<String> getDisplayedFeatureGroups();
 
   /**
    * display all features of these types
@@ -177,4 +177,19 @@ public interface FeatureRenderer
    */
   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();
 }