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 4fd89c1..839119d 100644 (file)
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -24,7 +24,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
-import java.util.Hashtable;
+import java.awt.Graphics;
 import java.util.List;
 import java.util.Map;
 
@@ -37,42 +37,159 @@ import java.util.Map;
 public interface FeatureRenderer
 {
 
-  Color findFeatureColour(Color col, SequenceI sequenceI, int r);
-
+  /**
+   * 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 sequence
+   * @param column
+   * @param g
+   * @return
+   */
+  Color findFeatureColour(SequenceI sequence, int column, Graphics g);
+
+  /**
+   * trigger the feature discovery process for a newly created feature renderer.
+   */
   void featuresAdded();
 
-  Object getFeatureStyle(String ft);
-
-  void setColour(String ft, Object ggc);
+  /**
+   * 
+   * @param ft
+   * @return display style for a feature
+   */
+  FeatureColourI getFeatureStyle(String ft);
+
+  /**
+   * update the feature style for a particular feature
+   * 
+   * @param ft
+   * @param ggc
+   */
+  void setColour(String ft, FeatureColourI ggc);
 
   AlignViewportI getViewport();
 
+  /**
+   * 
+   * @return container managing list of feature types and their visibility
+   */
   FeaturesDisplayedI getFeaturesDisplayed();
 
-  Map<String,Object> getFeatureColours();
-
+  /**
+   * get display style for all features types - visible or invisible
+   * 
+   * @return
+   */
+  Map<String, FeatureColourI> getFeatureColours();
+
+  /**
+   * query the alignment view to find all features
+   * 
+   * @param newMadeVisible
+   *          - when true, automatically make newly discovered types visible
+   */
   void findAllFeatures(boolean newMadeVisible);
 
-  Map<String,Object> getDisplayedFeatureCols();
-
+  /**
+   * get display style for all features types currently visible
+   * 
+   * @return
+   */
+  Map<String, FeatureColourI> getDisplayedFeatureCols();
+
+  /**
+   * get all registered groups
+   * 
+   * @return
+   */
   List<String> getFeatureGroups();
 
+  /**
+   * get groups that are visible/invisible
+   * 
+   * @param visible
+   * @return
+   */
   List<String> getGroups(boolean visible);
 
+  /**
+   * change visibility for a range of groups
+   * 
+   * @param toset
+   * @param visible
+   */
   void setGroupVisibility(List<String> toset, boolean visible);
 
+  /**
+   * change visibiilty of given group
+   * 
+   * @param group
+   * @param visible
+   */
   void setGroupVisibility(String group, boolean visible);
 
+  /**
+   * Returns features at the specified position on the given sequence.
+   * Non-positional features are not included.
+   * 
+   * @param sequence
+   * @param res
+   * @return
+   */
   List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res);
 
-  boolean isTransparencyAvailable();
-
-  String[] getDisplayedFeatureTypes();
-
-  String[] getDisplayedFeatureGroups();
-
+  /**
+   * get current displayed types, in ordering of rendering (on top last)
+   * 
+   * @return a (possibly empty) list of feature types
+   */
+
+  List<String> getDisplayedFeatureTypes();
+
+  /**
+   * get current displayed groups
+   * 
+   * @return a (possibly empty) list of feature groups
+   */
+  List<String> getDisplayedFeatureGroups();
+
+  /**
+   * display all features of these types
+   * 
+   * @param featureTypes
+   */
   void setAllVisible(List<String> featureTypes);
 
+  /**
+   * display featureType
+   * 
+   * @param featureType
+   */
   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();
 }