X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=5477f57f33ce6cf0a5a073e7b02affc112b0b2fb;hb=65d6d09cd08743d481d39521bb0298ea683888f8;hp=debad16c3b8cb1bce84692a2d9098ecbc2743d7d;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index debad16..5477f57 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
  * 
@@ -23,8 +23,6 @@ package jalview.api;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 
-import java.awt.Color;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 
@@ -37,42 +35,137 @@ import java.util.Map;
 public interface FeatureRenderer
 {
 
-  Color findFeatureColour(Color col, SequenceI sequenceI, int r);
-
+  /**
+   * compute the perceived colour for a given column position in sequenceI,
+   * taking transparency and feature visibility into account.
+   * 
+   * @param col
+   *          - background colour (due to alignment/group shading schemes, etc).
+   * @param sequenceI
+   *          - sequence providing features
+   * @param r
+   *          - column position
+   * @return
+   */
+  ColorI findFeatureColour(ColorI col, SequenceI sequenceI, int r);
+
+  /**
+   * 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 featureType
+   * @param featureColour
+   */
+  void setColour(String featureType, FeatureColourI featureColour);
 
   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);
 
+  /**
+   * locate features at a particular position on the given sequence
+   * 
+   * @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);
 
 }