X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=70c1e0726642bf3332398ca535bd06263d9f4cb0;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=22b0a457a2268a50a9b258eb87682c2fc133aee8;hpb=bcec956c0817f71f72a80a02066f1b57672304df;p=jalview.git

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 22b0a45..70c1e07 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -1,20 +1,180 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.api;
 
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Abstract feature renderer interface
+ * 
  * @author JimP
- *
+ * 
  */
 public interface FeatureRenderer
 {
 
+  /**
+   * 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
+   */
   Color findFeatureColour(Color col, SequenceI sequenceI, int r);
 
+  /**
+   * trigger the feature discovery process for a newly created feature renderer.
+   */
+  void featuresAdded();
+
+  /**
+   * 
+   * @param ft
+   * @return display style for a feature
+   */
+  Object 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);
+
+  AlignViewportI getViewport();
+
+  /**
+   * 
+   * @return container managing list of feature types and their visibility
+   */
+  FeaturesDisplayedI getFeaturesDisplayed();
+
+  /**
+   * get display style for all features types - visible or invisible
+   * 
+   * @return
+   */
+  Map<String, Object> getFeatureColours();
+
+  /**
+   * query the alignment view to find all features
+   * 
+   * @param newMadeVisible
+   *          - when true, automatically make newly discovered types visible
+   */
+  void findAllFeatures(boolean newMadeVisible);
+
+  /**
+   * get display style for all features types currently visible
+   * 
+   * @return
+   */
+  Map<String, Object> 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);
+
+  /**
+   * 
+   * @return true if the rendering platform supports transparency
+   */
+  boolean isTransparencyAvailable();
+
+  /**
+   * get current displayed types
+   * 
+   * @return
+   */
+
+  String[] getDisplayedFeatureTypes();
+
+  /**
+   * get current displayed groups
+   * 
+   * @return
+   */
+  String[] getDisplayedFeatureGroups();
+
+  /**
+   * display all features of these types
+   * 
+   * @param featureTypes
+   */
+  void setAllVisible(List<String> featureTypes);
+
+  /**
+   * display featureType
+   * 
+   * @param featureType
+   */
+  void setVisible(String featureType);
+
 }