X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=8aa28581842e88b557b84de0232f8f269119c32b;hb=1b378087ec2d5be9b290cd63c45bfdb9e75269fb;hp=ef0abbd1b95ea9487f33a1bebf35c3bb293ebb86;hpb=f8b17a9e7363b8a9e7cd12d61bc6d611c7c97d7d;p=jalview.git

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index ef0abbd..8aa2858 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -20,9 +20,10 @@
  */
 package jalview.api;
 
+import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.util.matcher.KeyedMatcherSetI;
+import jalview.datamodel.features.FeatureMatcherSetI;
 
 import java.awt.Color;
 import java.awt.Graphics;
@@ -161,15 +162,18 @@ public interface FeatureRenderer
   List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column);
 
   /**
-   * Returns features at the specified residue position on the given sequence.
-   * Non-positional features are not included.
+   * Returns features at the specified residue positions on the given sequence.
+   * Non-positional features are not included. Features are returned in render
+   * order of their feature type (last is on top). Within feature type, ordering
+   * is undefined.
    * 
    * @param sequence
-   * @param resNo
-   *          residue position (start..)
+   * @param fromResNo
+   * @param toResNo
    * @return
    */
-  List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence, int resNo);
+  List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
+          int fromResNo, int toResNo);
 
   /**
    * get current displayed types, in ordering of rendering (on top last)
@@ -223,14 +227,14 @@ public interface FeatureRenderer
    * @param featureType
    * @return
    */
-  KeyedMatcherSetI getFeatureFilter(String featureType);
+  FeatureMatcherSetI getFeatureFilter(String featureType);
 
   /**
-   * Answers a shallow copy of the feature filters map
+   * Answers the feature filters map
    * 
    * @return
    */
-  public Map<String, KeyedMatcherSetI> getFeatureFilters();
+  public Map<String, FeatureMatcherSetI> getFeatureFilters();
 
   /**
    * Sets the filters for the feature type, or removes them if a null or empty
@@ -239,14 +243,14 @@ public interface FeatureRenderer
    * @param featureType
    * @param filter
    */
-  void setFeatureFilter(String featureType, KeyedMatcherSetI filter);
+  void setFeatureFilter(String featureType, FeatureMatcherSetI filter);
 
   /**
    * Replaces all feature filters with the given map
    * 
    * @param filters
    */
-  void setFeatureFilters(Map<String, KeyedMatcherSetI> filters);
+  void setFeatureFilters(Map<String, FeatureMatcherSetI> filters);
 
   /**
    * Returns the colour for a particular feature instance. This includes
@@ -255,14 +259,42 @@ public interface FeatureRenderer
    * <p>
    * Returns null if
    * <ul>
-   * <li>feature type is not visible, or</li>
    * <li>feature group is not visible, or</li>
    * <li>feature values lie outside any colour threshold, or</li>
    * <li>feature is excluded by filter conditions</li>
    * </ul>
+   * This method does not check feature type visibility.
    * 
    * @param feature
    * @return
    */
   Color getColour(SequenceFeature feature);
+
+  /**
+   * Answers true if feature would be shown, else false. A feature is shown if
+   * <ul>
+   * <li>its feature type is set to visible</li>
+   * <li>its feature group is either null, or set to visible</li>
+   * <li>it is not excluded by a colour threshold on score or other numeric
+   * attribute</li>
+   * <li>it is not excluded by a filter condition</li>
+   * </ul>
+   * 
+   * @param feature
+   * @return
+   */
+  boolean isVisible(SequenceFeature feature);
+
+  /**
+   * Answers a bean containing a mapping, and a list of visible features in this
+   * alignment at a position (or range) which is mappable from the given sequence
+   * residue position in a mapped alignment. Features are returned in render order
+   * of feature type (on top last), with order within feature type undefined. If
+   * no features or mapping are found, answers null.
+   * 
+   * @param sequence
+   * @param pos
+   * @return
+   */
+  MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence, int pos);
 }