X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=fff3b38046f79cb282dd594b0998fe97c076a837;hb=1f029391e9e263b132a62eaefcc2fe68badacfd6;hp=cf3c8da9513d718ea8e3212e1a9fbe157eb17754;hpb=14b1b2a878190d5fffda298c4b9a901c72c74ad3;p=jalview.git

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index cf3c8da..fff3b38 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -20,6 +20,7 @@
  */
 package jalview.api;
 
+import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.FeatureMatcherSetI;
@@ -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)
@@ -255,14 +259,49 @@ 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);
+
+  /**
+   * Sends a message to let any registered parties know that something about
+   * feature rendering has changed
+   */
+  void notifyFeaturesChanged();
+
 }