3253-omnibus save

[jalview.git] / src / jalview / api / FeatureRenderer.java

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 404c497..8aa2858 100644 (file)
--- 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)
@@ -280,4 +284,17 @@ public interface FeatureRenderer
    * @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);
 }