X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=762350e161663cfb719fe71d99a63bab608535a7;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=861f337bb51e79622c8d2fb37f1aa601b44f0afa;hpb=3740241b6d0dfa109dc81847afe58f17497c39e8;p=jalview.git

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 861f337..762350e 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -20,15 +20,17 @@
  */
 package jalview.api;
 
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.FeatureMatcherSetI;
-
 import java.awt.Color;
 import java.awt.Graphics;
+import java.beans.PropertyChangeListener;
 import java.util.List;
 import java.util.Map;
 
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
+
 /**
  * Abstract feature renderer interface
  * 
@@ -150,19 +152,22 @@ public interface FeatureRenderer
 
   /**
    * Returns visible features at the specified aligned column on the given
-   * sequence. Non-positional features are not included. If the column has a gap,
-   * then enclosing features are included (but not contact features).
+   * sequence. Non-positional features are not included. If the column has a
+   * gap, then enclosing features are included (but not contact features).
    * 
    * @param sequence
    * @param column
    *          aligned column position (1..)
    * @return
    */
-  List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column);
+  List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence,
+          int column);
 
   /**
    * Returns features at the specified residue positions on the given sequence.
-   * Non-positional features are not included.
+   * 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 fromResNo
@@ -266,4 +271,61 @@ public interface FeatureRenderer
    * @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();
+
+  /**
+   * register as a listener for notifyFeaturesChanged events
+   * 
+   * @param ourListener
+   */
+  void addPropertyChangeListener(PropertyChangeListener ourListener);
+
+  /**
+   * remove a listener for notifyFeaturesChanged events
+   * 
+   * @param ourListener
+   */
+  void removePropertyChangeListener(PropertyChangeListener ourListener);
+
+  /**
+   * 
+   * @return associated alignment panel for this feature renderer (may return
+   *         null)
+   */
+  AlignmentViewPanel getAlignPanel();
+
 }