*/
package jalview.api;
+import jalview.datamodel.MappedFeatures;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcherSetI;
/**
* 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.
* @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();
+
}