*/
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
*
/**
* 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 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)
* <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
* @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();
+
}