import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.util.matcher.KeyedMatcherSetI;
+import jalview.datamodel.features.FeatureMatcherSetI;
import java.awt.Color;
import java.awt.Graphics;
* @param featureType
* @return
*/
- KeyedMatcherSetI getFeatureFilter(String featureType);
+ FeatureMatcherSetI getFeatureFilter(String featureType);
/**
- * Answers a shallow copy of the feature filters map
+ * Answers the feature filters map
*
* @return
*/
- public Map<String, KeyedMatcherSetI> getFeatureFilters();
+ public Map<String, FeatureMatcherSetI> getFeatureFilters();
/**
* Sets the filters for the feature type, or removes them if a null or empty
* @param featureType
* @param filter
*/
- void setFeatureFilter(String featureType, KeyedMatcherSetI filter);
+ void setFeatureFilter(String featureType, FeatureMatcherSetI filter);
/**
* Replaces all feature filters with the given map
*
* @param filters
*/
- void setFeatureFilters(Map<String, KeyedMatcherSetI> filters);
+ void setFeatureFilters(Map<String, FeatureMatcherSetI> filters);
/**
* Returns the colour for a particular feature instance. This includes
* <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);
}