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;
List<String> getGroups(boolean visible);
/**
- * change visibility for a range of groups
+ * Set visibility for a list of groups
*
* @param toset
* @param visible
void setGroupVisibility(List<String> toset, boolean visible);
/**
- * change visibiilty of given group
+ * Set visibility of the given feature group
*
* @param group
* @param visible
void setGroupVisibility(String group, boolean visible);
/**
- * Returns 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).
+ * 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).
*
* @param sequence
* @param column
* @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