*/
package jalview.api;
+import java.util.List;
+
/**
* prototype abstract controller for a Jalview alignment view
*
* @return true if operation affected state
*/
boolean markColumnsContainingFeatures(boolean invert,
- boolean extendCurrent, boolean clearColumns, String featureType);
+ boolean extendCurrent, boolean toggle, String featureType);
/**
- * sort the alignment or current selection by average score over the given set of features
- * @param typ list of feature names or null to use currently displayed features
+ * sort the alignment or current selection by average score over the given set
+ * of features
+ *
+ * @param typ
+ * list of feature names or null to use currently displayed features
*/
- void sortAlignmentByFeatureScore(String[] typ);
+ void sortAlignmentByFeatureScore(List<String> typ);
/**
- * sort the alignment or current selection by distribution of the given set of features
- * @param typ list of feature names or null to use currently displayed features
+ * sort the alignment or current selection by distribution of the given set of
+ * features
+ *
+ * @param typ
+ * list of feature names or null to use currently displayed features
*/
- void sortAlignmentByFeatureDensity(String[] typ);
+ void sortAlignmentByFeatureDensity(List<String> typ);
/**
* add a features file of some kind to the current view