/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
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
* @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
* @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