/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
boolean markColumnsContainingFeatures(boolean invert,
boolean extendCurrent, boolean clearColumns, 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
+ */
+ void sortAlignmentByFeatureScore(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
+ */
+ void sortAlignmentByFeatureDensity(String[] typ);
+
+ /**
+ * add a features file of some kind to the current view
+ *
+ * @param file
+ * @param protocol
+ * @param relaxedIdMatching
+ * if true, try harder to match up IDs with local sequence data
+ * @return true if parsing resulted in something being imported to the view or
+ * dataset
+ */
+ public boolean parseFeaturesFile(String file, String protocol,
+ boolean relaxedIdMatching);
+
}