+ boolean markColumnsContainingFeatures(boolean invert,
+ 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
+ */
+ 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
+ */
+ void sortAlignmentByFeatureDensity(List<String> typ);
+
+ /**
+ * add a features file of some kind to the current view
+ *
+ * @param file
+ * @param sourceType
+ * @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, DataSourceType sourceType,
+ boolean relaxedIdMatching);
+
+ /**
+ * mark columns containing highlighted regions (e.g. from search, structure
+ * highlight, or a mouse over event in another viewer)
+ *
+ * @param invert
+ * @param extendCurrent
+ * @param toggle
+ * @return
+ */
+ boolean markHighlightedColumns(boolean invert, boolean extendCurrent,
+ boolean toggle);