/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * 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 jalview.io.DataSourceType;
+
+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
*
* @param file
- * @param protocol
+ * @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, String protocol,
+ 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);
+
}