*/
package jalview.api;
-import jalview.io.DataSourceType;
-
import java.util.List;
+import jalview.io.DataSourceType;
+
/**
* prototype abstract controller for a Jalview alignment view
*
* @return true if parsing resulted in something being imported to the view or
* dataset
*/
- public boolean parseFeaturesFile(String file, DataSourceType sourceType,
+ public boolean parseFeaturesFile(Object 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);
+
+ /**
+ * copies each distinct highlighted region on the current view as a new
+ * sequence on the clipboard
+ *
+ * @return
+ */
+ boolean copyHighlightedRegionsToClipboard();
+
}