* @return
*/
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
+
+ /**
+ * Calculate the visible start and end index of an alignment. The result is
+ * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
+ *
+ * @param hiddenCols
+ * @return
+ */
+ public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
}