HiddenSequences getHiddenSequences();
+ HiddenColumns getHiddenColumns();
+
/**
* Compact representation of alignment
*
*/
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);
+ public void setHiddenColumns(HiddenColumns cols);
}