* @param columnSelection
* @param selectionGroup
*/
- public CigarArray(AlignmentI alignment, ColumnSelection columnSelection,
+ public CigarArray(AlignmentI alignment, HiddenColumns hidden,
SequenceGroup selectionGroup)
{
this(constructSeqCigarArray(alignment, selectionGroup));
constructFromAlignment(alignment,
- columnSelection != null ? columnSelection.getHiddenColumns()
+ hidden != null ? hidden.getHiddenRegions()
: null, selectionGroup);
}
}
/**
- * @see Cigar.getSequenceAndDeletions
+ * @see CigarBase.getSequenceAndDeletions
* @param GapChar
* char
* @return Object[][]