Formatter formatter = new AlFormatter(getOut());
if (alignmentList == null) {
alignmentList = parser.parse();
}
alignmentList = filter.apply(alignmentList);
formatter.format(alignmentList);
}
private AlignAlgorithm createAlgorithm(CommandLine commandLine,
List<Alignment> alignmentList) {
String cls = commandLine.getOptionValue('c');