/** @param args */
public static void main(String[] args) {
NWAligner nw = new NWAligner(100);
// Scanner scanner = new Scanner(System.in);
// Tools.debug("每行输入一个字符串");
// lcs.setSequences(scanner.nextLine(), scanner.nextLine());
String a = "A-";
String b = "A-";
Tools.debug(a);
Tools.debug(b);
nw.setScoringMatrixName("blosum50");
nw.setGapOpen(8);
// nw.setScoringMatrixName("pam250");
// nw.setGapOpen(5);
Tools.debug(nw.align(a, b).trace().getScore());
}
