/** @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()); }