java 完全匹配_全序列匹配（java)

importjava.util.Scanner;classData{intleft, diagonal, up;

Data(){}

Data(int a, int b, intc){

left=a;

diagonal=b;

up=c;

}publicString toString(){return String.format("(%2d, %2d, %2d)",left, diagonal, up);

}

}public classBlast {//反转字符串

public staticString reverse(String s) {

String str= "";char[] a =s.toCharArray();for (int i = a.length - 1; i >= 0; i--) {

str+=a[i];

}returnstr;

}public staticString pairaln(String s1, String s2) {//得分情况

int MATCH = 2; //匹配

int MISMATCH = -1; //匹配失败

int GAP = -1; //存在gap//初始化

int length1 = s1.length() + 1;int length2 = s2.length() + 1;int[][] score = new int[length2][length1];int[][] pointer = new int[length2][length1];

Data[][] data= newData[length2][length1];

score[0][0] = 0;

pointer[0][0] = 0; //记录选择了那个数据，按照left,diagonal,up顺序

data[0][0] = new Data(0, 0, 0);for (int j = 1; j < length1; j++) {

score[0][j] = GAP *j;

pointer[0][j] = 1;

data[0][j] = new Data(GAP * j, GAP * j, GAP *j);

}for (int i = 1; i < length2; i++) {

score[i][0] = GAP *i;

pointer[i][0] = 3;

data[i][0] = new Data(GAP * i, GAP * i, GAP *i);

}//dp

for (int i = 1; i < length2; i++) {int letter2 = s2.charAt(i - 1);for (int j = 1; j < length1; j++) {intdiagonal_score, left_score, up_score;int letter1 = s1.charAt(j - 1);

diagonal_score= letter1 == letter2 ?score[i- 1][j - 1] + MATCH : score[i - 1][j - 1] +MISMATCH;

up_score= score[i - 1][j] +GAP;

left_score= score[i][j - 1] +GAP;

data[i][j]= newData(left_score, diagonal_score, up_score);if (diagonal_score >=Math.max(up_score, left_score)) {

score[i][j]=diagonal_score;

pointer[i][j]= 2;

}else{if (up_score >=left_score) {

score[i][j]=up_score;

pointer[i][j]= 3;

}else{

score[i][j]=left_score;

pointer[i][j]= 1;

}

}

}

}//得分矩阵

for (int k = 0; k < length2; k++) {for (int l = 0; l < length1; l++) {

System.out.print(data[k][l]+ " ");

}

System.out.println();

}//回溯

int j = length1 - 1;int i = length2 - 1;

String align1= "";

String align2= "";while (true) {if (pointer[i][j] == 0) break;if (pointer[i][j] == 2) {

align1+= s1.charAt(j - 1);

align2+= s2.charAt(i - 1);

i--;

j--;

}if (pointer[i][j] == 1) {

align1+= s1.charAt(j - 1);

align2+= "-";

j--;

}if (pointer[i][j] == 3) {

align1+= "-";

align2+= s2.charAt(i - 1);

i--;

}

}//翻转

align1 =reverse(align1);

align2=reverse(align2);return "序列：\n" + s1 + "\n" + s2 + "\n" + "比对结果：\n" + align1 + "\n" + align2 + "\n";

}public static voidmain(String[] args) {

Scanner in= newScanner(System.in);

System.out.println("请输入第一条序列：");

String seq1=in.next();

System.out.println("请输入第二条序列：");

String seq2=in.next();

System.out.println(pairaln(seq1, seq2));

}

}