java实现基因序列比较的示例代码

package algorithmClassSet.three;

import java.util.HashMap;
import java.util.Map;

/**
 * s1 = result[i-1][j-1] + getScore(X[i], Y[j]) 这个是x，y序列使用坐标匹配
 * s2 = result[i-1][j] + getScore(X[i], '-')  这个是x序列匹配y的 ‘-'
 * s3 = result[i][j-1] + getScore('-', Y[j]) 这个是y序列匹配x的 ‘-'
 * result[i][j] = max(s1,s2,s3)  找出三个中最大的就是所求的值
 * m*n
 */

public class GeneSequenceComparison {
  public static void main(String[] args) {
    dealIt();
  }

  private static void dealIt() {
    String[] X = {"A", "G", "T", "G", "A", "T", "G"};
    String[] Y = {"G", "T", "T", "A", "G"};
    int m = X.length + 1;
    int n = Y.length + 1;
    int[][] result = new int[m][n];

    for (int i = 1; i < m; i++) {
      result[i][0] = result[i - 1][0] + getScore(X[i - 1], "-");
    }
    for (int j = 1; j < n; j++) {
      result[0][j] = result[0][j - 1] + getScore("-", Y[j - 1]);
    }

    for (int i = 1; i < m; i++) {
      for (int j = 1; j < n; j++) {
        int s1 = result[i - 1][j - 1] + getScore(X[i - 1], Y[j - 1]);
        int s2 = result[i - 1][j] + getScore(X[i - 1], "-");
        int s3 = result[i][j - 1] + getScore("-", Y[j - 1]);
        int maxs = getMax(s1, s2, s3);
        result[i][j] = maxs;
      }
    }
    System.out.println("结果为：" + result[m - 1][n - 1]);


    for (int i = 0; i < m; i++) {
      for (int j = 0; j < n; j++) {
        System.out.print(result[i][j] + " ");
      }
      System.out.println();
    }
  }

  private static int getMax(int s1, int s2, int s3) {
    int flag = s1;
    if (flag < s2) {
      flag = s2;
    }
    if (flag < s3) {
      flag = s3;
    }
    return flag;
  }


  //传入值获取分数
  private static int getScore(String x, String y) {
    //x和y必须属于 ACGT-
    Map<String, Integer> map = new HashMap<>();
    map.put("A", 0);
    map.put("C", 1);
    map.put("G", 2);
    map.put("T", 3);
    map.put("-", 4);
    int[][] score = {
        {5, -1, -2, -1, -3},
        {-1, 5, -3, -2, -4},
        {-2, -3, 5, -2, -2},
        {-1, -2, -2, 5, -1},
        {-3, -4, -2, -1, -10000000}};
    return score[map.get(x)][map.get(y)];
  }
}