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  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)];
  }
}