Rosalind Java|Matching Random Motifs

Rosalind编程问题之计算随机序列出现并匹配待比对序列的概率。
跟Rosalind Java|Introduction to Random Strings有异曲同工之妙。

Matching Random Motifs

Problem：
Our aim in this problem is to determine the probability with which a given motif (a known promoter, say) occurs in a randomly constructed genome. Unfortunately, finding this probability is tricky; instead of forming a long genome, we will form a large collection of smaller random strings having the same length as the motif; these smaller strings represent the genome’s substrings, which we can then test against our motif.

Given a probabilistic event A, the complement of A is the collection Ac of outcomes not belonging to A. Because Ac takes place precisely when A does not, we may also call Ac “not A.”

For a simple example, if A is the event that a rolled die is 2 or 4, then Pr(A)=13. Ac is the event that the die is 1, 3, 5, or 6, and Pr(Ac)=23. In general, for any event we will have the identity that Pr(A)+Pr(Ac)=1.

Given: A positive integer N≤100000, a number x between 0 and 1, and a DNA string s of length at most 10 bp.
Sample input：

90000 0.6
ATAGCCGA

Return: The probability that if N random DNA strings having the same length as s are constructed with GC-content x (see “Introduction to Random Strings”), then at least one of the strings equals s. We allow for the same random string to be created more than once.
Sample output：

0.689

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本题给出我们90000条长度和ATAGCCGA一样的序列，这些序列有相同的GC比例0.6。需要我们计算90000条序列中至少一条序列等于给出序列的概率（ATAGCCGA）。有些朋友可能提问，给出的GC比例为0.6，并不等于给出序列（ATAGCCGA）的GC比。在这里GC含量可以理解为GC出现的概率，从而反推AT出现的概率。否则两条GC比例不同但长度相同的序列永远不可能相等。

解题思路如下：
1.读取三个输入数据。
2.统计给出序列的GC数和AT数，根据GC比例计算G/C以及A/T出现的概率。
3.结合第二步，计算给出序列与未知序列相同的概率p。
4.结合第三步，计算给出序列与未知序列不相同的概率1-p。
5.至少一个匹配给出序列的概率等于1-（1-p）ⁿ，最后四舍五入到三位小数。

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代码如下：

public class Matching_Random_Motifs {
    public static void main(String[] args) {
        //1.输入序列个数
        Scanner sc = new Scanner(System.in);
        System.out.println("请输入序列个数n：");
        int n = sc.nextInt();
        //输入GC比例
        Scanner sr = new Scanner(System.in);
        System.out.println("请输入GC比例：");
        Double GC = sr.nextDouble();
        //输入待比对序列
        Scanner sk = new Scanner(System.in);
        System.out.println("请输入示例序列：");
        String DNA = sk.nextLine();

        //2.计算有相同GC比例和长度的序列中等于待比对DNA的概率
        int ATDNA = 0;
        int GCDNA = 0;
        for (int i = 0; i < DNA.length(); i++) {
            switch (DNA.charAt(i)) {
                //括号中的输出类型为char类型，匹配后面的字符时需要将字符加单引号转化为对应的ASCII码方可匹配。
                case 'A':
                case 'T':
                    ATDNA++;
                    break;
                case 'C':
                case 'G':
                    GCDNA++;
                    break;
                default:
                    break;
            }
        }
        double prob = Math.pow(GC / 2, GCDNA) * Math.pow((1 - GC) / 2, ATDNA);
        double randomprob = 1 - Math.pow(1 - prob, n);
        System.out.println((float) (Math.round(randomprob * 1000)) / 1000);//四舍五入时分子一定要转化成浮点型，否则会默认整数型输出并舍为0
    }
}