Repeated DNA Sequences

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最新推荐文章于 2022-07-28 15:01:27 发布

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All DNA is composed of a series of nucleotides abbreviated as A, C, G, and T, for example: "ACGAATTCCG". When studying DNA, it is sometimes useful to identify repeated sequences within the DNA.

Write a function to find all the 10-letter-long sequences (substrings) that occur more than once in a DNA molecule.

For example,

Given s = "AAAAACCCCCAAAAACCCCCCAAAAAGGGTTT",

Return:
["AAAAACCCCC", "CCCCCAAAAA"].

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解题技巧：

该题主要采用了两种技巧：位运算、hash。

考虑将ACGT进行二进制编码，即：A -> 00, C -> 01, G -> 10, T -> 11；在编码的情况下，每10位字符串的组合即为一个数字，且10位的字符串有20位，一般来说int有4个字节，32位，即可以用于对应一个10位的字符串。例如：ACGTACGTAC -> 00011011000110110001

20位的二进制数，至多有2^20种组合，因此hash table的大小为2^20，即1024 * 1024，将hash table设计为bool hashTable[1024 * 1024];

在处理字符串时，每次向右移动1位字符，相当于字符串对应的int值左移2位，再将其最低2位置为新的字符的编码值，最后将高2位置0；得到当前的子字符串对应的值val后，判断该值是否出现过，如果未出现，则将hasTable[val]设置为true，否则，将当前的子字符串存入到set容器中

代码：

#include <iostream>
#include <string>
#include <vector>
#include <set>
#include <mem.h>
#include <map>
using namespace std;

vector<string> findRepeatedDnaSequences(string s)
{
    vector<string> res;
    if(s.length() < 10) return res;

    map<char,int> mp;
    mp['A'] = 0;
    mp['C'] = 1;
    mp['G'] = 2;
    mp['T'] = 3;

    bool exist[1024*1024];
    memset(exist, false, sizeof(exist));

    int val = 0;
    for(int i = 0; i < 10; i ++)
    {
        val <<= 2;
        val |= mp[s[i]];
    }
    exist[val] = true;

    set<string> tmp;
    for(int i = 10; i < s.length(); i ++)
    {
        val <<= 2;
        val |= mp[s[i]];
        val &= ~(0x300000);
        if(exist[val]) tmp.insert(s.substr(i-9,10));
        else exist[val] = true;
    }
    set<string>::iterator it = tmp.begin();
    while(it != tmp.end())
    {
        res.push_back(*it);
        it++;
    }
    return res;
}

int main()
{
    vector<string> res;
    string s;
    cin >> s;
    res = findRepeatedDnaSequences(s);
    for(int i = 0; i < res.size(); i ++)
    {
        cout<<res[i]<<' ';
    }
}