dp-(LCS 基因匹配)

Human Gene Functions

Description

It is well known that a human gene can be considered as a sequence, consisting of four nucleotides, which are simply denoted by four letters, A, C, G, and T. Biologists have been interested in identifying human genes and determining their functions, because these can be used to diagnose human diseases and to design new drugs for them.

A human gene can be identified through a series of
time-consuming biological experiments, often with the help of computer
programs. Once a sequence of a gene is obtained, the next job is to
determine its function.

One of the methods for biologists to use in determining the function
of a new gene sequence that they have just identified is to search a
database with the new gene as a query. The database to be searched
stores many gene sequences and their functions – many researchers have
been submitting their genes and functions to the database and the
database is freely accessible through the Internet.

A database search will return a list of gene sequences from the database that are similar to the query gene.

Biologists assume that sequence similarity often implies
functional similarity. So, the function of the new gene might be
one of the functions that the genes from the list have. To exactly
determine which one is the right one another series of biological
experiments will be needed.

Your job is to make a program that compares two genes and determines
their similarity as explained below. Your program may be used as a part
of the database search if you can provide an efficient one.

Given two genes AGTGATG and GTTAG, how similar are they? One of the methods to measure the similarity

of two genes is called alignment. In an alignment, spaces are inserted, if necessary, in appropriate positions of

the genes to make them equally long and score the resulting genes according to a scoring matrix.

For example, one space is inserted into AGTGATG to result in
AGTGAT-G, and three spaces are inserted into GTTAG to result in
–GT--TAG. A space is denoted by a minus sign (-). The two genes
are now of equal

length. These two strings are aligned:

AGTGAT-G

-GT--TAG

In this alignment, there are four matches, namely, G in the second
position, T in the third, T in the sixth, and G in the eighth. Each
pair of aligned characters is assigned a score according to the
following scoring matrix.

denotes that a space-space match is not allowed. The score
of the alignment above is (-3)+5+5+(-2)+(-3)+5+(-3)+5=9.

Of course, many other alignments are possible. One is shown below (a
different number of spaces are inserted into different positions):

AGTGATG

-GTTA-G

This alignment gives a score of (-3)+5+5+(-2)+5+(-1) +5=14. So,
this one is better than the previous one. As a matter of fact, this one
is optimal since no other alignment can have a higher score. So, it is
said that the

similarity of the two genes is 14.

Input

The
input consists of T test cases. The number of test cases ) (T is
given in the first line of the input file. Each test case consists of
two lines: each line contains an integer, the length of a gene, followed
by a gene sequence. The length of each gene sequence is at least one
and does not exceed 100.

Output

The output should print the similarity of each test case, one per line.

Sample Input

2
7 AGTGATG
5 GTTAG
7 AGCTATT
9 AGCTTTAAA 

Sample Output

14
21 

题目大意 ：

　　给出一个基因匹配表格 ， 里面有一些数值 。　　设 dp[i][j] 为 s1 取第 i 个字符， s2 取第 j 个字符的最大值，决定dp[i][j] 最优的情况有 三种， 类似于最长公共子序列的三种情况。　　　　1 . s1 取第 i 个字母， s2 取 ‘-‘ ， temp1 = dp[i][j] = dp[i-1][j] + score[a[i]][‘-‘];　　2 . s2 取第 j 个字母, s1 取 ‘-‘ , temp2 = dp[i][j] = dp[i][j-1] + score[‘-‘][b[j]];　　3 . s1 取第 i 个字母 ， s2 取第 j 个字母 , temp3 = dp[i][j] = dp[i-1][j-1] + score[a[i]][b[j]];

　　则 dp[i][j] = max ( temp1, temp2, temp3 );

　　还有初始化问题 :

　　　　dp[0][0] = 0;　　　　dp[i][0] = dp[i-1][0] + score[a[i]][‘-‘];　　　　dp[0][j] = dp[0][j-1] + score[‘-‘][b[j]];

代码示例 ：　　

/*
 * Author:  ry
 * Created Time:  2017/9/3 8:00:06
 * File Name: 1.cpp
 */
#include <iostream>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <cmath>
#include <algorithm>
#include <string>
#include <vector>
#include <stack>
#include <queue>
#include <set>
#include <time.h>
using namespace std;
const int mm = 1e6+5;
#define ll long long

ll t_cnt;
void t_st(){t_cnt=clock();}
void t_ot(){printf("you spent : %lldms\n", clock()-t_cnt);}
//开始t_st();
//结束t_ot();

int dp[150][150];
int score[‘T‘+1][‘T‘+1];

void intial () {
    score[‘A‘][‘A‘] = 5;
    score[‘C‘][‘C‘] = 5;
    score[‘G‘][‘G‘] = 5;
    score[‘T‘][‘T‘] = 5;
    score[‘A‘][‘C‘] = score[‘C‘][‘A‘] = -1;
    score[‘A‘][‘G‘] = score[‘G‘][‘A‘] = -2;
    score[‘A‘][‘T‘] = score[‘T‘][‘A‘] = -1;
    score[‘A‘][‘-‘] = score[‘-‘][‘A‘] = -3;
    score[‘C‘][‘G‘] = score[‘G‘][‘C‘] = -3;
    score[‘C‘][‘T‘] = score[‘T‘][‘C‘] = -2;
    score[‘C‘][‘-‘] = score[‘-‘][‘C‘] = -4;
    score[‘G‘][‘T‘] = score[‘T‘][‘G‘] = -2;
    score[‘G‘][‘-‘] = score[‘-‘][‘G‘] = -2;
    score[‘T‘][‘-‘] = score[‘-‘][‘T‘] = -1;
}

int MAX (int x, int y, int z) {
    int k = (x>y?x:y);
    return z>k?z:k;
}

int main() {
    int t;
    int len1, len2;
    char a[105], b[105];

    intial();
    cin >> t;
    getchar();
    while ( t-- ){
        memset (dp, 0, sizeof(dp));
        scanf("%d %s", &len1, a);
        scanf("%d %s", &len2, b);

        for (int i = len1; i > 0; i--)
            a[i] = a[i-1];
        for (int i = len2; i > 0; i--)
            b[i] = b[i-1];

        dp[0][0] = 0;
        for (int i = 1; i <= len1; i++)
            dp[i][0] = dp[i-1][0] + score[a[i]][‘-‘];
        for (int j = 1; j <= len2; j++)
            dp[0][j] = dp[0][j-1] + score[‘-‘][b[j]];

        for (int i = 1; i <= len1; i++)
            for (int j = 1; j <= len2; j++){
                int temp1 = dp[i-1][j] + score[a[i]][‘-‘];
                int temp2 = dp[i][j-1] + score[‘-‘][b[j]];
                int temp3 = dp[i-1][j-1] + score[a[i]][b[j]];
                dp[i][j] = MAX (temp1, temp2, temp3);
            }

        printf ("%d\n", dp[len1][len2]);
    }

    return 0;
}