POJ-1080-Human Gene Functions

                       Time Limit: 1000MS       Memory Limit: 10000K
                        Total Submissions: 18823        Accepted: 10481

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

题意说明： n组测试数据，之后每两行为一个测试数据，每行前面的数字是后面的字符串长度。让你求出的给定的字符串的最高相似度(其实就是DNA序列) 而每个字母与其他字母或自身和空格对应都有一个打分(如图中)，求在这两个字符串中插入空格，让这两个字符串的匹配分数最大，并打印这个分数

解题思路：不难想到为了记录字母与字母或者空格的分数，可以采用打表方式(反正不多，也就25个。。)，开个二维数组ch[‘T’+1][‘T’+1]来记录这些分数。之后可以用搜索或者dp来AK这道题，其实很多dp都可以用搜索来AK，之后我们可以模仿dp里面经典的求最长公共子序列的方法。
字符串s1中的字符和字符串s2中的字符相比无非就三种情况 1.上面加‘-’ 2.下面加‘-’ 3.直接两个字符相比

dp[i][j]用来表示字符串s1 1-i的和字符串序列s2 1-j的最大相似度

ch[s1[i]][s2[j]]表示字符s1[i]和s2[j]的匹配值

dp[i][j] 为 dp[i-1][j-1] + ch[s1[i-1]][s2[j-1]], dp[i-1][j] + ch[s1[i-1]][‘-’], dp[i][j-1] + ch[‘-’][s2[j-1]]中的最大值

当然重要还有注意下dp的边界值 这也是经常可能会出错的地方

dp[0][j] = dp[0][j-1] + ch[‘-’][s2[j-1]]
dp[i][0] = dp[i-1][0] + ch[s1[i-1]][‘-’]

接下来就直接上AC的代码了…

#include <iostream>
#include <cstdio>
#include <cstring>
#include <cstdlib>
#include <algorithm>
#include <map>
#include <cmath>
#include <queue>
#include <string>
using namespace std;
int n,len1,len2;
int ch[100][100],dp[105][105];
char s1[105],s2[105];
void init()//打表
{
    ch['A']['A']=5;
    ch['A']['C']=-1;
    ch['A']['G']=-2;
    ch['A']['T']=-1;
    ch['A']['-']=-3;
    ch['C']['A']=-1;
    ch['C']['C']=5;
    ch['C']['G']=-3;
    ch['C']['T']=-2;
    ch['C']['-']=-4;
    ch['G']['A']=-2;
    ch['G']['C']=-3;
    ch['G']['G']=5;
    ch['G']['T']=-2;
    ch['G']['-']=-2;
    ch['T']['A']=-1;
    ch['T']['C']=-2;
    ch['T']['G']=-2;
    ch['T']['T']=5;
    ch['T']['-']=-1;
    ch['-']['A']=-3;
    ch['-']['C']=-4;
    ch['-']['G']=-2;
    ch['-']['T']=-1;
    ch['-']['-']=-1;//注意这里 因为题中没给 最好给小值
}
int main()
{
    init();//载入ch二维数组
    scanf("%d",&n);
     while(n--){
       scanf("%d%s%d%s",&len1,s1,&len2,s2);
       memset(dp,0,sizeof(dp));//初始化dp
      for (int i=1;i<=len1;i++)
        dp[i][0]=dp[i-1][0]+ch[s1[i-1]]['-'];//边界值
      for (int i=1;i<=len2;i++)
        dp[0][i]=dp[0][i-1]+ch['-'][s2[i-1]];//边界值
       for(int i=1;i<=len1;i++)
       {
           for(int j=1;j<=len2;j++)
           {
                dp[i][j]=max(max(dp[i-1][j-1]+ch[s1[i-1]][s2[j-1]],dp[i][j-1]+ch['-'][s2[j-1]]),dp[i-1][j]+ch[s1[i-1]]['-']);//取三种情况的最大值
           }
       }
       printf("%d\n",dp[len1][len2]);
     }
    return 0;
}

END！！！！！！！！！！！！！！！！！！！