hdu1080 Human Gene Functions最大公共子序列dp(java)

Human Gene Functions
Time Limit: 2000/1000 MS (Java/Others) Memory Limit: 65536/32768 K (Java/Others)
Total Submission(s): 5160 Accepted Submission(s): 2827

Problem 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. 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.
最大公共子序列变形，特别注意题目中要求单个序列长度不超过100，那么我们开辟数组空间时数组大小要比100大那么一点儿
核心代码块：

for(int i=1;i<=n1;i++){
                for(int j=1;j<=n2;j++){
                    dp[i][j]=Math.max(dp[i-1][j-1]+table[a1[i]][a2[j]],Math.max(dp[i-1][j]+table[a1[i]][4],dp[i][j-1]+table[4][a2[j]]));
                }
            }

对核心代码块的理解：
用第一层max省去了匹配相同字符的过程，因为大的那个一定是匹配成功的那个。第二层max可以理解为：如果i比j大，则当前应考虑dp[i-1][j]，因为dp[i][j-1]的过程中有可能第j个元素刚好是当前最大公共子序列的最右端，j-1使其被舍弃，故应考虑dp[i-1][j]；如果i比j小，则…也就是说第二层max算是实现了遍历过程中对两子序列相对大小（也就是i和j的相对大小）的实时处理，毕竟最大公共子序列总是在小的那一边儿。

import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.io.StreamTokenizer ;
import java.io.IOException ;
class Main{
    private static int[][] table = {
        {5,-1,-2,-1,-3},
        {-1,5,-3,-2,-4},
        {-2,-3,5,-2,-2},
        {-1,-2,-2,5,-1},
        {-3,-4,-2,-1,0}} ;
    private static int[][] dp ;
    private static int[] a1,a2 ;
    private static int transform(char c) {
        if (c == 'A') {
            return 0;
        }
        if (c == 'C') {
            return 1;
        }
        if (c == 'G') {
            return 2;
        }
        if (c == 'T') {
            return 3;
        }
        return 4;
    }
    public static void main(String arg[])throws IOException{
        StreamTokenizer in = new StreamTokenizer(new BufferedReader(new InputStreamReader(System.in))) ;
        in.nextToken() ;
        int T = (int)in.nval ;
        while(T-->0){
            in.nextToken() ;
            int n1 = (int)in.nval ;
            a1 = new int[105] ;//这里要注意数组大小
            in.nextToken() ;
            String str1 = in.sval ;
            for(int i=1;i<=n1;i++){
                a1[i] = transform(str1.charAt(i-1)) ;
            }
            in.nextToken() ;
            int n2 = (int)in.nval ;
            a2 = new int[105] ;//同样注意数组大小
            in.nextToken() ;
            String str2 = in.sval ;
            for(int i=1;i<=n2;i++){
                a2[i] = transform(str2.charAt(i-1)) ;
            }
            dp = new int[105][105] ;
            dp[0][0] = 0 ;
            //初始化二维数组的第0行和第0列,初始化中空格两两相连，所以是累加的过程。
            for(int i=1;i<=n1;i++)  dp[i][0]=dp[i-1][0]+table[a1[i]][4];
            for(int i=1;i<=n2;i++)  dp[0][i]=dp[0][i-1]+table[4][a2[i]];
            //最大公共子序列模板
            for(int i=1;i<=n1;i++){
                for(int j=1;j<=n2;j++){
                    dp[i][j]=Math.max(dp[i-1][j-1]+table[a1[i]][a2[j]],Math.max(dp[i-1][j]+table[a1[i]][4],dp[i][j-1]+table[4][a2[j]]));
                }
            }
            System.out.println(dp[n1][n2]) ;
        }
    }
}