JAVA才学了几天就开始学数据结构,这个程序怎么看都看不懂哪里出错了,能否帮忙指正一下?
不胜感激!
import java.until.random;
class SequenceAlignment1{
/*
using main with two command line arguments will align the
arguments with minimum cost according to the meassure +1 for
mismatches and indels, 0 for matches.
*/
private string[] character=[ A ,R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y,V];
private int[][] scores =
/* A R N D C Q E G H I L K M F P S T W Y V */
{ /* A */ { 5 },
/* R */ { -2, 7 },
/* N */ { -1,-1, 7 },
/* D */ { -2,-2, 2, 8 },
/* C */ { -1,-4,-2,-4,13 },
/* Q */ { -1, 1, 0, 0,-3, 7 },
/* E */ { -1, 0, 0, 2,-3, 2, 6 },
/* G */ { 0,-3, 0,-1,-3,-2,-3, 8 },
/* H */ { -2, 0, 1,-1,-3, 1, 0,-2,10 },
/* I */ { -1,-4,-3,-4,-2,-3,-4,-4,-4, 5 },
/* L */ { -2,-3,-4,-4,-2,-2,-3,-4,-3, 2, 5 },
/* K */ { -1, 3, 0,-1,-3, 2, 1,-2, 0,-3,-3, 6 },
/* M */ { -1,-2,-2,-4,-2, 0,-2,-3,-1, 2, 3,-2, 7 },
/* F */ { -3,-3,-4,-5,-2,-4,-3,-4,-1, 0, 1,-4, 0, 8 },
/* P */ { -1,-3,-2,-1,-4,-1,-1,-2,-2,-3,-4,-1,-3,-4,10 },
/* S */ { 1,-1, 1, 0,-1, 0,-1, 0,-1,-3,-3, 0,-2,-3,-1, 5 },
/* T */ { 0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 2, 5 },
/* W */ { -3,-3,-4,-5,-5,-1,-3,-3,-3,-3,-2,-3,-1, 1,-4,-4,-3,15 },
/* Y */ { -2,-1,-2,-3,-3,-1,-2,-3, 2,-1,-1,-2, 0, 4,-3,-2,-2, 2, 8 },
/* V */ { 0,-3,-3,-4,-1,-3,-3,-4,-4, 4, 1,-3, 1,-1,-3,-2, 0,-3,-1, 5 }
/* A R N D C Q E G H I L K M F P S T W Y V */
};
int convert(string x)
{ /* A R N D C Q E G H I L K M F P S T W Y V */
int index;
switch(x){
case A: index=0;break;
case R: index=1;break;
case N: index=2;break;
case D: index=3;break;
case C: index=4;break;
case Q: index=5;break;
case E: index=6;break;
case G: index=7;break;
case H: index=8;break;
case I: index=9;break;
case L: index=10;break;
case K: index=11;break;
case M: index=12;break;
case F: index=13;break;
case P: index=14;break;
case S: index=15;break;
case T: index=16;break;
case W: index=17;break;
case Y: index=18;break;
case V: index=19;break;
default:break;
}
return a;
}
int getscore(string a,string b){
int i,j;
i=convert(a);
j=convert(b);
if(score)
score=scores[i][j];
else
score=scores[j][i];
}
public static void main(String[] args){
/*SequenceAlignment1 sa1 = new SequenceAlignment1(string[] cmdLn);
String[] res = sa1.getAlignment();
System.out.println(sa1.getValue());
System.out.println(res[0]);
System.out.println(res[1]);*/
Random generator=new Random();
//int r=generator.nextInt();
for(int j=0;j<cmdLn.length;j++){
int randomIndex=generator.nextInt(19);
string b;
b=character[randomIndex];
}
String xs, ys; // the seqs to be aligned.
int n, m; // their lengths.
int[][] M; // the matrix used to compute the optimal values
Coord[][] traceback;
public SequenceAlignment1(String a, String b){
xs = a;
ys = b;
n = a.length();
m = b.length();
M = new int[n+1][m+1];
traceback = new Coord[n+1][m+1];
for(int i = 1; i<=n; i++){
M[i][0] = i*(-8);
traceback[i][0]=new Coord(i-1,0);
}
for(int j = 1; j<=m; j++){
M[0][j] = j*(-8);
traceback[0][j]=new Coord(0,j-1);
}
for(int i = 1; i<=n; i++)
for(int j = 1; j<=m; j++){
M[i][j] = max(M[i-1][j-1]+d(xs.charAt(i-1),ys.charAt(j-1)),
M[i-1][j]-8,
M[i][j-1]-8);
if(M[i][j] == M[i-1][j-1]+d(xs.charAt(i-1),ys.charAt(j-1)))
traceback[i][j] = new Coord(i-1,j-1);
else if (M[i][j]==M[i-1][j]-8)
traceback[i][j] = new Coord(i-1,j);
else traceback[i][j] = new Coord(i,j-1);
}
}
public int getValue(){return M[n][m];}
public String[] getAlignment(){
Coord tb = new Coord(n,m);
StringBuffer res1 = new StringBuffer();
StringBuffer res2 = new StringBuffer();
int i = tb.i;
int j = tb.j;
tb=traceback[n][m];
while(tb!=null){
if(i==tb.i)res1.append('-');
else res1.append(xs.charAt(i-1));
if(j==tb.j)res2.append('-');
else res2.append(ys.charAt(j-1));
i=tb.i;
j=tb.j;
tb = traceback[i][j];
}
String[] res = {res1.reverse().toString(),res2.reverse().toString()};
return res;
}
private static final int min(int a, int b, int c){
return Math.min(a,Math.min(b,c));
}
private static final int max(int a, int b, int c){
return Math.max(a,Math.max(b,c));
}
// The distance function:
private static final int d(char a, char b){
return a==b?0:1;
}
}
class Coord{
int i, j;
Coord(int x, int y){
i=x;j=y;
}
}
用JAVA程序，从命令行读取两个字符串，输出这两个输入的最优（佳）对比的花费（COST）和输出有着最优分数的对比（alignment）
要求用动态规划(dynamic programming)
有着最优分数(score)的一个对比(alignment)是:当对比两个各自都允许间隙(gap)的字符串时,有着最大分数(score)的对比.通过一个分数矩阵来表示字母(letter)对比的花费.假设一个间隙(gap)的花费是-8.两个字符串对比的花费是各自位置的花费的总和.
应该测量执行时间(execution time),并生成一个包含有测量及结论的文件.表示你应该写一个程序,测试序列对比中的输入(input)的大小,必须提供计算执行时间的证据
原文：
Write a java program that reads two strings from the command line and outputs the cost of an optimal alignment for the two inputs as well as one alignment with the optimal score.
The program should implement a dynamic programming algorithm.
hits:
An alignment with optimal score is one that maximizes the total score when aligning two strings alowing gaps in both strings. The cost for aligning letters is given by a score matrix 。Assume that the cost of introducing a gap is -8. The cost for the alignment of the two strings is the sum of the costs at each possition.
You should meassure the execution time of your implementation and produce the file with your meassurements and conclusions. This means that you should write a program that tests sequence alignment for some sizes of the input and that you should provide experimental evidence for the calculated asymptotic execution time
谢谢
[此贴子已经被作者于2007-10-1 18:50:09编辑过]
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2007/9/30 9:39:00
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