中文XML论坛--源码查错

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;
  }
}

[此贴子已经被作者于2007-9-30 23:11:44编辑过]


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