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GCG Format

ketchup Ketchup*REMOVE* at concentric.net
Fri May 15 11:44:34 EST 1998


Jennifer Hallinan <jsh at forbio.com.au> wrote:

>Can anyone tell me how to compute the checksum in the header of a GCG
>format DNA sequence file?

>Thanks,

>Jennifer



static const int MSFFILEtable[256] = {
    0x0, 0x1, 0x2, 0x3, 0x4, 0x5, 0x6, 0x7, 
    0x8, 0x9, 0xa, 0xb, 0xc, 0xd, 0xe, 0xf,
    0x10, 0x11, 0x12, 0x13, 0x14, 0x15, 0x16, 0x17, 
    0x18, 0x19, 0x1a, 0x1b, 0x1c, 0x1d, 0x1e, 0x1f,
    0x20, 0x21, 0x22, 0x23, 0x24, 0x25, 0x26, 0x27, 
    0x28, 0x29, 0x2a, 0x2b, 0x2c, 0x2d, 0x2e, 0x2f,
    0x30, 0x31, 0x32, 0x33, 0x34, 0x35, 0x36, 0x37, 
    0x38, 0x39, 0x3a, 0x3b, 0x3c, 0x3d, 0x3e, 0x3f,
    0x40, 0x41, 0x42, 0x43, 0x44, 0x45, 0x46, 0x47, 
    0x48, 0x49, 0x4a, 0x4b, 0x4c, 0x4d, 0x4e, 0x4f,
    0x50, 0x51, 0x52, 0x53, 0x54, 0x55, 0x56, 0x57, 
    0x58, 0x59, 0x5a, 0x5b, 0x5c, 0x5d, 0x5e, 0x5f,
    0x60, 0x41, 0x42, 0x43, 0x44, 0x45, 0x46, 0x47, 
    0x48, 0x49, 0x4a, 0x4b, 0x4c, 0x4d, 0x4e, 0x4f,
    0x50, 0x51, 0x52, 0x53, 0x54, 0x55, 0x56, 0x57, 
    0x58, 0x59, 0x5a, 0x7b, 0x7c, 0x7d, 0x7e, 0x7f,
    0x80, 0x81, 0x82, 0x83, 0x84, 0x85, 0x86, 0x87, 
    0x88, 0x89, 0x8a, 0x8b, 0x8c, 0x8d, 0x8e, 0x8f,
    0x90, 0x91, 0x92, 0x93, 0x94, 0x95, 0x96, 0x97, 
    0x98, 0x99, 0x9a, 0x9b, 0x9c, 0x9d, 0x9e, 0x9f,
    0xa0, 0xa1, 0xa2, 0xa3, 0xa4, 0xa5, 0xa6, 0xa7, 
    0xa8, 0xa9, 0xaa, 0xab, 0xac, 0xad, 0xae, 0xaf,
    0xb0, 0xb1, 0xb2, 0xb3, 0xb4, 0xb5, 0xb6, 0xb7, 
    0xb8, 0xb9, 0xba, 0xbb, 0xbc, 0xbd, 0xbe, 0xbf,
    0xc0, 0xc1, 0xc2, 0xc3, 0xc4, 0xc5, 0xc6, 0xc7, 
    0xc8, 0xc9, 0xca, 0xcb, 0xcc, 0xcd, 0xce, 0xcf,
    0xd0, 0xd1, 0xd2, 0xd3, 0xd4, 0xd5, 0xd6, 0xd7, 
    0xd8, 0xd9, 0xda, 0xdb, 0xdc, 0xdd, 0xde, 0xdf,
    0xe0, 0xe1, 0xe2, 0xe3, 0xe4, 0xe5, 0xe6, 0xe7, 
    0xe8, 0xe9, 0xea, 0xeb, 0xec, 0xed, 0xee, 0xef,
    0xf0, 0xf1, 0xf2, 0xf3, 0xf4, 0xf5, 0xf6, 0xf7, 
    0xf8, 0xf9, 0xfa, 0xfb, 0xfc, 0xfd, 0xfe, 0xff
  };
  

// 
static 
long
CheckSeq(const char *strand, DWORD Len) 
{
	long check;
	long count;

  /* this table is designed as a cheap way to perform toupper() */

  for(check = 0, count = 1; Len--; strand++) {
  	if ( (*strand == '-') || (*strand == '.') ) {
	    check = (check + count * MSFFILEtable[(int)'.']) % 10000L;
  	} else {
	    check = (check + count * MSFFILEtable[(int) *strand]) % 10000L;
	}
    if(count == 57) 
      count = 1;
    else
      count++;
  }
  return check;

} /* end CheckSeq */







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