YMODEMCLASS::YMODEMCLASS (OBJECTID oiFT, char *fileName, BOOL sORr) :XMODEMCLASS (oiFT, fileName, sORr)
{
char * p ;
FILETRANSFER fltr(oiFT) ;
fileCount = 0 ;
if (sORr)
{
filename = new char[2048] ;
p = filename ;
while(lstrlen(fileName))
{
CopyMemory(p, fileName, lstrlen(fileName)+1) ;
fileName = fileName+lstrlen(fileName)+1 ;
p=p+lstrlen(p)+1 ;
fileCount ++ ;
}
p = '\0' ;
}
else
{
filename = new char[256] ;
lstrcpy (filename, fileName) ;
}
lErrorCount =0 ;
maxTimeout = fltr.data0->maxTimeout*60 ;
maxTrytimes = fltr.data0->maxTrytimes ;
bSeq = 0 ;
fCRC = TRUE ;
dataBlock0 = TRUE ;
AObjSetRuntimeInfo (oiFT, (long)this) ;
}
void
rankSufmatch ( void *space,
Suffixarray *a,
PairSint *matches,
Uint len,
Uint maxmatches,
Uint S,
IntSequence **s,
Uint noofseqs,
double (*fltr)( void *,
Matchtype *,
IntSequence *,
IntSequence *,
Uint *,
Uint,
Uint,
void *),
Matchtype* (*sel)( void *,
Matchtype *,
Uint,
IntSequence *,
IntSequence **,
void *),
int (*handler)( void *,
Matchtype *,
IntSequence **,
Uint,
Uint,
void *),
IntSequence *queryseq,
void *info,
double *scores,
unsigned char depictsw
)
{
Matchtype key, *cur, *occ=NULL;
int i=0, j=0, k=0, l=0, r=0, retval=0;
int *hashTable;
double t;
Uint *ptr;
hashTable = ALLOCMEMORY(space, NULL, int, (noofseqs+1));
memset(hashTable, -1, sizeof(int)*(noofseqs+1));
for(i=0; i < len; i++) {
if(matches[i].b >= ((matches[i].a))) {
for(j=matches[i].a; j <= matches[i].b; j++) {
key.id = getMultiSeqIndex(a->seq, &a->seq->sequences[a->suftab[j]]);
r = hashTable[key.id];
if (r == -1) {
occ = ALLOCMEMORY(space, occ, Matchtype, k+1);
hashTable[key.id]=(&occ[k])-(occ);
initMatchtype(&occ[k], key.id);
cur = &occ[k];
k++;
} else {
cur = ((Matchtype*)(occ+r));
}
/*score the matches if no < maxmatches*/
if ((matches[i].b-matches[i].a) < maxmatches) {
ptr = &a->seq->sequences[a->suftab[j]]);
t=fltr(space, cur, queryseq, s[cur->id], ptr, S, i, info);
if (t == -1) break;
}
}
}
}
int main(int argc, char* argv[])
{
FILE *f; // исходный файл
FILE *f1; // файл для печати
int *n=0, *c=0; // указатель на начало и после конца массива
int *m=0, *d=0; // указатель на начало и после конца отфилтрованного массива
setlocale(0, "russian");
if (argc < 4)
{
printf("Нет достаточного числа аргументов!");
return BADARG;
}
f = fopen(argv[1], "r");
if (f == NULL)
{
printf("Невозможно открыть исходный файл!");
return BADINFILE;
}
if (readarray(f, &n, &c))
{
printf("Невозможно выделить память под исходный массив!");
fclose(f);
return FAILEDINMEM;
}
f1 = fopen(argv[2], "w");
if (f1 == NULL)
{
printf("Невозможно открыть файл результата!");\
fclose(f);
free(n);
return BADOUTFILE;
}
if (strcmp(argv[3], "-flt") == 0)
{
if (fltr(n, c, &m, &d))
{
printf("Невозможно выделить память под отфильтрованный массив!");
fclose(f);
fclose(f1);
free(n);
return FAILEDOUTMEM;
}
myqsort(m, d - m, sizeof(*m), compare_int);
printmass(f1, m, d);
free(n);
free(m);
}
else
{
myqsort(n, c - n, sizeof(*n), compare_int);
printmass(f1, n, c);
free(n);
}
fclose(f);
fclose(f1);
printf("Успешно!");
getch();
return 0;
}
bool NucleicAcidTools::symm_match( clipper::MiniMol& molwrk, const clipper::MiniMol& molref )
{
clipper::Spacegroup spg1 = clipper::Spacegroup(clipper::Spacegroup::P1);
clipper::Spacegroup spgr = molwrk.spacegroup();
clipper::Cell cell = molwrk.cell();
// calculate extent of model
clipper::Atom_list atomr = molref.atom_list();
clipper::Range<clipper::ftype> urange, vrange, wrange;
clipper::Coord_frac cfr( 0.0, 0.0, 0.0 );
for ( int i = 0; i < atomr.size(); i++ ) {
clipper::Coord_frac cf = atomr[i].coord_orth().coord_frac( cell );
cfr += cf;
urange.include( cf.u() );
vrange.include( cf.v() );
wrange.include( cf.w() );
}
clipper::Coord_frac cf0( urange.min(), vrange.min(), wrange.min() );
clipper::Coord_frac cf1( urange.max(), vrange.max(), wrange.max() );
cfr = (1.0/double(atomr.size())) * cfr;
// calculate mask using wrk cell and ref atoms
clipper::Resolution reso( 5.0 );
clipper::Grid_sampling grid( spg1, cell, reso );
clipper::Grid_range grng( grid, cf0, cf1 );
grng.add_border(4);
clipper::NXmap<float> nxmap( cell, grid, grng ), nxflt( cell, grid, grng );
clipper::EDcalc_mask<float> maskcalc( 2.0 );
nxmap = 0.0;
maskcalc( nxmap, atomr );
MapFilterFn_g5 fn;
clipper::MapFilter_fft<float>
fltr( fn, 1.0, clipper::MapFilter_fft<float>::Relative );
fltr( nxflt, nxmap );
// now score each chain, symmetry and offset in turn
for ( int c = 0; c < molwrk.size(); c++ ) {
double bestscr = 0.0;
int bestsym = 0;
clipper::Coord_frac bestoff( 0.0, 0.0, 0.0 );
const clipper::Coord_frac cfh( 0.5, 0.5, 0.5 );
for ( int sym = 0; sym < spgr.num_symops(); sym++ ) {
clipper::Atom_list atomw = molwrk[c].atom_list();
clipper::RTop_orth rtop = spgr.symop(sym).rtop_orth( cell );
clipper::Coord_orth cow( 0.0, 0.0, 0.0 );
for ( int a = 0; a < atomw.size(); a++ ) {
atomw[a].transform( rtop );
cow += atomw[a].coord_orth();
}
if ( atomw.size() > 0 ) cow = (1.0/double(atomw.size())) * cow;
clipper::Coord_frac cfw = cow.coord_frac( cell );
clipper::Coord_frac cfwt = cfw.lattice_copy_near( cfr - cfh );
clipper::Coord_frac off0 = cfwt - cfw;
// try offsets
for ( double du = 0.0; du <= 1.01; du += 1.0 )
for ( double dv = 0.0; dv < 1.01; dv += 1.0 )
for ( double dw = 0.0; dw < 1.01; dw += 1.0 ) {
clipper::Coord_frac off( rint( off0.u() ) + du,
rint( off0.v() ) + dv,
rint( off0.w() ) + dw );
clipper::Coord_orth ofo = off.coord_orth( cell );
double scr = 0.0;
for ( int a = 0; a < atomw.size(); a++ ) {
clipper::Coord_orth coa = atomw[a].coord_orth() + ofo;
clipper::Coord_grid cga = nxflt.coord_map( coa ).coord_grid();
if ( nxflt.in_map( cga ) ) scr += nxflt.get_data( cga );
}
if ( scr > bestscr ) {
bestscr = scr;
bestsym = sym;
bestoff = off;
}
}
}
// now transform using the best operator
clipper::Coord_orth cot = bestoff.coord_orth( cell );
clipper::RTop_orth rtop = spgr.symop(bestsym).rtop_orth( cell );
rtop = clipper::RTop_orth( rtop.rot(), rtop.trn()+cot );
molwrk[c].transform( rtop );
}
return true;
}