//-------------------------------------------------------------------------
void CSeqMaskerWindowPattern::FillWindow( Uint4 winstart )
{
first_unit = 0;
TUnit unit = 0;
Int4 iter = 0;
end = winstart + unit_size - 1;
Uint4 wstart = winstart;
for( ; iter < NumUnits() && end < data.size() && end < winend; )
if( MakeUnit( winstart, unit ) )
{
units[iter] = unit;
++iter;
end += unit_step;
winstart += unit_step;
}
else
{
iter = 0;
wstart += window_step;
winstart = wstart;
end = winstart + unit_size - 1;
}
end -= unit_step;
end += (window_size - unit_size)%unit_step;
start = end - window_size + 1;
state = (iter == NumUnits());
}
//-------------------------------------------------------------------------
void CSeqMaskerWindowPatternAmbig::FillWindow( Uint4 winstart )
{
first_unit = 0;
TUnit unit = 0;
Int4 iter = 0;
end = winstart + unit_size - 1;
for( ; iter < NumUnits() && end < data.size();
++iter, end += unit_step, winstart += unit_step ) {
if( MakeUnit( winstart, unit ) ) {
units[iter] = unit;
} else {
units[iter] = ambig_unit;
}
}
end -= unit_step;
end += (window_size - unit_size)%unit_step;
start = end - window_size + 1;
state = (iter == NumUnits());
}
//-------------------------------------------------------------------------
CSeqMaskerWindow::CSeqMaskerWindow( const CSeqVector & arg_data,
Uint1 arg_unit_size,
Uint1 arg_window_size,
Uint4 arg_window_step,
Uint1 arg_unit_step,
Uint4 winstart,
Uint4 arg_winend )
: data(arg_data), state( false ),
unit_size( arg_unit_size ), unit_step( arg_unit_step ),
window_size( arg_window_size ), window_step( arg_window_step ),
end( 0 ), first_unit( 0 ), unit_mask( 0 ), winend( arg_winend )
{
static bool first_call = true;
if( first_call )
{
LOOKUP[unsigned('A')] = 1;
LOOKUP[unsigned('C')] = 2;
LOOKUP[unsigned('G')] = 3;
LOOKUP[unsigned('T')] = 4;
first_call = false;
}
if( data.size() < window_size ) {
// TODO Throw an exception.
}
if( unit_size > window_size ) {
// TODO Throw an exception.
}
units.resize( NumUnits(), 0 );
unit_mask = (unit_size == 16) ? 0xFFFFFFFF : (1 << (unit_size << 1)) - 1;
if( winend == 0 )
winend = data.size();
FillWindow( winstart );
}
//-------------------------------------------------------------------------
void CSeqMaskerWindowAmbig::Advance( Uint4 step )
{
if( ambig || step >= window_size || unit_step > 1 )
{
FillWindow( start + step );
return;
}
Uint1 num_units = NumUnits();
Uint1 last_unit = first_unit ? first_unit - 1 : num_units - 1;
Uint4 unit = units[last_unit];
Uint4 iter = 0;
Uint4 newstart = start + step;
for( ; ++end < data.size() && iter < step ; ++iter )
{
Uint1 letter = LOOKUP[unsigned(data[end])];
if( !(letter--) )
{
FillWindow( newstart );
return;
}
unit = ((unit<<2)&unit_mask) + letter;
if( ++first_unit == num_units ) first_unit = 0;
if( ++last_unit == num_units ) last_unit = 0;
units[last_unit] = unit;
}
--end;
start = end - window_size + 1;
if( iter != step ) state = false;
}