void CBaseCountItem::x_GatherInfo(CBioseqContext& ctx)
{
if ( ctx.IsProt() ) {
x_SetSkip();
return;
}
CSeqVector v(ctx.GetLocation(), ctx.GetHandle().GetScope(),
CBioseq_Handle::eCoding_Iupac);
const size_t COUNT = kMax_UChar+1;
TSeqPos counters[COUNT] = {}; // "{}" will set all counters to zero
// every how many bases do we check if the flatfile generator is canceled?
// (feel free to adjust this number if it makes things faster)
const static TSeqPos kCancelCheckBases = 4096;
CSeqVector_CI it(v, 0, CSeqVector_CI::eCaseConversion_lower);
TSeqPos count = v.size();
while ( count > 0 ) {
const TSeqPos uBasesToCopyRightNow = min( kCancelCheckBases, count );
ITERATE_SIMPLE(uBasesToCopyRightNow) {
++counters[*it];
++it;
}
count -= uBasesToCopyRightNow;
ctx.ThrowIfCanceled();
}
m_A = counters[Uchar('a')];
m_C = counters[Uchar('c')];
m_G = counters[Uchar('g')];
m_T = counters[Uchar('t')];
m_Other = v.size() - m_A - m_C - m_G - m_T;
}
void CBaseCountItem::x_GatherInfo(CBioseqContext& ctx)
{
if ( ctx.IsProt() ) {
x_SetSkip();
return;
}
CSeqVector v(ctx.GetLocation(), ctx.GetHandle().GetScope(),
CBioseq_Handle::eCoding_Iupac);
const size_t COUNT = kMax_UChar+1;
TSeqPos counters[COUNT];
for ( size_t i = 0; i < COUNT; ++i) {
counters[i] = 0;
}
CSeqVector_CI it(v, 0, CSeqVector_CI::eCaseConversion_lower);
for ( TSeqPos count = v.size(); count; --count, ++it ) {
++counters[*it];
}
m_A = counters[Uchar('a')];
m_C = counters[Uchar('c')];
m_G = counters[Uchar('g')];
m_T = counters[Uchar('t')];
m_Other = v.size() - m_A - m_C - m_G - m_T;
}
