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;
}
bool s_ShowContig(CBioseqContext& ctx)
{
if ( (ctx.IsSegmented() && ctx.HasParts()) ||
(ctx.IsDelta() && !ctx.IsDeltaLitOnly()) ) {
return true;
}
return false;
}
void CGenbankGatherer::x_DoSingleSection(CBioseqContext& ctx) const
{
CConstRef<IFlatItem> item;
const CFlatFileConfig& cfg = ctx.Config();
// these macros make the code easier to read and less repetitive
#define GATHER_BLOCK(BlockType, ItemClassName) \
if( cfg.IsShownGenbankBlock(CFlatFileConfig::fGenbankBlocks_##BlockType) ) { \
item.Reset( new ItemClassName(ctx) ); \
ItemOS() << item; \
}
#define GATHER_ANCHOR(BlockType, block_str) \
if( cfg.IsShownGenbankBlock(CFlatFileConfig::fGenbankBlocks_##BlockType) ) { \
item.Reset( new CHtmlAnchorItem(ctx, (block_str) ) ); \
ItemOS() << item; \
}
#define GATHER_VIA_FUNC(BlockType, FuncName) \
if( cfg.IsShownGenbankBlock(CFlatFileConfig::fGenbankBlocks_##BlockType) ) { \
FuncName(); \
}
// if there's a callback, let it know we've entered another bioseq
if( cfg.GetGenbankBlockCallback() ) {
CFlatFileConfig::CGenbankBlockCallback::EBioseqSkip eBioseqSkip =
cfg.GetGenbankBlockCallback()->notify_bioseq( ctx );
if( eBioseqSkip == CFlatFileConfig::CGenbankBlockCallback::eBioseqSkip_Yes ) {
return;
}
}
// gather needed blocks
GATHER_BLOCK(Head, CStartSectionItem);
GATHER_ANCHOR(Locus, "locus");
GATHER_BLOCK(Locus, CLocusItem);
GATHER_BLOCK(Defline, CDeflineItem);
GATHER_BLOCK(Accession, CAccessionItem);
GATHER_BLOCK(Version, CVersionItem);
GATHER_BLOCK(Project, CGenomeProjectItem);
if ( ctx.IsProt() ) {
bool show_dbsource = true;
CBioseq_Handle& bsh = ctx.GetHandle();
FOR_EACH_SEQID_ON_BIOSEQ_HANDLE (sid_itr, bsh) {
CSeq_id_Handle sid = *sid_itr;
switch (sid.Which()) {
case NCBI_SEQID(Other):
{
CConstRef<CSeq_id> id = sid.GetSeqId();
const CTextseq_id& tsid = *id->GetTextseq_Id ();
if (tsid.IsSetAccession()) {
const string& acc = tsid.GetAccession ();
if (NStr::StartsWith (acc, "WP_")) {
show_dbsource = false;
}
}
break;
}
default:
break;
}
}
