int CSeq_id_Handle::CompareOrdered(const CSeq_id_Handle& id) const
{
// small optimization to avoid creation of temporary CSeq_id objects
if ( int diff = Which() - id.Which() ) {
return diff;
}
if ( IsGi() && id.IsGi() ) {
return GetGi() - id.GetGi();
}
return GetSeqId()->CompareOrdered(*id.GetSeqId());
}
static TReadId sx_GetReadId(const CSeq_id_Handle& idh)
{
if ( idh.Which() != CSeq_id::e_General ) {
return TReadId();
}
CConstRef<CSeq_id> id = idh.GetSeqId();
const CDbtag& general = id->GetGeneral();
if ( general.GetDb() != "SRA") {
return TReadId();
}
return sx_GetReadId(general.GetTag().GetStr(), true);
}
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;
}
}