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NCBI C++ ToolKit: src/app/table2asn/feature_table_reader.hpp Source File

(

objects::CSeq_entry& possible_proteins, objects::CSeq_entry& entry);

objects::CBioseq& bioseq,

objects::CSeq_feat& cd_feature,

(objects::CSeq_entry_Handle entry_h, objects::CSeq_annot::TData::TFtable& seq_ftable, objects::CSeq_annot::TData::TFtable& set_ftable,

&);

objects::CBioseq& protein,

partial5,

partial3);

void xParseCdregions(objects::CSeq_entry &entry, TAsyncToken &)

objects::CFastaReader::TPostponedModMap m_PrtModMap

void AddProteins(const objects::CSeq_entry &possible_proteins, objects::CSeq_entry &entry)

void MoveRegionsToProteins(objects::CSeq_entry &entry)

void MakeGapsFromFeatures(objects::CSeq_entry &entry) const

void xMoveCdRegions(objects::CSeq_entry_Handle entry_h, objects::CSeq_annot::TData::TFtable &seq_ftable, objects::CSeq_annot::TData::TFtable &set_ftable, TAsyncToken &)

void FindOpenReadingFrame(objects::CSeq_entry &entry) const

bool xAddProteinToSeqEntry(const objects::CBioseq &protein, objects::CSeq_entry_Handle seh)

void ConvertNucSetToSet(CRef< objects::CSeq_entry > &entry) const

CFeatureTableReader(CTable2AsnContext &context)

CTable2AsnContext & m_context

void MakeGapsFromFeatures(objects::CSeq_entry_Handle seh) const

CRef< objects::CSeq_entry > ReadProtein(ILineReader &line_reader)

void ChangeDeltaProteinToRawProtein(objects::CSeq_entry &entry) const

void xConvertSeqIntoSeqSet(objects::CSeq_entry &entry, bool nuc_prod_set) const

static void RemoveEmptyFtable(objects::CBioseq &bioseq)

CRef< objects::CSeq_feat > x_AddProteinFeatureToProtein(CRef< objects::CSeq_entry > nuc, CConstRef< objects::CSeq_loc > cds_loc, const list< CRef< objects::CSeq_id >> &pOriginalProtIds, objects::CBioseq &protein, bool partial5, bool partial3)

CRef< objects::CDelta_seq > MakeGap(objects::CBioseq &bioseq, const objects::CSeq_feat &feature_gap) const

void xMergeCDSFeatures_impl(objects::CSeq_entry &, TAsyncToken &)

void MergeCDSFeatures(objects::CSeq_entry &, TAsyncToken &)

void MoveProteinSpecificFeats(objects::CSeq_entry &entry)

CRef< objects::CSeq_entry > m_replacement_protein

bool xCheckIfNeedConversion(const objects::CSeq_entry &entry) const

CRef< objects::CSeq_entry > xTranslateProtein(const objects::CBioseq &bioseq, objects::CSeq_feat &cd_feature, list< CRef< CSeq_feat >> &seq_ftable, TAsyncToken &)

void MakeGapsFromFeatures(objects::CBioseq &bioseq) const

namespace ncbi::objects::

Base class for all serializable objects.

Abstract base class for lightweight line-by-line reading.

Operators to edit gaps in sequences.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

The NCBI C++/STL use hints.

static CS_CONTEXT * context

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