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NCBI C++ ToolKit: Parser Struct Reference

#include <objtools/flatfile/flatfile_parse_info.hpp>

enum class EOutput { BioseqSet , Seqsubmit } enum class EMode { Release , HTGS , HTGSCON , Relaxed } enum class ESource {
  unknown , NCBI , EMBL , GenBank ,
  DDBJ , LANL , SPROT , Refseq ,
  Flybase , USPTO , All
} enum class EFormat {
  unknown , EMBL , GenBank , SPROT ,
  DDBJ , XML , ALL
}

Definition at line 66 of file flatfile_parse_info.hpp.

◆ EFormat ◆ EMode ◆ EOutput ◆ ESource Enumerator unknown NCBI EMBL GenBank DDBJ LANL SPROT Refseq Flybase USPTO All

Definition at line 80 of file flatfile_parse_info.hpp.

◆ Parser() ◆ ~Parser() ◆ CurEntry() ◆ GetNumEntries() size_t Parser::GetNumEntries ( ) const inline ◆ InitializeKeywordParser() void Parser::InitializeKeywordParser ( EFormat fmt ) ◆ KeywordParser() ◆ accpref ◆ accver

Definition at line 181 of file flatfile_parse_info.hpp.

Referenced by add_entry(), CheckDupEntries(), CheckGene(), CkCdRegion(), CkProteinTransl(), CreateEntryBioseq(), EmblIndex(), FillAccsBySource(), flat2asn_range_func(), Flat2AsnCheck(), fta_add_hist(), fta_init_pp(), fta_parse_buf(), GenBankIndex(), get_sequence_text(), GetAccession(), GetEmblInstContig(), GetGenBankInstContig(), GetOneGeneRef(), GetProtRefSeqId(), GetSeqExt(), GetSeqLocation(), GetSprotDescr(), GetSPSeqLoc(), LoadFeat(), QSIndex(), sParseFlatfile(), SPFeatProtRef(), SPGetOneGeneRefNew(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), CSwissProt2Asn::xGetEntry(), CXml2Asn::xGetEntry(), XMLCheckRequiredTags(), XMLGetInstContig(), and XMLIndex().

◆ acprefix ◆ all ◆ allow_crossdb_featloc ◆ allow_uwsec ◆ authors_str ◆ buf ◆ citat ◆ cleanup ◆ convert ◆ curindx

Definition at line 108 of file flatfile_parse_info.hpp.

Referenced by check_short_CDS(), CheckDivCode(), CheckGene(), CkNonTerSP(), CMappedInput2Asn::CMappedInput2Asn(), CollectGapFeats(), CreateEntryBioseq(), CreateRawBioSources(), CurEntry(), DealWithGenes(), DescrRefs(), EmblIndex(), CFindPub::fix_pub_equiv(), flat2asn_range_func(), fta_fix_seq_loc_id(), fta_get_genetic_code(), fta_init_pp(), fta_is_con_div(), fta_replace_org(), GenBankIndex(), get_bioseq(), get_pat(), get_sub(), GetDescrEmblBlock(), GetDescrSPBlock(), GetEmblDescr(), GetEmblGBBlock(), GetEmblMolInfo(), GetFlatBiomol(), GetGBBlock(), GetGenBankDescr(), GetGenBankInst(), GetGenBankMolInfo(), GetOneGeneRef(), GetProtRefSeqId(), GetSeqData(), GetSeqExt(), GetSPAnnot(), GetSprotDescr(), GetSPSeqLoc(), InternalStopCodon(), Entry::IsAA(), LoadFeat(), CMappedInput2Asn::operator()(), OutputEmblAsn(), parse_entry(), ParseSourceFeat(), ProcFeatBlk(), ProcNucProt(), ResetParserStruct(), s_GetEmblInst(), SPFeatProtRef(), SPGetGeneRefsNew(), SPGetOneGeneRefNew(), SpPrepareEntry(), SprotIndex(), SrchCdRegion(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), CSwissProt2Asn::xGetEntry(), CXml2Asn::xGetEntry(), Entry::xInitSeqInst(), XMLGetDescr(), XMLGetEMBLBlock(), XMLGetGBBlock(), XMLGetInst(), XMLGetMolInfo(), XMLIndex(), and XMLLoadEntry().

◆ date ◆ debug ◆ diff_lt ◆ entrez_fetch Uint1 Parser::entrez_fetch = 0 ◆ entries ◆ entrylist

Definition at line 107 of file flatfile_parse_info.hpp.

Referenced by add_entry(), check_short_CDS(), CheckDivCode(), CheckDupEntries(), CheckGene(), CkNonTerSP(), CollectGapFeats(), CreateEntryBioseq(), CreateRawBioSources(), CurEntry(), DealWithGenes(), DescrRefs(), EmblIndex(), CFindPub::fix_pub_equiv(), flat2asn_range_func(), fta_fix_seq_loc_id(), fta_get_genetic_code(), fta_init_pp(), fta_is_con_div(), fta_parse_buf(), fta_replace_org(), GenBankIndex(), get_bioseq(), get_pat(), get_sub(), GetDescrEmblBlock(), GetDescrSPBlock(), GetEmblDescr(), GetEmblGBBlock(), GetEmblMolInfo(), GetFlatBiomol(), GetGBBlock(), GetGenBankDescr(), GetGenBankInst(), GetGenBankMolInfo(), GetOneGeneRef(), GetProtRefSeqId(), GetSeqData(), GetSeqExt(), GetSPAnnot(), GetSprotDescr(), GetSPSeqLoc(), InternalStopCodon(), Entry::IsAA(), LoadFeat(), OutputEmblAsn(), parse_entry(), ParseSourceFeat(), ProcFeatBlk(), ProcNucProt(), ResetParserStruct(), s_GetEmblInst(), sParseFlatfile(), SPFeatProtRef(), SPGetGeneRefsNew(), SPGetOneGeneRefNew(), SpPrepareEntry(), SprotIndex(), SrchCdRegion(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), CSwissProt2Asn::xGetEntry(), CXml2Asn::xGetEntry(), Entry::xInitSeqInst(), XMLGetDescr(), XMLGetEMBLBlock(), XMLGetGBBlock(), XMLGetInst(), XMLGetMolInfo(), XMLIndex(), XMLLoadEntry(), and XMLPerformIndex().

◆ errstat ◆ farseq ◆ ff_get_entry char*(* Parser::ff_get_entry) (const char *accession) = nullptr ◆ ff_get_entry_pp ◆ ff_get_entry_v ◆ ff_get_entry_v_pp ◆ ff_get_qscore ◆ ff_get_qscore_pp ◆ ffbuf ◆ ffdb ◆ format

Definition at line 128 of file flatfile_parse_info.hpp.

Referenced by add_entry(), CollectGapFeats(), DescrRefs(), FillAccsBySource(), Flat2AsnCheck(), FlatFileIndex(), fta_parse_buf(), fta_set_format_source(), get_art(), get_bioseq(), get_pat(), GetAccession(), GetDescrEmblBlock(), GetFlatBiomol(), GetGBBlock(), GetSeqData(), ImpFeatPub(), InitialEntry(), journal(), LoadEntry(), LoadEntryGenbank(), LoadFeat(), parse_entry(), s_GetInput2Asn(), SeqFeatPub(), SetReleaseStr(), sParseFlatfile(), SpPrepareEntry(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), CXml2Asn::xGetEntry(), and XMLGetGBBlock().

◆ fpo ◆ genenull ◆ histacc ◆ ign_bad_qs ◆ ign_prot_src ◆ ign_toks ◆ indx

Definition at line 105 of file flatfile_parse_info.hpp.

Referenced by add_entry(), CheckDupEntries(), EmblIndex(), flat2asn_range_func(), fta_init_pp(), fta_parse_buf(), GenBankIndex(), GetNumEntries(), CMappedInput2Asn::operator()(), CEmbl2Asn::PostTotals(), ResetParserStruct(), sParseFlatfile(), SprotIndex(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), CSwissProt2Asn::xGetEntry(), CXml2Asn::xGetEntry(), XMLIndex(), and XMLPerformIndex().

◆ limit ◆ medserver Uint1 Parser::medserver = 0 ◆ mode

Definition at line 187 of file flatfile_parse_info.hpp.

Referenced by CkCdRegion(), CreateEntryBioseq(), DescrRefs(), FillAccsBySource(), Flat2AsnCheck(), fta_init_pp(), GenBankIndex(), GetAccession(), GetGBBlock(), GetProtRefSeqId(), InitialEntry(), LoadFeat(), and CGenbank2Asn::xGetEntry().

◆ mpKeywordParser ◆ no_code ◆ no_date ◆ normalize ◆ num_drop Int4 Parser::num_drop = 0 ◆ output_format ◆ pbp

Definition at line 146 of file flatfile_parse_info.hpp.

Referenced by CkCdRegion(), FindCd(), fta_get_genetic_code(), fta_init_pp(), fta_parse_buf(), GetGcode(), GuessGeneticCode(), ProcNucProt(), ResetParserStruct(), sParseFlatfile(), and SrchCdRegion().

◆ qamode ◆ qsfd ◆ qsfile ◆ release_str ◆ seqtype Uint1 Parser::seqtype = 0 ◆ simple_genes ◆ sort ◆ source

Definition at line 129 of file flatfile_parse_info.hpp.

Referenced by BldProtRefSeqEntry(), CkCdRegion(), CollectGapFeats(), CreateEntryBioseq(), DealWithGenes(), DescrRefs(), EmblIndex(), FillAccsBySource(), FindCd(), CFindPub::fix_pub_annot(), flat2asn_range_func(), fta_add_hist(), fta_fix_seq_loc_id(), fta_replace_org(), GenBankIndex(), get_art(), get_pat(), get_sub(), get_sub_gsdb(), GetAccession(), GetAuthorsStr(), GetDescrEmblBlock(), GetDescrSPBlock(), GetEmblDescr(), GetEmblGBBlock(), GetFlatBiomol(), GetGBBlock(), GetGenBankDescr(), GetProtRefSeqId(), GetSeqData(), GetSprotDescr(), InitialEntry(), IsPatentedAccPrefix(), IsTLSAccPrefix(), IsTPAAccPrefix(), IsTSAAccPrefix(), IsWGSAccPrefix(), journal(), LoadEntry(), LoadEntryGenbank(), LoadFeat(), ParseSourceFeat(), s_GetEmblInst(), SetReleaseStr(), sp_refs(), SprotIndex(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), CXml2Asn::xGetEntry(), XMLCheckRequiredTags(), XMLGetDescr(), XMLGetEMBLBlock(), XMLGetGBBlock(), XMLIndex(), and XMLRefs().

◆ sp_dt_seq_ver ◆ taxserver Uint1 Parser::taxserver = 0

Definition at line 145 of file flatfile_parse_info.hpp.

Referenced by CkCdRegion(), Flat2AsnCheck(), fta_fix_orgref(), fta_fix_orgref_byid(), fta_get_genetic_code(), fta_init_pp(), fta_init_servers(), GetEmblDescr(), GetGenBankDescr(), InternalStopCodon(), LoadFeat(), ParseSourceFeat(), ProcNucProt(), XMLGetDescr(), and XMLGetGBBlock().

◆ transl ◆ user_data ◆ xml_comp

The documentation for this struct was generated from the following files:

include/objtools/flatfile/flatfile_parse_info.hpp
src/objtools/flatfile/flatfile_parse_info.cpp

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