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NCBI C++ ToolKit: Indexblk Struct Reference

Search Toolkit Book for Indexblk

#include "ftablock.h"
(Private to src/objtools/flatfile.)

Definition at line 148 of file ftablock.h.

◆ Indexblk() ◆ acnum Char Indexblk::acnum[200]

Definition at line 149 of file ftablock.h.

Referenced by AccsCmp(), add_entry(), CheckDupEntries(), CompareAccs(), CompareAccsV(), CompareData(), CompareDataV(), CreateEntryBioseq(), err_install(), fta_check_mga_line(), fta_create_wgs_seqid(), fta_fix_seq_loc_id(), GenBankIndex(), GetAccession(), GetDescrEmblBlock(), GetEmblDescr(), GetExtraAccession(), GetGBBlock(), GetGenBankDescr(), GetOneGeneRef(), GetSeqExt(), GetSprotDescr(), GetSPSeqLoc(), Indexblk(), IsTLSAccPrefix(), IsTSAAccPrefix(), LoadFeat(), ParseEmblVersion(), ParseGenBankVersion(), ParseSourceFeat(), SeqFeatPub(), SPFeatProtRef(), SPGetOneGeneRefNew(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), CSwissProt2Asn::xGetEntry(), XMLAccessionsCheck(), XMLCheckRequiredTags(), XMLGetDescr(), XMLGetEMBLBlock(), XMLGetGBBlock(), XMLInitialEntry(), and XMLParseVersion().

◆ assembly ◆ bases size_t Indexblk::bases = 0

Definition at line 155 of file ftablock.h.

Referenced by AddToIndexBlk(), CollectGapFeats(), fta_check_mga_line(), fta_create_imgt_misc_feat(), get_bioseq(), GetDescrEmblBlock(), GetGBBlock(), GetGenBankDescr(), GetSeqData(), GetSPSeqLoc(), ImpFeatPub(), InitialEntry(), LoadFeat(), ParseFeatureBlock(), ParseSourceFeat(), SpAddToIndexBlk(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), XMLGetEMBLBlock(), XMLGetGBBlock(), XMLIndex(), and XMLInitialEntry().

◆ biodrop ◆ blocusname Char Indexblk::blocusname[200] ◆ date CRef<objects::CDate_std> Indexblk::date ◆ division Char Indexblk::division[4]

Definition at line 154 of file ftablock.h.

Referenced by AddToIndexBlk(), CheckContigEverywhere(), CheckDivCode(), CheckEmblContigEverywhere(), CheckForENV(), CheckGene(), EmblGetDivision(), EmblGetDivisionNewID(), GetDescrEmblBlock(), GetEmblDescr(), GetFlatBiomol(), GetGBBlock(), GetGenBankDescr(), Indexblk(), ParseSourceFeat(), SpAddToIndexBlk(), UpdateRawBioSource(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), XMLCheckContigEverywhere(), XMLGetDescr(), XMLGetDivision(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLInitialEntry().

◆ drop

Definition at line 160 of file ftablock.h.

Referenced by CheckContigEverywhere(), CheckDupEntries(), CheckGene(), CollectGapFeats(), EmblIndex(), CFindPub::fix_pub_equiv(), fta_check_non_tpa_tsa_tls_locations(), fta_create_wgs_seqid(), fta_fix_seq_id(), fta_fix_seq_loc_id(), fta_replace_org(), GenBankIndex(), GetAccession(), GetDescrEmblBlock(), GetDescrSPBlock(), GetEmblDescr(), GetExtraAccession(), GetFlatBiomol(), GetGenBankDescr(), GetSeqData(), GetSprotDescr(), LoadFeat(), ParseEmblVersion(), ParseFeatureBlock(), ParseGenBankVersion(), SeqFeatPub(), SPFeatProtRef(), SPGetGeneRefsNew(), SPParseDefinition(), SprotIndex(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), CSwissProt2Asn::xGetEntry(), XMLAccessionsCheck(), XMLCheckContigEverywhere(), XMLGetDescr(), XMLGetEMBLBlock(), XMLIndex(), XMLKeywordsCheck(), XMLParseFeatureBlock(), and XMLParseVersion().

◆ embl_new_ID ◆ env_sample_qual ◆ EST ◆ experimental ◆ gaps ◆ gc_genomic int Indexblk::gc_genomic = 0 ◆ gc_mito int Indexblk::gc_mito = 0 ◆ got_plastid ◆ GSS ◆ HTC ◆ htg ◆ inferential ◆ is_contig

Definition at line 175 of file ftablock.h.

Referenced by CheckContigEverywhere(), CheckEmblContigEverywhere(), EmblIndex(), GenBankIndex(), get_bioseq(), GetDescrEmblBlock(), GetEmblDescr(), GetExtraAccession(), GetGBBlock(), GetGenBankDescr(), GetGenBankInst(), GetSeqData(), s_GetEmblInst(), XMLCheckContigEverywhere(), XMLCheckRequiredTags(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLGetInst().

◆ is_mga

Definition at line 177 of file ftablock.h.

Referenced by CheckContigEverywhere(), GenBankIndex(), GetAccession(), GetDescrEmblBlock(), GetGBBlock(), GetGenBankDescr(), GetGenBankInst(), GetGenBankMolInfo(), GetSeqData(), LoadFeat(), ParseFeatureBlock(), Entry::xInitSeqInst(), XMLGetEMBLBlock(), and XMLGetGBBlock().

◆ is_pat

Definition at line 180 of file ftablock.h.

Referenced by fta_replace_org(), get_pat(), GetAccession(), GetDescrEmblBlock(), GetEmblDescr(), GetGBBlock(), GetGenBankDescr(), GetSeqData(), InitialEntry(), ParseSourceFeat(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLInitialEntry().

◆ is_prot ◆ is_tls

Definition at line 186 of file ftablock.h.

Referenced by fta_check_non_tpa_tsa_tls_locations(), GetDescrEmblBlock(), GetEmblDescr(), GetEmblMolInfo(), GetGBBlock(), GetGenBankDescr(), GetGenBankMolInfo(), InitialEntry(), IsTLSAccPrefix(), LoadFeat(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), XMLGetDescr(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLGetMolInfo().

◆ is_tpa

Definition at line 184 of file ftablock.h.

Referenced by check_est_sts_gss_tpa_kwds(), CreateEntryBioseq(), EmblIndex(), fta_check_non_tpa_tsa_tls_locations(), GenBankIndex(), GetAccession(), GetDescrEmblBlock(), GetEmblDescr(), GetGBBlock(), GetGenBankDescr(), LoadFeat(), xCheckEstStsGssTpaKeywords(), XMLCheckRequiredTags(), XMLGetDescr(), XMLGetEMBLBlock(), and XMLGetGBBlock().

◆ is_tpa_wgs_con ◆ is_tsa

Definition at line 185 of file ftablock.h.

Referenced by fta_check_non_tpa_tsa_tls_locations(), fta_create_wgs_seqid(), GetDescrEmblBlock(), GetEmblDescr(), GetEmblMolInfo(), GetGBBlock(), GetGenBankDescr(), GetGenBankMolInfo(), InitialEntry(), IsTSAAccPrefix(), LoadFeat(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), XMLGetDescr(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLGetMolInfo().

◆ is_wgs

Definition at line 183 of file ftablock.h.

Referenced by EmblIndex(), GenBankIndex(), GetAccession(), GetEmblDescr(), GetEmblMolInfo(), GetGBBlock(), GetGenBankDescr(), GetGenBankMolInfo(), CGenbank2Asn::xGetEntry(), XMLCheckRequiredTags(), XMLGetDescr(), and XMLGetMolInfo().

◆ keywords ◆ lc

Definition at line 190 of file ftablock.h.

Referenced by add_entry(), AddToIndexBlk(), GenBankIndex(), GetGBBlock(), GetGenBankDescr(), GetGenBankInst(), GetGenBankMolInfo(), InitialEntry(), Entry::IsAA(), CGenbank2Asn::xGetEntry(), and Entry::xInitSeqInst().

◆ len ◆ linenum size_t Indexblk::linenum = 0 ◆ locusname Char Indexblk::locusname[200]

Definition at line 153 of file ftablock.h.

Referenced by CheckDupEntries(), CreateEntryBioseq(), EmblIndex(), err_install(), GetAccession(), Indexblk(), InitialEntry(), LoadFeat(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), CSwissProt2Asn::xGetEntry(), and XMLInitialEntry().

◆ moltype ◆ no_gbblock_source bool Indexblk::no_gbblock_source ◆ no_gc_warning ◆ offset size_t Indexblk::offset = 0

Definition at line 151 of file ftablock.h.

Referenced by AccsCmp(), CheckDupEntries(), CompareData(), CompareDataV(), EmblIndex(), GenBankIndex(), InitialEntry(), SprotIndex(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), CSwissProt2Asn::xGetEntry(), XMLLoadEntry(), and XMLPerformIndex().

◆ organism ◆ origin ◆ ppp ◆ psip CRef<objects::CPatent_seq_id> Indexblk::psip ◆ qslength size_t Indexblk::qslength = 0 ◆ qsoffset size_t Indexblk::qsoffset = 0 ◆ secaccs ◆ specialist_db ◆ STS ◆ submitter_seqid string Indexblk::submitter_seqid ◆ taxid ◆ tsa_allowed ◆ vernum Int2 Indexblk::vernum = 0

Definition at line 150 of file ftablock.h.

Referenced by AccsCmp(), add_entry(), CheckDupEntries(), CompareAccsV(), CompareDataV(), CreateEntryBioseq(), err_install(), GenBankIndex(), GetAccession(), GetEmblDescr(), GetGenBankDescr(), GetOneGeneRef(), GetSeqExt(), GetSPSeqLoc(), LoadFeat(), ParseEmblVersion(), ParseGenBankVersion(), SPFeatProtRef(), SPGetOneGeneRefNew(), SPGetVerNum(), SprotIndex(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), XMLGetDescr(), and XMLParseVersion().

◆ wgs_and_gi Int4 Indexblk::wgs_and_gi = 0 ◆ wgssec ◆ xip

Definition at line 195 of file ftablock.h.

Referenced by CollectGapFeats(), GetSeqData(), ImpFeatPub(), LoadFeat(), s_IsSegment(), SeqFeatPub(), XMLAccessionsCheck(), XMLCheckRequiredTags(), XMLGetDescr(), XMLGetDivision(), XMLGetEMBLBlock(), XMLGetGBBlock(), XMLGetInst(), XMLGetMolInfo(), XMLIndex(), XMLInitialEntry(), XMLKeywordsCheck(), and XMLPerformIndex().

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

src/objtools/flatfile/ftablock.h
src/objtools/flatfile/indx_blk.cpp

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