NCBI C++ ToolKit
Public Member Functions | Public Attributes | List of all members
Indexblk Struct Reference

Search Toolkit Book for Indexblk

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

+ Collaboration diagram for Indexblk:

Public Member Functions

 Indexblk ()
 

Public Attributes

Char acnum [200]
 
Int2 vernum = 0
 
size_t offset = 0
 
Char locusname [200]
 
Char division [4]
 
size_t bases = 0
 
Uint2 segnum = 0
 
Uint2 segtotal = 0
 
Char blocusname [200]
 
size_t linenum = 0
 
bool drop = false
 
size_t len = 0
 
CRef< objects::CDate_std > date
 
CRef< objects::CPatent_seq_id > psip
 
bool EST = false
 
bool STS = false
 
bool GSS = false
 
bool HTC = false
 
Int2 htg = 0
 
bool is_contig = false
 
bool is_mga = false
 
bool origin = false
 
bool is_pat = false
 
bool is_wgs = false
 
bool is_tpa = false
 
bool is_tsa = false
 
bool is_tls = false
 
bool is_tpa_wgs_con = false
 
bool tsa_allowed = false
 
LocusCont lc
 
string moltype
 
GapFeatsPtr gaps = nullptr
 
TokenBlkList secaccs
 
XmlIndexPtr xip = nullptr
 
bool embl_new_ID = false
 
bool env_sample_qual = false
 
bool is_prot = false
 
string organism
 
TTaxId taxid = ZERO_TAX_ID
 
bool no_gc_warning = false
 
size_t qsoffset = 0
 
size_t qslength = 0
 
Int4 wgs_and_gi = 0
 
bool got_plastid = false
 
string wgssec
 
int gc_genomic = 0
 
int gc_mito = 0
 
TKeywordList keywords
 
bool assembly = false
 
bool specialist_db = false
 
bool inferential = false
 
bool experimental = false
 
string submitter_seqid
 
Parser * ppp = nullptr
 

Detailed Description

Definition at line 165 of file ftablock.h.

Constructor & Destructor Documentation

◆ Indexblk()

Indexblk::Indexblk ( )

Definition at line 665 of file indx_blk.cpp.

References acnum, blocusname, division, locusname, and wgssec.

Member Data Documentation

◆ acnum

Char Indexblk::acnum[200]

Definition at line 166 of file ftablock.h.

Referenced by AccsCmp(), add_entry(), CheckContigEverywhere(), CheckDupEntries(), CheckEmblContigEverywhere(), CompareAccs(), CompareAccsV(), CompareData(), CompareDataV(), CreateEntryBioseq(), EmblAscii(), err_install(), fta_check_mga_line(), fta_create_wgs_seqid(), fta_fix_seq_loc_id(), GenBankAscii(), GenBankAsciiOrig(), GenBankIndex(), GetAccession(), GetBioseq(), GetDescrEmblBlock(), GetEmblDescr(), GetExtraAccession(), GetGBBlock(), GetGenBankDescr(), GetOneGeneRef(), GetSeqExt(), GetSprotDescr(), GetSPSeqLoc(), Indexblk(), IsTLSAccPrefix(), IsTSAAccPrefix(), LoadFeat(), ParseEmblVersion(), ParseGenBankVersion(), ParseSourceFeat(), SeqFeatPub(), SPFeatProtRef(), SPGetOneGeneRefNew(), SprotAscii(), XMLAccessionsCheck(), XMLAscii(), XMLCheckContigEverywhere(), XMLCheckRequiredTags(), XMLGetDescr(), XMLGetEMBLBlock(), XMLGetGBBlock(), XMLInitialEntry(), and XMLParseVersion().

◆ assembly

bool Indexblk::assembly = false

Definition at line 241 of file ftablock.h.

Referenced by GenBankIndex(), GetEmblDescr(), xCheckEstStsGssTpaKeywords(), and XMLKeywordsCheck().

◆ bases

size_t Indexblk::bases = 0

Definition at line 172 of file ftablock.h.

Referenced by AddToIndexBlk(), CollectGapFeats(), EmblAscii(), fta_check_mga_line(), fta_create_imgt_misc_feat(), GenBankAscii(), GenBankAsciiOrig(), get_bioseq(), GetDescrEmblBlock(), GetGBBlock(), GetGenBankDescr(), GetSeqData(), GetSPSeqLoc(), ImpFeatPub(), InitialEntry(), LoadFeat(), ParseFeatureBlock(), ParseSourceFeat(), SpAddToIndexBlk(), XMLAscii(), XMLGetEMBLBlock(), XMLGetGBBlock(), XMLIndex(), and XMLInitialEntry().

◆ blocusname

Char Indexblk::blocusname[200]

Definition at line 178 of file ftablock.h.

Referenced by CompareData(), CompareDataV(), DelSegnum(), EmblSegment(), GetBioseq(), GetSegment(), Indexblk(), InitialEntry(), XMLDelSegnum(), XMLGetSegment(), and XMLInitialEntry().

◆ date

CRef<objects::CDate_std> Indexblk::date

Definition at line 187 of file ftablock.h.

Referenced by CheckDupEntries(), EmblIndex(), InitialEntry(), SprotIndex(), and XMLInitialEntry().

◆ division

Char Indexblk::division[4]

Definition at line 171 of file ftablock.h.

Referenced by AddToIndexBlk(), CheckContigEverywhere(), CheckDivCode(), CheckEmblContigEverywhere(), CheckForENV(), CheckGene(), EmblAscii(), EmblGetDivision(), EmblGetDivisionNewID(), GenBankAscii(), GenBankAsciiOrig(), GetDescrEmblBlock(), GetEmblDescr(), GetFlatBiomol(), GetGBBlock(), GetGenBankDescr(), Indexblk(), ParseSourceFeat(), SpAddToIndexBlk(), UpdateRawBioSource(), XMLAscii(), XMLCheckContigEverywhere(), XMLGetDescr(), XMLGetDivision(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLInitialEntry().

◆ drop

bool Indexblk::drop = false

Definition at line 182 of file ftablock.h.

Referenced by BuildBioSegHeader(), CheckContigEverywhere(), CheckDupEntries(), CheckGene(), CollectGapFeats(), DelSegnum(), EmblAscii(), 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(), GenBankAscii(), GenBankAsciiOrig(), GenBankIndex(), GetAccession(), GetDescrEmblBlock(), GetDescrSPBlock(), GetEmblDescr(), GetExtraAccession(), GetFlatBiomol(), GetGenBankDescr(), GetSeqData(), GetSprotDescr(), LoadFeat(), ParseEmblVersion(), ParseFeatureBlock(), ParseGenBankVersion(), SeqFeatPub(), SPFeatProtRef(), SPGetGeneRefsNew(), SPParseDefinition(), SprotAscii(), SprotIndex(), XMLAccessionsCheck(), XMLAscii(), XMLCheckContigEverywhere(), XMLDelSegnum(), XMLGetDescr(), XMLGetEMBLBlock(), XMLIndex(), XMLKeywordsCheck(), and XMLParseVersion().

◆ embl_new_ID

bool Indexblk::embl_new_ID = false

Definition at line 218 of file ftablock.h.

Referenced by CreateEntryBioseq(), EmblAscii(), EmblIndex(), GetDescrEmblBlock(), GetEmblInst(), GetEmblMolInfo(), GetFlatBiomol(), and InitialEntry().

◆ env_sample_qual

bool Indexblk::env_sample_qual = false

Definition at line 219 of file ftablock.h.

Referenced by CheckForENV(), GetDescrEmblBlock(), GetGBBlock(), XMLGetEMBLBlock(), and XMLGetGBBlock().

◆ EST

bool Indexblk::EST = false

Definition at line 192 of file ftablock.h.

Referenced by check_est_sts_gss_tpa_kwds(), GetDescrEmblBlock(), GetGBBlock(), InitialEntry(), xCheckEstStsGssTpaKeywords(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLInitialEntry().

◆ experimental

bool Indexblk::experimental = false

Definition at line 247 of file ftablock.h.

Referenced by GenBankIndex(), GetEmblDescr(), GetGenBankDescr(), xCheckEstStsGssTpaKeywords(), XMLGetDescr(), and XMLKeywordsCheck().

◆ gaps

GapFeatsPtr Indexblk::gaps = nullptr

Definition at line 214 of file ftablock.h.

Referenced by CollectGapFeats(), EmblAscii(), FreeIndexblk(), fta_set_molinfo_completeness(), GenBankAsciiOrig(), and XMLAscii().

◆ gc_genomic

int Indexblk::gc_genomic = 0

Definition at line 238 of file ftablock.h.

Referenced by fta_get_gcode_from_biosource(), and fta_get_genetic_code().

◆ gc_mito

int Indexblk::gc_mito = 0

Definition at line 239 of file ftablock.h.

Referenced by fta_get_gcode_from_biosource(), and fta_get_genetic_code().

◆ got_plastid

bool Indexblk::got_plastid = false

Definition at line 233 of file ftablock.h.

Referenced by CheckGene(), and UpdateRawBioSource().

◆ GSS

bool Indexblk::GSS = false

Definition at line 194 of file ftablock.h.

Referenced by check_est_sts_gss_tpa_kwds(), GetDescrEmblBlock(), GetGBBlock(), InitialEntry(), xCheckEstStsGssTpaKeywords(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLInitialEntry().

◆ HTC

bool Indexblk::HTC = false

Definition at line 195 of file ftablock.h.

Referenced by check_est_sts_gss_tpa_kwds(), GetDescrEmblBlock(), GetGBBlock(), InitialEntry(), xCheckEstStsGssTpaKeywords(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLInitialEntry().

◆ htg

Int2 Indexblk::htg = 0

Definition at line 196 of file ftablock.h.

Referenced by EmblAscii(), fta_check_htg_kwds(), GenBankAsciiOrig(), GetDescrEmblBlock(), GetGBBlock(), XMLAscii(), XMLGetEMBLBlock(), and XMLGetGBBlock().

◆ inferential

bool Indexblk::inferential = false

Definition at line 245 of file ftablock.h.

Referenced by GenBankIndex(), GetEmblDescr(), GetGenBankDescr(), xCheckEstStsGssTpaKeywords(), XMLGetDescr(), and XMLKeywordsCheck().

◆ is_contig

bool Indexblk::is_contig = false

Definition at line 197 of file ftablock.h.

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

◆ is_mga

bool Indexblk::is_mga = false

Definition at line 199 of file ftablock.h.

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

◆ is_pat

bool Indexblk::is_pat = false

Definition at line 202 of file ftablock.h.

Referenced by EmblAscii(), fta_replace_org(), GenBankAsciiOrig(), get_pat(), GetAccession(), GetDescrEmblBlock(), GetEmblDescr(), GetGBBlock(), GetGenBankDescr(), GetSeqData(), InitialEntry(), ParseSourceFeat(), XMLAscii(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLInitialEntry().

◆ is_prot

bool Indexblk::is_prot = false

Definition at line 222 of file ftablock.h.

Referenced by GenBankAscii(), GenBankAsciiOrig(), GetFlatBiomol(), GetGenBankInst(), GetSeqData(), ParseFeatureBlock(), SeqFeatPub(), XMLAscii(), XMLGetInst(), and XMLInitialEntry().

◆ is_tls

bool Indexblk::is_tls = false

Definition at line 208 of file ftablock.h.

Referenced by EmblAscii(), fta_check_non_tpa_tsa_tls_locations(), GenBankAsciiOrig(), GetDescrEmblBlock(), GetEmblDescr(), GetEmblMolInfo(), GetGBBlock(), GetGenBankDescr(), GetGenBankMolInfo(), InitialEntry(), IsTLSAccPrefix(), LoadFeat(), XMLAscii(), XMLGetDescr(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLGetMolInfo().

◆ is_tpa

bool Indexblk::is_tpa = false

Definition at line 206 of file ftablock.h.

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

◆ is_tpa_wgs_con

bool Indexblk::is_tpa_wgs_con = false

Definition at line 209 of file ftablock.h.

Referenced by EmblIndex(), GenBankIndex(), and XMLCheckRequiredTags().

◆ is_tsa

bool Indexblk::is_tsa = false

Definition at line 207 of file ftablock.h.

Referenced by EmblAscii(), fta_check_non_tpa_tsa_tls_locations(), fta_create_wgs_seqid(), GenBankAscii(), GenBankAsciiOrig(), GetDescrEmblBlock(), GetEmblDescr(), GetEmblMolInfo(), GetGBBlock(), GetGenBankDescr(), GetGenBankMolInfo(), InitialEntry(), IsTSAAccPrefix(), LoadFeat(), XMLAscii(), XMLGetDescr(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLGetMolInfo().

◆ is_wgs

bool Indexblk::is_wgs = false

Definition at line 205 of file ftablock.h.

Referenced by EmblIndex(), GenBankAsciiOrig(), GenBankIndex(), GetAccession(), GetEmblDescr(), GetEmblMolInfo(), GetGBBlock(), GetGenBankDescr(), GetGenBankMolInfo(), XMLAscii(), XMLCheckRequiredTags(), XMLGetDescr(), and XMLGetMolInfo().

◆ keywords

TKeywordList Indexblk::keywords

Definition at line 240 of file ftablock.h.

Referenced by CollectGapFeats(), GetGBBlock(), XMLGetEMBLBlock(), and XMLGetGBBlock().

◆ lc

LocusCont Indexblk::lc

Definition at line 212 of file ftablock.h.

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

◆ len

size_t Indexblk::len = 0

Definition at line 184 of file ftablock.h.

Referenced by EmblAscii(), EmblIndex(), GenBankAscii(), GenBankAsciiOrig(), GenBankIndex(), SprotAscii(), SprotIndex(), XMLIndex(), XMLLoadEntry(), and XMLPerformIndex().

◆ linenum

size_t Indexblk::linenum = 0

Definition at line 180 of file ftablock.h.

Referenced by GenBankIndex(), GetAccession(), GetSegment(), InitialEntry(), XMLIndex(), XMLLoadEntry(), and XMLPerformIndex().

◆ locusname

Char Indexblk::locusname[200]

Definition at line 170 of file ftablock.h.

Referenced by CheckContigEverywhere(), CheckDupEntries(), CheckEmblContigEverywhere(), CreateEntryBioseq(), EmblAscii(), EmblIndex(), err_install(), GenBankAscii(), GenBankAsciiOrig(), GetAccession(), Indexblk(), InitialEntry(), LoadFeat(), SprotAscii(), XMLAscii(), XMLCheckContigEverywhere(), and XMLInitialEntry().

◆ moltype

string Indexblk::moltype

Definition at line 213 of file ftablock.h.

Referenced by GetFlatBiomol(), and ParseSourceFeat().

◆ no_gc_warning

bool Indexblk::no_gc_warning = false

Definition at line 226 of file ftablock.h.

Referenced by fta_replace_org().

◆ offset

size_t Indexblk::offset = 0

Definition at line 168 of file ftablock.h.

Referenced by AccsCmp(), CheckDupEntries(), CompareData(), CompareDataV(), EmblAscii(), EmblIndex(), GenBankAscii(), GenBankAsciiOrig(), GenBankIndex(), InitialEntry(), SprotAscii(), SprotIndex(), XMLLoadEntry(), and XMLPerformIndex().

◆ organism

string Indexblk::organism

Definition at line 223 of file ftablock.h.

Referenced by fta_replace_org(), and SourceFeatStructFillIn().

◆ origin

bool Indexblk::origin = false

Definition at line 201 of file ftablock.h.

Referenced by CheckContigEverywhere(), CheckEmblContigEverywhere(), EmblIndex(), GenBankIndex(), XMLCheckContigEverywhere(), and XMLCheckRequiredTags().

◆ ppp

Parser* Indexblk::ppp = nullptr

Definition at line 250 of file ftablock.h.

Referenced by add_entry(), and InitialEntry().

◆ psip

CRef<objects::CPatent_seq_id> Indexblk::psip

Definition at line 190 of file ftablock.h.

Referenced by EmblAscii(), GenBankAsciiOrig(), get_pat(), GetDescrEmblBlock(), GetGBBlock(), XMLAscii(), XMLGetEMBLBlock(), and XMLGetGBBlock().

◆ qslength

size_t Indexblk::qslength = 0

Definition at line 230 of file ftablock.h.

Referenced by EmblAscii(), GenBankAsciiOrig(), GetQSFromFile(), and XMLAscii().

◆ qsoffset

size_t Indexblk::qsoffset = 0

Definition at line 229 of file ftablock.h.

Referenced by GetQSFromFile().

◆ secaccs

TokenBlkList Indexblk::secaccs

Definition at line 216 of file ftablock.h.

Referenced by fta_create_wgs_seqid(), GetAccession(), and GetExtraAccession().

◆ segnum

Uint2 Indexblk::segnum = 0

Definition at line 173 of file ftablock.h.

Referenced by CheckContigEverywhere(), CheckEmblContigEverywhere(), CompareData(), CompareDataV(), EmblSegment(), GenBankAscii(), GenBankAsciiOrig(), GenBankIndex(), GetSegment(), ParseSourceFeat(), XMLAscii(), XMLCheckContigEverywhere(), XMLCheckRequiredTags(), and XMLGetSegment().

◆ segtotal

Uint2 Indexblk::segtotal = 0

Definition at line 175 of file ftablock.h.

Referenced by CompareData(), CompareDataV(), EmblSegment(), GenBankAsciiOrig(), GetSegment(), ParseSourceFeat(), XMLAscii(), and XMLGetSegment().

◆ specialist_db

bool Indexblk::specialist_db = false

Definition at line 243 of file ftablock.h.

Referenced by GenBankIndex(), GetEmblDescr(), GetGenBankDescr(), xCheckEstStsGssTpaKeywords(), XMLGetDescr(), and XMLKeywordsCheck().

◆ STS

bool Indexblk::STS = false

Definition at line 193 of file ftablock.h.

Referenced by check_est_sts_gss_tpa_kwds(), GetDescrEmblBlock(), GetGBBlock(), InitialEntry(), xCheckEstStsGssTpaKeywords(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLInitialEntry().

◆ submitter_seqid

string Indexblk::submitter_seqid

Definition at line 249 of file ftablock.h.

Referenced by fta_create_wgs_seqid(), LoadFeat(), ParseSourceFeat(), and SourceFeatStructFillIn().

◆ taxid

TTaxId Indexblk::taxid = ZERO_TAX_ID

Definition at line 224 of file ftablock.h.

Referenced by fta_replace_org(), and SourceFeatStructFillIn().

◆ tsa_allowed

bool Indexblk::tsa_allowed = false

Definition at line 211 of file ftablock.h.

Referenced by EmblAscii(), EmblIndex(), GenBankAscii(), GenBankAsciiOrig(), GenBankIndex(), IsTSAAccPrefix(), XMLAscii(), and XMLCheckRequiredTags().

◆ vernum

Int2 Indexblk::vernum = 0

Definition at line 167 of file ftablock.h.

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

◆ wgs_and_gi

Int4 Indexblk::wgs_and_gi = 0

Definition at line 231 of file ftablock.h.

Referenced by GenBankAsciiOrig(), GenBankIndex(), and GetAccession().

◆ wgssec

string Indexblk::wgssec

Definition at line 236 of file ftablock.h.

Referenced by GetDescrEmblBlock(), GetDescrSPBlock(), GetEmblGBBlock(), GetExtraAccession(), GetGBBlock(), Indexblk(), XMLGetEMBLBlock(), and XMLGetGBBlock().

◆ xip

XmlIndexPtr Indexblk::xip = nullptr

Definition at line 217 of file ftablock.h.

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

The documentation for this struct was generated from the following files:
Generated by doxygen 1.9.0
Modified on Fri Sep 20 14:57:54 2024 by modify_doxy.py rev. 669887