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Indexblk Struct Reference

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#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
 
TokenBlkPtr secaccs = nullptr
 
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
 
Parserppp = nullptr
 

Detailed Description

Definition at line 168 of file ftablock.h.

Constructor & Destructor Documentation

◆ Indexblk()

Indexblk::Indexblk ( )

Definition at line 666 of file indx_blk.cpp.

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

Member Data Documentation

◆ acnum

Char Indexblk::acnum[200]

◆ assembly

bool Indexblk::assembly = false

◆ bases

size_t Indexblk::bases = 0

◆ blocusname

Char Indexblk::blocusname[200]

◆ date

CRef<objects::CDate_std> Indexblk::date

Definition at line 190 of file ftablock.h.

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

◆ division

Char Indexblk::division[4]

◆ drop

bool Indexblk::drop = false

◆ embl_new_ID

bool Indexblk::embl_new_ID = false

◆ env_sample_qual

bool Indexblk::env_sample_qual = false

◆ EST

bool Indexblk::EST = false

◆ experimental

bool Indexblk::experimental = false

◆ gaps

GapFeatsPtr Indexblk::gaps = nullptr

◆ gc_genomic

int Indexblk::gc_genomic = 0

Definition at line 241 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 242 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 236 of file ftablock.h.

Referenced by CheckGene(), and UpdateRawBioSource().

◆ GSS

bool Indexblk::GSS = false

◆ HTC

bool Indexblk::HTC = false

◆ htg

Int2 Indexblk::htg = 0

◆ inferential

bool Indexblk::inferential = false

◆ is_contig

bool Indexblk::is_contig = false

◆ is_mga

bool Indexblk::is_mga = false

◆ is_pat

bool Indexblk::is_pat = false

◆ is_prot

bool Indexblk::is_prot = false

◆ is_tls

bool Indexblk::is_tls = false

◆ is_tpa

bool Indexblk::is_tpa = false

◆ is_tpa_wgs_con

bool Indexblk::is_tpa_wgs_con = false

Definition at line 212 of file ftablock.h.

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

◆ is_tsa

bool Indexblk::is_tsa = false

◆ is_wgs

bool Indexblk::is_wgs = false

◆ keywords

TKeywordList Indexblk::keywords

Definition at line 243 of file ftablock.h.

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

◆ lc

LocusCont Indexblk::lc

◆ len

size_t Indexblk::len = 0

◆ linenum

size_t Indexblk::linenum = 0

◆ locusname

Char Indexblk::locusname[200]

◆ moltype

string Indexblk::moltype

Definition at line 216 of file ftablock.h.

Referenced by GetFlatBiomol(), and ParseSourceFeat().

◆ no_gc_warning

bool Indexblk::no_gc_warning = false

Definition at line 229 of file ftablock.h.

Referenced by fta_replace_org().

◆ offset

size_t Indexblk::offset = 0

◆ organism

string Indexblk::organism

Definition at line 226 of file ftablock.h.

Referenced by fta_replace_org(), and SourceFeatStructFillIn().

◆ origin

bool Indexblk::origin = false

◆ ppp

Parser* Indexblk::ppp = nullptr

Definition at line 253 of file ftablock.h.

Referenced by add_entry(), and InitialEntry().

◆ psip

CRef<objects::CPatent_seq_id> Indexblk::psip

◆ qslength

size_t Indexblk::qslength = 0

Definition at line 233 of file ftablock.h.

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

◆ qsoffset

size_t Indexblk::qsoffset = 0

Definition at line 232 of file ftablock.h.

Referenced by GetQSFromFile().

◆ secaccs

TokenBlkPtr Indexblk::secaccs = nullptr

Definition at line 219 of file ftablock.h.

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

◆ segnum

Uint2 Indexblk::segnum = 0

◆ segtotal

Uint2 Indexblk::segtotal = 0

◆ specialist_db

bool Indexblk::specialist_db = false

◆ STS

bool Indexblk::STS = false

◆ submitter_seqid

string Indexblk::submitter_seqid

◆ taxid

TTaxId Indexblk::taxid = ZERO_TAX_ID

Definition at line 227 of file ftablock.h.

Referenced by fta_replace_org(), and SourceFeatStructFillIn().

◆ tsa_allowed

bool Indexblk::tsa_allowed = false

◆ vernum

Int2 Indexblk::vernum = 0

◆ wgs_and_gi

Int4 Indexblk::wgs_and_gi = 0

Definition at line 234 of file ftablock.h.

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

◆ wgssec

string Indexblk::wgssec

◆ xip

XmlIndexPtr Indexblk::xip = nullptr

The documentation for this struct was generated from the following files:
Modified on Thu Feb 29 12:23:29 2024 by modify_doxy.py rev. 669887