NCBI C++ ToolKit
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Parser Struct Reference

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#include <objtools/flatfile/flatfile_parse_info.hpp>

+ Collaboration diagram for Parser:

Classes

struct  SFindPubOptions
 

Public Types

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
}
 

Public Member Functions

IndexblkCurEntry ()
 
size_t GetNumEntries () const
 
 Parser ()
 
virtual ~Parser ()
 
void InitializeKeywordParser (EFormat)
 
CKeywordParserKeywordParser ()
 

Public Attributes

Int4 indx = 0
 
vector< IndexblkPtrentrylist
 
Int4 curindx = 0
 
FileBuf ffbuf
 
string release_str
 
string authors_str
 
TEntryList entries
 
Int4 limit = 0
 
EFormat format = EFormat::unknown
 
ESource source = ESource::unknown
 
bool all = false
 
Uint1 seqtype = 0
 
Int4 num_drop = 0
 
const char * acprefix = nullptr
 
Uint1 entrez_fetch = 0
 
Uint1 taxserver = 0
 
ProtBlkPtr pbp = nullptr
 
Uint1 medserver = 0
 
bool normalize = false
 
SFindPubOptions fpo
 
bool date = false
 
bool no_date = false
 
bool citat = false
 
bool transl = false
 
bool sort = false
 
bool debug = false
 
bool segment = false
 
bool no_code = false
 
bool seg_acc = false
 
bool convert = false
 
const char ** accpref = nullptr
 
bool accver = false
 
bool histacc = false
 
bool ign_toks = false
 
bool ign_prot_src = false
 
bool ign_bad_qs = false
 
EMode mode = EMode::Release
 
bool diff_lt = false
 
Int4 errstat = 0
 
bool allow_uwsec = false
 
bool xml_comp = false
 
bool sp_dt_seq_ver = true
 
bool simple_genes = false
 
Int4 cleanup = 0
 
bool allow_crossdb_featloc = false
 
bool genenull = false
 
const char * qsfile = nullptr
 
FILE * qsfd = nullptr
 
bool qamode = false
 
char * buf = nullptr
 
EOutput output_format = EOutput::BioseqSet
 
bool ffdb = false
 
bool farseq = false
 
void * user_data = nullptr
 
char *(* ff_get_entry )(const char *accession) = nullptr
 
char *(* ff_get_entry_v )(const char *accession, Int2 vernum) = nullptr
 
char *(* ff_get_qscore )(const char *accession, Int2 v) = nullptr
 
char *(* ff_get_qscore_pp )(const char *accession, Int2 v, Parser *pp) = nullptr
 
char *(* ff_get_entry_pp )(const char *accession, Parser *pp) = nullptr
 
char *(* ff_get_entry_v_pp )(const char *accession, Int2 vernum, Parser *pp) = nullptr
 

Private Attributes

CKeywordParsermpKeywordParser
 

Detailed Description

Definition at line 65 of file flatfile_parse_info.hpp.

Member Enumeration Documentation

◆ EFormat

enum Parser::EFormat
strong
Enumerator
unknown 
EMBL 
GenBank 
SPROT 
DDBJ 
XML 
ALL 

Definition at line 93 of file flatfile_parse_info.hpp.

◆ EMode

enum Parser::EMode
strong
Enumerator
Release 
HTGS 
HTGSCON 
Relaxed 

Definition at line 72 of file flatfile_parse_info.hpp.

◆ EOutput

enum Parser::EOutput
strong
Enumerator
BioseqSet 
Seqsubmit 

Definition at line 67 of file flatfile_parse_info.hpp.

◆ ESource

enum Parser::ESource
strong
Enumerator
unknown 
NCBI 
EMBL 
GenBank 
DDBJ 
LANL 
SPROT 
Refseq 
Flybase 
USPTO 
All 

Definition at line 79 of file flatfile_parse_info.hpp.

Constructor & Destructor Documentation

◆ Parser()

Parser::Parser ( )

Definition at line 44 of file flatfile_parse_info.cpp.

◆ ~Parser()

Parser::~Parser ( )
virtual

Definition at line 62 of file flatfile_parse_info.cpp.

References mpKeywordParser, and ResetParserStruct().

Member Function Documentation

◆ CurEntry()

Indexblk* Parser::CurEntry ( )
inline

Definition at line 108 of file flatfile_parse_info.hpp.

References curindx, and entrylist.

◆ GetNumEntries()

size_t Parser::GetNumEntries ( ) const
inline

Definition at line 109 of file flatfile_parse_info.hpp.

References indx.

◆ InitializeKeywordParser()

void Parser::InitializeKeywordParser ( EFormat  fmt)

Definition at line 49 of file flatfile_parse_info.cpp.

References mpKeywordParser.

Referenced by sParseFlatfile().

◆ KeywordParser()

CKeywordParser & Parser::KeywordParser ( )

Definition at line 56 of file flatfile_parse_info.cpp.

References _ASSERT, and mpKeywordParser.

Referenced by EmblIndex(), GetDescrEmblBlock(), and GetEmblGBBlock().

Member Data Documentation

◆ accpref

const char** Parser::accpref = nullptr

Definition at line 179 of file flatfile_parse_info.hpp.

Referenced by FillAccsBySource(), fta_init_pp(), and GetAccession().

◆ accver

bool Parser::accver = false

◆ acprefix

const char* Parser::acprefix = nullptr

Definition at line 134 of file flatfile_parse_info.hpp.

Referenced by FillAccsBySource(), fta_init_pp(), and GetAccession().

◆ all

bool Parser::all = false

◆ allow_crossdb_featloc

bool Parser::allow_crossdb_featloc = false

◆ allow_uwsec

bool Parser::allow_uwsec = false

◆ authors_str

string Parser::authors_str

Definition at line 117 of file flatfile_parse_info.hpp.

Referenced by GetAuthorsStr(), and MakeSeqSubmit().

◆ buf

char* Parser::buf = nullptr

◆ citat

bool Parser::citat = false

◆ cleanup

Int4 Parser::cleanup = 0

◆ convert

bool Parser::convert = false

◆ curindx

Int4 Parser::curindx = 0

◆ date

bool Parser::date = false

Definition at line 167 of file flatfile_parse_info.hpp.

Referenced by fta_init_pp(), GetGenBankDescr(), and XMLGetDescr().

◆ debug

bool Parser::debug = false

◆ diff_lt

bool Parser::diff_lt = false

Definition at line 190 of file flatfile_parse_info.hpp.

Referenced by CheckGene().

◆ entrez_fetch

Uint1 Parser::entrez_fetch = 0

Definition at line 139 of file flatfile_parse_info.hpp.

Referenced by fta_add_hist(), fta_init_pp(), fta_is_con_div(), and fta_parse_buf().

◆ entries

TEntryList Parser::entries

◆ entrylist

vector<IndexblkPtr> Parser::entrylist

◆ errstat

Int4 Parser::errstat = 0

Definition at line 192 of file flatfile_parse_info.hpp.

Referenced by ParseSourceFeat().

◆ farseq

bool Parser::farseq = false

Definition at line 221 of file flatfile_parse_info.hpp.

Referenced by flat2asn_range_func(), and get_bioseq().

◆ ff_get_entry

char*(* Parser::ff_get_entry) (const char *accession) = nullptr

Definition at line 223 of file flatfile_parse_info.hpp.

Referenced by fta_init_pp(), and get_sequence_text().

◆ ff_get_entry_pp

char*(* Parser::ff_get_entry_pp) (const char *accession, Parser *pp) = nullptr

Definition at line 227 of file flatfile_parse_info.hpp.

Referenced by fta_init_pp(), and get_sequence_text().

◆ ff_get_entry_v

char*(* Parser::ff_get_entry_v) (const char *accession, Int2 vernum) = nullptr

Definition at line 224 of file flatfile_parse_info.hpp.

Referenced by fta_init_pp(), and get_sequence_text().

◆ ff_get_entry_v_pp

char*(* Parser::ff_get_entry_v_pp) (const char *accession, Int2 vernum, Parser *pp) = nullptr

Definition at line 228 of file flatfile_parse_info.hpp.

Referenced by fta_init_pp(), and get_sequence_text().

◆ ff_get_qscore

char*(* Parser::ff_get_qscore) (const char *accession, Int2 v) = nullptr

Definition at line 225 of file flatfile_parse_info.hpp.

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

◆ ff_get_qscore_pp

char*(* Parser::ff_get_qscore_pp) (const char *accession, Int2 v, Parser *pp) = nullptr

Definition at line 226 of file flatfile_parse_info.hpp.

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

◆ ffbuf

FileBuf Parser::ffbuf

◆ ffdb

bool Parser::ffdb = false

Definition at line 220 of file flatfile_parse_info.hpp.

Referenced by flat2asn_range_func(), and fta_init_pp().

◆ format

EFormat Parser::format = EFormat::unknown

◆ fpo

SFindPubOptions Parser::fpo

Definition at line 166 of file flatfile_parse_info.hpp.

Referenced by CFindPub::CFindPub(), and fta_fill_find_pub_option().

◆ genenull

bool Parser::genenull = false

Definition at line 210 of file flatfile_parse_info.hpp.

Referenced by DealWithGenes(), Flat2AsnCheck(), and fta_init_pp().

◆ histacc

bool Parser::histacc = false

Definition at line 183 of file flatfile_parse_info.hpp.

Referenced by fta_add_hist(), fta_init_pp(), and GetSprotDescr().

◆ ign_bad_qs

bool Parser::ign_bad_qs = false

Definition at line 187 of file flatfile_parse_info.hpp.

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

◆ ign_prot_src

bool Parser::ign_prot_src = false

Definition at line 185 of file flatfile_parse_info.hpp.

Referenced by GetProtRefSeqId().

◆ ign_toks

bool Parser::ign_toks = false

Definition at line 184 of file flatfile_parse_info.hpp.

Referenced by fta_init_pp(), and GenBankIndex().

◆ indx

Int4 Parser::indx = 0

◆ limit

Int4 Parser::limit = 0

◆ medserver

Uint1 Parser::medserver = 0

◆ mode

EMode Parser::mode = EMode::Release

◆ mpKeywordParser

CKeywordParser* Parser::mpKeywordParser
private

Definition at line 240 of file flatfile_parse_info.hpp.

Referenced by InitializeKeywordParser(), KeywordParser(), and ~Parser().

◆ no_code

bool Parser::no_code = false

◆ no_date

bool Parser::no_date = false

◆ normalize

bool Parser::normalize = false

Definition at line 149 of file flatfile_parse_info.hpp.

Referenced by fta_find_pub_explore(), and fta_init_servers().

◆ num_drop

Int4 Parser::num_drop = 0

◆ output_format

EOutput Parser::output_format = EOutput::BioseqSet

Definition at line 217 of file flatfile_parse_info.hpp.

Referenced by CloseAll(), and sParseFlatfile().

◆ pbp

ProtBlkPtr Parser::pbp = nullptr

◆ qamode

bool Parser::qamode = false

◆ qsfd

FILE* Parser::qsfd = nullptr

◆ qsfile

const char* Parser::qsfile = nullptr

Definition at line 211 of file flatfile_parse_info.hpp.

Referenced by Flat2AsnCheck(), fta_init_pp(), and QSIndex().

◆ release_str

string Parser::release_str

Definition at line 116 of file flatfile_parse_info.hpp.

Referenced by MakeBioseqSet(), and SetReleaseStr().

◆ seg_acc

bool Parser::seg_acc = false

Definition at line 177 of file flatfile_parse_info.hpp.

Referenced by fta_init_pp(), and GetBioseq().

◆ segment

bool Parser::segment = false

Definition at line 175 of file flatfile_parse_info.hpp.

Referenced by EmblAscii(), EmblIndex(), and fta_init_pp().

◆ seqtype

Uint1 Parser::seqtype = 0

◆ simple_genes

bool Parser::simple_genes = false

Definition at line 201 of file flatfile_parse_info.hpp.

Referenced by CheckGene(), and fta_init_pp().

◆ sort

bool Parser::sort = false

Definition at line 173 of file flatfile_parse_info.hpp.

Referenced by Flat2AsnCheck(), fta_init_pp(), fta_parse_buf(), and sParseFlatfile().

◆ source

ESource Parser::source = ESource::unknown

◆ sp_dt_seq_ver

bool Parser::sp_dt_seq_ver = true

Definition at line 197 of file flatfile_parse_info.hpp.

Referenced by Flat2AsnCheck(), fta_init_pp(), GetDescrSPBlock(), and SprotIndex().

◆ taxserver

Uint1 Parser::taxserver = 0

◆ transl

bool Parser::transl = false

Definition at line 172 of file flatfile_parse_info.hpp.

Referenced by CkProteinTransl(), and fta_init_pp().

◆ user_data

void* Parser::user_data = nullptr

Definition at line 222 of file flatfile_parse_info.hpp.

Referenced by fta_init_pp().

◆ xml_comp

bool Parser::xml_comp = false

The documentation for this struct was generated from the following files:
Modified on Tue Feb 27 05:51:22 2024 by modify_doxy.py rev. 669887