NCBI C++ ToolKit
Macros | Functions | Variables
indx_blk.cpp File Reference
#include <ncbi_pch.hpp>
#include "ftacpp.hpp"
#include "index.h"
#include <objtools/flatfile/flatfile_parse_info.hpp>
#include "ftaerr.hpp"
#include "indx_blk.h"
#include "indx_def.h"
#include "utilfun.h"
#include <map>
+ Include dependency graph for indx_blk.cpp:

Go to the source code of this file.

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Macros

#define THIS_FILE   "indx_blk.cpp"
 

Functions

 USING_SCOPE (objects)
 
bool EmblIndex (ParserPtr pp, void(*fun)(IndexblkPtr entry, char *offset, Int4 len))
 
bool GenBankIndex (ParserPtr pp)
 
bool SprotIndex (ParserPtr pp, void(*fun)(IndexblkPtr entry, char *offset, Int4 len))
 
bool XMLIndex (ParserPtr pp)
 
static const char * GetResidue (TokenStatBlkPtr stoken)
 
static bool XReadFile (FILE *fp, FinfoBlk &finfo)
 
static Int2 FileGetsBuf (char *res, Int4 size, FileBuf &fbuf)
 
bool XReadFileBuf (FileBuf &fbuf, FinfoBlk &finfo)
 
NCBI_UNUSED bool SkipTitle (FILE *fp, FinfoBlk &finfo, const char *str, size_t len)
 
NCBI_UNUSED bool SkipTitle (FILE *fp, FinfoBlk &finfo, const CTempString &keyword)
 
bool SkipTitleBuf (FileBuf &fbuf, FinfoBlk &finfo, const CTempString &keyword)
 
static bool CheckLocus (const char *locus, Parser::ESource source)
 
static bool CheckLocusSP (const char *locus)
 
static bool CkDateFormat (const char *date)
 
int CheckSTRAND (const string &str)
 
Int2 XMLCheckSTRAND (const char *str)
 
Int2 XMLCheckTPG (const char *str)
 
int CheckTPG (const string &str)
 
Int2 CheckNADDBJ (const char *str)
 
Int2 CheckNA (const char *str)
 
Int2 CheckDIV (const char *str)
 
bool CkLocusLinePos (char *offset, Parser::ESource source, LocusContPtr lcp, bool is_mga)
 
CRef< CDate_stdGetUpdateDate (const char *ptr, Parser::ESource source)
 
static bool fta_check_embl_moltype (char *str)
 
static bool isSpace (char c)
 
static CTempString::const_iterator sFindNextSpace (const CTempString &tempString, CTempString::const_iterator current_it)
 
static CTempString::const_iterator sFindNextNonSpace (const CTempString &tempString, CTempString::const_iterator current_it)
 
static void sSetLocusLineOffsets (const CTempString &locusLine, LocusCont &offsets)
 
IndexblkPtr InitialEntry (ParserPtr pp, FinfoBlk &finfo)
 
void DelNoneDigitTail (char *str)
 
void DelNonDigitTail (string &str)
 
static bool sIsUpperAlpha (char c)
 
Int4 IsNewAccessFormat (const Char *acnum)
 
static bool IsValidAccessPrefix (const char *acc, const char **accpref)
 
static bool fta_if_master_wgs_accession (const char *acnum, Int4 accformat)
 
static bool s_IsVDBWGSScaffold (string_view accession)
 
static int s_RefineWGSType (string_view accession, int initialType)
 
int fta_if_wgs_acc (string_view accession)
 
bool IsSPROTAccession (const char *acc)
 
static bool sNotAllDigits (const char *first, const char *last)
 
static bool CheckAccession (TokenStatBlkPtr stoken, Parser::ESource source, Parser::EMode mode, char *priacc, unsigned skip)
 
static bool IsPatentedAccPrefix (const Parser &parseInfo, const char *acc)
 
static bool IsTPAAccPrefix (const Parser &parseInfo, const char *acc)
 
static bool IsWGSAccPrefix (const Parser &parseInfo, const char *acc)
 
static void IsTSAAccPrefix (const Parser &parseInfo, const char *acc, IndexblkPtr ibp)
 
static void IsTLSAccPrefix (const Parser &parseInfo, const char *acc, IndexblkPtr ibp)
 
bool GetAccession (ParserPtr pp, const char *str, IndexblkPtr entry, unsigned skip)
 
void ResetParserStruct (ParserPtr pp)
 
void CloseFiles (ParserPtr pp)
 
void MsgSkipTitleFail (const char *flatfile, FinfoBlk &finfo)
 
bool FindNextEntryBuf (bool end_of_file, FileBuf &fbuf, FinfoBlk &finfo, const CTempString &keyword)
 
bool FlatFileIndex (ParserPtr pp, void(*fun)(IndexblkPtr entry, char *offset, Int4 len))
 
const char ** GetAccArray (Parser::ESource source)
 
bool isSupportedAccession (CSeq_id::E_Choice type)
 
CSeq_id::E_Choice GetNucAccOwner (const CTempString &acc)
 
CSeq_id::E_Choice GetProtAccOwner (const CTempString &acc)
 

Variables

static const char * XML_STRAND_array []
 
static const char * XML_TPG_array []
 
static const char * ParFlat_NA_array_DDBJ []
 
static const char * ParFlat_AA_array_DDBJ []
 
static const char * ParFlat_NA_array []
 
static const char * ParFlat_DIV_array []
 
static const char * embl_accpref []
 
static const char * lanl_accpref []
 
static const char * sprot_accpref []
 
static const char * ddbj_accpref []
 
static const char * ncbi_accpref []
 
static const char * refseq_accpref []
 
static const char * acc_tsa_allowed []
 
static const char * ncbi_tpa_accpref []
 
static const char * ddbj_tpa_accpref []
 
static const char * ncbi_wgs_accpref []
 
static const char * ddbj_wgs_accpref []
 
static const set< string_view > k_WgsScaffoldPrefix
 
static const map< Parser::ESource, stringsourceNames
 
static const char * month_name []
 
static const char * ParFlat_RESIDUE_STR []
 
static const char * ValidMolTypes []
 

Macro Definition Documentation

◆ THIS_FILE

#define THIS_FILE   "indx_blk.cpp"

Definition at line 51 of file indx_blk.cpp.

Function Documentation

◆ CheckAccession()

static bool CheckAccession ( TokenStatBlkPtr  stoken,
Parser::ESource  source,
Parser::EMode  mode,
char *  priacc,
unsigned  skip 
)
static

◆ CheckDIV()

Int2 CheckDIV ( const char *  str)

Definition at line 530 of file indx_blk.cpp.

References fta_StringMatch(), ParFlat_DIV_array, and str().

Referenced by CkLocusLinePos(), GetGBBlock(), and XMLGetGBBlock().

◆ CheckLocus()

static bool CheckLocus ( const char *  locus,
Parser::ESource  source 
)
static

◆ CheckLocusSP()

static bool CheckLocusSP ( const char *  locus)
static

Definition at line 417 of file indx_blk.cpp.

References ERR_LOCUS_BadLocusName, ErrPostEx, and SEV_ERROR.

Referenced by InitialEntry().

◆ CheckNA()

Int2 CheckNA ( const char *  str)

Definition at line 524 of file indx_blk.cpp.

References fta_StringMatch(), ParFlat_NA_array, and str().

Referenced by GetFlatBiomol().

◆ CheckNADDBJ()

Int2 CheckNADDBJ ( const char *  str)

Definition at line 518 of file indx_blk.cpp.

References fta_StringMatch(), ParFlat_NA_array_DDBJ, and str().

Referenced by GetFlatBiomol().

◆ CheckSTRAND()

int CheckSTRAND ( const string str)

◆ CheckTPG()

int CheckTPG ( const string str)

Definition at line 500 of file indx_blk.cpp.

References i, NStr::StartsWith(), str(), and NStr::ToLower().

Referenced by CkLocusLinePos(), GetGenBankInst(), and Entry::xInitSeqInst().

◆ CkDateFormat()

static bool CkDateFormat ( const char *  date)
static

Definition at line 452 of file indx_blk.cpp.

References isdigit(), MatchArraySubString(), and month_name.

Referenced by CkLocusLinePos(), and GetUpdateDate().

◆ CkLocusLinePos()

bool CkLocusLinePos ( char *  offset,
Parser::ESource  source,
LocusContPtr  lcp,
bool  is_mga 
)

◆ CloseFiles()

void CloseFiles ( ParserPtr  pp)

Definition at line 2145 of file indx_blk.cpp.

References Parser::qsfd.

Referenced by CloseAll().

◆ DelNonDigitTail()

void DelNonDigitTail ( string str)

Definition at line 957 of file indx_blk.cpp.

References str().

Referenced by GetExtraAccession().

◆ DelNoneDigitTail()

void DelNoneDigitTail ( char *  str)

Definition at line 943 of file indx_blk.cpp.

References str().

Referenced by GetAccession().

◆ EmblIndex()

bool EmblIndex ( ParserPtr  pp,
void(*)(IndexblkPtr entry, char *offset, Int4 len fun 
)

◆ FileGetsBuf()

static Int2 FileGetsBuf ( char *  res,
Int4  size,
FileBuf fbuf 
)
static

Definition at line 287 of file indx_blk.cpp.

References FileBuf::current, i, and ncbi::grid::netcache::search::fields::size.

Referenced by XReadFileBuf().

◆ FindNextEntryBuf()

bool FindNextEntryBuf ( bool  end_of_file,
FileBuf fbuf,
FinfoBlk finfo,
const CTempString keyword 
)

◆ FlatFileIndex()

bool FlatFileIndex ( ParserPtr  pp,
void(*)(IndexblkPtr entry, char *offset, Int4 len fun 
)

◆ fta_check_embl_moltype()

static bool fta_check_embl_moltype ( char *  str)
static

◆ fta_if_master_wgs_accession()

static bool fta_if_master_wgs_accession ( const char *  acnum,
Int4  accformat 
)
static

Definition at line 1062 of file indx_blk.cpp.

Referenced by CheckAccession().

◆ fta_if_wgs_acc()

int fta_if_wgs_acc ( string_view  accession)

◆ GenBankIndex()

bool GenBankIndex ( ParserPtr  pp)

Definition at line 337 of file gb_index.cpp.

References Parser::accver, Indexblk::acnum, Indexblk::assembly, check_est_sts_gss_tpa_kwds(), CheckLineType(), CkLocusLinePos(), ConstructValNode(), Parser::curindx, Parser::DDBJ, Indexblk::drop, e_not_set, Parser::EMBL, Parser::entrylist, ERR_ACCESSION_NoAccessNum, ERR_ENTRY_InvalidLineType, ERR_FORMAT_ContigInSegset, ERR_FORMAT_IncorrectMGALine, ERR_FORMAT_LineTypeOrder, ErrPostEx, Indexblk::experimental, Parser::ffbuf, FindNextEntryBuf(), Parser::Flybase, fta_check_mga_line(), FtaDeletePrefix(), gb_err_field(), genbankKeywords, FileBuf::get_offs(), GetAccession(), GetSegment(), Parser::HTGSCON, i, IndBlkNode::ibp, if(), Parser::ign_toks, Parser::indx, Indexblk::inferential, InitialEntry(), Indexblk::is_contig, Indexblk::is_mga, Indexblk::is_tpa, Indexblk::is_tpa_wgs_con, Indexblk::is_wgs, NStr::IsBlank(), Indexblk::lc, Indexblk::len, FinfoBlk::line, Indexblk::linenum, MemFree(), Parser::mode, MsgSkipTitleFail(), IndBlkNode::next, Parser::num_drop, Indexblk::offset, Indexblk::origin, ParFlat_ACCESSION, ParFlat_COL_DATA, ParFlat_COMMENT, ParFlat_CONTIG, ParFlat_DBLINK, ParFlat_DEFINITION, ParFlat_END, ParFlat_FEATURES, ParFlat_KEYWORDS, ParFlat_LOCUS, ParFlat_MGA, ParFlat_NCBI_GI, ParFlat_ORIGIN, ParFlat_PRIMARY, ParFlat_REFERENCE, ParFlat_SEGMENT, ParFlat_SOURCE, ParFlat_UNKW, ParFlat_USER, ParFlat_VERSION, ParseGenBankVersion(), PREFIX_ACCESSION, PREFIX_LOCUS, Parser::qsfd, QSIndex(), Parser::Refseq, Parser::Relaxed, Indexblk::segnum, SEV_ERROR, SEV_REJECT, SkipTitleBuf(), Parser::source, Indexblk::specialist_db, SrchKeyword(), FinfoBlk::str, StringEquN(), StringLen(), StringNCpy(), StringNew(), StringSave, StringStr, Indexblk::tsa_allowed, ValNodeFreeData(), ValNodeNew(), Indexblk::vernum, Indexblk::wgs_and_gi, and XReadFileBuf().

Referenced by FlatFileIndex().

◆ GetAccArray()

const char** GetAccArray ( Parser::ESource  source)

◆ GetAccession()

bool GetAccession ( ParserPtr  pp,
const char *  str,
IndexblkPtr  entry,
unsigned  skip 
)

◆ GetNucAccOwner()

CSeq_id::E_Choice GetNucAccOwner ( const CTempString acc)

◆ GetProtAccOwner()

CSeq_id::E_Choice GetProtAccOwner ( const CTempString acc)

◆ GetResidue()

static const char* GetResidue ( TokenStatBlkPtr  stoken)
static

◆ GetUpdateDate()

CRef<CDate_std> GetUpdateDate ( const char *  ptr,
Parser::ESource  source 
)

◆ InitialEntry()

IndexblkPtr InitialEntry ( ParserPtr  pp,
FinfoBlk finfo 
)

◆ IsNewAccessFormat()

Int4 IsNewAccessFormat ( const Char acnum)

◆ IsPatentedAccPrefix()

static bool IsPatentedAccPrefix ( const Parser parseInfo,
const char *  acc 
)
static

Definition at line 1606 of file indx_blk.cpp.

References Parser::all, Parser::DDBJ, Parser::EMBL, Parser::NCBI, Parser::source, StringEqu(), and StringEquN().

Referenced by GetAccession().

◆ isSpace()

static bool isSpace ( char  c)
static

Definition at line 673 of file indx_blk.cpp.

References isspace().

Referenced by sFindNextNonSpace(), and sFindNextSpace().

◆ IsSPROTAccession()

bool IsSPROTAccession ( const char *  acc)

Definition at line 1253 of file indx_blk.cpp.

References b, len, sprot_accpref, StringEquN(), and StringLen().

Referenced by CheckAccession(), and GetSprotDescr().

◆ isSupportedAccession()

bool isSupportedAccession ( CSeq_id::E_Choice  type)

◆ IsTLSAccPrefix()

static void IsTLSAccPrefix ( const Parser parseInfo,
const char *  acc,
IndexblkPtr  ibp 
)
static

◆ IsTPAAccPrefix()

static bool IsTPAAccPrefix ( const Parser parseInfo,
const char *  acc 
)
static

◆ IsTSAAccPrefix()

static void IsTSAAccPrefix ( const Parser parseInfo,
const char *  acc,
IndexblkPtr  ibp 
)
static

◆ IsValidAccessPrefix()

static bool IsValidAccessPrefix ( const char *  acc,
const char **  accpref 
)
static

Definition at line 1043 of file indx_blk.cpp.

References b, i, IsNewAccessFormat(), StringEquN(), and StringLen().

Referenced by GetAccession().

◆ IsWGSAccPrefix()

static bool IsWGSAccPrefix ( const Parser parseInfo,
const char *  acc 
)
static

◆ MsgSkipTitleFail()

void MsgSkipTitleFail ( const char *  flatfile,
FinfoBlk finfo 
)

Definition at line 2160 of file indx_blk.cpp.

References ERR_ENTRY_Begin, ErrPostEx, and SEV_ERROR.

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

◆ ResetParserStruct()

void ResetParserStruct ( ParserPtr  pp)

◆ s_IsVDBWGSScaffold()

static bool s_IsVDBWGSScaffold ( string_view  accession)
static

Definition at line 1086 of file indx_blk.cpp.

References isalpha(), and isdigit().

Referenced by fta_if_wgs_acc().

◆ s_RefineWGSType()

static int s_RefineWGSType ( string_view  accession,
int  initialType 
)
static

Definition at line 1128 of file indx_blk.cpp.

Referenced by fta_if_wgs_acc().

◆ sFindNextNonSpace()

static CTempString::const_iterator sFindNextNonSpace ( const CTempString tempString,
CTempString::const_iterator  current_it 
)
static

Definition at line 687 of file indx_blk.cpp.

References CTempString::end(), and isSpace().

Referenced by sSetLocusLineOffsets().

◆ sFindNextSpace()

static CTempString::const_iterator sFindNextSpace ( const CTempString tempString,
CTempString::const_iterator  current_it 
)
static

Definition at line 679 of file indx_blk.cpp.

References CTempString::end(), and isSpace().

Referenced by sSetLocusLineOffsets().

◆ sIsUpperAlpha()

static bool sIsUpperAlpha ( char  c)
static

Definition at line 986 of file indx_blk.cpp.

Referenced by CheckAccession(), and IsNewAccessFormat().

◆ SkipTitle() [1/2]

NCBI_UNUSED bool SkipTitle ( FILE *  fp,
FinfoBlk finfo,
const char *  str,
size_t  len 
)

Definition at line 340 of file indx_blk.cpp.

References fp, len, str(), FinfoBlk::str, StringEquN(), and XReadFile().

Referenced by SkipTitle().

◆ SkipTitle() [2/2]

NCBI_UNUSED bool SkipTitle ( FILE *  fp,
FinfoBlk finfo,
const CTempString keyword 
)

Definition at line 350 of file indx_blk.cpp.

References CTempString::data(), fp, CTempString::size(), and SkipTitle().

◆ SkipTitleBuf()

bool SkipTitleBuf ( FileBuf fbuf,
FinfoBlk finfo,
const CTempString keyword 
)

◆ sNotAllDigits()

static bool sNotAllDigits ( const char *  first,
const char *  last 
)
static

Definition at line 1489 of file indx_blk.cpp.

References first(), isdigit(), and last().

Referenced by CheckAccession().

◆ SprotIndex()

bool SprotIndex ( ParserPtr  pp,
void(*)(IndexblkPtr entry, char *offset, Int4 len fun 
)

◆ sSetLocusLineOffsets()

static void sSetLocusLineOffsets ( const CTempString locusLine,
LocusCont offsets 
)
static

◆ USING_SCOPE()

USING_SCOPE ( objects  )

◆ XMLCheckSTRAND()

Int2 XMLCheckSTRAND ( const char *  str)

Definition at line 483 of file indx_blk.cpp.

References str(), StringMatchIcase(), and XML_STRAND_array.

Referenced by XMLGetInst().

◆ XMLCheckTPG()

Int2 XMLCheckTPG ( const char *  str)

Definition at line 489 of file indx_blk.cpp.

References i, str(), StringMatchIcase(), and XML_TPG_array.

Referenced by XMLGetInst().

◆ XMLIndex()

bool XMLIndex ( ParserPtr  pp)

◆ XReadFile()

static bool XReadFile ( FILE *  fp,
FinfoBlk finfo 
)
static

Definition at line 261 of file indx_blk.cpp.

References fp, FinfoBlk::line, n, FinfoBlk::pos, FinfoBlk::str, StringCpy(), and StringEquN().

Referenced by SkipTitle().

◆ XReadFileBuf()

bool XReadFileBuf ( FileBuf fbuf,
FinfoBlk finfo 
)

Variable Documentation

◆ acc_tsa_allowed

const char* acc_tsa_allowed[]
static
Initial value:
= {
"AF", "AY", "DQ", "EF", "EU", "FJ", "GQ", "HQ", "JF", "JN", "JQ", "JX",
"KC", "KF", "KJ", "KM", "KP", "KR", "KT", "KU", "KX", "KY", "MF", "MG",
"MH", "MK", "MN", "MT", nullptr
}

Definition at line 145 of file indx_blk.cpp.

Referenced by IsTSAAccPrefix().

◆ ddbj_accpref

const char* ddbj_accpref[]
static
Initial value:
= {
"AB", "AG", "AK", "AP", "AT", "AU", "AV", "BA", "BB", "BD", "BJ", "BP",
"BR", "BS", "BW", "BY", "CI", "CJ", "DA", "DB", "DC", "DD", "DE", "DF",
"DG", "DH", "DI", "DJ", "DK", "DL", "DM", "FS", "FT", "FU", "FV", "FW",
"FX", "FY", "FZ", "GA", "GB", "HT", "HU", "HV", "HW", "HX", "HY", "HZ",
"LA", "LB", "LC", "LD", "LE", "LF", "LG", "LH", "LI", "LJ", "LU", "LV",
"LX", "LY", "LZ", "MA", "MB", "MC", "MD", "ME", "OF", "OG", "OH", "OI",
"OJ", "PA", "PE", "PF", "PG", "PH", "PI", "PJ", "PK", nullptr
}

Definition at line 104 of file indx_blk.cpp.

Referenced by GetAccArray().

◆ ddbj_tpa_accpref

const char* ddbj_tpa_accpref[]
static
Initial value:
= {
"BR", "HT", "HU", nullptr
}

Definition at line 155 of file indx_blk.cpp.

Referenced by IsTPAAccPrefix().

◆ ddbj_wgs_accpref

const char* ddbj_wgs_accpref[]
static
Initial value:
= {
"HT", "HU", nullptr
}

Definition at line 163 of file indx_blk.cpp.

Referenced by IsWGSAccPrefix().

◆ embl_accpref

const char* embl_accpref[]
static
Initial value:
= {
"AJ", "AL", "AM", "AN", "AX", "BN", "BX", "CQ", "CR", "CS", "CT", "CU",
"FB", "FM", "FN", "FO", "FP", "FQ", "FR", "GM", "GN", "HA", "HB", "HC",
"HD", "HE", "HF", "HG", "HH", "HI", "JA", "JB", "JC", "JD", "JE", "LK",
"LL", "LM", "LN", "LO", "LP", "LQ", "LR", "LS", "LT", "MP", "MQ", "MR",
"MS", "OA", "OB", "OC", "OD", "OE", "OU", "OV", "OW", "OX", "OY", "OZ",
nullptr
}

Definition at line 87 of file indx_blk.cpp.

Referenced by GetAccArray().

◆ k_WgsScaffoldPrefix

const set<string_view> k_WgsScaffoldPrefix
static
Initial value:
= {
"CH", "CT", "CU", "DF", "DG", "DS",
"EM", "EN", "EP", "EQ", "FA", "FM",
"GG", "GJ", "GK", "GL", "HT", "HU",
"JH", "KB", "KD", "KE", "KI", "KK",
"KL", "KN", "KQ", "KV", "KZ", "LD",
"ML", "MU", "PS"
}

Definition at line 167 of file indx_blk.cpp.

Referenced by fta_if_wgs_acc().

◆ lanl_accpref

const char* lanl_accpref[]
static
Initial value:
= {
"AD", nullptr
}

Definition at line 96 of file indx_blk.cpp.

Referenced by GetAccArray().

◆ month_name

const char* month_name[]
static
Initial value:
= {
"Ill", "JAN", "FEB", "MAR", "APR", "MAY", "JUN", "JUL", "AUG", "SEP", "OCT", "NOV", "DEC", nullptr
}

Definition at line 187 of file indx_blk.cpp.

Referenced by CkDateFormat(), and get_month_code_by_name().

◆ ncbi_accpref

const char* ncbi_accpref[]
static
Initial value:
= {
"AA", "AC", "AD", "AE", "AF", "AH", "AI", "AQ", "AR", "AS", "AW", "AY",
"AZ", "BC", "BE", "BF", "BG", "BH", "BI", "BK", "BL", "BM", "BQ", "BT",
"BU", "BV", "BZ", "CA", "CB", "CC", "CD", "CE", "CF", "CG", "CH", "CK",
"CL", "CM", "CN", "CO", "CP", "CV", "CW", "CX", "CY", "CZ", "DN", "DP",
"DQ", "DR", "DS", "DT", "DU", "DV", "DW", "DX", "DY", "DZ", "EA", "EB",
"EC", "ED", "EE", "EF", "EG", "EH", "EI", "EJ", "EK", "EL", "EM", "EN",
"EP", "EQ", "ER", "ES", "ET", "EU", "EV", "EW", "EX", "EY", "EZ", "FA",
"FC", "FD", "FE", "FF", "FG", "FH", "FI", "FJ", "FK", "FL", "GC", "GD",
"GE", "GF", "GG", "GH", "GJ", "GK", "GL", "GO", "GP", "GQ", "GR", "GS",
"GT", "GU", "GV", "GW", "GX", "GY", "GZ", "HJ", "HK", "HL", "HM", "HN",
"HO", "HP", "HQ", "HR", "HS", "JF", "JG", "JH", "JI", "JJ", "JK", "JL",
"JM", "JN", "JO", "JP", "JQ", "JR", "JS", "JT", "JU", "JV", "JW", "JX",
"JY", "JZ", "KA", "KB", "KC", "KD", "KE", "KF", "KG", "KH", "KI", "KJ",
"KK", "KL", "KM", "KN", "KO", "KP", "KQ", "KR", "KS", "KT", "KU", "KV",
"KX", "KY", "KZ", "MF", "MG", "MH", "MI", "MJ", "MK", "ML", "MM", "MN",
"MO", "MT", "MU", "MV", "MW", "MX", "MY", "MZ", "OK", "OL", "OM", "ON",
"OO", "OP", "OQ", "OR", "OS", "OT", "PP", "PR", "PS", "PT", nullptr
}

Definition at line 114 of file indx_blk.cpp.

Referenced by GetAccArray().

◆ ncbi_tpa_accpref

const char* ncbi_tpa_accpref[]
static
Initial value:
= {
"BK", "BL", "GJ", "GK", nullptr
}

Definition at line 151 of file indx_blk.cpp.

Referenced by IsTPAAccPrefix().

◆ ncbi_wgs_accpref

const char* ncbi_wgs_accpref[]
static
Initial value:
= {
"GJ", "GK", nullptr
}

Definition at line 159 of file indx_blk.cpp.

Referenced by IsWGSAccPrefix().

◆ ParFlat_AA_array_DDBJ

const char* ParFlat_AA_array_DDBJ[]
static
Initial value:
= {
"PRT", nullptr
}

Definition at line 70 of file indx_blk.cpp.

Referenced by CkLocusLinePos().

◆ ParFlat_DIV_array

const char* ParFlat_DIV_array[]
static
Initial value:
= {
" ", "PRI", "ROD", "MAM", "VRT", "INV", "PLN", "BCT", "RNA",
"VRL", "PHG", "SYN", "UNA", "EST", "PAT", "STS", "ORG", "GSS",
"HUM", "HTG", "CON", "HTC", "ENV", "TSA", nullptr
}

Definition at line 81 of file indx_blk.cpp.

Referenced by CheckDIV().

◆ ParFlat_NA_array

const char* ParFlat_NA_array[]
static
Initial value:
= {
" ", "NA", "DNA", "genomic DNA", "other DNA", "unassigned DNA", "RNA",
"mRNA", "rRNA", "tRNA", "uRNA", "scRNA", "snRNA", "snoRNA", "pre-RNA",
"pre-mRNA", "genomic RNA", "other RNA", "unassigned RNA", "cRNA",
"viral cRNA", nullptr
}

Definition at line 74 of file indx_blk.cpp.

Referenced by CheckNA(), and CkLocusLinePos().

◆ ParFlat_NA_array_DDBJ

const char* ParFlat_NA_array_DDBJ[]
static
Initial value:
= {
"cDNA", nullptr
}

Definition at line 66 of file indx_blk.cpp.

Referenced by CheckNADDBJ(), and CkLocusLinePos().

◆ ParFlat_RESIDUE_STR

const char* ParFlat_RESIDUE_STR[]
static
Initial value:
= {
"bp", "bp.", "bp,", "AA", "AA.", "AA,", nullptr
}

Definition at line 191 of file indx_blk.cpp.

Referenced by GetResidue().

◆ refseq_accpref

const char* refseq_accpref[]
static
Initial value:
= {
"NC_", "NG_", "NM_", "NP_", "NR_", "NT_", "NW_", "XM_", "XP_", "XR_",
"NZ_", nullptr
}

Definition at line 134 of file indx_blk.cpp.

Referenced by GetAccArray().

◆ sourceNames

const map<Parser::ESource, string> sourceNames
static
Initial value:

Definition at line 176 of file indx_blk.cpp.

Referenced by GetAccession().

◆ sprot_accpref

const char* sprot_accpref[]
static
Initial value:
= {
"DD", nullptr
}

Definition at line 100 of file indx_blk.cpp.

Referenced by GetAccArray(), and IsSPROTAccession().

◆ ValidMolTypes

const char* ValidMolTypes[]
static
Initial value:
= {
"genomic DNA",
"genomic RNA",
"mRNA",
"tRNA",
"rRNA",
"snoRNA",
"snRNA",
"scRNA",
"pre-RNA",
"pre-mRNA",
"other RNA",
"other DNA",
"transcribed RNA",
"unassigned RNA",
"unassigned DNA",
"viral cRNA",
nullptr
}

Definition at line 195 of file indx_blk.cpp.

Referenced by fta_check_embl_moltype().

◆ XML_STRAND_array

const char* XML_STRAND_array[]
static
Initial value:
= {
" ", "single", "double", "mixed", nullptr
}

Definition at line 58 of file indx_blk.cpp.

Referenced by XMLCheckSTRAND().

◆ XML_TPG_array

const char* XML_TPG_array[]
static
Initial value:
= {
" ", "Linear", "Circular", "Tandem", nullptr
}

Definition at line 62 of file indx_blk.cpp.

Referenced by XMLCheckTPG().

Modified on Fri May 24 14:54:53 2024 by modify_doxy.py rev. 669887