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NCBI C++ ToolKit: src/objtools/flatfile/ftacpp.hpp File Reference

#include <cstring>
#include <charconv>
#include <corelib/ncbistr.hpp>

Go to the source code of this file.

Go to the SVN repository for this file.

char *  StringNew (size_t sz)   void  MemSet (void *p, int n, size_t sz)   void  MemCpy (void *p, const void *q, size_t sz)   void  MemFree (char *p)   size_t  StringLen (const char *s)   char *  StringSave (const char *s)   char *  StringSave (string_view s)   char *  StringSave (unique_ptr< string > s)   const char *  StringStr (const char *s1, const char *s2)   char *  StringStr (char *s1, const char *s2)   void  StringCat (char *d, const char *s)   void  StringCpy (char *d, const char *s)   void  StringNCpy (char *d, const char *s, size_t n)   const char *  StringChr (const char *s, const char c)   char *  StringChr (char *s, const char c)   char *  StringRChr (char *s, const char c)   int  StringCmp (const char *s1, const char *s2)   bool  StringEqu (const char *s1, const char *s2)   bool  StringEquN (const char *s1, const char *s2, size_t n)   bool  fta_StartsWith (const char *s1, string_view s2)   bool  StringEquNI (const char *s1, const char *s2, size_t n)   bool  StringHasNoText (const char *s)   bool  StringDoesHaveText (const char *s)   int  fta_atoi (string_view sv)   ◆ fta_atoi() int fta_atoi ( string_view  sv ) inline

Definition at line 153 of file ftacpp.hpp.

References n.

Referenced by AddToIndexBlk(), check_mix_pages_range(), CheckCollectionDate(), CheckSourceFeatCoverage(), CkInitMetSP(), DbxrefQualToDbtag(), fta_check_mga_line(), fta_check_rpt_unit_span(), fta_get_citgen(), fta_get_dblink_user_object(), fta_get_project_user_object(), fta_get_user_field(), fta_parse_tpa_tsa_block(), fta_sort_quals(), FtaErrGetMsgCodes(), get_lanl_date(), get_pat(), GetCitSerialFromQual(), GetDRlineDataSP(), GetLenSubNode(), GetProtRefSeqId(), GetSPDate(), GetSprotIds(), GetSPSegLocInfo(), GetSPSeqLoc(), GetTaxIdFrom_OX(), GetViralHostsFrom_OH(), InitialEntry(), MakeUsptoPatSeqId(), ParseEmblVersion(), ParseGenBankVersion(), ParseSPFeat(), QSIndex(), SourceFeatStructFillIn(), SpAddToIndexBlk(), SPGetVerNum(), UnwrapAccessionRange(), valid_pages_range(), xgbgap(), xgbload_number(), and XMLInitialEntry().

◆ fta_StartsWith() bool fta_StartsWith ( const char *  s1, string_view  s2  ) inline

Definition at line 132 of file ftacpp.hpp.

Referenced by add_entry(), CkLocusLinePos(), DefVsHTGKeywords(), embl_refs(), EmblIndex(), FindNextEntryBuf(), fta_check_mult_ids(), fta_get_user_object(), gb_refs_common(), GenBankIndex(), get_art(), get_book(), get_error(), GetDescrComment(), GetDescrEmblBlock(), GetDRlineDataSP(), GetEmblBlockXref(), GetEmblDate(), GetEmblMolInfo(), GetFlatBiomol(), GetGBBlock(), GetGenBankMolInfo(), journal(), ParsePcrPrimers(), SprotIndex(), CGenbank2Asn::xGetEntry(), CXml2Asn::xGetEntry(), XMLCheckCDS(), XMLCheckRequiredTags(), XMLGetEMBLBlock(), XMLGetGBBlock(), XMLGetMolInfo(), and XMLRefs().

◆ MemCpy() void MemCpy ( void *  p, const void *  q, size_t  sz  ) inline ◆ MemFree() void MemFree ( char *  p ) inline

Definition at line 56 of file ftacpp.hpp.

Referenced by CObjectOStream::AsnIo::AsnIo(), CheckCollectionDate(), CheckDelGbblockSourceFromDescrs(), CheckOutsideEntry(), CheckQualsInSourceFeat(), CheckSourceFeatCoverage(), CollectSubNames(), CreateRawBioSources(), DefVsHTGKeywords(), embl_refs(), fta_check_mga_line(), fta_check_non_tpa_tsa_tls_locations(), fta_create_wgs_seqid(), fta_get_mga_user_object(), fta_get_str_user_field(), fta_get_trna_from_comment(), fta_get_trna_from_product(), fta_get_user_field(), fta_get_user_object(), fta_parse_rrna_feat(), GenBankIndex(), get_book(), get_parts(), get_pat(), GetCitBook(), GetDescrComment(), GetDescrEmblBlock(), GetDRlineDataSP(), GetEmblBlockXref(), GetEmblDescr(), GetEmblInstContig(), GetExtraAccession(), GetGBBlock(), GetGenBankDescr(), GetGenBankInstContig(), GetOrganismFrom_OS_OC(), GetSeqData(), GetSetOfSpecies(), GetSPDescrTitle(), GetTaxIdFrom_OX(), GetViralHostsFrom_OH(), LoadEntry(), LoadEntryGenbank(), MakeChainPDBSeqId(), ParseSourceFeat(), ParseSpComment(), SetOfSpeciesFree(), SourceFeatStructFillIn(), SPFeatProtRef(), SPFreeGenRefTokens(), SPGetGeneRefsNew(), SPGetPEValue(), SPPostProcVarSeq(), SprotRefString(), SPValidateEcnum(), StripCDSComment(), UpdateRawBioSource(), CXml2Asn::xGetEntry(), XMLDefVsHTGKeywords(), XMLGetDescr(), XMLGetDivision(), XMLGetEMBLBlock(), XMLGetGBBlock(), XMLGetInstContig(), XMLGetMolInfo(), XMLIndex(), XMLLoadEntry(), XMLRefs(), DataBlk::~DataBlk(), FTATpaBlock::~FTATpaBlock(), and SourceFeatBlk::~SourceFeatBlk().

◆ MemSet() void MemSet ( void *  p, int  n, size_t  sz  ) inline ◆ StringCat() void StringCat ( char *  d, const char *  s  ) inline ◆ StringChr() [1/2] char* StringChr ( char *  s, const char  c  ) inline

Definition at line 93 of file ftacpp.hpp.

◆ StringChr() [2/2] ◆ StringCmp() ◆ StringCpy() void StringCpy ( char *  d, const char *  s  ) inline

Definition at line 90 of file ftacpp.hpp.

Referenced by add_entry(), CheckAccession(), fta_get_trna_from_product(), get_art(), GetAccession(), GetDescrEmblBlock(), GetDRlineDataSP(), GetGBBlock(), InitialEntry(), QSbuf_ParseDefline(), xGenBankGetDivision(), XMLGetDivision(), XMLGetEMBLBlock(), XMLGetGBBlock(), XMLInitialEntry(), XReadFile(), and XReadFileBuf().

◆ StringDoesHaveText() ◆ StringEqu()

Definition at line 112 of file ftacpp.hpp.

References util::strcmp().

Referenced by add_entry(), check_mix_pages_range(), CheckCollectionDate(), CheckFocusInOrgs(), CheckGene(), CheckHTGDivision(), CheckMoltypeConsistency(), CheckSubmitterSeqidQuals(), CheckSYNTGNDivision(), CollectGapFeats(), CreateEntryBioseq(), fta_check_embl_moltype(), fta_get_trna_from_comment(), fta_get_trna_from_product(), fta_strings_same(), GetAccession(), GetDescrEmblBlock(), GetDRlineDataSP(), GetFeatNameAndLoc(), GetFlatBiomol(), GetGBBlock(), ParseGenBankVersion(), QSbuf_ParseScores(), QSbuf_To_Single_Qscore_SeqGraph(), UpdateRawBioSource(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), CXml2Asn::xGetEntry(), XMLGetEMBLBlock(), XMLGetGBBlock(), XMLGetRefTypePos(), XMLIndexSameSubTags(), XMLIndexSubTags(), XMLInitialEntry(), and XMLPerformIndex().

◆ StringEquN()

Definition at line 122 of file ftacpp.hpp.

References n, and util::strncmp().

Referenced by AddToIndexBlk(), check_book_tit(), CheckDelGbblockSourceFromDescrs(), CheckLocus(), CheckPcrPrimersTag(), FakeGenBankBioSources(), fta_check_mga_line(), fta_create_wgs_seqid(), fta_fix_seq_id(), fta_fix_seq_loc_id(), fta_get_trna_from_comment(), fta_get_trna_from_product(), fta_get_user_field(), fta_parse_rrna_feat(), fta_parse_structured_comment(), get_book(), get_sub(), get_sub_gsdb(), GetCitSubmit(), GetDescrComment(), GetDescrEmblBlock(), GetExtraAccession(), GetFlatBiomol(), GetGBBlock(), GetLineOSorOC(), IsSPROTAccession(), IsValidAccessPrefix(), ParseFeatureBlock(), ParseGenBankVersion(), ParseSpComment(), ParseSPFeat(), SkipTitle(), SkipTitleBuf(), SpAddToIndexBlk(), StringRStr(), XMLGetDescrComment(), XMLGetEMBLBlock(), and XMLGetGBBlock().

◆ StringEquNI()

Definition at line 136 of file ftacpp.hpp.

References NStr::EqualNocase(), and n.

Referenced by CheckDelGbblockSourceFromDescrs(), CkQualPosaa(), CkQualSeqaa(), CkQualSite(), DbxrefQualToDbtag(), fill_orgref(), fta_parse_rrna_feat(), fta_parse_tpa_tsa_block(), get_book(), get_lanl_date(), get_pat(), get_s_date(), get_sub(), GetDRlineDataSP(), GetSPGenomeFrom_OS_OG(), GetSprotIds(), GetTaxIdFrom_OX(), GetViralHostsFrom_OH(), journal(), ParseRLDataSP(), SPGetGeneRefsNew(), and SprotRefString().

◆ StringHasNoText() ◆ StringLen() size_t StringLen ( const char *  s ) inline

Definition at line 61 of file ftacpp.hpp.

Referenced by add_entry(), check_translation(), CheckAccession(), CheckCollectionDate(), CheckDelGbblockSourceFromDescrs(), CheckForENV(), CheckMoltypeConsistency(), CheckQualsInSourceFeat(), CheckSourceFeatLocFuzz(), CheckSYNTGNDivision(), CkProteinTransl(), clean_up(), CollectSubNames(), embl_refs(), fill_orgref(), fta_check_mga_line(), fta_check_non_tpa_tsa_tls_locations(), fta_get_str_user_field(), fta_get_trna_from_comment(), fta_get_trna_from_product(), fta_number_is_huge(), fta_parse_rrna_feat(), fta_parse_tpa_tsa_block(), fta_StringMatch(), GenBankIndex(), get_art(), get_embl_str_pub_id(), get_error(), get_pat(), get_plasmid(), get_sub(), get_sub_gsdb(), GetAccession(), GetCitPatent(), GetDescrEmblBlock(), GetExtraAccession(), GetSPSitesMod(), GetTaxIdFrom_OX(), GetViralHostsFrom_OH(), ind_subdbp(), InitialEntry(), IsSPROTAccession(), IsValidAccessPrefix(), journal(), make_entry(), ParseSpComment(), QSbuf_To_Single_Qscore_SeqGraph(), QSIndex(), SPFeatProtRef(), SprotRefString(), StringMatchIcase(), StringRStr(), stripStr(), CXml2Asn::xGetEntry(), XMLAccessionsCheck(), XMLGetEMBLBlock(), XMLPerformIndex(), and XMLRefs().

◆ StringNCpy() void StringNCpy ( char *  d, const char *  s, size_t  n  ) inline ◆ StringNew() char* StringNew ( size_t  sz ) inline ◆ StringRChr() char* StringRChr ( char *  s, const char  c  ) inline ◆ StringSave() [1/3] char* StringSave ( const char *  s ) inline ◆ StringSave() [2/3] char* StringSave ( string_view  s ) inline ◆ StringSave() [3/3] char* StringSave ( unique_ptr< string >  s ) inline ◆ StringStr() [1/2] char* StringStr ( char *  s1, const char *  s2  ) inline

Definition at line 88 of file ftacpp.hpp.

◆ StringStr() [2/2]

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