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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/asci__blk_8cpp.html below:

NCBI C++ ToolKit: src/objtools/flatfile/asci_blk.cpp File Reference

USING_SCOPE (objects) void ShrinkSpaces (char *line) void ShrinkSpaces (string &line) static void InsertDatablkVal (TDataBlkList &dbl, Int2 type, char *offset, size_t len) void xGetGenBankBlocks (Entry &entry) char * GetGenBankBlock (TDataBlkList &chain, char *ptr, Int2 *retkw, char *eptr) static void GetGenBankRefType (DataBlk &dbp, size_t bases) static void BuildFeatureBlock (DataBlk &dbp) static void fta_check_mult_ids (const DataBlk &dbp, string_view mtag, string_view ptag) void GetGenBankSubBlock (const DataBlk &entry, size_t bases) void xGetGenBankSubBlocks (Entry &entry, size_t bases) char * GetEmblBlock (TDataBlkList &chain, char *ptr, short *retkw, Parser::EFormat format, char *eptr) static bool TrimEmblFeatBlk (DataBlk &dbp) static bool GetSubNodeType (string_view subkw, char *&bptr, char *eptr) static void GetEmblRefType (size_t bases, Parser::ESource source, DataBlk &dbp) void GetEmblSubBlock (size_t bases, Parser::ESource source, const DataBlk &entry) void BuildSubBlock (DataBlk &dbp, Int2 subtype, string_view subkw) void GetLenSubNode (DataBlk &dbp) CRef< CPatent_seq_id > MakeUsptoPatSeqId (const char *acc) static Uint1 ValidSeqType (const char *accession, Uint1 type) CRef< CSeq_id > MakeAccSeqId (const char *acc, Uint1 seqtype, bool accver, Int2 vernum) CRef< CSeq_id > MakeLocusSeqId (const char *locus, CSeq_id::E_Choice seqtype) char * SrchNodeSubType (const DataBlk &entry, Int2 type, Int2 subtype, size_t *len) static void SetEmptyId (CBioseq &bioseq) CRef< CBioseq > CreateEntryBioseq (ParserPtr pp) char * GetDescrComment (char *offset, size_t len, Uint2 col_data, bool is_htg, bool is_pat) static void fta_fix_secondaries (TokenBlkList &secondaries) void GetExtraAccession (IndexblkPtr ibp, bool allow_uwsec, Parser::ESource source, TAccessionList &accessions) static void fta_fix_tpa_keywords (TKeywordList &keywords) void xFixEMBLKeywords (string &keywordData) void GetSequenceOfKeywords (const DataBlk &entry, int type, Uint2 col_data, TKeywordList &keywords) Int4 ScanSequence (bool warn, char **seqptr, std::vector< char > &bsp, unsigned char *conv, Char replacechar, int *numns) bool GetSeqData (ParserPtr pp, const DataBlk &entry, CBioseq &bioseq, Int4 nodetype, unsigned char *seqconv, Uint1 seq_data_type) unique_ptr< unsigned char[]> GetDNAConv (void) DEFINE_STATIC_MUTEX (s_DNAConvMutex) unsigned char *const GetDNAConvTable () unique_ptr< unsigned char[]> GetProteinConv (void) DEFINE_STATIC_MUTEX (s_ProtConvMutex) unsigned char *const GetProtConvTable () void GetSeqExt (ParserPtr pp, CSeq_loc &seq_loc) bool check_div (bool pat_acc, bool pat_ref, bool est_kwd, bool sts_kwd, bool gss_kwd, bool if_cds, string &div, CMolInfo::TTech *tech, size_t bases, Parser::ESource source, bool &drop) CRef< CSeq_id > StrToSeqId (const char *pch, bool pid) void AddNIDSeqId (CBioseq &bioseq, const DataBlk &entry, Int2 type, Int2 coldata, Parser::ESource source) static void CheckDivCode (TEntryList &seq_entries, ParserPtr pp) static const CBioSource * GetTopBiosource (const CSeq_entry &entry) static bool SeqEntryCheckTaxonDiv (const CSeq_entry &entry) void EntryCheckDivCode (TEntryList &seq_entries, ParserPtr pp) void DefVsHTGKeywords (CMolInfo::TTech tech, const DataBlk &entry, Int2 what, Int2 ori, bool cancelled) void XMLDefVsHTGKeywords (CMolInfo::TTech tech, const char *entry, const TXmlIndexList &xil, bool cancelled) void CheckHTGDivision (const char *div, CMolInfo::TTech tech) const CSeq_descr & GetDescrPointer (const CSeq_entry &entry) static void CleanVisString (string &str) static void CleanVisStringList (list< string > &str_list) static void CheckGBBlock (TSeqdescList &descrs, bool &got) bool fta_EntryCheckGBBlock (TEntryList &seq_entries) static int GetSerialNumFromPubEquiv (const CPub_equiv &pub_eq) static bool fta_if_pubs_sorted (const CPub_equiv &pub1, const CPub_equiv &pub2) static bool descr_cmp (const CRef< CSeqdesc > &desc1, const CRef< CSeqdesc > &desc2) void fta_sort_descr (TEntryList &seq_entries) static bool pub_cmp (const CRef< CPub > &pub1, const CRef< CPub > &pub2) static void sort_feat_cit (CBioseq::TAnnot &annots) void fta_sort_seqfeat_cit (TEntryList &seq_entries) bool fta_orgref_has_taxid (const COrg_ref::TDb &dbtags) void fta_fix_orgref_div (const CBioseq::TAnnot &annots, COrg_ref *org_ref, CGB_block &gbb) bool XMLCheckCDS (const char *entry, const TXmlIndexList &xil) void fta_set_strandedness (TEntryList &seq_entries) static bool SwissProtIDPresent (const TEntryList &seq_entries) static bool IsCitEmpty (const CCit_gen &cit) static void RemoveSerials (TPubList &pubs) void StripSerialNumbers (TEntryList &seq_entries) static void PackSeqData (CSeq_data::E_Choice code, CSeq_data &seq_data) static void RawBioseqPack (CBioseq &bioseq) static void DeltaBioseqPack (CBioseq &bioseq) void PackEntries (TEntryList &seq_entries) ◆ Seq_descr_pub_same #define Seq_descr_pub_same 50

Definition at line 98 of file asci_blk.cpp.

◆ THIS_FILE #define THIS_FILE "asci_blk.cpp"

Definition at line 96 of file asci_blk.cpp.

◆ AddNIDSeqId()

Definition at line 2006 of file asci_blk.cpp.

References Parser::DDBJ, Parser::EMBL, CRef< C, Locker >::Empty(), DataBlk::mBuf, offset, DataBlk::ptr, CBioseq_Base::SetId(), rapidjson::source, StrToSeqId(), and TrackNodeType().

Referenced by CEmbl2Asn::xGetEntry(), and CGenbank2Asn::xGetEntry().

◆ BuildFeatureBlock() ◆ BuildSubBlock() void BuildSubBlock ( DataBlk & dbp, Int2 subtype, string_view subkw ) ◆ check_div() bool check_div ( bool pat_acc, bool pat_ref, bool est_kwd, bool sts_kwd, bool gss_kwd, bool if_cds, string & div, CMolInfo::TTech * tech, size_t bases, Parser::ESource source, bool & drop )

Definition at line 1849 of file asci_blk.cpp.

References Parser::EMBL, ERR_DIVISION_ESTHasCDSFeature, ERR_DIVISION_ESTHasSTSKeywords, ERR_DIVISION_GSSHasCDSFeature, ERR_DIVISION_LongESTSequence, ERR_DIVISION_LongGSSSequence, ERR_DIVISION_LongSTSSequence, ERR_DIVISION_MappedtoEST, ERR_DIVISION_MappedtoGSS, ERR_DIVISION_MappedtoPAT, ERR_DIVISION_MappedtoSTS, ERR_DIVISION_MissingESTKeywords, ERR_DIVISION_MissingGSSKeywords, ERR_DIVISION_MissingPatentRef, ERR_DIVISION_MissingSTSKeywords, ERR_DIVISION_NotMappedtoEST, ERR_DIVISION_NotMappedtoGSS, ERR_DIVISION_NotMappedtoSTS, ERR_DIVISION_PATHasCDSFeature, ERR_DIVISION_PATHasESTKeywords, ERR_DIVISION_PATHasGSSKeywords, ERR_DIVISION_PATHasSTSKeywords, ERR_DIVISION_ShouldBePAT, ERR_DIVISION_STSHasCDSFeature, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_survey, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_unknown, FtaErrPost, SEV_INFO, SEV_REJECT, SEV_WARNING, and rapidjson::source.

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

◆ CheckDivCode()

Definition at line 2022 of file asci_blk.cpp.

References Begin(), Parser::curindx, Indexblk::division, Parser::entrylist, NStr::EqualCase(), NStr::EqualNocase(), ERR_DIVISION_GBBlockDivision, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_unknown, FtaErrPost, CGB_block_Base::GetDiv(), CMolInfo_Base::GetTech(), CGB_block_Base::IsSetDiv(), CGB_block_Base::ResetDiv(), CGB_block_Base::SetDiv(), and SEV_WARNING.

Referenced by EntryCheckDivCode().

◆ CheckGBBlock()

Definition at line 2324 of file asci_blk.cpp.

Referenced by fta_EntryCheckGBBlock().

◆ CheckHTGDivision()

Definition at line 2242 of file asci_blk.cpp.

References ERR_DIVISION_ShouldBeHTG, ERR_DIVISION_ShouldNotBeHTG, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, FtaErrPost, SEV_ERROR, SEV_WARNING, and StringEqu().

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

◆ CleanVisString() ◆ CleanVisStringList() static void CleanVisStringList ( list< string > & str_list ) static ◆ CreateEntryBioseq()

Definition at line 1022 of file asci_blk.cpp.

References Parser::accver, Indexblk::acnum, Parser::curindx, CSeq_id_Base::e_Local, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Tpe, Parser::EMBL, Indexblk::embl_new_ID, Parser::entrylist, Indexblk::is_tpa, NStr::IsBlank(), Indexblk::locusname, MakeUsptoPatSeqId(), Parser::mode, Ref(), Parser::Relaxed, Parser::seqtype, SetEmptyId(), CBioseq_Base::SetId(), SetTextId(), Parser::source, StringEqu(), Parser::USPTO, ValidSeqType(), and Indexblk::vernum.

Referenced by SpPrepareEntry(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), and CXml2Asn::xGetEntry().

◆ DEFINE_STATIC_MUTEX() [1/2] DEFINE_STATIC_MUTEX ( s_DNAConvMutex ) ◆ DEFINE_STATIC_MUTEX() [2/2] DEFINE_STATIC_MUTEX ( s_ProtConvMutex ) ◆ DefVsHTGKeywords()

Definition at line 2118 of file asci_blk.cpp.

References b, count, ERR_DEFINITION_HTGNotInProgress, ERR_DEFINITION_HTGShouldBeComplete, ERR_SEQUENCE_UnknownBaseHTG3, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, fta_StartsWith(), fta_StringCpy(), FtaErrPost, DataBlk::len, magic_phrases, DataBlk::mBuf, MemFree(), DataBlk::ptr, r(), SEV_ERROR, SEV_WARNING, StringNCpy(), StringSave, StringStr, tmp, and TrackNodeType().

Referenced by GetDescrEmblBlock(), and GetGBBlock().

◆ DeltaBioseqPack() ◆ descr_cmp()

Definition at line 2454 of file asci_blk.cpp.

References fta_if_pubs_sorted(), CPubdesc_Base::GetPub(), CSeqdesc_Base::GetPub(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CSeqdesc_Base::GetUser(), CSeqdesc_Base::IsPub(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), CSeqdesc_Base::IsUser(), util::strcmp(), and CSeqdesc_Base::Which().

Referenced by fta_sort_descr().

◆ EntryCheckDivCode() ◆ fta_check_mult_ids() static void fta_check_mult_ids ( const DataBlk & dbp, string_view mtag, string_view ptag ) static ◆ fta_EntryCheckGBBlock() ◆ fta_fix_orgref_div()

Definition at line 2566 of file asci_blk.cpp.

References count, fta_orgref_has_taxid(), COrg_ref_Base::GetDb(), CGB_block_Base::GetDiv(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CGB_block_Base::IsSetDiv(), COrgName_Base::IsSetDiv(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), CGB_block_Base::ResetDiv(), and COrg_ref_Base::SetOrgname().

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

◆ fta_fix_secondaries() ◆ fta_fix_tpa_keywords() ◆ fta_if_pubs_sorted() ◆ fta_orgref_has_taxid() ◆ fta_set_strandedness() void fta_set_strandedness ( TEntryList & seq_entries ) ◆ fta_sort_descr() ◆ fta_sort_seqfeat_cit() void fta_sort_seqfeat_cit ( TEntryList & seq_entries ) ◆ GetDescrComment() char* GetDescrComment ( char * offset, size_t len, Uint2 col_data, bool is_htg, bool is_pat )

Definition at line 1108 of file asci_blk.cpp.

References fta_StartsWith(), fta_StringCpy(), len, MemCpy(), MemFree(), offset, ncbi::grid::netcache::search::fields::size, SrchTheChar(), SrchTheStr(), str(), StringChr, StringEquN(), StringNew(), and StringStr.

Referenced by GetEmblDescr(), and GetGenBankDescr().

◆ GetDescrPointer() ◆ GetDNAConv() unique_ptr<unsigned char[]> GetDNAConv ( void ) ◆ GetDNAConvTable() unsigned char* const GetDNAConvTable ( ) ◆ GetEmblBlock()

Definition at line 541 of file asci_blk.cpp.

References emblKeywords, format, InsertDatablkVal(), len, offset, ParFlat_END, ParFlat_UNKW, Parser::SPROT, SrchKeyword(), and swissProtKeywords.

Referenced by CheckOutsideEntry(), get_bioseq(), SpPrepareEntry(), and CEmbl2Asn::xGetEntry().

◆ GetEmblRefType()

Definition at line 670 of file asci_blk.cpp.

References Parser::EMBL, GetSubNodeType(), DataBlk::len, DataBlk::mBuf, DataBlk::mType, Parser::NCBI, ParFlat_REF_BTW, ParFlat_REF_END, ParFlat_REF_NO_TARGET, ParFlat_REF_SITES, DataBlk::ptr, rapidjson::source, SrchTheStr(), and str().

Referenced by GetEmblSubBlock().

◆ GetEmblSubBlock()

Definition at line 723 of file asci_blk.cpp.

References BuildFeatureBlock(), BuildSubBlock(), ERR_FEATURE_NoFeatData, fta_check_mult_ids(), FtaErrPost, GetEmblRefType(), GetLenSubNode(), next(), ParFlat_FH, ParFlat_OC, ParFlat_OG, ParFlat_OS, ParFlat_RA, ParFlat_RC, ParFlat_RG, ParFlat_RL, ParFlat_RN, ParFlat_RP, ParFlat_RT, ParFlat_RX, SEV_WARNING, rapidjson::source, TrackNodes(), and TrimEmblFeatBlk().

Referenced by CEmbl2Asn::xGetEntry().

◆ GetExtraAccession()

Definition at line 1237 of file asci_blk.cpp.

References a, Indexblk::acnum, NStr::CommonSuffixSize(), Parser::DDBJ, DelNonDigitTail(), Indexblk::drop, CSeq_id_Base::e_Embl, Parser::EMBL, ERR_ACCESSION_ScfldHasWGSContigSec, ERR_ACCESSION_UnusualWGS_Secondary, ERR_ACCESSION_WGSMasterAsSecondary, ERR_ACCESSION_WGSWithNonWGS_Sec, fta_fix_secondaries(), fta_if_wgs_acc(), FtaErrPost, GetNucAccOwner(), i, Indexblk::is_contig, MemFree(), Parser::NCBI, Parser::Refseq, Indexblk::secaccs, SEV_REJECT, SEV_WARNING, rapidjson::source, StringEquN(), StringLen(), StringSave, text(), and Indexblk::wgssec.

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

◆ GetGenBankBlock() char* GetGenBankBlock ( TDataBlkList & chain, char * ptr, Int2 * retkw, char * eptr ) ◆ GetGenBankRefType()

Definition at line 337 of file asci_blk.cpp.

References NStr::Find(), DataBlk::len, DataBlk::mBuf, DataBlk::mType, NPOS, ParFlat_REF_BTW, ParFlat_REF_END, ParFlat_REF_NO_TARGET, ParFlat_REF_SITES, DataBlk::ptr, and str().

Referenced by GetGenBankSubBlock().

◆ GetGenBankSubBlock() void GetGenBankSubBlock ( const DataBlk & entry, size_t bases )

Definition at line 452 of file asci_blk.cpp.

References BuildFeatureBlock(), BuildSubBlock(), fta_check_mult_ids(), GetGenBankRefType(), GetLenSubNode(), ParFlat_AUTHORS, ParFlat_CONSRTM, ParFlat_FEATURES, ParFlat_JOURNAL, ParFlat_MEDLINE, ParFlat_ORGANISM, ParFlat_PUBMED, ParFlat_REFERENCE, ParFlat_REMARK, ParFlat_SOURCE, ParFlat_STANDARD, ParFlat_TITLE, TrackNodes(), and TrackNodeType().

Referenced by CGenbank2Asn::xGetEntry().

◆ GetLenSubNode() void GetLenSubNode ( DataBlk & dbp )

Definition at line 809 of file asci_blk.cpp.

References done, ERR_FORMAT_LineTypeOrder, fta_atoi(), FtaErrPost, isdigit(), l(), DataBlk::len, DataBlk::mBuf, DataBlk::mData, n, next(), offset, DataBlk::ptr, and SEV_WARNING.

Referenced by GetEmblSubBlock(), GetGenBankSubBlock(), and GetSprotSubBlock().

◆ GetProtConvTable() unsigned char* const GetProtConvTable ( ) ◆ GetProteinConv() unique_ptr<unsigned char[]> GetProteinConv ( void ) ◆ GetSeqData()

Definition at line 1594 of file asci_blk.cpp.

References Indexblk::bases, buf, Parser::curindx, Parser::DDBJ, Indexblk::drop, CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Iupacna, Parser::EMBL, Parser::entrylist, ERR_SEQUENCE_AllNs, ERR_SEQUENCE_SeqLenNotEq, ERR_SEQUENCE_TooShort, ERR_SEQUENCE_TooShortIsPatent, Parser::format, FtaErrPost, Parser::GenBank, CBioseq::GetLength(), INSDSEQ_SEQUENCE, Indexblk::is_contig, Indexblk::is_mga, Indexblk::is_pat, Indexblk::is_prot, isalpha(), len, DataBlk::mBuf, MemFree(), DataBlk::ptr, ScanSequence(), CBioseq_Base::SetInst(), SEV_INFO, SEV_REJECT, SEV_WARNING, Parser::source, SrchNodeType(), str(), StringSave, tmp, Parser::USPTO, Indexblk::xip, Parser::XML, and XMLFindTagValue().

Referenced by get_bioseq(), GetGenBankInst(), GetSPInst(), s_DoNWalign(), s_GetCdsSequence(), s_GetEmblInst(), COligoSpecificityCheck::x_NW_alignment(), and XMLGetInst().

◆ GetSeqExt() ◆ GetSequenceOfKeywords()

Definition at line 1467 of file asci_blk.cpp.

References fta_fix_tpa_keywords(), GetBlkDataReplaceNewLine(), GetNodeData(), last(), ParFlatSP_KW, NStr::Split(), StripECO(), tmp, NStr::TrimSuffixInPlace(), NStr::TruncateSpacesInPlace(), and xFixEMBLKeywords().

Referenced by CollectGapFeats(), GetDescrSPBlock(), and GetGBBlock().

◆ GetSerialNumFromPubEquiv() ◆ GetSubNodeType() static bool GetSubNodeType ( string_view subkw, char *& bptr, char * eptr ) static ◆ GetTopBiosource() ◆ InsertDatablkVal() ◆ IsCitEmpty()

Definition at line 2673 of file asci_blk.cpp.

References CCit_gen_Base::IsSetAuthors(), CCit_gen_Base::IsSetCit(), CCit_gen_Base::IsSetDate(), CCit_gen_Base::IsSetIssue(), CCit_gen_Base::IsSetJournal(), CCit_gen_Base::IsSetMuid(), CCit_gen_Base::IsSetPages(), CCit_gen_Base::IsSetPmid(), CCit_gen_Base::IsSetSerial_number(), CCit_gen_Base::IsSetTitle(), and CCit_gen_Base::IsSetVolume().

Referenced by RemoveSerials().

◆ MakeAccSeqId() ◆ MakeLocusSeqId() ◆ MakeUsptoPatSeqId() ◆ PackEntries() ◆ PackSeqData()

Definition at line 2735 of file asci_blk.cpp.

References CSeqConvert::Convert(), CSeq_data_Base::e_Iupacaa, CSeqUtil::e_Iupacaa, CSeq_data_Base::e_Ncbi8aa, CSeqUtil::e_Ncbi8aa, CSeqUtil::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, CSeqUtil::e_Ncbistdaa, CSeqUtil::e_not_set, CAliasBase< TPrim >::Get(), CSeq_data_Base::GetIupacaa(), CSeq_data_Base::GetNcbi8aa(), CSeq_data_Base::GetNcbistdaa(), CAliasBase< TPrim >::Set(), and CSeq_data_Base::SetNcbieaa().

Referenced by RawBioseqPack().

◆ pub_cmp() ◆ RawBioseqPack() ◆ RemoveSerials() ◆ ScanSequence() Int4 ScanSequence ( bool warn, char ** seqptr, std::vector< char > & bsp, unsigned char * conv, Char replacechar, int * numns ) ◆ SeqEntryCheckTaxonDiv() ◆ SetEmptyId() ◆ ShrinkSpaces() [1/2] void ShrinkSpaces ( char * line )

Definition at line 117 of file asci_blk.cpp.

References fta_StringCpy().

Referenced by CheckDelGbblockSourceFromDescrs(), DescrRefs(), fta_fix_affil(), fta_get_trna_from_comment(), fta_get_trna_from_product(), fta_remark_is_er(), fta_strip_pub_comment(), fta_vnp_structured_comment(), GetSPDescrTitle(), GetViralHostsFrom_OH(), ParseFeatureBlock(), RemoveSourceFeatSpaces(), SPFeatProtRef(), StripCDSComment(), and XMLParseFeatureBlock().

◆ ShrinkSpaces() [2/2] void ShrinkSpaces ( string & line ) ◆ sort_feat_cit() ◆ SrchNodeSubType() ◆ StripSerialNumbers() void StripSerialNumbers ( TEntryList & seq_entries ) ◆ StrToSeqId() ◆ SwissProtIDPresent() ◆ TrimEmblFeatBlk() ◆ USING_SCOPE() ◆ ValidSeqType()

Definition at line 892 of file asci_blk.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id::GetAccType(), CSeq_id::IdentifyAccession(), and type.

Referenced by CreateEntryBioseq(), and MakeAccSeqId().

◆ xFixEMBLKeywords() void xFixEMBLKeywords ( string & keywordData ) ◆ xGetGenBankBlocks() void xGetGenBankBlocks ( Entry & entry ) ◆ xGetGenBankSubBlocks() void xGetGenBankSubBlocks ( Entry & entry, size_t bases )

Definition at line 489 of file asci_blk.cpp.

References Entry::mSections, ParFlat_AUTHORS, ParFlat_CONSRTM, ParFlat_FEATURES, ParFlat_JOURNAL, ParFlat_MEDLINE, ParFlat_ORGANISM, ParFlat_PUBMED, ParFlat_REFERENCE, ParFlat_REMARK, ParFlat_SOURCE, ParFlat_STANDARD, and ParFlat_TITLE.