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USING_SCOPE (objects) string tata_save (string_view t) bool no_date (Parser::EFormat format, const TSeqdescList &descrs) bool no_reference (const CBioseq &bioseq) bool check_cds (const DataBlk &entry, Parser::EFormat format) void err_install (const Indexblk *ibp, bool accver) static void CreateSeqGap (CSeq_literal &seq_lit, GapFeats &gfp) void AssemblyGapsToDelta (CBioseq &bioseq, TGapFeatsList &gf, bool *drop) void GapsToDelta (CBioseq &bioseq, TGapFeatsList &gf, bool *drop) void SeqToDelta (CBioseq &bioseq, Int2 tech) static bool fta_ranges_to_hist (const CGB_block::TExtra_accessions &extra_accs) static bool s_IsConOrScaffold (CBioseq_Handle bsh) static bool s_IsAccession (const CSeq_id &id) bool g_DoesNotReferencePrimary (const CDelta_ext &delta_ext, const CSeq_id &primary, CScope &scope) static int sGetPrefixLength (string_view accession) void fta_add_hist (ParserPtr pp, CBioseq &bioseq, CGB_block::TExtra_accessions &extra_accs, Parser::ESource source, CSeq_id::E_Choice acctype, bool pricon, const char *acc) bool fta_strings_same (const char *s1, const char *s2) bool fta_check_htg_kwds (TKeywordList &kwds, IndexblkPtr ibp, CMolInfo &mol_info) static void fta_check_tpa_tsa_coverage (const FTATpaBlockList &ftbp, Int4 length, bool tpa) bool fta_number_is_huge (const Char *s) bool fta_parse_tpa_tsa_block (CBioseq &bioseq, char *offset, char *acnum, Int2 vernum, size_t len, Int2 col_data, bool tpa) char * StringRStr (char *where, const char *what) CRef< CSeq_loc > fta_get_seqloc_int_whole (const CSeq_id &seq_id, size_t len) static void fta_validate_assembly (string_view name) static bool fta_validate_bioproject (string_view name, Parser::ESource source) static forward_list< string > fta_tokenize_project (string str, Parser::ESource source, bool newstyle) void fta_get_project_user_object (TSeqdescList &descrs, const char *offset, Parser::EFormat format, bool *drop, Parser::ESource source) bool fta_if_valid_sra (string_view id, bool dblink) bool fta_if_valid_biosample (string_view id, bool dblink) static forward_list< string > fta_tokenize_dblink (string str, Parser::ESource source) void fta_get_dblink_user_object (TSeqdescList &descrs, char *offset, size_t len, Parser::ESource source, bool *drop, CRef< CUser_object > &dbuop) CMolInfo::TTech fta_check_con_for_wgs (CBioseq &bioseq) static void fta_fix_seq_id (CSeq_loc &loc, CSeq_id &id, IndexblkPtr ibp, string_view location, string_view name, SeqLocIdsPtr slip, bool iscon, Parser::ESource source) static void fta_do_fix_seq_loc_id (TSeqLocList &locs, IndexblkPtr ibp, string_view location, string_view name, SeqLocIdsPtr slip, bool iscon, Parser::ESource source) Int4 fta_fix_seq_loc_id (TSeqLocList &locs, ParserPtr pp, string_view location, string_view name, bool iscon) static forward_list< string > fta_vnp_structured_comment (string buf) static CRef< CUser_object > fta_build_structured_comment (string_view tag, string_view scomment) void fta_parse_structured_comment (char *str, bool &bad, TUserObjVector &objs) string GetQSFromFile (FILE *fd, const Indexblk *ibp) void fta_remove_cleanup_user_object (CSeq_entry &seq_entry) void fta_tsa_tls_comment_dblink_check (const CBioseq &bioseq, bool is_tsa) void fta_set_molinfo_completeness (CBioseq &bioseq, const Indexblk *ibp) void fta_create_far_fetch_policy_user_object (CBioseq &bsp, Int4 num) void StripECO (string &str) bool fta_dblink_has_sra (const CRef< CUser_object > &uop) ◆ HTG_GAP ◆ SHORT_GAP ◆ THIS_FILE #define THIS_FILE "add.cpp"Definition at line 80 of file add.cpp.
◆ FTATpaBlockList ◆ SeqLocIdsPtr ◆ AssemblyGapsToDelta()Definition at line 327 of file add.cpp.
References CreateSeqGap(), delta(), ERR_FORMAT_ContigVersusAssemblyGapMissmatch, FtaErrPost, CSeq_inst_Base::GetExt(), CBioseq_Base::GetInst(), CSeq_ext_Base::IsDelta(), CSeq_inst_Base::IsSetExt(), literal(), CBioseq_Base::SetInst(), and SEV_REJECT.
Referenced by CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), and CXml2Asn::xGetEntry().
◆ check_cds()Definition at line 254 of file add.cpp.
References Parser::EMBL, format, Parser::GenBank, len, ParFlat_FEATURES, ParFlat_FH, SrchTheStr(), str(), TrackNodes(), and type.
Referenced by GetDescrEmblBlock(), GetGBBlock(), and CDemoApp::Run().
◆ CreateSeqGap() ◆ err_install() ◆ fta_add_hist()Definition at line 795 of file add.cpp.
References Parser::accver, Parser::allow_uwsec, CSeq_id_Base::e_not_set, Parser::entrez_fetch, NStr::EqualNocase(), ERR_ACCESSION_CannotGetDivForSecondary, fta_if_wgs_acc(), fta_ranges_to_hist(), FtaErrPost, g_DoesNotReferencePrimary(), CScope::GetBioseqHandles(), CSeq_id_Handle::GetHandle(), GetNucAccOwner(), GetScope(), Parser::histacc, i, isdigit(), s_IsConOrScaffold(), CBioseq_Base::SetInst(), SEV_ERROR, sGetPrefixLength(), rapidjson::source, Parser::source, and UnwrapAccessionRange().
Referenced by GetEmblDescr(), GetGenBankDescr(), and XMLGetDescr().
◆ fta_build_structured_comment() ◆ fta_check_con_for_wgs()Definition at line 1970 of file add.cpp.
References delta(), CSeq_inst_Base::eRepr_delta, CMolInfo_Base::eTech_unknown, CMolInfo_Base::eTech_wgs, fta_if_wgs_acc(), CDelta_ext_Base::Get(), CTextseq_id_Base::GetAccession(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CBioseq_Base::GetInst(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_inst_Base::GetRepr(), CSeq_loc_CI::GetSeq_id(), CSeq_id_Base::IsDdbj(), CSeq_ext_Base::IsDelta(), CSeq_id_Base::IsEmbl(), CSeq_loc_Base::IsEmpty(), CSeq_id_Base::IsGenbank(), CSeq_loc_Base::IsInt(), CSeq_id_Base::IsOther(), CSeq_loc_Base::IsPacked_pnt(), CSeq_loc_Base::IsPnt(), CTextseq_id_Base::IsSetAccession(), CSeq_inst_Base::IsSetExt(), CSeq_id_Base::IsTpd(), CSeq_id_Base::IsTpe(), CSeq_id_Base::IsTpg(), and CSeq_loc_Base::IsWhole().
Referenced by GetEmblDescr(), and GetGenBankDescr().
◆ fta_check_htg_kwds()Definition at line 917 of file add.cpp.
References ERR_KEYWORD_MultipleHTGPhases, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, FtaErrPost, Indexblk::htg, ncbi::grid::netcache::search::fields::key, CMolInfo_Base::SetTech(), and SEV_ERROR.
Referenced by GetDescrEmblBlock(), GetGBBlock(), XMLGetEMBLBlock(), and XMLGetGBBlock().
◆ fta_check_tpa_tsa_coverage() ◆ fta_create_far_fetch_policy_user_object() void fta_create_far_fetch_policy_user_object ( CBioseq & bsp, Int4 num )Definition at line 2642 of file add.cpp.
References ERR_SEQUENCE_HasManyComponents, FtaErrPost, CUser_field_Base::SetData(), CUser_object_Base::SetData(), CBioseq_Base::SetDescr(), CUser_field_Base::SetLabel(), CUser_object_Base::SetType(), CSeqdesc_Base::SetUser(), and SEV_INFO.
Referenced by GetEmblInstContig(), GetGenBankInstContig(), and XMLGetInstContig().
◆ fta_dblink_has_sra()Definition at line 2683 of file add.cpp.
References CRef< C, Locker >::Empty(), CUser_object_Base::GetData(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CUser_object_Base::IsSetData(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), and str().
Referenced by GetEmblDescr(), GetGenBankDescr(), and XMLGetDescr().
◆ fta_do_fix_seq_loc_id() ◆ fta_fix_seq_id()Definition at line 2023 of file add.cpp.
References Parser::All, SeqLocIds::badslp, Parser::DDBJ, SeqLocIds::ddbj, Indexblk::drop, Parser::EMBL, SeqLocIds::embl, ERR_LOCATION_SeqIdProblem, Parser::Flybase, FtaErrPost, SeqLocIds::genbank, CTextseq_id_Base::GetAccession(), CSeq_id::GetAccType(), i, CSeq_id::IdentifyAccession(), IsNewAccessFormat(), CTextseq_id_Base::IsSetAccession(), isSupportedAccession(), Parser::LANL, location, MakeUsptoPatSeqId(), Parser::NCBI, SeqLocIds::other, SeqLocIds::pir, SeqLocIds::prf, Parser::Refseq, SetTextId(), SEV_REJECT, rapidjson::source, Parser::SPROT, StringEquN(), SeqLocIds::swissprot, tag, SeqLocIds::total, SeqLocIds::tpd, SeqLocIds::tpe, SeqLocIds::tpg, Parser::USPTO, SeqLocIds::wgsacc, SeqLocIds::wgscont, and SeqLocIds::wgsscaf.
Referenced by fta_do_fix_seq_loc_id().
◆ fta_fix_seq_loc_id()Definition at line 2194 of file add.cpp.
References Indexblk::acnum, Parser::allow_crossdb_featloc, SeqLocIds::badslp, Parser::curindx, SeqLocIds::ddbj, Indexblk::drop, SeqLocIds::embl, Parser::entrylist, ERR_ACCESSION_WGSPrefixMismatch, ERR_LOCATION_ContigAndScaffold, ERR_LOCATION_CrossDatabaseFeatLoc, ERR_LOCATION_TpaAndNonTpa, ERR_SEQUENCE_MultipleWGSProjects, fta_do_fix_seq_loc_id(), FtaErrPost, SeqLocIds::genbank, CSeq_loc::GetLabel(), i, IsNewAccessFormat(), label, location, msg(), SeqLocIds::other, SeqLocIds::pir, SeqLocIds::prf, SEV_ERROR, SEV_REJECT, SEV_WARNING, Parser::source, StringEquN(), StringNCpy(), SeqLocIds::swissprot, SeqLocIds::total, SeqLocIds::tpd, SeqLocIds::tpe, SeqLocIds::tpg, SeqLocIds::wgsacc, SeqLocIds::wgscont, and SeqLocIds::wgsscaf.
Referenced by GetEmblInstContig(), GetGenBankInstContig(), GetSeqLocation(), and XMLGetInstContig().
◆ fta_get_dblink_user_object()Definition at line 1855 of file add.cpp.
References CRef< C, Locker >::Empty(), ERR_FORMAT_IncorrectDBLINK, fta_atoi(), fta_tokenize_dblink(), FtaErrPost, i, CUser_object_Base::IsSetData(), len, next(), CRef< C, Locker >::NotEmpty(), offset, ParFlat_COL_DATA, CRef< C, Locker >::Reset(), CUser_field_Base::SetData(), CUser_object_Base::SetData(), CUser_field_Base::SetLabel(), CUser_field_Base::SetNum(), CUser_object_Base::SetType(), CSeqdesc_Base::SetUser(), SEV_ERROR, rapidjson::source, and str().
Referenced by GetGenBankDescr().
◆ fta_get_project_user_object()Definition at line 1572 of file add.cpp.
References Parser::EMBL, ERR_FORMAT_InvalidBioProjectAcc, format, fta_atoi(), fta_tokenize_project(), FtaErrPost, Parser::GenBank, CRef< C, Locker >::GetNCPointer(), CObject_id_Base::GetStr(), i, CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), len, n, offset, ParFlat_COL_DATA, ParFlat_COL_DATA_EMBL, CRef< C, Locker >::Reset(), CUser_field_Base::SetData(), CUser_object_Base::SetData(), CUser_field_Base::SetLabel(), CUser_field_Base::SetNum(), CUser_object_Base::SetType(), CSeqdesc_Base::SetUser(), SEV_REJECT, rapidjson::source, and str().
Referenced by GetEmblDescr(), and GetGenBankDescr().
◆ fta_get_seqloc_int_whole() ◆ fta_if_valid_biosample() bool fta_if_valid_biosample ( string_view id, bool dblink ) ◆ fta_if_valid_sra() bool fta_if_valid_sra ( string_view id, bool dblink ) ◆ fta_number_is_huge() ◆ fta_parse_structured_comment()Definition at line 2423 of file add.cpp.
References CRef< C, Locker >::Empty(), ERR_COMMENT_InvalidStructuredComment, ERR_COMMENT_SameStructuredCommentTags, ERR_COMMENT_StructuredCommentLacksDelim, fta_build_structured_comment(), fta_StringCpy(), FtaErrPost, i, next(), r(), SEV_ERROR, SEV_REJECT, str(), string, StringEquN(), StringStr, and tag.
Referenced by GetEmblDescr(), GetGenBankDescr(), and XMLGetDescr().
◆ fta_parse_tpa_tsa_block() bool fta_parse_tpa_tsa_block ( CBioseq & bioseq, char * offset, char * acnum, Int2 vernum, size_t len, Int2 col_data, bool tpa )Definition at line 1119 of file add.cpp.
References buf, CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Tpg, eNa_strand_minus, eNa_strand_plus, ERR_TPA_InvalidPrimaryBlock, ERR_TPA_InvalidPrimarySeqId, ERR_TPA_InvalidPrimarySpan, ERR_TSA_InvalidPrimaryBlock, ERR_TSA_InvalidPrimarySeqId, ERR_TSA_InvalidPrimarySpan, CSeq_align_Base::eType_not_set, CSeq_align_Base::eType_partial, fta_atoi(), fta_check_tpa_tsa_coverage(), fta_number_is_huge(), FtaErrPost, CBioseq::GetLength(), GetNucAccOwner(), len, next(), CRef< C, Locker >::NotEmpty(), offset, r(), CRef< C, Locker >::Reset(), CSeq_align_set_Base::Set(), CSeq_align_Base::SetDim(), CSeq_id_Base::SetGeneral(), CBioseq_Base::SetInst(), CSeq_align_Base::SetSegs(), SetTextId(), CSeq_align_Base::SetType(), SEV_REJECT, SrchTheChar(), StringChr, StringEquNI(), StringLen(), StringSave, t, and tag.
Referenced by GetEmblDescr(), GetGenBankDescr(), and XMLGetDescr().
◆ fta_ranges_to_hist() ◆ fta_remove_cleanup_user_object() void fta_remove_cleanup_user_object ( CSeq_entry & seq_entry )Definition at line 2539 of file add.cpp.
References CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_Base::IsSetDescr(), CBioseq_set_Base::IsSetDescr(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), CBioseq_Base::SetDescr(), CBioseq_set_Base::SetDescr(), CSeq_entry_Base::SetSeq(), and CSeq_entry_Base::SetSet().
Referenced by OutputEmblAsn(), CGenbank2Asn::xGetEntry(), and CXml2Asn::xGetEntry().
◆ fta_set_molinfo_completeness() ◆ fta_strings_same() ◆ fta_tokenize_dblink()Definition at line 1725 of file add.cpp.
References ERR_DBLINK_DuplicateIdentifierRemoved, ERR_FORMAT_IncorrectDBLINK, fta_if_valid_biosample(), fta_if_valid_sra(), fta_validate_assembly(), fta_validate_bioproject(), FtaErrPost, next(), SEV_REJECT, SEV_WARNING, rapidjson::source, str(), t, and tag.
Referenced by fta_get_dblink_user_object().
◆ fta_tokenize_project() ◆ fta_tsa_tls_comment_dblink_check()Definition at line 2572 of file add.cpp.
References ERR_ENTRY_TLSLacksBioProjectLink, ERR_ENTRY_TLSLacksStructuredComment, ERR_ENTRY_TSALacksBioProjectLink, ERR_ENTRY_TSALacksStructuredComment, FtaErrPost, CSeq_descr_Base::Get(), CUser_object_Base::GetData(), CBioseq_Base::GetDescr(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), and SEV_WARNING.
Referenced by CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), and CXml2Asn::xGetEntry().
◆ fta_validate_assembly() static void fta_validate_assembly ( string_view name ) static ◆ fta_validate_bioproject() ◆ fta_vnp_structured_comment() ◆ g_DoesNotReferencePrimary() ◆ GapsToDelta()Definition at line 380 of file add.cpp.
References CreateSeqGap(), delta(), CSeq_inst_Base::eRepr_delta, ERR_FEATURE_AllNsBetweenGaps, ERR_FEATURE_InvalidGapSequence, ERR_FEATURE_NsAbutGap, FtaErrPost, CBioseq_Base::GetInst(), CSeq_data_Base::GetIupacna(), CBioseq::GetLength(), CSeq_inst_Base::GetSeq_data(), i, CSeq_inst_Base::IsSetSeq_data(), len, next(), CBioseq_Base::SetInst(), SEV_ERROR, SEV_REJECT, and SEV_WARNING.
Referenced by CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), and CXml2Asn::xGetEntry().
◆ GetQSFromFile() ◆ no_date() ◆ no_reference() ◆ s_IsAccession() ◆ s_IsConOrScaffold() ◆ SeqToDelta()Definition at line 508 of file add.cpp.
References buf, delta(), CSeq_inst_Base::eRepr_delta, ERR_SEQUENCE_HTGPhaseZeroHasGap, ERR_SEQUENCE_HTGPossibleShortGap, ERR_SEQUENCE_HTGWithoutGaps, FtaErrPost, CBioseq_Base::GetInst(), CSeq_data_Base::GetIupacna(), CBioseq::GetLength(), CSeq_inst_Base::GetRepr(), CSeq_inst_Base::GetSeq_data(), HTG_GAP, i, CSeq_inst_Base::IsSetSeq_data(), r(), CBioseq_Base::SetInst(), SEV_WARNING, and SHORT_GAP.
Referenced by CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), and CXml2Asn::xGetEntry().
◆ sGetPrefixLength() static int sGetPrefixLength ( string_view accession ) static ◆ StringRStr() char* StringRStr ( char * where, const char * what ) ◆ StripECO() void StripECO ( string & str ) ◆ tata_save() string tata_save ( string_view t ) ◆ USING_SCOPE()RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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