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

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Definition at line 95 of file em_ascii.cpp.

Definition at line 724 of file em_ascii.cpp.

References Parser::DDBJ, Indexblk::division, Parser::EMBL, NStr::EqualNocase(), ERR_DIVISION_ConDivLacksContig, ERR_DIVISION_MappedtoCON, ERR_FORMAT_ContigWithSequenceData, ERR_FORMAT_MissingContigFeature, ERR_FORMAT_MissingSequenceData, FtaErrPost, Indexblk::is_contig, Indexblk::origin, result, SEV_ERROR, SEV_INFO, SEV_REJECT, SEV_WARNING, and rapidjson::source.

Referenced by CEmbl2Asn::xGetEntry().

Definition at line 1987 of file em_ascii.cpp.

References count, CBioSource_Base::eGenome_plasmid, CRef< C, Locker >::Empty(), ERR_ORGANISM_NoOrganism, FtaErrPost, GetEmblOrgRef(), CBioSource_Base::GetGenome(), GetGenomeInfo(), COrg_ref_Base::IsSetOrgname(), ParFlat_COL_DATA_EMBL, ParFlat_OC, ParFlat_OG, ParFlat_OS, CBioseq_Base::SetDescr(), CBioSource_Base::SetOrg(), COrg_ref_Base::SetOrgname(), CSeqdesc_Base::SetSource(), COrg_ref_Base::SetTaxname(), SEV_WARNING, and TrackNodes().

Referenced by CEmbl2Asn::xGetEntry().

Definition at line 1501 of file em_ascii.cpp.

References CSerialObject::Assign(), CRef< C, Locker >::Empty(), fta_create_user_field(), CRef< C, Locker >::GetPointer(), CObject_id_Base::GetStr(), CObject_id_Base::IsStr(), CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CUser_object_Base::SetData(), CUser_object_Base::SetType(), and CSeqdesc_Base::SetUser().

Referenced by GetEmblDescr(), and XMLGetDescr().

Definition at line 1564 of file em_ascii.cpp.

References Indexblk::bases, ctll::empty(), fta_get_seqloc_int_whole(), CEMBL_block_Base::GetXref(), CEMBL_block_Base::IsSetXref(), CBioseq_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetDbxref(), CBioseq_Base::SetId(), CImp_feat_Base::SetKey(), CSeq_feat_Base::SetLocation(), and tag.

Referenced by GetEmblDescr().

Definition at line 931 of file em_ascii.cpp.

References Indexblk::acnum, Parser::allow_uwsec, Indexblk::bases, check_cds(), check_div(), CheckHTGDivision(), CKeywordParser::Cleanup(), Parser::curindx, DefVsHTGKeywords(), Indexblk::division, Indexblk::drop, CEMBL_block_Base::eClass_not_set, CEMBL_block_Base::eClass_other, CEMBL_block_Base::eClass_unannotated, CEMBL_block_Base::eDiv_pri, CEMBL_block_Base::eDiv_sts, CEMBL_block_Base::eDiv_una, Parser::EMBL, Indexblk::embl_new_ID, NStr::eNocase, Parser::entrylist, Indexblk::env_sample_qual, CBioSource_Base::eOrigin_synthetic, ERR_DIVISION_BadTPADivcode, ERR_DIVISION_BadTSADivcode, ERR_DIVISION_HTCWrongMolType, ERR_DIVISION_InvalidHTCKeyword, ERR_DIVISION_MissingHTCKeyword, ERR_DIVISION_MissingHTGKeywords, ERR_DIVISION_UnknownDivCode, ERR_KEYWORD_ConflictingKeywords, ERR_KEYWORD_ENV_NoMatchingQualifier, ERR_KEYWORD_ESTSubstring, ERR_KEYWORD_GSSSubstring, ERR_KEYWORD_HTGPlusENV, ERR_KEYWORD_IllegalForCON, ERR_KEYWORD_MissingTLS, ERR_KEYWORD_MissingTPA, ERR_KEYWORD_MissingTSA, ERR_KEYWORD_NoGeneExpressionKeywords, ERR_KEYWORD_ShouldNotBeCAGE, ERR_KEYWORD_ShouldNotBeTLS, ERR_KEYWORD_ShouldNotBeTPA, ERR_KEYWORD_ShouldNotBeTSA, ERR_KEYWORD_STSSubstring, Indexblk::EST, CSubSource_Base::eSubtype_environmental_sample, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_fli_cdna, CMolInfo_Base::eTech_htc, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_survey, CMolInfo_Base::eTech_unknown, CMolInfo_Base::eTech_wgs, Parser::format, fta_check_htg_kwds(), fta_if_wgs_acc(), fta_keywords_check(), fta_remove_env_keywords(), fta_remove_keywords(), fta_remove_tls_keywords(), fta_remove_tpa_keywords(), fta_remove_tsa_keywords(), fta_StartsWith(), fta_StringMatch(), fta_tls_keywords_check(), fta_tpa_keywords_check(), fta_tsa_keywords_check(), FtaErrPost, GetBlkDataReplaceNewLine(), GetEmblBlockXref(), GetEmblDate(), GetExtraAccession(), CBioSource_Base::GetOrigin(), CBioSource_Base::GetSubtype(), CMolInfo_Base::GetTech(), Indexblk::GSS, HasHtc(), HasHtg(), Indexblk::HTC, Indexblk::htg, i, Indexblk::is_contig, Indexblk::is_mga, Indexblk::is_pat, Indexblk::is_tls, Indexblk::is_tpa, Indexblk::is_tsa, IsCancelled(), CBioSource_Base::IsSetOrigin(), CBioSource_Base::IsSetSubtype(), CMolInfo_Base::IsSetTech(), ncbi::grid::netcache::search::fields::key, CKeywordParser::KeywordList(), Parser::KeywordParser(), len, DataBlk::mBuf, MemFree(), CRef< C, Locker >::NotEmpty(), ParFlat_COL_DATA_EMBL, ParFlat_DE, ParFlat_Embl_dataclass_array, ParFlat_Embl_DIV_array, ParFlat_GBDIV_array, ParFlat_KW, ParFlat_SQ, PointToNextToken(), Indexblk::psip, DataBlk::ptr, RemoveHtgPhase(), CMolInfo_Base::ResetTech(), CMolInfo_Base::SetTech(), SEV_ERROR, SEV_REJECT, SEV_WARNING, Parser::source, SrchNodeType(), NStr::StartsWith(), StringChr, StringCpy(), StringEqu(), StringEquN(), StringLen(), StringNCpy(), StringSave, Indexblk::STS, and Indexblk::wgssec.

Referenced by GetEmblDescr().

Definition at line 410 of file em_ascii.cpp.

References b, CleanTailNonAlphaChar(), ctll::empty(), NStr::Equal(), NStr::EqualNocase(), ERR_DRXREF_DuplicatedBioSamples, ERR_DRXREF_DuplicatedSRA, ERR_DRXREF_InvalidBioSample, ERR_DRXREF_InvalidSRA, ERR_DRXREF_UnknownDBname, fta_if_valid_biosample(), fta_if_valid_sra(), fta_StartsWith(), fta_StringMatch(), FtaErrPost, INSDSEQ_DATABASE_REFERENCE, len, MemFree(), ParFlat_COL_DATA_EMBL, ParFlat_DBname_array, ParFlat_DR, ParFlat_DRname_array, PointToNextToken(), CEMBL_block_Base::SetXref(), SetXrefObjId(), SEV_REJECT, SEV_WARNING, SrchNodeType(), SrchTheChar(), StringChr, StringSave, tmp, val, and XMLFindTagValue().

Referenced by GetDescrEmblBlock(), and XMLGetEMBLBlock().

Definition at line 273 of file em_ascii.cpp.

References CRef< C, Locker >::Empty(), fta_StartsWith(), CDate_std_Base::GetDay(), CDate_std_Base::GetMonth(), GetUpdateDate(), CDate_std_Base::GetYear(), len, offset, ParFlat_COL_DATA_EMBL, ParFlat_DT, CRef< C, Locker >::Reset(), CDate_std_Base::SetDay(), CDate_std_Base::SetMonth(), CDate_std_Base::SetYear(), rapidjson::source, SrchNodeType(), and SrchTheChar().

Referenced by GetDescrEmblBlock(), and GetEmblDescr().

Definition at line 1638 of file em_ascii.cpp.

References Indexblk::acnum, Indexblk::assembly, CDate_std::Compare(), Parser::curindx, Parser::DDBJ, DescrRefs(), Indexblk::division, Indexblk::drop, CSeq_id_Base::e_Embl, CDate::eCompare_after, Parser::EMBL, CRef< C, Locker >::Empty(), NStr::eNocase, Parser::entrylist, ERR_DATE_IllegalDate, ERR_DEFINITION_MissingTLS, ERR_DEFINITION_MissingTPA, ERR_DEFINITION_MissingTSA, ERR_DEFINITION_ShouldNotBeTLS, ERR_DEFINITION_ShouldNotBeTPA, ERR_DEFINITION_ShouldNotBeTSA, ERR_TPA_TpaCommentMissing, ERR_TPA_TpaSpansMissing, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_unknown, Indexblk::experimental, fta_add_hist(), fta_build_ena_user_object(), fta_check_con_for_wgs(), fta_create_imgt_misc_feat(), fta_dblink_has_sra(), fta_fix_orgref_div(), fta_get_project_user_object(), fta_orgref_has_taxid(), fta_parse_structured_comment(), fta_parse_tpa_tsa_block(), FtaErrPost, CBioseq_Base::GetAnnot(), GetBlkDataReplaceNewLine(), CDate_std::GetDate(), COrg_ref_Base::GetDb(), GetDescrComment(), GetDescrEmblBlock(), GetEmblDate(), GetEmblGBBlock(), GetEmblMolInfo(), COrg_ref_Base::GetOrgname(), i, Indexblk::inferential, Indexblk::is_contig, Indexblk::is_pat, Indexblk::is_tls, Indexblk::is_tpa, Indexblk::is_tsa, Indexblk::is_wgs, CBioseq_Base::IsSetAnnot(), COrg_ref_Base::IsSetDb(), COrgName_Base::IsSetDiv(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), len, MemFree(), Parser::NCBI, Parser::no_date, CRef< C, Locker >::NotEmpty(), offset, ParFlat_AH, ParFlat_CC, ParFlat_COL_DATA_EMBL, ParFlat_DE, ParFlat_GBDIV_array, ParFlat_PR, ParFlat_REF_END, ParFlat_REF_NO_TARGET, CRef< C, Locker >::Reset(), s_HasTPAPrefix(), CBioseq_Base::SetAnnot(), CSeqdesc_Base::SetComment(), CSeqdesc_Base::SetCreate_date(), CBioseq_Base::SetDescr(), CSeqdesc_Base::SetEmbl(), CSeqdesc_Base::SetGenbank(), CSeqdesc_Base::SetMolinfo(), CBioSource_Base::SetOrg(), COrg_ref_Base::SetOrgname(), CSeqdesc_Base::SetPub(), CDate_Base::SetStd(), CSeqdesc_Base::SetTitle(), CSeqdesc_Base::SetUpdate_date(), CSeqdesc_Base::SetUser(), SEV_ERROR, SEV_REJECT, Parser::source, Indexblk::specialist_db, SrchNodeType(), NStr::StartsWith(), str(), Parser::taxserver, TrackNodes(), TrackNodeType(), Indexblk::vernum, and Parser::xml_comp.

Referenced by CEmbl2Asn::xGetEntry().

Definition at line 1365 of file em_ascii.cpp.

References Parser::allow_uwsec, CKeywordParser::Cleanup(), Parser::curindx, Parser::entrylist, NStr::EqualNocase(), CSubSource_Base::eSubtype_environmental_sample, GetExtraAccession(), CBioSource_Base::GetSubtype(), CBioSource_Base::IsSetSubtype(), CKeywordParser::KeywordList(), Parser::KeywordParser(), Parser::NCBI, CRef< C, Locker >::Reset(), s_DuplicatesBiosource(), Parser::source, and Indexblk::wgssec.

Referenced by GetEmblDescr().

Definition at line 755 of file em_ascii.cpp.

References Parser::accver, Parser::allow_crossdb_featloc, Parser::buf, CSeq_inst_Base::eRepr_delta, ERR_LOCATION_ContigHasNull, fta_create_far_fetch_policy_user_object(), fta_fix_seq_loc_id(), FtaErrPost, CBioseq_Base::GetId(), CSeq_loc_Base::GetMix(), i, CSeq_loc_Base::IsMix(), DataBlk::len, DataBlk::mBuf, MemFree(), CRef< C, Locker >::NotEmpty(), ParFlat_CO, ParFlat_COL_DATA_EMBL, DataBlk::ptr, r(), CBioseq_Base::SetInst(), SEV_REJECT, StringSave, TrackNodeType(), XGappedSeqLocsToDeltaSeqs(), and xgbparseint_ver().

Referenced by s_GetEmblInst().

Definition at line 1411 of file em_ascii.cpp.

References CheckSTRAND(), Parser::curindx, CMolInfo_Base::eBiomol_unknown, Indexblk::embl_new_ID, NStr::eNocase, Parser::entrylist, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_targeted, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_wgs, fta_StartsWith(), GetFlatBiomol(), i, Indexblk::is_tls, Indexblk::is_tsa, Indexblk::is_wgs, DataBlk::mBuf, ParFlat_COL_DATA_EMBL, PointToNextToken(), DataBlk::ptr, r(), NStr::StartsWith(), and StringChr.

Referenced by GetEmblDescr().

Definition at line 649 of file em_ascii.cpp.

References NStr::fAllowTrailingSymbols, DataBlk::GetEntryData(), len, offset, ParFlat_DT, PointToNextToken(), EntryBlk::seq_entry, CBioseq_Base::SetId(), SetTextIdRef(), SrchNodeType(), SrchTheChar(), SrchTheStr(), and NStr::StringToInt().

Referenced by CEmbl2Asn::xGetEntry().

Definition at line 312 of file em_ascii.cpp.

References CheckDupDates(), Parser::citat, Parser::cleanup, Parser::convert, Parser::curindx, DealWithGenes(), EntryCheckDivCode(), Parser::entrylist, ERR_ENTRY_GBBlock_not_Empty, ERR_ENTRY_LongSequence, FinalCleanup(), fta_EntryCheckGBBlock(), fta_find_pub_explore(), fta_remove_cleanup_user_object(), fta_set_strandedness(), fta_sort_descr(), fta_sort_seqfeat_cit(), FtaErrPost, GetScope(), Parser::limit, MaybeCutGbblockSource(), PackEntries(), ProcessCitations(), Parser::qamode, CScope::ResetDataAndHistory(), result, SEV_REJECT, SEV_WARNING, StripSerialNumbers(), and Parser::xml_comp.

Referenced by CEmbl2Asn::xGetEntry().

Definition at line 833 of file em_ascii.cpp.

References CheckSTRAND(), Parser::curindx, Parser::EMBL, Indexblk::embl_new_ID, NStr::eNocase, Parser::entrylist, CSeq_inst_Base::eRepr_raw, ERR_LOCUS_WrongTopology, eSeq_code_type_iupacna, CSeq_inst_Base::eTopology_circular, FtaErrPost, GetEmblInstContig(), DataBlk::GetEntryData(), GetSeqData(), CSeq_inst_Base::GetTopology(), i, Indexblk::is_contig, DataBlk::mBuf, Parser::NCBI, ParFlat_COL_DATA_EMBL, ParFlat_SQ, PointToNextToken(), DataBlk::ptr, r(), EntryBlk::seq_entry, CBioseq_Base::SetInst(), CSeq_inst_Base::SetRepr(), CSeq_inst_Base::SetStrand(), CSeq_inst_Base::SetTopology(), SEV_WARNING, Parser::source, NStr::StartsWith(), StringChr, and StringStr.

Referenced by CEmbl2Asn::xGetEntry().

Definition at line 613 of file em_ascii.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_Other, 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, and CSeq_id_Base::e_Tpg.

Referenced by GetReleaseInfo().

Definition at line 2310 of file em_ascii.cpp.

References Indexblk::acnum, Parser::allow_uwsec, Indexblk::bases, check_div(), CheckHTGDivision(), Parser::curindx, Indexblk::division, Indexblk::drop, CEMBL_block_Base::eDiv_pri, CEMBL_block_Base::eDiv_sts, CEMBL_block_Base::eDiv_una, Parser::EMBL, CRef< C, Locker >::Empty(), Parser::entrylist, Indexblk::env_sample_qual, CBioSource_Base::eOrigin_synthetic, ERR_DIVISION_BadTPADivcode, ERR_DIVISION_BadTSADivcode, ERR_DIVISION_HTCWrongMolType, ERR_DIVISION_InvalidHTCKeyword, ERR_DIVISION_MissingHTCKeyword, ERR_DIVISION_MissingHTGKeywords, ERR_DIVISION_UnknownDivCode, ERR_KEYWORD_ConflictingKeywords, ERR_KEYWORD_ENV_NoMatchingQualifier, ERR_KEYWORD_ESTSubstring, ERR_KEYWORD_GSSSubstring, ERR_KEYWORD_HTGPlusENV, ERR_KEYWORD_IllegalForCON, ERR_KEYWORD_MissingTLS, ERR_KEYWORD_MissingTPA, ERR_KEYWORD_MissingTSA, ERR_KEYWORD_NoGeneExpressionKeywords, ERR_KEYWORD_ShouldNotBeCAGE, ERR_KEYWORD_ShouldNotBeTLS, ERR_KEYWORD_ShouldNotBeTPA, ERR_KEYWORD_ShouldNotBeTSA, ERR_KEYWORD_STSSubstring, Indexblk::EST, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_fli_cdna, CMolInfo_Base::eTech_htc, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_survey, CMolInfo_Base::eTech_unknown, CMolInfo_Base::eTech_wgs, fta_check_htg_kwds(), fta_if_wgs_acc(), fta_keywords_check(), fta_remove_keywords(), fta_remove_tls_keywords(), fta_remove_tpa_keywords(), fta_remove_tsa_keywords(), fta_StartsWith(), fta_StringMatch(), FtaErrPost, GetEmblBlockXref(), GetExtraAccession(), CBioSource_Base::GetOrigin(), CMolInfo_Base::GetTech(), GetUpdateDate(), Indexblk::GSS, HasHtc(), HasHtg(), Indexblk::HTC, Indexblk::htg, i, INSDSEQ_CREATE_DATE, INSDSEQ_DIVISION, INSDSEQ_KEYWORDS, INSDSEQ_MOLTYPE, INSDSEQ_UPDATE_DATE, Indexblk::is_contig, Indexblk::is_mga, Indexblk::is_pat, Indexblk::is_tls, Indexblk::is_tpa, Indexblk::is_tsa, IsCancelled(), CBioSource_Base::IsSetOrigin(), CMolInfo_Base::IsSetTech(), ncbi::grid::netcache::search::fields::key, Indexblk::keywords, MemFree(), CRef< C, Locker >::NotEmpty(), ParFlat_Embl_DIV_array, ParFlat_GBDIV_array, Indexblk::psip, r(), RemoveHtgPhase(), CMolInfo_Base::ResetTech(), CMolInfo_Base::SetTech(), SEV_ERROR, SEV_REJECT, SEV_WARNING, Parser::source, StringCpy(), StringEqu(), StringEquN(), StringLen(), StringSave, Indexblk::STS, Indexblk::wgssec, Indexblk::xip, XMLCheckCDS(), XMLConcatSubTags(), XMLDefVsHTGKeywords(), XMLFindTagValue(), and XMLGetKeywords().

Referenced by XMLGetDescr().

= {

"EMBL",

"GENBANK",

"DDBJ",

"GENINFO",

"MEDLINE",

"SWISS-PROT",

"PIR",

"PDB",

"EPD",

"ECD",

"TFD",

"FLYBASE",

"PROSITE",

"ENZYME",

"MIM",

"ECOSEQ",

"HIV",

nullptr

}

Definition at line 132 of file em_ascii.cpp.

Referenced by GetEmblBlockXref().

= {

"ANN", "CON", "PAT", "EST", "GSS", "HTC", "HTG", "STS", "TSA",

nullptr

}

Definition at line 106 of file em_ascii.cpp.

Referenced by EmblGetDivisionNewID(), and GetDescrEmblBlock().

= {

"FUN", "INV", "MAM", "ORG", "PHG", "PLN", "PRI", "PRO", "ROD",

"SYN", "UNA", "VRL", "VRT", "PAT", "EST", "STS", "UNC", "GSS",

"HUM", "HTG", "HTC", "CON", "ENV", "MUS", "TGN", "TSA",

nullptr

}

Definition at line 113 of file em_ascii.cpp.

Referenced by GetDescrEmblBlock(), GetEmblDiv(), and XMLGetEMBLBlock().

= {

"PLN", "INV", "MAM", "UNA", "PHG", "PLN", "PRI", "BCT", "ROD",

"SYN", "UNA", "VRL", "VRT", "PAT", "EST", "STS", "UNA", "GSS",

"PRI", "HTG", "HTC", "CON", "ENV", "ROD", "SYN", "TSA",

nullptr

}

Definition at line 123 of file em_ascii.cpp.

Referenced by GetDescrEmblBlock(), GetEmblDescr(), and XMLGetEMBLBlock().

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