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USING_SCOPE (objects) static void XMLCheckContigEverywhere (IndexblkPtr ibp, Parser::ESource source) static bool XMLGetInstContig (const TXmlIndexList &xil, const DataBlk &dbp, CBioseq &bioseq, ParserPtr pp) bool XMLGetInst (ParserPtr pp, const DataBlk &dbp, unsigned char *dnaconv, CBioseq &bioseq) static CRef< CGB_block > XMLGetGBBlock (ParserPtr pp, const char *entry, CMolInfo &mol_info, CBioSource *bio_src) static CRef< CMolInfo > XMLGetMolInfo (ParserPtr pp, const DataBlk &entry, COrg_ref *org_ref) static void XMLFakeBioSources (const TXmlIndexList &xil, const char *entry, CBioseq &bioseq, Parser::ESource source) static void XMLGetDescrComment (char *offset) static void XMLGetDescr (ParserPtr pp, const DataBlk &entry, CBioseq &bioseq) static void XMLGetDivision (const char *entry, IndexblkPtr ibp) ◆ THIS_FILE #define THIS_FILE "xm_ascii.cpp"Definition at line 89 of file xm_ascii.cpp.
◆ USING_SCOPE() ◆ XMLCheckContigEverywhere()Definition at line 95 of file xm_ascii.cpp.
References Parser::DDBJ, Indexblk::division, Indexblk::drop, 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, SEV_ERROR, SEV_INFO, SEV_REJECT, SEV_WARNING, and rapidjson::source.
Referenced by CXml2Asn::xGetEntry().
◆ XMLFakeBioSources()Definition at line 645 of file xm_ascii.cpp.
References CBioSource_Base::eGenome_plasmid, Parser::EMBL, ERR_ORGANISM_NoOrganism, FtaErrPost, CBioSource_Base::GetGenome(), GetGenomeInfo(), COrg_ref_Base::GetTaxname(), INSDSEQ_ORGANISM, INSDSEQ_TAXONOMY, COrg_ref_Base::SetCommon(), CBioseq_Base::SetDescr(), CBioSource_Base::SetOrg(), COrg_ref_Base::SetOrgname(), CSeqdesc_Base::SetSource(), COrg_ref_Base::SetTaxname(), SEV_WARNING, rapidjson::source, StringChr, and XMLGetTagValue().
Referenced by CXml2Asn::xGetEntry().
◆ XMLGetDescr()Definition at line 771 of file xm_ascii.cpp.
References Indexblk::acnum, CDate_std::Compare(), Parser::curindx, Parser::date, Parser::DDBJ, DescrRefs(), Indexblk::division, Indexblk::drop, CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CDate::eCompare_after, CTime::eCurrent, 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, Indexblk::experimental, fta_add_hist(), fta_build_ena_user_object(), fta_dblink_has_sra(), fta_fix_orgref_div(), fta_parse_structured_comment(), fta_parse_tpa_tsa_block(), fta_StringCpy(), FtaErrPost, GetUpdateDate(), Indexblk::inferential, INSDSEQ_COMMENT, INSDSEQ_CREATE_DATE, INSDSEQ_DEFINITION, INSDSEQ_PRIMARY, INSDSEQ_UPDATE_DATE, Indexblk::is_tls, Indexblk::is_tpa, Indexblk::is_tsa, Indexblk::is_wgs, CBioSource_Base::IsSetOrg(), DataBlk::mBuf, MemFree(), Parser::no_date, CRef< C, Locker >::NotEmpty(), offset, ParFlat_REF_END, ParFlat_REF_NO_TARGET, DataBlk::ptr, CRef< C, Locker >::Reset(), 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(), CSeqdesc_Base::SetPub(), CDate_Base::SetStd(), CSeqdesc_Base::SetTitle(), CDate_std::SetToTime(), CSeqdesc_Base::SetUpdate_date(), CSeqdesc_Base::SetUser(), SEV_ERROR, SEV_REJECT, Parser::source, Indexblk::specialist_db, NStr::StartsWith(), str(), StringRChr(), StringSave, Parser::taxserver, Indexblk::vernum, Indexblk::xip, Parser::xml_comp, XMLBuildRefDataBlk(), XMLFindTagValue(), XMLGetDescrComment(), XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLGetMolInfo().
Referenced by CXml2Asn::xGetEntry().
◆ XMLGetDescrComment() static void XMLGetDescrComment ( char * offset ) static ◆ XMLGetDivision() ◆ XMLGetGBBlock()Definition at line 228 of file xm_ascii.cpp.
References Indexblk::acnum, Parser::allow_uwsec, Indexblk::bases, Indexblk::biodrop, check_div(), CheckDIV(), CheckHTGDivision(), Parser::curindx, Indexblk::division, Parser::EMBL, Parser::entrylist, Indexblk::env_sample_qual, ERR_DIVISION_BadTPADivcode, ERR_DIVISION_BadTSADivcode, ERR_DIVISION_HTCWrongMolType, ERR_DIVISION_InvalidHTCKeyword, ERR_DIVISION_MappedtoEST, ERR_DIVISION_MissingHTCKeyword, ERR_DIVISION_MissingHTGKeywords, ERR_DIVISION_UnknownDivCode, ERR_KEYWORD_ConflictingKeywords, ERR_KEYWORD_ENV_NoMatchingQualifier, ERR_KEYWORD_ESTSubstring, 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, Parser::format, fta_check_htg_kwds(), fta_check_mga_keywords(), 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_tls_keywords_check(), fta_tpa_keywords_check(), fta_tsa_keywords_check(), FtaErrPost, COrgName_Base::GetDiv(), GetExtraAccession(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CBioSource_Base::GetOrigin(), CBioSource_Base::GetSubtype(), CMolInfo_Base::GetTech(), Indexblk::GSS, HasHtc(), HasHtg(), Indexblk::HTC, Indexblk::htg, i, INSDSEQ_DIVISION, INSDSEQ_KEYWORDS, INSDSEQ_MOLTYPE, INSDSEQ_SOURCE, Indexblk::is_contig, Indexblk::is_mga, Indexblk::is_pat, Indexblk::is_tls, Indexblk::is_tpa, Indexblk::is_tsa, IsCancelled(), IsNewAccessFormat(), COrgName_Base::IsSetDiv(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), CBioSource_Base::IsSetOrigin(), CBioSource_Base::IsSetSubtype(), CMolInfo_Base::IsSetTech(), ncbi::grid::netcache::search::fields::key, Indexblk::keywords, MemCpy(), MemFree(), msg(), Indexblk::no_gbblock_source, CRef< C, Locker >::NotEmpty(), Indexblk::psip, RemoveHtgPhase(), CMolInfo_Base::ResetTech(), CMolInfo_Base::SetTech(), SEV_ERROR, SEV_INFO, SEV_REJECT, SEV_WARNING, Parser::source, str(), StringCpy(), StringEqu(), StringEquN(), StringRChr(), StringSave, Indexblk::STS, Parser::taxserver, Parser::USPTO, Indexblk::wgssec, Indexblk::xip, Parser::XML, XMLCheckCDS(), XMLConcatSubTags(), XMLDefVsHTGKeywords(), XMLFindTagValue(), and XMLGetKeywords().
Referenced by XMLGetDescr().
◆ XMLGetInst()Definition at line 184 of file xm_ascii.cpp.
References Parser::curindx, Parser::entrylist, CSeq_inst_Base::eRepr_raw, eSeq_code_type_iupacaa, eSeq_code_type_iupacna, GetSeqData(), INSDSEQ_STRANDEDNESS, INSDSEQ_TOPOLOGY, Indexblk::is_contig, Indexblk::is_prot, DataBlk::mBuf, DataBlk::ptr, CBioseq_Base::SetInst(), CSeq_inst_Base::SetRepr(), CSeq_inst_Base::SetStrand(), CSeq_inst_Base::SetTopology(), Indexblk::xip, XMLCheckSTRAND(), XMLCheckTPG(), XMLGetInstContig(), and XMLGetTagValue().
Referenced by CXml2Asn::xGetEntry().
◆ XMLGetInstContig()Definition at line 123 of file xm_ascii.cpp.
References Parser::accver, Parser::allow_crossdb_featloc, Parser::buf, CRef< C, Locker >::Empty(), 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, INSDSEQ_CONTIG, CSeq_loc_Base::IsMix(), DataBlk::mBuf, MemFree(), DataBlk::ptr, r(), CBioseq_Base::SetInst(), SEV_REJECT, StringSave, XGappedSeqLocsToDeltaSeqs(), xgbparseint_ver(), and XMLFindTagValue().
Referenced by XMLGetInst().
◆ XMLGetMolInfo()Definition at line 599 of file xm_ascii.cpp.
References Parser::curindx, CMolInfo_Base::eBiomol_unknown, Parser::entrylist, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_survey, CMolInfo_Base::eTech_targeted, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_wgs, fta_StartsWith(), GetFlatBiomol(), INSDSEQ_DIVISION, INSDSEQ_MOLTYPE, Indexblk::is_tls, Indexblk::is_tsa, Indexblk::is_wgs, DataBlk::mBuf, MemFree(), DataBlk::ptr, StringSave, Indexblk::xip, and XMLFindTagValue().
Referenced by XMLGetDescr().
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