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Functions | |
| bool | GetGenBankInstContig (const DataBlk &entry, objects::CBioseq &bsp, ParserPtr pp) |
| void | CheckFeatSeqLoc (TEntryList &seq_entries) |
| bool | GenBankAscii (ParserPtr pp) |
| bool | GenBankAsciiOrig (ParserPtr pp) |
Function Documentation
◆ CheckFeatSeqLoc()
| void CheckFeatSeqLoc | ( | TEntryList & | seq_entries | ) |
Definition at line 2375 of file gb_ascii.cpp.
References FindFeatSeqLoc(), CBioseq_set_Base::GetAnnot(), GetParts(), CBioseq_set_Base::SetAnnot(), and CSeq_annot_Base::SetData().
Referenced by GenBankAsciiOrig(), and XMLAscii().
◆ GenBankAscii()
Definition at line 1784 of file gb_ascii.cpp.
References Parser::accver, Indexblk::acnum, CScope::AddBioseq(), Indexblk::bases, CheckContigEverywhere(), conv, CreateEntryBioseq(), Parser::curindx, Indexblk::division, Indexblk::drop, Parser::entrylist, ERR_ENTRY_ParsingComplete, ERR_ENTRY_Skipped, ERR_FORMAT_MissingEnd, err_install(), ERR_SEQUENCE_BadData, ERR_TSA_UnexpectedPrimaryAccession, ErrPostEx, ErrPostStr, FtaDeletePrefix(), GetDNAConv(), GetProteinConv(), GetScope(), i, Parser::indx, Indexblk::is_prot, Indexblk::is_tsa, Indexblk::len, LoadEntryGenbank(), Indexblk::locusname, Indexblk::offset, ParFlat_COL_DATA, ParFlat_END, ParFlat_NCBI_GI, PREFIX_ACCESSION, PREFIX_LOCUS, Indexblk::segnum, SEV_ERROR, SEV_INFO, SEV_REJECT, SEV_WARNING, Parser::source, StringEqu(), Indexblk::tsa_allowed, xGenBankGetDivision(), xGetGenBankBlocks(), and xGetGenBankSubBlocks().
Referenced by fta_parse_buf().
◆ GenBankAsciiOrig()
Definition at line 1363 of file gb_ascii.cpp.
References Parser::accver, Indexblk::acnum, CScope::AddBioseq(), AddNIDSeqId(), AssemblyGapsToDelta(), Indexblk::bases, LocusCont::bp, BuildBioSegHeader(), EntryBlk::chain, CheckContigEverywhere(), CheckDupDates(), CheckFeatSeqLoc(), Parser::citat, Parser::cleanup, conv, Parser::convert, CreateEntryBioseq(), Parser::curindx, Parser::DDBJ, DealWithGenes(), Parser::debug, Indexblk::division, Indexblk::drop, Parser::entries, EntryCheckDivCode(), Parser::entrylist, CSeq_inst_Base::eRepr_raw, ERR_DATE_IllegalDate, ERR_DIVISION_Mismatch, ERR_ENTRY_GBBlock_not_Empty, ERR_ENTRY_LongHTGSSequence, ERR_ENTRY_LongSequence, ERR_ENTRY_Parsed, ERR_ENTRY_ParsingComplete, ERR_ENTRY_Skipped, ERR_FORMAT_MissingEnd, err_install(), ERR_QSCORE_FailedToParse, ERR_REFERENCE_No_references, ERR_SEGMENT_OnlyOneMember, ERR_SEGMENT_Rejected, ERR_SEQUENCE_BadData, ERR_TSA_UnexpectedPrimaryAccession, ErrPostEx, ErrPostStr, FakeGenBankBioSources(), Parser::ff_get_qscore, Parser::ff_get_qscore_pp, FinalCleanup(), Parser::Flybase, Parser::format, fta_EntryCheckGBBlock(), fta_find_pub_explore(), fta_get_user_object(), fta_remove_cleanup_user_object(), fta_set_molinfo_completeness(), fta_set_strandedness(), fta_sort_descr(), fta_sort_seqfeat_cit(), fta_tsa_tls_comment_dblink_check(), FtaDeletePrefix(), g_InstantiateMissingProteins(), Indexblk::gaps, GapsToDelta(), GenBankGetDivision(), CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), GetDNAConv(), GetGenBankBlock(), GetGenBankDescr(), GetGenBankInst(), GetGenBankSubBlock(), CBioseq_Base::GetInst(), CObjectManager::GetInstance(), GetProteinConv(), GetQSFromFile(), CSeq_inst_Base::GetRepr(), GetScope(), GetSeqExt(), Indexblk::htg, i, Parser::ign_bad_qs, Parser::indx, Indexblk::is_pat, Indexblk::is_prot, Indexblk::is_tls, Indexblk::is_tsa, Indexblk::is_wgs, CSeq_inst::IsNa(), CBioseq_Base::IsSetAnnot(), Indexblk::lc, Indexblk::len, Parser::limit, LoadEntry(), LoadFeat(), Indexblk::locusname, MaybeCutGbblockSource(), Parser::mode, Parser::no_date, no_date(), no_reference(), CRef< C, Locker >::NotEmpty(), Indexblk::offset, PackEntries(), ParFlat_COL_DATA, ParFlat_END, ParFlat_LOCUS, ParFlat_NCBI_GI, PREFIX_ACCESSION, PREFIX_LOCUS, ProcessCitations(), Indexblk::psip, Parser::qamode, QscoreToSeqAnnot(), Parser::qsfd, Indexblk::qslength, Ref(), Parser::Refseq, Parser::Relaxed, CRef< C, Locker >::Reset(), Indexblk::segnum, Indexblk::segtotal, EntryBlk::seq_entry, SeqToDelta(), CBioseq_Base::SetId(), SEV_ERROR, SEV_INFO, SEV_REJECT, SEV_WARNING, Parser::source, StringEqu(), StringEquN(), StripSerialNumbers(), Indexblk::tsa_allowed, Indexblk::vernum, Indexblk::wgs_and_gi, xFreeEntry(), and Parser::xml_comp.
Referenced by sParseFlatfile().
