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static char * get_sequence_text (ParserPtr parser, const string &accession, int version) static bool get_accession_from_id (const CSeq_id &id, string &accession, int &version) static int add_entry (ParserPtr pp, const char *acc, Int2 vernum, const DataBlk &entry) static void AddToIndexBlk (const DataBlk &entry, IndexblkPtr ibp, Parser::EFormat format) static CRef< CBioseq > get_bioseq (ParserPtr pp, const DataBlk &entry, const CSeq_id &id) static DataBlk * make_entry (char *entry_str) static CRef< CBioseq > parse_entry (ParserPtr pp, char *entry_str, const string &accession, int ver, const CSeq_id &id) size_t CheckOutsideEntry (ParserPtr pp, const char *acc, Int2 vernum) ◆ THIS_FILE ◆ add_entry()Definition at line 165 of file buf_data_loader.cpp.
References Parser::accver, Indexblk::acnum, LocusCont::bases, LocusCont::bp, LocusCont::date, LocusCont::div, Parser::entrylist, Parser::format, fta_StartsWith(), Parser::GenBank, i, Parser::indx, Indexblk::lc, DataBlk::len, DataBlk::mBuf, LocusCont::molecule, ParFlat_COL_BASES, ParFlat_COL_BASES_NEW, ParFlat_COL_BP, ParFlat_COL_BP_NEW, ParFlat_COL_DATE, ParFlat_COL_DATE_NEW, ParFlat_COL_DIV, ParFlat_COL_DIV_NEW, ParFlat_COL_MOLECULE, ParFlat_COL_MOLECULE_NEW, ParFlat_COL_STRAND, ParFlat_COL_STRAND_NEW, ParFlat_COL_TOPOLOGY, ParFlat_COL_TOPOLOGY_NEW, Indexblk::ppp, DataBlk::ptr, LocusCont::strand, StringChr, StringCpy(), StringEqu(), StringLen(), LocusCont::topology, and Indexblk::vernum.
Referenced by CheckOutsideEntry(), and parse_entry().
◆ AddToIndexBlk()Definition at line 218 of file buf_data_loader.cpp.
References LocusCont::bases, Indexblk::bases, LocusCont::div, Indexblk::division, Parser::EMBL, format, fta_atoi(), Parser::GenBank, isalpha(), isdigit(), Indexblk::lc, len, DataBlk::len, DataBlk::mBuf, offset, DataBlk::ptr, StringChr, StringEquN(), and StringNCpy().
Referenced by CheckOutsideEntry(), and parse_entry().
◆ CheckOutsideEntry()Definition at line 434 of file buf_data_loader.cpp.
References add_entry(), AddToIndexBlk(), EntryBlk::chain, ERR_FORMAT_MissingEnd, FtaErrPost, get_sequence_text(), GetEmblBlock(), DataBlk::GetEntryData(), DataBlk::len, make_entry(), DataBlk::mBuf, MemFree(), ParFlat_ID, ParFlatEM_END, DataBlk::ptr, and SEV_ERROR.
Referenced by flat2asn_range_func().
◆ get_accession_from_id() ◆ get_bioseq()Definition at line 273 of file buf_data_loader.cpp.
References CSeq_id::Assign(), Indexblk::bases, EntryBlk::chain, Parser::curindx, Parser::EMBL, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, Parser::entrylist, CSeq_inst_Base::eRepr_raw, eSeq_code_type_iupacna, CSeq_inst_Base::eStrand_ss, CSeq_inst_Base::eTopology_linear, Parser::farseq, Parser::format, Parser::GenBank, GetDNAConv(), GetEmblBlock(), GetEmblInstContig(), DataBlk::GetEntryData(), GetGenBankBlock(), GetGenBankInstContig(), GetProteinConv(), GetSeqData(), Indexblk::is_contig, DataBlk::len, DataBlk::mBuf, ParFlat_END, ParFlat_ID, ParFlat_LOCUS, ParFlat_ORIGIN, ParFlat_SQ, ParFlatEM_END, ParFlatSP_END, DataBlk::ptr, CRef< C, Locker >::Reset(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), and Parser::SPROT.
Referenced by parse_entry().
◆ get_sequence_text() ◆ make_entry() ◆ parse_entry()RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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