/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/ |
H A D | asci_blk.h | 49 void StripSerialNumbers(TEntryList& seq_entries); 50 void PackEntries(TEntryList& seq_entries); 77 void BuildBioSegHeader(ParserPtr pp, TEntryList& entries, 85 void EntryCheckDivCode(TEntryList& seq_entries, ParserPtr pp); 91 bool fta_EntryCheckGBBlock(TEntryList& seq_entries); 93 void fta_sort_descr(TEntryList& seq_entries); 94 void fta_sort_seqfeat_cit(TEntryList& seq_entries); 96 void fta_set_strandedness(TEntryList& seq_entries);
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H A D | nucprot.h | 76 void CheckDupDates(TEntryList& seq_entries); 77 void ProcNucProt(ParserPtr pp, TEntryList& seq_entries, GeneRefFeats& gene_refs);
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H A D | asci_blk.cpp | 2126 TEntryList::iterator next_seq = entries.begin(); in CheckSegPub() 2447 NON_CONST_ITERATE(TEntryList, entry, entries) in GetSegSetDblink() 2610 ITERATE(TEntryList, entry, entries) in SrchSegSeqMol() 2638 ITERATE(TEntryList, entry, entries) in SrchSegLength() 3538 bool fta_EntryCheckGBBlock(TEntryList& seq_entries) in fta_EntryCheckGBBlock() 3619 void fta_sort_descr(TEntryList& seq_entries) in fta_sort_descr() 3689 void fta_sort_seqfeat_cit(TEntryList& seq_entries) in fta_sort_seqfeat_cit() 3797 void fta_set_strandedness(TEntryList& seq_entries) in fta_set_strandedness() 3821 ITERATE(TEntryList, entry, seq_entries) in SwissProtIDPresent() 3872 void StripSerialNumbers(TEntryList& seq_entries) in StripSerialNumbers() [all …]
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H A D | utilfeat.cpp | 347 static void GetTaxnameName(TEntryList& seq_entries, std::vector<std::string>& names) in GetTaxnameName() 351 NON_CONST_ITERATE(TEntryList, entry, seq_entries) in GetTaxnameName() 474 static void CheckDelGbblockSource(TEntryList& seq_entries, std::vector<std::string>& names) in CheckDelGbblockSource() 476 NON_CONST_ITERATE(TEntryList, entry, seq_entries) in CheckDelGbblockSource() 488 void MaybeCutGbblockSource(TEntryList& seq_entries) in MaybeCutGbblockSource()
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H A D | fcleanup.cpp | 172 NON_CONST_ITERATE(TEntryList, entry, bio_set.SetSeq_set()) in MoveAnnotToTop() 207 NON_CONST_ITERATE(TEntryList, entry, bio_set.SetSeq_set()) in MoveBiomolToTop() 219 ITERATE(TEntryList, entry, parts->GetSeq_set()) in MoveBiomolToTop() 243 NON_CONST_ITERATE(TEntryList, entry, parts->SetSeq_set()) in MoveBiomolToTop() 465 void FinalCleanup(TEntryList& seq_entries) in FinalCleanup() 481 NON_CONST_ITERATE(TEntryList, entry, seq_entries) in FinalCleanup()
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H A D | fcleanup.h | 46 void FinalCleanup(TEntryList& seq_entries);
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H A D | citation.cpp | 344 void ProcessCitations(TEntryList& seq_entries) in ProcessCitations() 348 ITERATE(TEntryList, entry, seq_entries) in ProcessCitations() 369 NON_CONST_ITERATE(TEntryList, entry, seq_entries) in ProcessCitations()
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H A D | gb_ascii.h | 49 void CheckFeatSeqLoc(TEntryList& seq_entries);
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H A D | utilfeat.h | 52 void MaybeCutGbblockSource(TEntryList& seq_entries);
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H A D | citation.h | 65 void ProcessCitations(TEntryList& seq_entries);
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H A D | ftanet.h | 52 void fta_find_pub_explore(ParserPtr pp, TEntryList& seq_entries);
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H A D | utilref.h | 56 void DealWithGenes(TEntryList& seq_entries, ParserPtr pp);
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H A D | nucprot.cpp | 252 static void GetGcode(TEntryList& seq_entries, ParserPtr pp) in GetGcode() 255 ITERATE(TEntryList, entry, seq_entries) in GetGcode() 293 static void AssignBioseqSetLevel(TEntryList& seq_entries) in AssignBioseqSetLevel() 296 NON_CONST_ITERATE(TEntryList, entry, seq_entries) in AssignBioseqSetLevel() 2607 NON_CONST_ITERATE(TEntryList, entry, seq_entries) in FindCd() 2619 NON_CONST_ITERATE(TEntryList, entry, seq_entries) in FindCd() 2744 static void BuildProtBioseqSet(ProtBlkPtr pbp, TEntryList& entries) in BuildProtBioseqSet() 2835 NON_CONST_ITERATE(TEntryList, entry, bio_set.SetSeq_set()) in FixDupDates() 2892 NON_CONST_ITERATE(TEntryList, entry, bio_set.SetSeq_set()) in FixEmblUpdateDates() 2929 void CheckDupDates(TEntryList& seq_entries) in CheckDupDates() [all …]
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H A D | ftablock.h | 92 TEntryList entries; /* a ProtRef SeqEntry list, link to above
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H A D | gb_ascii.cpp | 1594 TEntryList seq_entries; in GenBankAscii() 2172 static void FindFeatSeqLoc(TEntryList& seq_entries, TSeqFeatList& feats) in FindFeatSeqLoc() 2174 NON_CONST_ITERATE(TEntryList, entry, seq_entries) in FindFeatSeqLoc() 2209 static objects::CBioseq_set* GetParts(TEntryList& seq_entries) in GetParts() 2211 NON_CONST_ITERATE(TEntryList, entry, seq_entries) in GetParts() 2234 void CheckFeatSeqLoc(TEntryList& seq_entries) in CheckFeatSeqLoc()
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H A D | ftanet.cpp | 620 using TEntryList = list<CRef<CSeq_entry>>; typedef in CFindPub 621 void Apply(TEntryList& entries); 908 void fta_find_pub_explore(ParserPtr pp, TEntryList& seq_entries) in fta_find_pub_explore()
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H A D | genref.cpp | 2871 static void CheckGene(TEntryList& seq_entries, ParserPtr pp, GeneRefFeats& gene_refs) in CheckGene() 2901 NON_CONST_ITERATE(TEntryList, entry, seq_entries) in CheckGene() 3158 static void GeneQuals(TEntryList& seq_entries, const Char* acnum, GeneRefFeats& gene_refs) in GeneQuals() 3176 NON_CONST_ITERATE(TEntryList, entry, seq_entries) in GeneQuals() 3253 void DealWithGenes(TEntryList& seq_entries, ParserPtr pp) in DealWithGenes() 3258 ITERATE(TEntryList, entry, seq_entries) in DealWithGenes() 3268 NON_CONST_ITERATE(TEntryList, entry, seq_entries) in DealWithGenes()
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H A D | ftamain.cpp | 402 TEntryList& entries = seq_submit->SetData().SetEntrys(); in MakeSeqSubmit() 935 TEntryList& fta_parse_buf(Parser& pp, const char* buf) in fta_parse_buf()
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H A D | prf_ascii.cpp | 966 TEntryList entries; in PrfPrepareEntry()
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H A D | em_ascii.cpp | 303 static bool OutputEmblAsn(bool seq_long, ParserPtr pp, TEntryList& seq_entries) in OutputEmblAsn() 2490 TEntryList seq_entries; in EmblAscii()
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H A D | xm_ascii.cpp | 1356 TEntryList seq_entries; in XMLAscii()
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H A D | pir_ascii.cpp | 2434 TEntryList entries; in ind2asn()
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H A D | sp_ascii.cpp | 5323 TEntryList entries; in SpPrepareEntry()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/flatfile/ |
H A D | fta_parse_buf.h | 48 typedef std::list<CRef<objects::CSeq_entry>> TEntryList; typedef 50 TEntryList& fta_parse_buf(Parser& pp, const char* buf);
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H A D | flatfile_parse_info.hpp | 57 using TEntryList = list<CRef<objects::CSeq_entry>>; typedef 115 TEntryList entries;
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