| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seqfeat/ |
| H A D | RNA_ref.cpp | 131 static CTempString s_GetTrnaProduct(const CTrna_ext& trna) in s_GetTrnaProduct()
163 static void s_SetTrnaProduct(CTrna_ext& trna, const string& product, string& remainder) in s_SetTrnaProduct()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seqfeat/ |
| H A D | RNA_ref.cpp | 131 static CTempString s_GetTrnaProduct(const CTrna_ext& trna) in s_GetTrnaProduct()
163 static void s_SetTrnaProduct(CTrna_ext& trna, const string& product, string& remainder) in s_SetTrnaProduct()
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| /dports/biology/ncbi-toolkit/ncbi/demo/ |
| H A D | releasescan.c | 78 tRNAPtr trna; in DoFeat() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/ |
| H A D | write_util.cpp | 306 const CTrna_ext& trna, in GetTrnaCodons()
349 const CTrna_ext& trna, in GetTrnaProductName()
373 const CTrna_ext& trna, in GetTrnaAntiCodon()
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| H A D | fasta_writer.cpp | 1015 const auto& trna = rna.GetExt().GetTRNA(); in x_AddRNAProductAttribute() local
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| H A D | gff_writer.cpp | 826 const CTrna_ext& trna = display_range.IsWhole() ? in xAssignFeatureAttributeProduct() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/unit_test/ |
| H A D | unit_test_gap_trim.cpp | 917 CRef<CSeq_feat> trna = AddMiscFeature(entry); in MakeTrnaWithAnticodon() local
938 CRef<CFeatGapInfo> trna = MakeTrnaWithAnticodon(start, stop, anticodon_start); in TestAnticodonSplit() local
949 CRef<CFeatGapInfo> trna = MakeTrnaWithAnticodon(start, stop, anticodon_start); in TestAnticodonTrim() local
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| H A D | unit_test_feature_propagate.cpp | 277 CRef<CSeq_feat> trna = unit_test_util::AddMiscFeature(seq, 15); in CreateTrna() local
283 void AddAnticodon(CRef<CSeq_feat> trna, CRef<CSeq_loc> subloc) in AddAnticodon()
473 CRef<CSeq_feat> trna = CreateTrna(main_loc, seq1); in TestTrnaAnticodon() local
515 CRef<CSeq_feat> trna = CreateTrna(main_loc, seq1); in TestTrnaAnticodonFromLastBioseq() local
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| H A D | unit_test_loc_edit.cpp | 523 CRef<objects::CSeq_feat> trna = unit_test_util::BuildGoodtRNA(id); in BOOST_AUTO_TEST_CASE() local
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| /dports/biology/ncbi-toolkit/ncbi/object/ |
| H A D | objfeat.h | 566 typedef struct trna { struct
567 Uint1 aatype, /* 0=not set, 1=iupacaa, 2=ncbieaa, 3=ncbi8aa 4=ncbistdaa */
568 aa; /* the aa transferred in above code */
569 Uint1 codon[6]; /* codons recognized, coded as for Genetic-code */
570 SeqLocPtr anticodon; /* location of anticodon */
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
| H A D | gap_trim.cpp | 467 CTrna_ext& trna = feat.SetData().SetRna().SetExt().SetTRNA(); in x_AdjustAnticodons() local
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| H A D | loc_edit.cpp | 1060 void ReverseComplementTrna(CTrna_ext& trna, CScope& scope) in ReverseComplementTrna()
2071 void TrnaAdjustForTrim(CTrna_ext& trna, in TrnaAdjustForTrim()
2131 void TrnaAdjustForInsert(CTrna_ext& trna, in TrnaAdjustForInsert()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
| H A D | gap_trim.cpp | 467 CTrna_ext& trna = feat.SetData().SetRna().SetExt().SetTRNA(); in x_AdjustAnticodons() local
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| H A D | loc_edit.cpp | 1060 void ReverseComplementTrna(CTrna_ext& trna, CScope& scope) in ReverseComplementTrna()
2071 void TrnaAdjustForTrim(CTrna_ext& trna, in TrnaAdjustForTrim()
2131 void TrnaAdjustForInsert(CTrna_ext& trna, in TrnaAdjustForInsert()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/unit_test/ |
| H A D | unit_test_validator.cpp | 12369 CRef<CSeq_feat> trna = unit_test_util::BuildtRNA(entry->SetSeq().SetId().front()); in BOOST_AUTO_TEST_CASE() local
12508 CRef<CSeq_feat> trna = unit_test_util::BuildtRNA(entry->SetSeq().SetId().front()); in BOOST_AUTO_TEST_CASE() local
12580 CRef<CSeq_feat> trna = unit_test_util::BuildtRNA(entry->SetSeq().SetId().front()); in BOOST_AUTO_TEST_CASE() local
13926 CRef<CSeq_feat> trna = unit_test_util::AddMiscFeature (entry); in BOOST_AUTO_TEST_CASE() local
14543 CRef<CSeq_feat> trna = unit_test_util::BuildtRNA(entry->SetSeq().SetId().front()); in BOOST_AUTO_TEST_CASE() local
14740 CRef<CSeq_feat> trna = unit_test_util::BuildtRNA(entry->SetSeq().SetId().front()); in BOOST_AUTO_TEST_CASE() local
18090 CRef<CSeq_feat> trna = unit_test_util::BuildtRNA(entry->SetSeq().SetId().front()); in BOOST_AUTO_TEST_CASE() local
18111 CRef<CSeq_feat> trna = unit_test_util::BuildtRNA(entry->SetSeq().SetId().front()); in BOOST_AUTO_TEST_CASE() local
23706 CRef<CSeq_feat> trna = unit_test_util::AddMiscFeature(entry); in BOOST_AUTO_TEST_CASE() local
23727 CRef<CSeq_feat> trna = unit_test_util::AddMiscFeature(entry); in BOOST_AUTO_TEST_CASE() local
[all …]
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| /dports/biology/ncbi-toolkit/ncbi/api/ |
| H A D | asn2ff3.c | 1591 static CharPtr GettRNAaa (tRNAPtr trna, Boolean error_msgs) in GettRNAaa()
1631 static void ComposetRNANote(Asn2ffJobPtr ajp, NoteStructPtr nsp, tRNAPtr trna) in ComposetRNANote()
1722 tRNAPtr trna=NULL; in DotRNAQuals() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cleanup/test/ |
| H A D | unit_test_basic_cleanup.cpp | 1104 CRef<CSeq_feat> trna(new CSeq_feat()); in TestMoveTrnaProductQualToNote() local
1133 CRef<CSeq_feat> trna(new CSeq_feat()); in BOOST_AUTO_TEST_CASE() local
1950 CRef<CSeq_feat> trna = AddMiscFeature(entry); in BOOST_AUTO_TEST_CASE() local
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| /dports/biology/bbmap/bbmap/current/prok/ |
| H A D | GeneModel.java | 98 ArrayList<GffLine> trna=allGffLines[2]; in process() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/ |
| H A D | loadfeat.cpp | 1756 static int get_aa_from_trna(const objects::CTrna_ext& trna) in get_aa_from_trna()
2019 static int get_first_codon_from_trna(const objects::CTrna_ext& trna) in get_first_codon_from_trna()
2317 const objects::CTrna_ext& trna = rna_ref->GetExt().GetTRNA(); in GetRnaRef() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/format/items/ |
| H A D | qualifiers.hpp | 658 CFlatTrnaCodonsQVal(const CTrna_ext& trna, const string& comment) : in CFlatTrnaCodonsQVal()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/format/items/ |
| H A D | qualifiers.hpp | 658 CFlatTrnaCodonsQVal(const CTrna_ext& trna, const string& comment) : in CFlatTrnaCodonsQVal()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
| H A D | single_feat_validator.cpp | 3168 const CTrna_ext& trna = m_Feat.GetData().GetRna().GetExt ().GetTRNA (); in x_ValidateTrnaData() local
3382 const CTrna_ext& trna = m_Feat.GetData().GetRna().GetExt().GetTRNA(); in x_ValidateTrnaCodons() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cleanup/ |
| H A D | newcleanupp.cpp | 3952 CRef<CTrna_ext> trna; in s_ParseTRnaFromAnticodonString() local
4213 CRNA_ref_Base::C_Ext::TTRNA& trna = rna.SetExt().SetTRNA(); in x_HandleTrnaProductGBQual() local
4407 CRef<CTrna_ext> trna = s_ParseTRnaFromAnticodonString(gb_qual.GetVal(), feat, m_Scope); in x_SeqFeatRnaGBQualBC() local
7853 static bool s_IsEmpty(const CTrna_ext& trna) in s_IsEmpty()
9061 unsigned char s_GetAaAsChar(const CTrna_ext& trna) in s_GetAaAsChar()
9167 CTrna_ext& trna = seq_feat.SetData().SetRna().SetExt().SetTRNA(); in x_tRNACodonEC() local
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/cleanup/ |
| H A D | newcleanupp.cpp | 3891 CRef<CTrna_ext> trna; in s_ParseTRnaFromAnticodonString() local
4152 CRNA_ref_Base::C_Ext::TTRNA& trna = rna.SetExt().SetTRNA(); in x_HandleTrnaProductGBQual() local
4346 CRef<CTrna_ext> trna = s_ParseTRnaFromAnticodonString(gb_qual.GetVal(), feat, m_Scope); in x_SeqFeatRnaGBQualBC() local
7792 static bool s_IsEmpty(const CTrna_ext& trna) in s_IsEmpty()
9002 unsigned char s_GetAaAsChar(const CTrna_ext& trna) in s_GetAaAsChar()
9108 CTrna_ext& trna = seq_feat.SetData().SetRna().SetExt().SetTRNA(); in x_tRNACodonEC() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/ |
| H A D | autodef_feature_clause_base.cpp | 2014 …CAutoDefParsedtRNAClause* trna = s_tRNAClauseFromNote(bh, cf, mapped_loc, phrase, first, last, opt… in ClauseFromPhrase() local
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