| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/validator/ |
| H A D | feature_match.hpp | 86 CMatchmRNA(const CMappedFeat &mrna) : CMatchFeat(mrna), m_AccountedFor(false) {}; in CMatchmRNA()
121 void AddmRNA(CMatchmRNA& mrna) { m_OverlappingmRNAs.push_back(Ref(&mrna)); } in AddmRNA()
122 void SetXrefMatch(CMatchmRNA& mrna) { m_XrefMatch = true; m_AssignedMrna = &mrna; } in SetXrefMatch()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
| H A D | feature_match.cpp | 114 const CSeq_feat& mrna = mrna_match.GetFeat(); in s_SetUpXrefPairs() local
358 CRef<CMatchmRNA> CmRNAAndCDSIndex::FindMatchmRNA(const CMappedFeat& mrna) in FindMatchmRNA()
370 bool CmRNAAndCDSIndex::MatchmRNAToCDSEnd(const CMappedFeat& mrna, unsigned int partial_type) in MatchmRNAToCDSEnd()
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| H A D | cdregion_validator.cpp | 1057 CConstRef<CSeq_feat> mrna = GetBestOverlappingFeat( in x_ValidateBadMRNAOverlap() local
1195 CMappedFeat mrna = feat_tree->GetParent(fh, CSeqFeatData::eSubtype_mRNA); in x_ValidateFarProducts() local
1868 CConstRef<CSeq_feat> mrna = GetmRNAforCDS(m_Feat, m_Scope); in x_ValidateParentPartialness() local
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| /dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqFeature/Gene/ |
| H A D | TranscriptI.pm | 191 sub mrna { subroutine
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| H A D | Transcript.pm | 569 sub mrna { subroutine
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| /dports/biology/ncbi-toolkit/ncbi/demo/ |
| H A D | nps2gps.c | 109 SeqFeatPtr mrna; in LclMakeNucProtCDS() local
588 SeqFeatPtr mrna in MakeIdFromLocusTag()
627 SeqFeatPtr mrna in MakeIdFromTscriptID()
666 SeqFeatPtr mrna in MakeIdFromTempID()
817 SeqFeatPtr mrna, in InstantiateMrnaIntoProt()
995 SeqFeatPtr mrna; member
1319 SeqFeatPtr mrna in ReciprocalTranscriptIDs()
1347 SeqFeatPtr mrna in GetCDSByProteinID()
1889 SeqFeatPtr cds, gene, mrna, lastmrna, sfp, lastsfp; in NPStoGPS() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/discrepancy/ |
| H A D | suspect_product_names.cpp | 295 …t void GetProtAndRnaForCDS(const CSeq_feat& cds, CScope& scope, CSeq_feat*& prot, CSeq_feat*& mrna) in GetProtAndRnaForCDS()
340 auto mrna = get_mrna(); in FixProductName() local
360 CSeq_feat* mrna; in DISCREPANCY_AUTOFIX() local
436 CSeq_feat* mrna; in DISCREPANCY_AUTOFIX() 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_cds_fix.cpp | 329 CRef<CSeq_feat> mrna = edit::MakemRNAforCDS(*cds, scope); in BOOST_AUTO_TEST_CASE() local
393 CRef<CSeq_feat> mrna = edit::MakemRNAforCDS(*cds, scope); in BOOST_AUTO_TEST_CASE() local
454 CConstRef<CSeq_feat> mrna = edit::GetmRNAforCDS(*cds, scope); in BOOST_AUTO_TEST_CASE() local
626 CRef<CSeq_feat> mrna(new CSeq_feat()); in BOOST_AUTO_TEST_CASE() local
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| H A D | unit_test_feature_propagate.cpp | 1609 CRef<CSeq_feat> mrna = unit_test_util::AddMiscFeature(first, 15); in GetGoodSeqEntryWithFeatureIds() local
1690 CConstRef<CSeq_feat> mrna = mrna_it->GetOriginalSeq_feat(); in BOOST_AUTO_TEST_CASE() local
1799 CConstRef<CSeq_feat> mrna = mrna_it->GetOriginalSeq_feat(); in BOOST_AUTO_TEST_CASE() local
1878 CRef<CSeq_feat> mrna = unit_test_util::AddMiscFeature(first, 15); in BOOST_AUTO_TEST_CASE() local
1942 CRef<CSeq_feat> mrna = unit_test_util::AddMiscFeature(first, 15); in BOOST_AUTO_TEST_CASE() local
1998 CRef<CSeq_feat> mrna = unit_test_util::AddMiscFeature(first, 15); in BOOST_AUTO_TEST_CASE() local
2062 CRef<CSeq_feat> mrna = unit_test_util::AddMiscFeature(first, 15); in BOOST_AUTO_TEST_CASE() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
| H A D | feattable_edit.cpp | 471 CMappedFeat mrna = *it; in GenerateProteinAndTranscriptIds() local
490 static string s_GetTranscriptIdFromMrna(const CMappedFeat& mrna) in s_GetTranscriptIdFromMrna()
506 CMappedFeat mrna = feature::GetBestMrnaForCds(cds, &mTree); in xAddTranscriptAndProteinIdsToCdsAndParentMrna() local
592 CMappedFeat& mrna) in xAddTranscriptAndProteinIdsToMrna()
642 void CFeatTableEdit::xAddTranscriptAndProteinIdsToUnmatchedMrna(CMappedFeat& mrna) in xAddTranscriptAndProteinIdsToUnmatchedMrna()
1751 const CMappedFeat& mrna) in xPutErrorDifferingProteinIds()
1769 const CMappedFeat& mrna) in xPutErrorDifferingTranscriptIds()
1972 CConstRef<CSeq_feat> mrna = xGetLinkedFeature(cd_feature, false); in xGenerate_mRNA_Product() local
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| H A D | promote.cpp | 262 CBioseq_Handle mrna; in x_PromoteCdregion() local
298 CBioseq_Handle& mrna, in x_CopyCdregionToRNA()
386 CBioseq_EditHandle mrna = in x_PromoteRna() local
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| H A D | link_cds_mrna.cpp | 151 CRef<CSeq_feat> cds, mrna; in xLinkCDSmRNAbyLabelAndLocation() local
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| H A D | cds_fix.cpp | 504 string s_GetmRNAName (const CSeq_feat& mrna) in s_GetmRNAName()
531 CConstRef <CSeq_feat> mrna(NULL); in MakemRNAforCDS() local
672 CConstRef<CSeq_feat> mrna; in GetmRNAforCDS() local
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
| H A D | feattable_edit.cpp | 474 CMappedFeat mrna = *it; in GenerateProteinAndTranscriptIds() local
494 static string s_GetTranscriptIdFromMrna(const CMappedFeat& mrna) in s_GetTranscriptIdFromMrna()
510 CMappedFeat mrna = feature::GetBestMrnaForCds(cds, &mTree); in xAddTranscriptAndProteinIdsToCdsAndParentMrna() local
605 CMappedFeat& mrna) in xAddTranscriptAndProteinIdsToMrna()
655 void CFeatTableEdit::xAddTranscriptAndProteinIdsToUnmatchedMrna(CMappedFeat& mrna) in xAddTranscriptAndProteinIdsToUnmatchedMrna()
1764 const CMappedFeat& mrna) in xPutErrorDifferingProteinIds()
1782 const CMappedFeat& mrna) in xPutErrorDifferingTranscriptIds()
1985 CConstRef<CSeq_feat> mrna = xGetLinkedFeature(cd_feature, false); in xGenerate_mRNA_Product() local
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| H A D | promote.cpp | 262 CBioseq_Handle mrna; in x_PromoteCdregion() local
298 CBioseq_Handle& mrna, in x_CopyCdregionToRNA()
386 CBioseq_EditHandle mrna = in x_PromoteRna() local
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| H A D | link_cds_mrna.cpp | 151 CRef<CSeq_feat> cds, mrna; in xLinkCDSmRNAbyLabelAndLocation() local
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| H A D | cds_fix.cpp | 504 string s_GetmRNAName (const CSeq_feat& mrna) in s_GetmRNAName()
531 CConstRef <CSeq_feat> mrna(NULL); in MakemRNAforCDS() local
672 CConstRef<CSeq_feat> mrna; in GetmRNAforCDS() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/table2asn/ |
| H A D | suspect_feat.cpp | 129 … auto mrna = feature::GetBestParentForFeat(mapped, CSeqFeatData::eSubtype_mRNA, m_feattree); in FixSuspectProductNames() local
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| /dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
| H A D | coderet.c | 62 AjPStr mrna = NULL; in main() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
| H A D | gnomon_seq.cpp | 147 void FindAllCodonInstances(TIVec positions[], const EResidue codon[], const CEResidueVec& mrna, TSi… in FindAllCodonInstances()
157 void FindAllStarts(TIVec starts[], const CEResidueVec& mrna, TSignedSeqRange search_region, int fix… in FindAllStarts()
162 void FindAllStops(TIVec stops[], const CEResidueVec& mrna, TSignedSeqRange search_region, int fixed… in FindAllStops()
182 …sStops(const CGeneModel& model, const CEResidueVec& contig_seq, const CEResidueVec& mrna, const CA… in FindStartsStops()
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| /dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/src/ |
| H A D | gtf_tracking.h | 170 GffObj* mrna; variable
532 bool add_mRNA(GffObj* mrna) { in add_mRNA()
602 void mrnas_add(GffObj* mrna) { in mrnas_add()
937 GffObj* mrna=loc->mrnas[m]; variable
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/nw/ |
| H A D | nw_formatter.cpp | 740 int CNWFormatter::SSegment::CanExtendRight(const vector<char>& mrna, const vector<char>& genomic) c… in CanExtendRight() argument
753 int CNWFormatter::SSegment::CanExtendLeft(const vector<char>& mrna, const vector<char>& genomic) co… in CanExtendLeft() argument
765 void CNWFormatter::SSegment::ExtendRight(const vector<char>& mrna, const vector<char>& genomic, int… in ExtendRight()
782 void CNWFormatter::SSegment::ExtendLeft(const vector<char>& mrna, const vector<char>& genomic, int … in ExtendLeft()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cleanup/test/ |
| H A D | unit_test_extended_cleanup.cpp | 858 CRef<CSeq_feat> mrna = unit_test_util::MakemRNAForCDS(cds); in BOOST_AUTO_TEST_CASE() local
1410 CRef<CSeq_feat> mrna = AddMiscFeature(entry); in Test_WGSCleanup() local
1478 CRef<CSeq_feat> mrna = AddMiscFeature(entry); in Test_WGSCleanupNoProt() local
1572 CRef<CSeq_feat> mrna = unit_test_util::MakemRNAForCDS(cds); in MakeMrnaGeneTripletForCDS() local
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| /dports/biology/viennarna/ViennaRNA-2.4.18/src/bin/ |
| H A D | RNAsnoop.c | 105 FILE *sno, *mrna; in main() local
1137 FILE *sno, *mrna; in redraw_output() local
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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 | 10978 CRef<CSeq_feat> mrna (new CSeq_feat()); in BOOST_AUTO_TEST_CASE() local
14056 CRef<CSeq_feat> mrna(new CSeq_feat()); in BOOST_AUTO_TEST_CASE() local
16448 CRef<CSeq_feat> mrna = unit_test_util::MakemRNAForCDS(cds); in BOOST_FIXTURE_TEST_CASE() local
16633 CRef<CSeq_feat> mrna = unit_test_util::MakemRNAForCDS(cds); in BOOST_AUTO_TEST_CASE() local
17254 CRef<CSeq_feat> mrna = unit_test_util::MakemRNAForCDS(cds); in BuildGenProdSetWithBigProduct() local
17918 CRef<CSeq_feat> mrna = unit_test_util::MakemRNAForCDS(cds); in BOOST_AUTO_TEST_CASE() local
18574 CRef<CSeq_feat> mrna = unit_test_util::MakemRNAForCDS(cds); in BOOST_AUTO_TEST_CASE() local
18632 CRef<CSeq_feat> mrna = unit_test_util::MakemRNAForCDS(cds); in BOOST_AUTO_TEST_CASE() local
18669 CRef<CSeq_feat> mrna = unit_test_util::MakemRNAForCDS(cds); in BOOST_AUTO_TEST_CASE() local
18773 CRef<CSeq_feat> mrna = unit_test_util::MakemRNAForCDS(cds); in BOOST_AUTO_TEST_CASE() local
[all …]
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