| /dports/biology/emboss/EMBOSS-6.6.0/ajax/ensembl/ |
| H A D | ensexon.c | 1024 EnsPExon ensExonNewCpy(const EnsPExon exon) in ensExonNewCpy()
1126 EnsPExon exon = NULL; in ensExonNewIni() local
1220 EnsPExon ensExonNewRef(EnsPExon exon) in ensExonNewRef()
1413 AjBool ensExonGetCurrent(const EnsPExon exon) in ensExonGetCurrent()
1521 ajint ensExonGetPhaseEnd(const EnsPExon exon) in ensExonGetPhaseEnd()
1565 ajint ensExonGetPhaseStart(const EnsPExon exon) in ensExonGetPhaseStart()
1607 ajuint ensExonGetVersion(const EnsPExon exon) in ensExonGetVersion()
2764 EnsPExon ensExonTransform(EnsPExon exon, in ensExonTransform()
4291 EnsPExon exon = NULL; in exonadaptorFetchAllbyStatement() local
4878 EnsPExon exon = NULL; in ensExonadaptorFetchAllbyTranscript() local
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| H A D | enstranscript.c | 402 EnsPExon exon = NULL; in ensTranscriptNewCpy() local
651 EnsPExon exon = NULL; in ensTranscriptNewIni() local
1026 EnsPExon exon = NULL; in ensTranscriptDel() local
2945 EnsPExon exon, in ensTranscriptAddExon()
3307 EnsPExon exon = NULL; in ensTranscriptTrace() local
3591 EnsPExon exon = NULL; in ensTranscriptCalculateCoordinates() local
3716 EnsPExon exon = NULL; in ensTranscriptCalculateLength() local
3791 EnsPExon exon = NULL; in ensTranscriptCalculateMemsize() local
3985 EnsPExon exon = NULL; in ensTranscriptCalculatePhaseStart() local
4023 EnsPExon exon = NULL; in ensTranscriptCalculateSliceCodingEnd() local
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| H A D | enstranslation.c | 1473 EnsPExon exon) in ensTranslationSetEndexon()
1645 EnsPExon exon) in ensTranslationSetStartexon()
3056 EnsPExon exon = NULL; in translationadaptorFetchAllbyStatement() local
3642 EnsPExon exon = NULL; in ensTranslationadaptorFetchAllbyTranscript() local
3828 EnsPExon exon = NULL; in translationadaptorFetchAllbyIdentifiers() local
4445 EnsPExon exon = NULL; in ensTranslationadaptorFetchByTranscript() local
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| /dports/biology/sim4/sim4.2003-09-21/ |
| H A D | sim4.h | 62 typedef struct exon { struct
74 struct exon *next_exon; argument
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
| H A D | transform_align.cpp | 92 const CSpliced_exon& exon = **it; in GetExonStructure() local
185 CSpliced_exon& exon = **it; in StitchSmallHoles() local
483 RecalculateExonIdty(CSpliced_exon &exon) in RecalculateExonIdty()
635 CSpliced_exon& exon = **exon_it; in MaximizeTranslation() local
798 CSpliced_exon& exon = **exon_it; in AdjustAlignment() local
933 CRef<CSpliced_exon> exon(new CSpliced_exon); in AdjustAlignment() local
950 CRef<CSpliced_exon> exon(new CSpliced_exon); in AdjustAlignment() local
967 CRef<CSpliced_exon> exon(new CSpliced_exon); in AdjustAlignment() local
1018 CSpliced_exon& exon = **exon_it; in AdjustAlignment() local
1026 CSpliced_exon& exon = **exon_it; in AdjustAlignment() local
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/util/ |
| H A D | VariationPropertiesUtils.h | 93 static inline bool isInDonorSpliceSite(const U2Region &exon, qint64 varPos, int spliceSiteLen) { in isInDonorSpliceSite()
98 …static inline bool isInAcceptorSpliceSite(const U2Region &exon, qint64 varPos, int spliceSiteLen) { in isInAcceptorSpliceSite()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/prosplign/ |
| H A D | AliSeqAlign.cpp | 85 void CAliToSeq_align::SetExonBioStart(CRef<CSpliced_exon> exon, int nulpos, int nultripos) const in SetExonBioStart()
94 void CAliToSeq_align::SetExonBioEnd(CRef<CSpliced_exon> exon, int nulpos, int nultripos) const in SetExonBioEnd()
145 CRef<CSpliced_exon> exon; in MakeSeq_align() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/unit_test/ |
| H A D | unit_test_gene_model.cpp | 535 CRef<CSpliced_exon> exon; in BOOST_AUTO_TEST_CASE() local
574 CRef<CSpliced_exon> exon; in BOOST_AUTO_TEST_CASE() local
649 CRef<CSpliced_exon> exon; in BOOST_AUTO_TEST_CASE() local
858 CRef<CSpliced_exon> exon; in BOOST_AUTO_TEST_CASE() local
973 CRef<CSpliced_exon> exon; in BOOST_AUTO_TEST_CASE() local
1029 const CSpliced_exon& exon = **modified_align->GetSegs().GetSpliced().GetExons().begin(); in BOOST_AUTO_TEST_CASE() local
1099 CRef<CSpliced_exon> exon; in BOOST_AUTO_TEST_CASE() local
1155 const CSpliced_exon& exon = **modified_align->GetSegs().GetSpliced().GetExons().begin(); in BOOST_AUTO_TEST_CASE() local
1226 CRef<CSpliced_exon> exon; in BOOST_AUTO_TEST_CASE() local
1326 CRef<CSpliced_exon> exon; in BOOST_AUTO_TEST_CASE() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/ |
| H A D | best_placement.cpp | 269 for(const auto& exon : aln.GetSegs().GetSpliced().GetExons()) { in GetLongestMatchrunLen() local
369 for(const auto& exon : aln.GetSegs().GetSpliced().GetExons()) { in s_GetIdentOdds_nucSS() local
466 for(const auto& exon : ss.GetExons()) { in GetSplicesOdds() local
503 for(const auto& exon : ss.GetExons()) { in GetExonsOdds() local
533 for(const auto& exon : aln.GetSegs().GetSpliced().GetExons()) { in GetNumGapopensBetweenExons() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/ |
| H A D | DataProviderForExampleGencodeGtfGene.java | 537 final GencodeGtfExonFeature exon = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); in createStopCodonExon() local
569 … final GencodeGtfExonFeature exon, final Strand codingDirection) { in create3pUtr()
583 … final GencodeGtfExonFeature exon, final Strand codingDirection) { in create5pUtr()
607 … final GencodeGtfExonFeature exon = (GencodeGtfExonFeature) GencodeGtfFeature.create(tmpExon); in createStartCodonExon() local
664 … final GencodeGtfExonFeature exon = (GencodeGtfExonFeature) GencodeGtfFeature.create(tmpExon); in createMiddleExon() local
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
| H A D | magicblast_unit_test.cpp | 198 SExon exon; in BOOST_AUTO_TEST_CASE() local
323 for (auto exon: seg.GetExons()) { in BOOST_AUTO_TEST_CASE() local
396 SExon exon; in BOOST_AUTO_TEST_CASE() local
518 for (auto exon: seg.GetExons()) { in BOOST_AUTO_TEST_CASE() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
| H A D | magicblast_unit_test.cpp | 198 SExon exon; in BOOST_AUTO_TEST_CASE() local
323 for (auto exon: seg.GetExons()) { in BOOST_AUTO_TEST_CASE() local
396 SExon exon; in BOOST_AUTO_TEST_CASE() local
518 for (auto exon: seg.GetExons()) { in BOOST_AUTO_TEST_CASE() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/ |
| H A D | gff3flybase_writer.cpp | 203 const CSpliced_exon& exon) in xAssignAlignmentSplicedLocation()
245 const CSpliced_exon& exon) in xAssignAlignmentSplicedTarget()
279 const CSpliced_exon& exon) in xAssignAlignmentSplicedSeqId()
295 const CSpliced_exon& exon) in xAssignAlignmentSplicedScores()
477 const CSpliced_exon& exon) in xAssignAlignmentSplicedGap()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seqalign/ |
| H A D | Spliced_seg.cpp | 121 const CSpliced_exon& exon = **exon_it; in Validate() local
322 s_ExonToDenseg(const CSpliced_exon& exon, in s_ExonToDenseg()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seqalign/ |
| H A D | Spliced_seg.cpp | 121 const CSpliced_exon& exon = **exon_it; in Validate() local
322 s_ExonToDenseg(const CSpliced_exon& exon, in s_ExonToDenseg()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/genebuilder/ |
| H A D | BasicProteinMapPanel.java | 97 uk.ac.sanger.artemis.Feature exon = in paintComponent() local
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| H A D | BasicGeneBuilderFrame.java | 484 Feature exon = (Feature)embl_exon.getUserData(); in addListeners() local
708 Feature exon = (Feature)embl_exon.getUserData(); in stopListeningAll() local
1074 Feature exon = (Feature) exons.get(0).getUserData(); in setQualifiers() local
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/genebuilder/gff/ |
| H A D | BasicPropertiesPanel.java | 71 Feature exon = (Feature) exons.get(0).getUserData(); in BasicPropertiesPanel() local
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| /dports/biology/wise/wise2.4.1/src/models/ |
| H A D | syexonmodel.h | 49 SyExon ** exon; member
66 SyExonScoreUnit ** exon; member
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| /dports/biology/kallisto/kallisto-0.46.1/src/ |
| H A D | GeneModel.cpp | 60 auto& exon = model.exons[i]; in translateTrPosition() local
98 auto& exon = model.exons[i]; in translateTrPosition() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/ |
| H A D | GencodeGtfTranscriptFeature.java | 46 public void addExon( final GencodeGtfExonFeature exon ) { in addExon()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/segment/ |
| H A D | SegmentExonUtils.java | 91 …final GencodeGtfExonFeature exon = gencodeGtfExonFeatureNode != null ? gencodeGtfExonFeatureNode.g… in findInclusiveExonIndex() local
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| /dports/biology/star/STAR-2.7.9a/source/ |
| H A D | Genome_transformGenome.cpp | 130 for (auto & exon : exonLoci1[1]) {//shift gene/tanscript IDs for 2nd haplotype in transformGenome() local
287 for (auto & exon : exonLoci) { in transformExonLoci() local
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| /dports/biology/stringtie/stringtie-2.1.1/gclib/ |
| H A D | GBam.cpp | 344 GSeg exon(exstart+1,c->pos+l); in setupCoordinates() local
359 GSeg exon(exstart+1,c->pos+l); in setupCoordinates() local
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| /dports/biology/hisat2/hisat2-2.2.1/ |
| H A D | alt.h | 86 bool exon() const { return type == ALT_EXON; } in exon() function
270 void setExons(bool exon) { _exon = exon; } in setExons()
|