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Searched refs:TExons (Results 1 – 25 of 54) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seqalign/
H A DSpliced_seg.cpp119 ITERATE (CSpliced_seg::TExons, exon_it, GetExons()) { in Validate()
238 ITERATE(TExons, exon_it, GetExons()) { in GetSeqRange()
246 ITERATE(TExons, exon_it, GetExons()) { in GetSeqRange()
260 ITERATE(TExons, exon_it, GetExons()) { in GetSeqRange()
440 ITERATE (CSpliced_seg::TExons, exon, GetExons()) { in AsDiscSeg()
463 ITERATE (CSpliced_seg::TExons, exon, GetExons()) { in AsDiscSeg()
H A DSeq_align.cpp1512 ITERATE (CSpliced_seg::TExons, iter, align.GetSegs().GetSpliced().GetExons()) { in s_GetGapCount()
1820 ITERATE (CSpliced_seg::TExons, iter, GetSegs().GetSpliced().GetExons()) { in GetAlignedBases()
1957 ITERATE (CSpliced_seg::TExons, iter, in s_GetAlignmentLength()
2061 ITERATE(TSegs::TSpliced::TExons, ex, spl.GetExons()) { in CreateRowSeq_loc()
2153 ITERATE (CSpliced_seg::TExons, iter, in GapLengthRange()
2186 ITERATE (CSpliced_seg::TExons, iter, in IntronLengthRange()
2212 ITERATE (CSpliced_seg::TExons, iter, in ExonLengthRange()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seqalign/
H A DSpliced_seg.cpp119 ITERATE (CSpliced_seg::TExons, exon_it, GetExons()) { in Validate()
238 ITERATE(TExons, exon_it, GetExons()) { in GetSeqRange()
246 ITERATE(TExons, exon_it, GetExons()) { in GetSeqRange()
260 ITERATE(TExons, exon_it, GetExons()) { in GetSeqRange()
440 ITERATE (CSpliced_seg::TExons, exon, GetExons()) { in AsDiscSeg()
463 ITERATE (CSpliced_seg::TExons, exon, GetExons()) { in AsDiscSeg()
H A DSeq_align.cpp1512 ITERATE (CSpliced_seg::TExons, iter, align.GetSegs().GetSpliced().GetExons()) { in s_GetGapCount()
1820 ITERATE (CSpliced_seg::TExons, iter, GetSegs().GetSpliced().GetExons()) { in GetAlignedBases()
1957 ITERATE (CSpliced_seg::TExons, iter, in s_GetAlignmentLength()
2061 ITERATE(TSegs::TSpliced::TExons, ex, spl.GetExons()) { in CreateRowSeq_loc()
2153 ITERATE (CSpliced_seg::TExons, iter, in GapLengthRange()
2186 ITERATE (CSpliced_seg::TExons, iter, in IntronLengthRange()
2212 ITERATE (CSpliced_seg::TExons, iter, in ExonLengthRange()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/
H A Dtransform_align.cpp91 ITERATE(CSpliced_seg::TExons, it, spliced_seg.GetExons()) { in GetExonStructure()
181 CSpliced_seg::TExons::iterator it = spliced_seg.SetExons().begin(); in StitchSmallHoles()
402 CSpliced_seg::TExons::iterator save_it = it; in StitchSmallHoles()
432 NON_CONST_ITERATE (CSpliced_seg::TExons, exon_it, in ClearScores()
456 NON_CONST_ITERATE (CSpliced_seg::TExons, exon_it, in RecalculateScores()
576 CSpliced_seg::TExons::reverse_iterator left_spl_exon_it(right_spl_exon_it); in TrimHolesToCodons()
632 CSpliced_seg::TExons::iterator prev_exon_it = spliced_seg.SetExons().end(); in MaximizeTranslation()
634 NON_CONST_ITERATE (CSpliced_seg::TExons, exon_it, spliced_seg.SetExons()) { in MaximizeTranslation()
797 NON_CONST_ITERATE(CSpliced_seg::TExons, exon_it, spliced_seg.SetExons()) { in AdjustAlignment()
830 CSpliced_seg::TExons::reverse_iterator left_spl_exon_it(right_spl_exon_it); in AdjustAlignment()
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H A Dfeature_generator.hpp126 objects::CSpliced_seg::TExons::reverse_iterator& spl_exon_it,
132 objects::CSpliced_seg::TExons::iterator& spl_exon_it,
H A Dproject_exons.cpp135 ITERATE(CSpliced_seg::TExons, it, spliced_aln.GetSegs().GetSpliced().GetExons()) { in GetExonPartialness()
228 ITERATE(CSpliced_seg::TExons, it, in GetTerminalPartialness()
1524 ITERATE(CSpliced_seg::TExons, it, in ProjectExons()
1735 NON_CONST_ITERATE(CSpliced_seg::TExons, it, spliced_aln.SetSegs().SetSpliced().SetExons()) {
H A Dinternal_stops.cpp310 ITERATE( CSpliced_seg::TExons, exon, spliced_seg.GetExons() ) { in GetCDSNucleotideSequence()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/
H A Dseq_align_util.cpp173 const CSpliced_seg::TExons& exons = spliced_seg.GetExons(); in GetProductString()
176 REVERSE_ITERATE(CSpliced_seg::TExons, ex_it, exons) { in GetProductString()
181 ITERATE(CSpliced_seg::TExons, ex_it, exons) { in GetProductString()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/util/
H A Dseq_align_util.cpp173 const CSpliced_seg::TExons& exons = spliced_seg.GetExons(); in GetProductString()
176 REVERSE_ITERATE(CSpliced_seg::TExons, ex_it, exons) { in GetProductString()
181 ITERATE(CSpliced_seg::TExons, ex_it, exons) { in GetProductString()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/unit_test/
H A Dunit_test_gene_model.cpp534 CSpliced_seg::TExons& exons = seg.SetExons(); in BOOST_AUTO_TEST_CASE()
573 CSpliced_seg::TExons& exons = seg.SetExons(); in BOOST_AUTO_TEST_CASE()
623 … CSpliced_seg::TExons::const_iterator i = trimmed_align->GetSegs().GetSpliced().GetExons().begin(); in BOOST_AUTO_TEST_CASE()
648 CSpliced_seg::TExons& exons = seg.SetExons(); in BOOST_AUTO_TEST_CASE()
704 … CSpliced_seg::TExons::const_iterator i = trimmed_align->GetSegs().GetSpliced().GetExons().begin(); in BOOST_AUTO_TEST_CASE()
772 … CSpliced_seg::TExons::const_iterator i = trimmed_align->GetSegs().GetSpliced().GetExons().begin(); in BOOST_AUTO_TEST_CASE()
857 CSpliced_seg::TExons& exons = seg.SetExons(); in BOOST_AUTO_TEST_CASE()
972 CSpliced_seg::TExons& exons = seg.SetExons(); in BOOST_AUTO_TEST_CASE()
1098 CSpliced_seg::TExons& exons = seg.SetExons(); in BOOST_AUTO_TEST_CASE()
1225 CSpliced_seg::TExons& exons = seg.SetExons(); in BOOST_AUTO_TEST_CASE()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon_model.hpp405 typedef vector<CModelExon> TExons; typedef in CGeneModel
406 const TExons& Exons() const { return m_exons; } in Exons()
585 void TrimEdgesToFrameInOtherAlignGaps(const TExons& exons_with_gaps);
594 TExons m_exons;
595 TExons& MyExons() { return m_exons; } in MyExons()
646 …CAlignMap(const CGeneModel::TExons& exons, const vector<TSignedSeqRange>& transcript_exons, const …
647 …CAlignMap(const CGeneModel::TExons& exons, const TInDels& frameshifts, EStrand strand, TSignedSeqR…
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Daligncollapser.cpp153 const CGeneModel::TExons& e = align.Exons(); in CAlignCommon()
328 ITERATE(CGeneModel::TExons, i, align.Exons()) { in AlignmentIsSupportedBySR()
356 ITERATE(CGeneModel::TExons, e, align.Exons()) { in ClipNotSupportedFlanks()
592 ITERATE(CGeneModel::TExons, e, a.Exons()) { in RemoveNotSupportedIntronsFromTranscript()
673 CGeneModel::TExons exons = align.Exons(); in CleanSelfTranscript()
720 CGeneModel::TExons edited_exons; in CleanSelfTranscript()
1342 ITERATE(CGeneModel::TExons, e, align.Exons()) { in FilterAlignments()
1823 ITERATE(CGeneModel::TExons, i, align.Exons()) { in CheckAndInsert()
1875 bool operator() (const CGeneModel::TExons& a, const CGeneModel::TExons& b) const { in operator ()()
2042 CGeneModel::TExons exons = i->Exons(); in GetCollapsedAlgnments()
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H A Dgnomon_objmgr.cpp149 ITERATE(CSpliced_seg::TExons, e_it, sps.GetExons()) { in CAlignModel()
366 …for (CGeneModel::TExons::const_iterator piece_begin = Exons().begin(); piece_begin != Exons().end(… in CAlignModel()
375 CGeneModel::TExons::const_iterator piece_end; in CAlignModel()
379 CGeneModel::TExons::const_iterator piece_end_g = piece_end; in CAlignModel()
H A Dgnomon_model.cpp70 TExons::const_iterator e = Exons().begin(); in GetInDels()
186 NON_CONST_ITERATE(TExons, it, MyExons()) { in ReverseComplementModel()
260 NON_CONST_ITERATE(TExons, e, MyExons()) { in Remap()
665 TExons new_exons; in RemoveShortHolesAndRescore()
816 ITERATE(TExons, e, Exons()) in Clip()
846 for (TExons::iterator e = MyExons().begin(); e != MyExons().end();) { in Clip()
882 …for(CGeneModel::TExons::const_iterator e = Exons().begin(); e != Exons().end() && indl != m_fshift… in RemoveExtraFShifts()
1068 ITERATE(CGeneModel::TExons, k, Exons()) { in IsSubAlignOf()
1180 void CGeneModel::TrimEdgesToFrameInOtherAlignGaps(const TExons& exons_with_gaps) in TrimEdgesToFrameInOtherAlignGaps()
1235 TExons a = MyExons(); in Extend()
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H A Dchainer.cpp63 bool BelongToExon(const CGeneModel::TExons& exons, int pos) { in BEGIN_SCOPE()
64 ITERATE(CGeneModel::TExons, i, exons) { in BEGIN_SCOPE()
421 ITERATE(CGeneModel::TExons, ib, b.Exons()) { in LargeCdsOverlap()
422 ITERATE(CGeneModel::TExons, ia, a.Exons()) { in LargeCdsOverlap()
464 ITERATE(CGeneModel::TExons, e, front()->Exons()) { in IsAllowedAlternative()
469 ITERATE(CGeneModel::TExons, e, a.Exons()) { in IsAllowedAlternative()
2082 ITERATE(CGeneModel::TExons, ie, algn.Exons()) { in CalculateSpliceWeights()
4197 NON_CONST_ITERATE(TExons, e, MyExons()) { in CChain()
5446 ITERATE (CGeneModel::TExons, e, Exons()) { in ClipLowCoverageUTR()
6064 ITERATE(CGeneModel::TExons, e, a.Exons()) in s_ExonLen()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/
H A Dscore_lookup.cpp358 CSpliced_seg::TExons::const_reverse_iterator it = in Get()
360 CSpliced_seg::TExons::const_reverse_iterator prev = in Get()
362 CSpliced_seg::TExons::const_reverse_iterator end = in Get()
379 CSpliced_seg::TExons::const_iterator it = in Get()
381 CSpliced_seg::TExons::const_iterator prev = in Get()
383 CSpliced_seg::TExons::const_iterator end = in Get()
702 ITERATE (CSpliced_seg::TExons, exon_it, seg.GetExons()) { in Get()
1598 const CSpliced_seg::TExons &exons = in Get()
H A Dscore_builder.cpp378 ITERATE (CSpliced_seg::TExons, it, in GetBlastScoreSpliced()
837 NON_CONST_ITERATE(CSpliced_seg::TExons, exon_iter, in s_CleanSeqAlign()
H A Dalign_compare.cpp208 ITERATE (CSpliced_seg::TExons, it, align.GetSegs().GetSpliced().GetExons()) in s_GetAlignmentMismatches()
299 ITERATE (CSpliced_seg::TExons, it, in s_GetAlignmentSpans_Exon()
336 ITERATE (CSpliced_seg::TExons, it, in s_GetAlignmentSpans_Intron()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/prosplign/
H A DInfo.cpp669 …CAliChunk(TSeqPos ali_pos, TSeqPos nuc_pos, TSeqPos prot_pos, CSpliced_seg::TExons::iterator exon_… in CAliChunk()
702 CSpliced_seg::TExons::iterator m_exon_iter;
724 NON_CONST_ITERATE (CSpliced_seg::TExons, e_it, sps.SetExons()) { in ExtractChunks()
855 void DropExon(CSpliced_seg::TExons& exons, CSpliced_seg::TExons::iterator& exon_iter) in DropExon()
888 void SplitExon(CSpliced_seg::TExons& exons, TAliChunkIterator chunk_iter, bool genomic_plus) in SplitExon()
1025 CSpliced_seg::TExons::iterator prev_exon_iter = sps.SetExons().end(); in RefineAlignment()
1056 ITERATE (CSpliced_seg::TExons, e_it, sps.GetExons()) { in RefineAlignment()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/
H A Dscore_builder_base.cpp369 ITERATE (CSpliced_seg::TExons, iter, in s_GetCountIdentityMismatch()
1024 typedef TSpliced::TExons TExons; in AddSplignScores() typedef
1025 const TExons & exons (spliced.GetExons()); in AddSplignScores()
1042 ITERATE(TExons, ii2, exons) { in AddSplignScores()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/alnmgr/
H A Dscore_builder_base.cpp369 ITERATE (CSpliced_seg::TExons, iter, in s_GetCountIdentityMismatch()
1024 typedef TSpliced::TExons TExons; in AddSplignScores() typedef
1025 const TExons & exons (spliced.GetExons()); in AddSplignScores()
1042 ITERATE(TExons, ii2, exons) { in AddSplignScores()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/magicblast/
H A Dmagicblast_util.cpp825 s_GetSpliceSiteOrientation(const CSpliced_seg::TExons::const_iterator& exon, in s_GetSpliceSiteOrientation()
826 const CSpliced_seg::TExons::const_iterator& next_exon) in s_GetSpliceSiteOrientation()
1187 ITERATE (CSpliced_seg::TExons, exon, spliced.GetExons()) { in PrintSAM()
1246 CSpliced_seg::TExons::const_iterator next_exon(exon); in PrintSAM()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/splign/unit_test/
H A Dunit_test_splign.cpp122 … NON_CONST_ITERATE(CSpliced_seg::TExons, exot, (*sait)->SetSegs().SetSpliced().SetExons()) { in s_RoundScores()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/split/
H A Did_range.cpp308 ITERATE ( CSpliced_seg::TExons, it, spliced.GetExons() ) { in Add()

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