/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seqalign/ |
H A D | Spliced_seg.cpp | 119 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 D | Seq_align.cpp | 1512 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 D | Spliced_seg.cpp | 119 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 D | Seq_align.cpp | 1512 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 D | transform_align.cpp | 91 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() [all …]
|
H A D | feature_generator.hpp | 126 objects::CSpliced_seg::TExons::reverse_iterator& spl_exon_it, 132 objects::CSpliced_seg::TExons::iterator& spl_exon_it,
|
H A D | project_exons.cpp | 135 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 D | internal_stops.cpp | 310 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 D | seq_align_util.cpp | 173 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 D | seq_align_util.cpp | 173 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 D | unit_test_gene_model.cpp | 534 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() [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
H A D | gnomon_model.hpp | 405 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 D | aligncollapser.cpp | 153 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() [all …]
|
H A D | gnomon_objmgr.cpp | 149 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 D | gnomon_model.cpp | 70 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() [all …]
|
H A D | chainer.cpp | 63 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() [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/ |
H A D | score_lookup.cpp | 358 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 D | score_builder.cpp | 378 ITERATE (CSpliced_seg::TExons, it, in GetBlastScoreSpliced() 837 NON_CONST_ITERATE(CSpliced_seg::TExons, exon_iter, in s_CleanSeqAlign()
|
H A D | align_compare.cpp | 208 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 D | Info.cpp | 669 …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 D | score_builder_base.cpp | 369 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 D | score_builder_base.cpp | 369 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 D | magicblast_util.cpp | 825 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 D | unit_test_splign.cpp | 122 … 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 D | id_range.cpp | 308 ITERATE ( CSpliced_seg::TExons, it, spliced.GetExons() ) { in Add()
|