/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
H A D | score.cpp | 66 if(strand == ePlus) { in isReadingFrameLeftEnd() 75 if(strand == ePlus) { in isReadingFrameRightEnd() 102 … if(strand == ePlus) return (m_dscr[ePlus][i-1] != BadScore()) && (m_ascr[ePlus][j] != BadScore()); in isConsensusIntron() 368 m_seq[ePlus][i] = l; in Init() 633 int otherstrand = (strand == ePlus) ? eMinus : ePlus; in Init() 742 if(strand == ePlus) in Init() 790 if(strand == ePlus) in Init() 1003 if(strand == ePlus) in Init() 1119 if(strand == ePlus) { in Init() 1160 if(strand == ePlus) in Init() [all …]
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H A D | parse.cpp | 342 m_igplus.reserve(m_seqscr.StartNumber(ePlus)+1); in CParse() 345 m_leplus.reserve(m_seqscr.StopNumber(ePlus)+1); in CParse() 346 m_seplus.reserve(m_seqscr.StopNumber(ePlus)+2); in CParse() 370 m_seplus.push_back(CSingleExon(ePlus,0,m_seqscr,exon_params)); in CParse() 376 if(m_seqscr.AcceptorScore(i,ePlus) != BadScore()) in CParse() 387 if(m_seqscr.DonorScore(i,ePlus) != BadScore()) in CParse() 389 s_MakeStep(m_seqscr, exon_params, ePlus,i,m_inplus,m_ieplus); in CParse() 390 s_MakeStep(m_seqscr, exon_params, ePlus,i,m_igplus,m_feplus); in CParse() 398 if(m_seqscr.StartScore(i,ePlus) != BadScore()) in CParse() 413 if(m_seqscr.StopScore(i,ePlus) != BadScore()) in CParse() [all …]
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H A D | gnomon_objmgr.cpp | 211 fill_src.m_strand = ePlus; in CAlignModel() 251 if (Strand() == ePlus) in CAlignModel() 258 if (Strand()==ePlus) in CAlignModel() 274 if(Strand() == ePlus) { in CAlignModel() 287 if(Strand() == ePlus) in CAlignModel() 301 EStrand orientation = (is_product_reversed == minusstrand) ? ePlus : eMinus; in CAlignModel() 311 if (Strand() == ePlus) { in CAlignModel() 610 if (strand == ePlus) { in GetAnnot() 627 (strand == ePlus ? eNa_strand_plus : eNa_strand_minus), id)); in GetAnnot() 641 (strand == ePlus ? eNa_strand_plus : eNa_strand_minus), id)); in GetAnnot() [all …]
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H A D | gnomon_seq.cpp | 53 Convert(src,dst[ePlus]); in Convert() 54 ReverseComplement(dst[ePlus],dst[eMinus]); in Convert() 110 if(strand == ePlus) in IsStartCodon() 125 if(strand == ePlus) { in IsStopCodon() 525 …TSignedSeqPos estart = (m_orientation == ePlus) ? transcript_exons.front().GetFrom() : transcript_… in CAlignMap() 552 if(m_orientation == ePlus) { in CAlignMap() 626 …int l = (m_orientation == ePlus) ? m_edited_ranges.front().GetFrom() : CAlignMap::TargetLen()-m_ed… in EditedSequence() 767 if((m_orientation == ePlus && tp%3 == 0) || (m_orientation == eMinus && tp%3 == 2)) { in ShrinkToRealPoints() 795 if((m_orientation == ePlus && tp%3 == 2) || (m_orientation == eMinus && tp%3==0)) { in ShrinkToRealPoints() 817 if(m_orientation == ePlus) in FShiftedMove() [all …]
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H A D | aligncollapser.cpp | 75 if(a.Strand() == ePlus) in GetAlignment() 83 if(a.Strand() == ePlus) { in GetAlignment() 94 if(a.Strand() == ePlus) in GetAlignment() 147 } else if(align.Strand() == ePlus){ in CAlignCommon() 157 if(align.Strand() == ePlus) in CAlignCommon() 339 SIntron intron_notoriented_nosig(a, b, ePlus, false, ""); in isGoodIntron() 2149 left_src.m_strand = ePlus; in FillGapsInAlignmentAndAddToGenomicGaps() 2156 right_src.m_strand = ePlus; in FillGapsInAlignmentAndAddToGenomicGaps() 2195 src.m_strand = ePlus; in FillGapsInAlignmentAndAddToGenomicGaps() 2310 if(a.Strand() == ePlus) { in AddAlignment() [all …]
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H A D | chainer.cpp | 4123 if(algn.Strand() == ePlus) { in GoodCDNAScore() 4715 if(Strand() == ePlus) { in RestoreReasonableConfirmedStart() 4800 if(Strand() == ePlus) in RestoreReasonableConfirmedStart() 5119 if(Strand() == ePlus) in ValidPolyA() 5131 if(Strand() == ePlus) { in ValidPolyA() 5543 if(Strand() == ePlus) in ClipLowCoverageUTR() 5693 if(Strand() == ePlus) in CalculateDropLimits() 5707 if(Strand() == ePlus) in CalculateDropLimits() 5728 if(Strand() == ePlus) in CalculateDropLimits() 5742 if(Strand() == ePlus) in CalculateDropLimits() [all …]
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H A D | gnomon_model.cpp | 102 if(Orientation() == ePlus) in TranscriptExon() 109 if(Orientation() == ePlus) in TranscriptExon() 121 if(Orientation() == ePlus) { in TranscriptLimits() 164 if (Strand() == ePlus) { in isNMD() 184 SetStrand(Strand() == ePlus ? eMinus : ePlus); in ReverseComplementModel() 1328 if (Strand()==ePlus) in RealCdsLimits() 2038 if(a.Strand() == ePlus) in printGFF3() 2120 if(a.Strand() == ePlus) { in printGFF3() 2183 if (a.Strand()==ePlus) in printGFF3() 2263 a.SetStrand(ePlus); in readGFF3() [all …]
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H A D | asn1.cpp | 357 ENa_strand strand = model.Strand()==ePlus?eNa_strand_plus:eNa_strand_minus; in create_packed_int_seqloc() 711 se->SetGenomic_strand(e.m_source.m_strand==ePlus?eNa_strand_plus:eNa_strand_minus); in spliced_exon() 727 if (strand==ePlus) { in spliced_exon() 735 if (strand==ePlus) { in spliced_exon() 782 spliced_seg.SetGenomic_strand(model.Strand()==ePlus?eNa_strand_plus:eNa_strand_minus); in AlignModelToSeqalign() 892 if(model.Orientation() == ePlus) in AlignModelToSeqalign()
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H A D | gnomon_engine.cpp | 119 EResidue c = m_data->m_ds[ePlus][i]; in ResetRange()
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H A D | variations.cpp | 263 CGeneModel a(ePlus, 0, CGeneModel::eSR); in GetVariationAlignList() 282 CGeneModel a(ePlus, 0, CGeneModel::eSR); in GetVariationAlignList() 308 CGeneModel a(ePlus, 0, CGeneModel::eSR); in GetVariationAlignList()
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H A D | annot.cpp | 575 if(nested.back().Strand() == ePlus) in Predict() 663 FindPartials(models, aligns, ePlus); in Predict()
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H A D | hmm.hpp | 280 bool isPlus() const { return (m_strand == ePlus); } in isPlus()
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/dports/devel/csmith/csmith-2.3.0/src/ |
H A D | FunctionInvocationUnary.cpp | 133 case ePlus: in get_type() 185 case ePlus: out << "+"; break; in OutputStandardFuncName() 244 case ePlus: in Output() 282 case ePlus: in indented_output()
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H A D | FunctionInvocation.h | 62 ePlus, enumerator
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
H A D | gnomon_model.hpp | 65 enum EStrand { ePlus, eMinus}; enumerator 66 inline EStrand OtherStrand(EStrand s) { return (s == ePlus ? eMinus : ePlus); } in OtherStrand() 104 SSource() : m_strand(ePlus) {} in SSource() 396 CGeneModel(EStrand s = ePlus, Int8 id = 0, int type = 0) : in CGeneModel() 464 bool plusstrand = Strand() == ePlus; in Orientation() 465 return (notreversed == plusstrand) ? ePlus : eMinus; in Orientation() 503 bool LeftComplete() const { return Strand() == ePlus ? HasStart() : HasStop(); } in LeftComplete() 516 return (Strand() == ePlus ? OpenLeftEnd() : OpenRightEnd()); in Open5primeEnd() 626 CAlignMap(TSignedSeqPos orig_a, TSignedSeqPos orig_b) : m_orientation(ePlus) { in CAlignMap() 923 if(algn.Strand() == ePlus) in GetAlignParts() [all …]
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/dports/math/hs-Agda/Agda-2.6.2/src/full/Agda/Syntax/ |
H A D | IdiomBrackets.hs | 23 ePlus a b = App r (App r (Ident qPlus) (defaultNamedArg a)) (defaultNamedArg b) function 30 return $ foldr1 ePlus es'
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/dports/science/jdftx/jdftx-1.6.0/jdftx/electronic/ |
H A D | TetrahedralDOS.cpp | 461 auto eIterPlus = eIter; eIterPlus++; double ePlus = *eIterPlus; in mergeLsplines() local 462 startScale[e] = (ePlus-e) / (ePlus-eMinus); in mergeLsplines() 470 auto eIterPlus = eIter; eIterPlus++; double ePlus = *eIterPlus; in mergeLsplines() local 471 stopScale[e] = (e-eMinus) / (ePlus-eMinus); in mergeLsplines()
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/dports/science/clhep/2.4.1.0/CLHEP/Evaluator/src/ |
H A D | setSystemOfUnits.cc | 367 const double ePlus = e_SI * C; // positron charge in setSystemOfUnits() local 368 const double eV = ePlus * V; in setSystemOfUnits()
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/kqsh/ |
H A D | kqsh-open.c | 87 case ePlus: in kqsh_open_row()
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/interfaces/klib/ |
H A D | token.h | 112 ePlus, eMinus, eAssign, eFwdSlash, eBackSlash, ePipe, enumerator
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/interfaces/klib/ |
H A D | token.h | 112 ePlus, eMinus, eAssign, eFwdSlash, eBackSlash, ePipe, enumerator
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/dports/science/openbabel/openbabel-3.1.1/src/formats/libinchi/ |
H A D | ichirvr6.c | 1140 int aN, aC, i1, i2, ePlus; in FixRestoredStructureStereo() local 1171 if ( 0 > (ePlus = pVA[aN].nCPlusGroupEdge-1) || in FixRestoredStructureStereo() 1172 (pePlus = pBNS->edge + ePlus)->flow || /* must be (+) charged */ in FixRestoredStructureStereo()
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H A D | ichirvr2.c | 2722 int ret, ePlus, eMinus; in RearrangePlusMinusEdgesFlow() local 2732 ePlus = pVA[i].nCPlusGroupEdge - 1; in RearrangePlusMinusEdgesFlow() 2733 num_tot += (eMinus >= 0) + (ePlus >= 0); in RearrangePlusMinusEdgesFlow() 2734 if ( eMinus >= 0 && ePlus >= 0 ) { in RearrangePlusMinusEdgesFlow() 2735 pPlus = pBNS->edge + ePlus; in RearrangePlusMinusEdgesFlow() 2751 ePlus = pVA[i].nCPlusGroupEdge - 1; in RearrangePlusMinusEdgesFlow() 2752 num_tot += (eMinus >= 0) + (ePlus >= 0); in RearrangePlusMinusEdgesFlow() 2753 if ( eMinus >= 0 && ePlus >= 0 ) { in RearrangePlusMinusEdgesFlow() 2754 pPlus = pBNS->edge + ePlus; in RearrangePlusMinusEdgesFlow() 2782 if ( ePlus >= 0 ) { in RearrangePlusMinusEdgesFlow() [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/vdb/ |
H A D | schema-expr.c | 1353 case ePlus: in const_expr() 1575 case ePlus: in fact_value() 1602 case ePlus: in old_fact_value() 1948 case ePlus: in expression()
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/vdb/ |
H A D | schema-expr.c | 1353 case ePlus: in const_expr() 1575 case ePlus: in fact_value() 1602 case ePlus: in old_fact_value() 1948 case ePlus: in expression()
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