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bool BelongToExon (const CGeneModel::TExons &exons, int pos) static bool DescendingModelOrder (const CChain &a, const CChain &b) static bool DescendingModelOrderP (const TChainPtr &a, const TChainPtr &b) static bool DescendingModelOrderPConsistentCoverage (const TChainPtr &a, const TChainPtr &b) TIdLim AlignIdLimits (SChainMember *mp) template<class C > void uniq (C &container) TSignedSeqRange ExtendedMaxCdsLimits (const CGeneModel &a, const CCDSInfo &cds) bool MemberIsMarkedForDeletion (const SChainMember *mp) TInDels StrictlyContainedInDels (const TInDels &indels, const TSignedSeqRange &lim) bool MemberIsCoding (const SChainMember *mp) string GetLinkedIdsForMember (const SChainMember &mi) bool GoodSupportForIntrons (const CGeneModel &chain, const SMinScor &minscor, map< TSignedSeqRange, int > &mrna_count, map< TSignedSeqRange, int > &est_count, map< TSignedSeqRange, int > &rnaseq_count) void MarkUnwantedLowSupportIntrons (TContained &pointers, const SMinScor &minscor, map< TSignedSeqRange, int > &mrna_count, map< TSignedSeqRange, int > &est_count, map< TSignedSeqRange, int > &rnaseq_count) pair< string, int > GetAccVer (const CAlignModel &a, CScope &scope) static int s_ExonLen (const CGeneModel &a) string FindMultiplyIncluded (CAlignModel &algn, TAlignModelList &clust) double InframeFraction (const CGeneModel &a, TSignedSeqPos left, TSignedSeqPos right) bool LeftAndLongFirst (const CGeneModel &a, const CGeneModel &b) bool OverlappingIndel (int pos, const CInDelInfo &indl) TInDels CombineCorrectionsAndIndels (const TSignedSeqRange exona, int extra_left, int extra_right, const TSignedSeqRange exonb, const TInDels &editing_indels_frombtoa, const TInDels &exona_indels) int EffectiveExonLength (const CModelExon &e, const CAlignMap &alignmap, bool snap_to_codons) ◆ BLOCK_OF_Ns ◆ COVERAGE_BUMP ◆ COVERAGE_DROP ◆ MIN_PART ◆ MIN_UTR_EXON ◆ NON_CDNA_INTRON_PENALTY #define NON_CDNA_INTRON_PENALTY 20Definition at line 2697 of file chainer.cpp.
◆ PGAP_PENALTY ◆ PROT_CLIP ◆ PROT_CLIP_FRAC ◆ SCAN_WINDOW ◆ SMALL_GAP_UTR ◆ START_BONUS ◆ TChainList ◆ TChainPointerList ◆ TChainPtr ◆ TContained ◆ TIdLim ◆ TLinkers ◆ TMemberPtrSet ◆ TMemeberGeneVec ◆ TOrigAligns ◆ TRangePrecedeSet ◆ TUnmodAligns ◆ anonymous enum Enumerator eCDS eLeftUTR eRightUTRDefinition at line 245 of file chainer.cpp.
◆ AlignIdLimits() ◆ BelongToExon() ◆ CombineCorrectionsAndIndels()Definition at line 7994 of file chainer.cpp.
References _ASSERT, count, CInDelInfo::eDel, CInDelInfo::eGenomeNotCorrect, CInDelInfo::eIns, ERASE_ITERATE, CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CRange_Base::GetTo(), ip, len, max(), min(), OverlappingIndel(), and pb.
Referenced by CGnomonAnnotator_Base::MapOneModelToEditedContig(), and CGnomonAnnotator_Base::MapOneModelToOrigContig().
◆ DescendingModelOrder() ◆ DescendingModelOrderP() ◆ DescendingModelOrderPConsistentCoverage() ◆ EffectiveExonLength() ◆ ExtendedMaxCdsLimits() ◆ FindMultiplyIncluded()Definition at line 6879 of file chainer.cpp.
References CGeneModel::AlignLen(), CGeneModel::Continuous(), CGeneModel::eProt, CGeneModel::IdenticalAlign(), set< Key, Compare >::insert(), CGeneModel::isCompatible(), kEmptyStr, len, NON_CONST_ITERATE, CGeneModel::Strand(), CAlignModel::TargetAccession(), and CGeneModel::Type().
Referenced by ConnectsParalogs::align_predicate().
◆ GetAccVer()Definition at line 6600 of file chainer.cpp.
References a, CSeq_id_Handle::AsString(), eGetId_ForceAcc, CGeneModel::eProt, CTextseq_id_Base::GetAccession(), GetId(), CSeq_id_Handle::GetSeqId(), CSeq_id::GetTextseq_Id(), CTextseq_id_Base::GetVersion(), CTextseq_id_Base::IsSetAccession(), and CTextseq_id_Base::IsSetVersion().
Referenced by s_ByAccVerLen::operator()(), and OverlapsSameAccessionAlignment::OverlapsSameAccessionAlignment().
◆ GetLinkedIdsForMember() ◆ GoodSupportForIntrons() ◆ InframeFraction() ◆ LeftAndLongFirst() ◆ MarkUnwantedLowSupportIntrons() ◆ MemberIsCoding() ◆ MemberIsMarkedForDeletion() ◆ OverlappingIndel() ◆ s_ExonLen() ◆ StrictlyContainedInDels() ◆ uniq()template<class C >
void uniq ( C & container )Definition at line 1963 of file chainer.cpp.
References ct::sort().
Referenced by CChainer::CChainerImpl::AddIfCompatible(), CChainer::CChainerImpl::CDNACounts(), CChainer::CChainerImpl::ReplicatePStops(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::SortAndExtractUniq(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::SortAndUniq(), and CDiscrepancyVisitorImpl< _Name >::Summarize().
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