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NCBI C++ ToolKit: CAlignModel Class Reference
Search Toolkit Book for CAlignModel
#include <algo/gnomon/gnomon_model.hpp>
CAlignModel () CAlignModel (const objects::CSeq_align &seq_align) CAlignModel (const CGeneModel &g, const CAlignMap &a) virtual CAlignMap GetAlignMap () const void ResetAlignMap () virtual void Clip (TSignedSeqRange limits, EClipMode mode, bool ensure_cds_invariant=true) virtual void CutExons (TSignedSeqRange hole) string TargetAccession () const void SetTargetId (const objects::CSeq_id &id) CConstRef< objects::CSeq_id > GetTargetId () const int TargetLen () const int PolyALen () const CRef< objects::CSeq_align > MakeSeqAlign (const string &contig) const CGeneModel (EStrand s=ePlus, Int8 id=0, int type=0) virtual ~CGeneModel () void AddExon (TSignedSeqRange exon, const string &fs="", const string &ss="", double ident=0, const string &seq="", const CInDelInfo::SSource &src=CInDelInfo::SSource()) void AddHole () void AddGgapExon (double ident, const string &seq, const CInDelInfo::SSource &src, bool infront) void AddNormalExon (TSignedSeqRange exon, const string &fs, const string &ss, double ident, bool infront) const TExons & Exons () const TExons & Exons () void ClearExons () void SetSplices (int i, const string &f_sig, const string &s_sig) void ReverseComplementModel () void Remap (const CRangeMapper &mapper) void ExtendLeft (int amount) void ExtendRight (int amount) void Extend (const CGeneModel &a, bool ensure_cds_invariant=true) void RemoveShortHolesAndRescore (const CGnomonEngine &gnomon) TSignedSeqRange TranscriptExon (int i) const TSignedSeqRange Limits () const TSignedSeqRange TranscriptLimits () const int AlignLen () const void RecalculateLimits () TSignedSeqRange ReadingFrame () const TSignedSeqRange RealCdsLimits () const int RealCdsLen () const TSignedSeqRange MaxCdsLimits () const const CCDSInfo & GetCdsInfo () const void SetCdsInfo (const CCDSInfo &cds_info) void SetCdsInfo (const CGeneModel &a) void CombineCdsInfo (const CGeneModel &a, bool ensure_cds_invariant=true) void CombineCdsInfo (const CCDSInfo &cds_info, bool ensure_cds_invariant=true) bool IntersectingWith (const CGeneModel &a) const double Ident () const void SetIdent (double i) double Weight () const void SetWeight (double w) void SetStrand (EStrand s) EStrand Strand () const EStrand Orientation () const void SetType (int t) int Type () const Int8 GeneID () const void SetGeneID (Int8 id) int RankInGene () const void SetRankInGene (int rank) Int8 ID () const void SetID (Int8 id) const CSupportInfoSet & Support () const bool AddSupport (const CSupportInfo &support) void ReplaceSupport (const CSupportInfoSet &support_set) const string & ProteinHit () const string & ProteinHit () unsigned int & Status () const unsigned int & Status () const void ClearStatus () const string & GetComment () const void SetComment (const string &comment) void AddComment (const string &comment) bool operator< (const CGeneModel &a) const double Score () const bool Continuous () const bool HasStart () const bool HasStop () const bool LeftComplete () const bool RightComplete () const bool FullCds () const bool CompleteCds () const bool GoodEnoughToBeAnnotation () const bool Open5primeEnd () const bool OpenLeftEnd () const bool OpenRightEnd () const bool OpenCds () const bool PStop (bool includeall=true) const bool ConfirmedStart () const bool ConfirmedStop () const bool isNMD (int limit=50) const TInDels & FrameShifts () const TInDels & FrameShifts () const TInDels FrameShifts (TSignedSeqPos a, TSignedSeqPos b) const TInDels GetInDels (bool fs_only) const TInDels GetInDels (TSignedSeqPos a, TSignedSeqPos b, bool fs_only) const int FShiftedLen (TSignedSeqRange ab, bool withextras=true) const int FShiftedLen (TSignedSeqPos a, TSignedSeqPos b, bool withextras=true) const TSignedSeqPos FShiftedMove (TSignedSeqPos pos, int len) const string GetCdsDnaSequence (const CResidueVec &contig_sequence) const string GetProtein (const CResidueVec &contig_sequence) const string GetProtein (const CResidueVec &contig_sequence, const CGenetic_code *gencode) const int HasCompatibleOverlap (const CGeneModel &a, int min_overlap=2) const int isCompatible (const CGeneModel &a) const bool IsSubAlignOf (const CGeneModel &a) const int MutualExtension (const CGeneModel &a) const bool IdenticalAlign (const CGeneModel &a) const bool operator== (const CGeneModel &a) const const list< CRef< CSeq_id > > & TrustedmRNA () const void InsertTrustedmRNA (CRef< CSeq_id > g) void ClearTrustedmRNA () const list< CRef< CSeq_id > > & TrustedProt () const void InsertTrustedProt (CRef< CSeq_id > g) void ClearTrustedProt () void SetTrustedGroup (int tgr) int TrustedGroup () const void SetTrustedCds (const TSignedSeqRange &r) TSignedSeqRange TrustedCds () const const vector< CCDSInfo > * GetEdgeReadingFrames () const vector< CCDSInfo > * SetEdgeReadingFrames () enum EType {
eWall = 1 , eNested = 2 , eSR = 4 , eEST = 8 ,
emRNA = 16 , eProt = 32 , eNotForChaining = 64 , eChain = 128 ,
eGnomon = 256
} enum EStatus {
ecDNAIntrons = 1 , eReversed = 2 , eSkipped = 4 , eLeftTrimmed = 8 ,
eRightTrimmed = 16 , eFullSupCDS = 32 , ePseudo = 64 , ePolyA = 128 ,
eCap = 256 , eBestPlacement = 512 , eUnknownOrientation = 1024 , eConsistentCoverage = 2048 ,
eGapFiller = 4096 , eUnmodifiedAlign = 8192 , eChangedByFilter = 16384 , eTSA = 32768 ,
eLeftConfirmed = 65536 , eRightConfirmed = 131072 , eLeftFlexible = 262144 , eRightFlexible = 524288 ,
eExcludedReadthrough = 1048576
} enum EClipMode { eRemoveExons , eDontRemoveExons } enum EGeneModelCreateFlags {
fCreateGene = CFeatureGenerator::fCreateGene , fCreateMrna = CFeatureGenerator::fCreateMrna , fCreateCdregion = CFeatureGenerator::fCreateCdregion , fForceTranslateCds = CFeatureGenerator::fForceTranslateCds ,
fForceTranscribeMrna = CFeatureGenerator::fForceTranscribeMrna , fDefaults = fCreateGene | fCreateMrna | fCreateCdregion
} typedef vector< CModelExon > TExons typedef int TGeneModelCreateFlags static string TypeToString (int type) static void CreateGeneModelFromAlign (const objects::CSeq_align &align, objects::CScope &scope, objects::CSeq_annot &annot, objects::CBioseq_set &seqs, TGeneModelCreateFlags flags=fDefaults, TSeqPos allowed_unaligned=10) Create a gene model from an alignment this will optionally promote all features through the alignment. More...
static void CreateGeneModelsFromAligns (const list< CRef< objects::CSeq_align > > &aligns, objects::CScope &scope, objects::CSeq_annot &annot, objects::CBioseq_set &seqs, TGeneModelCreateFlags flags=fDefaults, TSeqPos allowed_unaligned=10) static void SetFeatureExceptions (objects::CSeq_feat &feat, objects::CScope &scope, const objects::CSeq_align *align=NULL) Correctly mark exceptions on a feature. More...
static void SetPartialFlags (objects::CScope &scope, CRef< objects::CSeq_feat > gene_feat, CRef< objects::CSeq_feat > mrna_feat, CRef< objects::CSeq_feat > cds_feat) static void RecomputePartialFlags (objects::CScope &scope, objects::CSeq_annot &annot) Int8 oid
Definition at line 746 of file gnomon_model.hpp.
◆ CAlignModel() [1/3] ◆ CAlignModel() [2/3] CAlignModel::CAlignModel ( const objects::CSeq_align & seq_align ) ◆ CAlignModel() [3/3]
Definition at line 196 of file gnomon_model.cpp.
References _ASSERT, a, CGeneModel::eReversed, CGeneModel::Exons(), CGeneModel::FrameShifts(), g(), COpenRange< Position >::GetLength(), CIdHandler::GnomonMRNA(), i, CGeneModel::ID(), int, ITERATE, SetTargetId(), CGeneModel::Status(), and CGeneModel::TranscriptExon().
◆ Clip() ◆ CutExons() ◆ GetAlignMap() virtual CAlignMap CAlignModel::GetAlignMap ( ) const inlinevirtual
Reimplemented from CGeneModel.
Definition at line 751 of file gnomon_model.hpp.
References m_alignmap.
Referenced by CAlignCollapser::ClipNotSupportedFlanks(), CAnnotationASN1::CImplementationData::create_internal_feature(), CAlignCollapser::FillGapsInAlignmentAndAddToGenomicGaps(), CAlignCollapser::FilterAlignments(), PolyALen(), CAlignCollapser::RemoveNotSupportedIntronsFromProt(), CAlignCollapser::RemoveNotSupportedIntronsFromTranscript(), RestoreModelAttributes(), RestoreModelReadingFrame(), CChain::SetConfirmedStartStopForCompleteProteins(), CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments(), CChainer::CChainerImpl::SetFlagsForChains(), SModelData::SModelData(), ProjectCDS::transform_align(), and TrimAlignment::transform_align().
◆ GetTargetId() CConstRef<objects::CSeq_id> CAlignModel::GetTargetId ( ) const inline
Definition at line 765 of file gnomon_model.hpp.
References m_target_id.
Referenced by CAlignCollapser::CleanSelfTranscript(), CChain::CollectTrustedmRNAsProts(), CAnnotationASN1::CImplementationData::create_internal_feature(), CAnnotationASN1::CImplementationData::create_ModelEvidence_user_object(), CAlignCollapser::FillGapsInAlignmentAndAddToGenomicGaps(), CAlignCollapser::FilterAlignments(), CAlignCollapser::RemoveNotSupportedIntronsFromTranscript(), TargetAccession(), MarkupCappedEst::transform_align(), MarkupTrustedGenes::transform_align(), and ProjectCDS::transform_align().
◆ MakeSeqAlign() CRef< objects::CSeq_align > CAlignModel::MakeSeqAlign ( const string & contig ) const ◆ PolyALen() int CAlignModel::PolyALen ( ) const ◆ RecalculateAlignMap() void CAlignModel::RecalculateAlignMap ( int left, int right ) private
Definition at line 230 of file gnomon_model.cpp.
References CAlignMap::eLeftEnd, ctll::empty(), COpenRange< Position >::Empty(), CAlignMap::eRightEnd, CAlignMap::eSinglePoint, CGeneModel::Exons(), CGeneModel::FrameShifts(), CModelExon::GetFrom(), CModelExon::GetTo(), int, l(), CModelExon::Limits(), m_alignmap, CAlignMap::MapRangeOrigToEdited(), CGeneModel::Orientation(), r(), CAlignMap::TargetLen(), and CGeneModel::TranscriptExon().
Referenced by Clip(), and CutExons().
◆ ResetAlignMap() void CAlignModel::ResetAlignMap ( ) ◆ SetTargetId() void CAlignModel::SetTargetId ( const objects::CSeq_id & id ) inline ◆ TargetAccession() string CAlignModel::TargetAccession ( ) const ◆ TargetLen() int CAlignModel::TargetLen ( ) const inline
Definition at line 766 of file gnomon_model.hpp.
References m_alignmap, and CAlignMap::TargetLen().
Referenced by AlignModelToSeqalign(), CAlignCollapser::CleanSelfTranscript(), CAlignCollapser::ClipNotSupportedFlanks(), CChain::CollectTrustedmRNAsProts(), CAlignCollapser::FillGapsInAlignmentAndAddToGenomicGaps(), CChainer::CChainerImpl::FilterOutChimeras(), PolyALen(), CChain::SetConfirmedStartStopForCompleteProteins(), CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments(), and CChain::SetOpenForPartialyAlignedProteins().
◆ m_alignmap ◆ m_target_id CConstRef<objects::CSeq_id> CAlignModel::m_target_id private
The documentation for this class was generated from the following files:
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