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CAlignModel Class Reference

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#include <algo/gnomon/gnomon_model.hpp>

+ Inheritance diagram for CAlignModel:
+ Collaboration diagram for CAlignModel:

Public Member Functions

 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
 
- Public Member Functions inherited from CGeneModel
 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 TExonsExons () const
 
TExonsExons ()
 
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 CCDSInfoGetCdsInfo () 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 CSupportInfoSetSupport () const
 
bool AddSupport (const CSupportInfo &support)
 
void ReplaceSupport (const CSupportInfoSet &support_set)
 
const stringProteinHit () const
 
stringProteinHit ()
 
unsigned intStatus ()
 
const unsigned intStatus () const
 
void ClearStatus ()
 
const stringGetComment () 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
 
TInDelsFrameShifts ()
 
const TInDelsFrameShifts () 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 ()
 
const vector< CCDSInfo > * GetEdgeReadingFrames () const
 
vector< CCDSInfo > * SetEdgeReadingFrames ()
 

Private Member Functions

void RecalculateAlignMap (int left, int right)
 

Private Attributes

CAlignMap m_alignmap
 
CConstRef< objects::CSeq_id > m_target_id
 

Additional Inherited Members

- Public Types inherited from CGeneModel
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
}
 
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< CModelExonTExons
 
typedef int TGeneModelCreateFlags
 
- Static Public Member Functions inherited from CGeneModel
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)
 
- Public Attributes inherited from CGeneModel
Int8 oid
 

Detailed Description

Definition at line 738 of file gnomon_model.hpp.

Constructor & Destructor Documentation

◆ CAlignModel() [1/3]

CAlignModel::CAlignModel ( )
inline

Definition at line 740 of file gnomon_model.hpp.

◆ CAlignModel() [2/3]

CAlignModel::CAlignModel ( const objects::CSeq_align &  seq_align)

◆ CAlignModel() [3/3]

CAlignModel::CAlignModel ( const CGeneModel g,
const CAlignMap a 
)

Member Function Documentation

◆ Clip()

virtual void CAlignModel::Clip ( TSignedSeqRange  limits,
EClipMode  mode,
bool  ensure_cds_invariant = true 
)
inlinevirtual

◆ CutExons()

virtual void CAlignModel::CutExons ( TSignedSeqRange  hole)
inlinevirtual

◆ GetAlignMap()

virtual CAlignMap CAlignModel::GetAlignMap ( ) const
inlinevirtual

◆ GetTargetId()

CConstRef<objects::CSeq_id> CAlignModel::GetTargetId ( ) const
inline

◆ 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

◆ 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

Member Data Documentation

◆ m_alignmap

CAlignMap CAlignModel::m_alignmap
private

Definition at line 764 of file gnomon_model.hpp.

Referenced by GetAlignMap(), RecalculateAlignMap(), ResetAlignMap(), and TargetLen().

◆ m_target_id

CConstRef<objects::CSeq_id> CAlignModel::m_target_id
private

Definition at line 765 of file gnomon_model.hpp.

Referenced by GetTargetId(), and SetTargetId().


The documentation for this class was generated from the following files:
Modified on Mon May 27 04:34:48 2024 by modify_doxy.py rev. 669887