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CChainer Class Reference

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#include <algo/gnomon/chainer.hpp>

+ Inheritance diagram for CChainer:
+ Collaboration diagram for CChainer:

Classes

class  CChainerImpl
 

Public Member Functions

 CChainer ()
 
 ~CChainer ()
 
void SetIntersectLimit (int value)
 
void SetTrim (int trim)
 
void SetMinPolyA (int minpolya)
 
SMinScorSetMinScor ()
 
void SetMinInframeFrac (double mininframefrac)
 
map< string, pair< bool, bool > > & SetProtComplet ()
 
map< string, TSignedSeqRange > & SetMrnaCDS ()
 
void SetGenomicRange (const TAlignModelList &alignments)
 
void SetNumbering (int idnext, int idinc)
 
void SetOnlyBestFs (bool onlybestfs)
 
TransformFunctionTrimAlignment ()
 
TransformFunctionDoNotBelieveShortPolyATail ()
 
PredicateOverlapsSameAccessionAlignment (TAlignModelList &alignments)
 
PredicateConnectsParalogs (TAlignModelList &alignments)
 
TransformFunctionProjectCDS (objects::CScope &scope)
 
TransformFunctionDoNotBelieveFrameShiftsWithoutCdsEvidence ()
 
void SetConfirmedStartStopForProteinAlignments (TAlignModelList &alignments)
 
void DropAlignmentInfo (TAlignModelList &alignments, TGeneModelList &models)
 
void FilterOutChimeras (TGeneModelList &clust)
 
void ScoreCDSes_FilterOutPoorAlignments (TGeneModelList &clust)
 
void FindSelenoproteinsClipProteinsToStartStop (TGeneModelList &clust)
 
void CutParts (TGeneModelList &models)
 
TGeneModelList MakeChains (TGeneModelList &models)
 
- Public Member Functions inherited from CGnomonAnnotator_Base
 CGnomonAnnotator_Base ()
 
virtual ~CGnomonAnnotator_Base ()
 
void SetHMMParameters (CHMMParameters *params)
 
void EnableSeqMasking ()
 
void SetGenomic (const CResidueVec &seq)
 
void SetGenomic (const CSeq_id &seqid, objects::CScope &scope, const string &mask_annots=kEmptyStr, const TGeneModelList *models=0)
 
void SetGenomic (const CSeq_id &seqid, objects::CScope &scope, const SCorrectionData &correction_data, TSignedSeqRange range=TSignedSeqRange::GetWhole(), const string &mask_annots=kEmptyStr)
 
void SetPCSF (const CPhyloCSFData *pcsf_datap)
 
CGnomonEngineGetGnomon ()
 
void MapAlignmentsToEditedContig (TAlignModelList &alignments) const
 
void MapModelsToEditedContig (TGeneModelList &models) const
 
void MapModelsToOrigContig (TGeneModelList &models) const
 

Private Member Functions

 CChainer (const CChainer &value)
 
CChaineroperator= (const CChainer &value)
 

Private Attributes

unique_ptr< CChainerImplm_data
 

Friends

class CChainerArgUtil
 

Additional Inherited Members

- Public Types inherited from CGnomonAnnotator_Base
typedef map< int, TInDels::const_iterator > TGgapInfo
 
typedef map< int, intTIntMap
 
- Protected Member Functions inherited from CGnomonAnnotator_Base
CAlignModel MapOneModelToEditedContig (const CGeneModel &align) const
 
CGeneModel MapOneModelToOrigContig (const CGeneModel &srcmodel) const
 
- Protected Attributes inherited from CGnomonAnnotator_Base
bool m_masking
 
CRef< CHMMParametersm_hmm_params
 
unique_ptr< CGnomonEnginem_gnomon
 
CAlignMap m_edited_contig_map
 
TInDels m_editing_indels
 
TInDels m_reversed_corrections
 
TIntMap m_confirmed_bases_len
 
TIntMap m_confirmed_bases_orig_len
 
map< int, char > m_replacements
 
map< int, char > m_replaced_bases
 
TGgapInfo m_inserted_seqs
 
TIntMap m_notbridgeable_gaps_len
 
TSignedSeqRange m_limits
 
string m_contig_acc
 
unique_ptr< SPhyloCSFSlicem_pcsf_slice
 
const CPhyloCSFDatam_pcsf_data = nullptr
 
double m_pcsf_factor = 0.
 

Detailed Description

Definition at line 160 of file chainer.hpp.

Constructor & Destructor Documentation

◆ CChainer() [1/2]

CChainer::CChainer ( )

◆ ~CChainer()

CChainer::~CChainer ( )

Definition at line 206 of file chainer.cpp.

◆ CChainer() [2/2]

CChainer::CChainer ( const CChainer value)
private

Member Function Documentation

◆ ConnectsParalogs()

Predicate * CChainer::ConnectsParalogs ( TAlignModelList alignments)

Definition at line 6583 of file chainer.cpp.

◆ CutParts()

void CChainer::CutParts ( TGeneModelList models)

Definition at line 2098 of file chainer.cpp.

References m_data.

Referenced by CChainer::CChainerImpl::CreateChainsForPartialProteins().

◆ DoNotBelieveFrameShiftsWithoutCdsEvidence()

TransformFunction * CChainer::DoNotBelieveFrameShiftsWithoutCdsEvidence ( )

Definition at line 7269 of file chainer.cpp.

◆ DoNotBelieveShortPolyATail()

TransformFunction * CChainer::DoNotBelieveShortPolyATail ( )

Definition at line 7203 of file chainer.cpp.

References m_data.

◆ DropAlignmentInfo()

void CChainer::DropAlignmentInfo ( TAlignModelList alignments,
TGeneModelList models 
)

◆ FilterOutChimeras()

void CChainer::FilterOutChimeras ( TGeneModelList clust)

Definition at line 6388 of file chainer.cpp.

References m_data.

◆ FindSelenoproteinsClipProteinsToStartStop()

void CChainer::FindSelenoproteinsClipProteinsToStartStop ( TGeneModelList clust)

◆ MakeChains()

TGeneModelList CChainer::MakeChains ( TGeneModelList models)

Definition at line 215 of file chainer.cpp.

References m_data.

◆ operator=()

CChainer& CChainer::operator= ( const CChainer value)
private

◆ OverlapsSameAccessionAlignment()

Predicate * CChainer::OverlapsSameAccessionAlignment ( TAlignModelList alignments)

Definition at line 6529 of file chainer.cpp.

◆ ProjectCDS()

TransformFunction * CChainer::ProjectCDS ( objects::CScope &  scope)

Definition at line 7254 of file chainer.cpp.

References m_data, CGnomonAnnotator_Base::m_gnomon, and NULL.

◆ ScoreCDSes_FilterOutPoorAlignments()

void CChainer::ScoreCDSes_FilterOutPoorAlignments ( TGeneModelList clust)

◆ SetConfirmedStartStopForProteinAlignments()

void CChainer::SetConfirmedStartStopForProteinAlignments ( TAlignModelList alignments)

Definition at line 7287 of file chainer.cpp.

References m_data.

◆ SetGenomicRange()

void CChainer::SetGenomicRange ( const TAlignModelList alignments)

Definition at line 7215 of file chainer.cpp.

References m_data.

◆ SetIntersectLimit()

void CChainer::SetIntersectLimit ( int  value)

Definition at line 7565 of file chainer.cpp.

References m_data, and rapidjson::value.

Referenced by CChainerArgUtil::ArgsToChainer().

◆ SetMinInframeFrac()

void CChainer::SetMinInframeFrac ( double  mininframefrac)

Definition at line 7582 of file chainer.cpp.

References m_data.

Referenced by CChainerArgUtil::ArgsToChainer().

◆ SetMinPolyA()

void CChainer::SetMinPolyA ( int  minpolya)

Definition at line 7574 of file chainer.cpp.

References m_data.

Referenced by CChainerArgUtil::ArgsToChainer().

◆ SetMinScor()

SMinScor & CChainer::SetMinScor ( )

Definition at line 7578 of file chainer.cpp.

References m_data.

Referenced by CChainerArgUtil::ArgsToChainer().

◆ SetMrnaCDS()

map< string, TSignedSeqRange > & CChainer::SetMrnaCDS ( )

Definition at line 7590 of file chainer.cpp.

References m_data.

Referenced by CChainerArgUtil::ArgsToChainer().

◆ SetNumbering()

void CChainer::SetNumbering ( int  idnext,
int  idinc 
)

Definition at line 7209 of file chainer.cpp.

References m_data.

◆ SetOnlyBestFs()

void CChainer::SetOnlyBestFs ( bool  onlybestfs)

◆ SetProtComplet()

map< string, pair< bool, bool > > & CChainer::SetProtComplet ( )

Definition at line 7586 of file chainer.cpp.

References m_data.

Referenced by CChainerArgUtil::ArgsToChainer().

◆ SetTrim()

void CChainer::SetTrim ( int  trim)

Definition at line 7569 of file chainer.cpp.

References m_data.

Referenced by CChainerArgUtil::ArgsToChainer().

◆ TrimAlignment()

TransformFunction * CChainer::TrimAlignment ( )

Definition at line 7184 of file chainer.cpp.

References m_data.

Friends And Related Function Documentation

◆ CChainerArgUtil

friend class CChainerArgUtil
friend

Definition at line 198 of file chainer.hpp.

Member Data Documentation

◆ m_data

unique_ptr<CChainerImpl> CChainer::m_data
private

The documentation for this class was generated from the following files:
Modified on Tue Apr 23 07:40:26 2024 by modify_doxy.py rev. 669887