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CGnomonAnnotator_Base Class Reference

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#include <algo/gnomon/chainer.hpp>

+ Inheritance diagram for CGnomonAnnotator_Base:
+ Collaboration diagram for CGnomonAnnotator_Base:

Public Types

typedef map< int, TInDels::const_iterator > TGgapInfo
 
typedef map< int, intTIntMap
 

Public Member Functions

 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
 

Protected Member Functions

CAlignModel MapOneModelToEditedContig (const CGeneModel &align) const
 
CGeneModel MapOneModelToOrigContig (const CGeneModel &srcmodel) const
 

Protected Attributes

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 114 of file chainer.hpp.

Member Typedef Documentation

◆ TGgapInfo

typedef map<int,TInDels::const_iterator> CGnomonAnnotator_Base::TGgapInfo

Definition at line 131 of file chainer.hpp.

◆ TIntMap

Definition at line 132 of file chainer.hpp.

Constructor & Destructor Documentation

◆ CGnomonAnnotator_Base()

CGnomonAnnotator_Base::CGnomonAnnotator_Base ( )

Definition at line 192 of file chainer.cpp.

◆ ~CGnomonAnnotator_Base()

CGnomonAnnotator_Base::~CGnomonAnnotator_Base ( )
virtual

Definition at line 194 of file chainer.cpp.

Member Function Documentation

◆ EnableSeqMasking()

void CGnomonAnnotator_Base::EnableSeqMasking ( )

Definition at line 196 of file chainer.cpp.

References m_masking.

Referenced by CGnomonAnnotatorArgUtil::ReadArgs().

◆ GetGnomon()

CGnomonEngine & CGnomonAnnotator_Base::GetGnomon ( )

Definition at line 8518 of file chainer.cpp.

References m_gnomon.

◆ MapAlignmentsToEditedContig()

void CGnomonAnnotator_Base::MapAlignmentsToEditedContig ( TAlignModelList alignments) const

Definition at line 8213 of file chainer.cpp.

References a, ERASE_ITERATE, and MapOneModelToEditedContig().

◆ MapModelsToEditedContig()

void CGnomonAnnotator_Base::MapModelsToEditedContig ( TGeneModelList models) const

Definition at line 8226 of file chainer.cpp.

References _ASSERT, MapOneModelToEditedContig(), and NON_CONST_ITERATE.

◆ MapModelsToOrigContig()

void CGnomonAnnotator_Base::MapModelsToOrigContig ( TGeneModelList models) const

◆ MapOneModelToEditedContig()

CAlignModel CGnomonAnnotator_Base::MapOneModelToEditedContig ( const CGeneModel align) const
protected

Definition at line 7987 of file chainer.cpp.

References _ASSERT, CGeneModel::AddExon(), CGeneModel::AddHole(), CGeneModel::ClearExons(), CCDSInfo::Clip(), CombineCorrectionsAndIndels(), CInDelInfo::eGenomeNotCorrect, CAlignMap::eLeftEnd, eMinus, COpenRange< Position >::Empty(), ePlus, CGeneModel::eProt, CAlignMap::eRightEnd, CAlignMap::eSinglePoint, CGeneModel::Exons(), CGeneModel::FrameShifts(), CGeneModel::GetAlignMap(), CGeneModel::GetCdsInfo(), CGeneModel::GetEdgeReadingFrames(), CModelExon::GetFrom(), CRange_Base::GetFrom(), CGeneModel::GetInDels(), COpenRange< Position >::GetLength(), CModelExon::GetTo(), CRange_Base::GetTo(), i, int, CCDSInfo::IsMappedToGenome(), ITERATE, Len, CModelExon::Limits(), m_edited_contig_map, m_editing_indels, CModelExon::m_fsplice, CModelExon::m_fsplice_sig, CModelExon::m_ident, m_limits, m_reversed_corrections, CModelExon::m_seq, CModelExon::m_ssplice, CModelExon::m_ssplice_sig, CCDSInfo::MapFromEditedToOrig(), CCDSInfo::MapFromOrigToEdited(), CAlignMap::MapOrigToEdited(), CAlignMap::MapRangeEditedToOrig(), CAlignMap::MapRangeOrigToEdited(), min(), CAlignMap::MoveOrigin(), COpenRange< Position >::NotEmpty(), CCDSInfo::OpenCds(), CGeneModel::Orientation(), OverlappingIndel(), CGeneModel::ReadingFrame(), ReverseComplement(), CCDSInfo::Score(), CGeneModel::SetCdsInfo(), CRange_Base::SetFrom(), CCDSInfo::SetScore(), CRange_Base::SetTo(), CAlignMap::ShrinkToRealPoints(), CCDSInfo::Start(), CCDSInfo::Stop(), CGeneModel::Strand(), CAlignMap::TargetLen(), CGeneModel::TranscriptExon(), CGeneModel::TranscriptLimits(), and CGeneModel::Type().

Referenced by MapAlignmentsToEditedContig(), and MapModelsToEditedContig().

◆ MapOneModelToOrigContig()

CGeneModel CGnomonAnnotator_Base::MapOneModelToOrigContig ( const CGeneModel srcmodel) const
protected

◆ SetGenomic() [1/3]

void CGnomonAnnotator_Base::SetGenomic ( const CResidueVec seq)

◆ SetGenomic() [2/3]

void CGnomonAnnotator_Base::SetGenomic ( const CSeq_id seqid,
objects::CScope &  scope,
const SCorrectionData correction_data,
TSignedSeqRange  range = TSignedSeqRange::GetWhole(),
const string mask_annots = kEmptyStr 
)

◆ SetGenomic() [3/3]

void CGnomonAnnotator_Base::SetGenomic ( const CSeq_id seqid,
objects::CScope &  scope,
const string mask_annots = kEmptyStr,
const TGeneModelList models = 0 
)

◆ SetHMMParameters()

void CGnomonAnnotator_Base::SetHMMParameters ( CHMMParameters params)

Definition at line 7560 of file chainer.cpp.

References m_hmm_params.

Referenced by CChainerArgUtil::ArgsToChainer(), and CGnomonAnnotatorArgUtil::ReadArgs().

◆ SetPCSF()

void CGnomonAnnotator_Base::SetPCSF ( const CPhyloCSFData pcsf_datap)
inline

Definition at line 124 of file chainer.hpp.

References m_pcsf_data.

Member Data Documentation

◆ m_confirmed_bases_len

TIntMap CGnomonAnnotator_Base::m_confirmed_bases_len
protected

◆ m_confirmed_bases_orig_len

TIntMap CGnomonAnnotator_Base::m_confirmed_bases_orig_len
protected

Definition at line 145 of file chainer.hpp.

Referenced by MapModelsToOrigContig(), and SetGenomic().

◆ m_contig_acc

string CGnomonAnnotator_Base::m_contig_acc
protected

Definition at line 151 of file chainer.hpp.

Referenced by CChainer::CChainer(), and SetGenomic().

◆ m_edited_contig_map

CAlignMap CGnomonAnnotator_Base::m_edited_contig_map
protected

◆ m_editing_indels

TInDels CGnomonAnnotator_Base::m_editing_indels
protected

◆ m_gnomon

unique_ptr<CGnomonEngine> CGnomonAnnotator_Base::m_gnomon
protected

◆ m_hmm_params

CRef<CHMMParameters> CGnomonAnnotator_Base::m_hmm_params
protected

Definition at line 139 of file chainer.hpp.

Referenced by CChainer::CChainer(), SetGenomic(), and SetHMMParameters().

◆ m_inserted_seqs

TGgapInfo CGnomonAnnotator_Base::m_inserted_seqs
protected

◆ m_limits

TSignedSeqRange CGnomonAnnotator_Base::m_limits
protected

◆ m_masking

bool CGnomonAnnotator_Base::m_masking
protected

Definition at line 138 of file chainer.hpp.

Referenced by EnableSeqMasking().

◆ m_notbridgeable_gaps_len

TIntMap CGnomonAnnotator_Base::m_notbridgeable_gaps_len
protected

◆ m_pcsf_data

const CPhyloCSFData* CGnomonAnnotator_Base::m_pcsf_data = nullptr
protected

Definition at line 153 of file chainer.hpp.

Referenced by SetPCSF().

◆ m_pcsf_factor

double CGnomonAnnotator_Base::m_pcsf_factor = 0.
protected

◆ m_pcsf_slice

unique_ptr<SPhyloCSFSlice> CGnomonAnnotator_Base::m_pcsf_slice
protected

◆ m_replaced_bases

map<int,char> CGnomonAnnotator_Base::m_replaced_bases
protected

Definition at line 147 of file chainer.hpp.

◆ m_replacements

map<int,char> CGnomonAnnotator_Base::m_replacements
protected

Definition at line 146 of file chainer.hpp.

Referenced by MapOneModelToOrigContig(), and SetGenomic().

◆ m_reversed_corrections

TInDels CGnomonAnnotator_Base::m_reversed_corrections
protected

Definition at line 143 of file chainer.hpp.

Referenced by MapOneModelToEditedContig(), and SetGenomic().


The documentation for this class was generated from the following files:
Modified on Wed Jun 12 11:17:40 2024 by modify_doxy.py rev. 669887