NCBI C++ ToolKit
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CGffBaseColumns Class Reference

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#include <objtools/readers/gff_base_columns.hpp>

+ Inheritance diagram for CGffBaseColumns:

Public Types

using TFrame = CCdregion::EFrame
 
using TReaderFlags = long
 
using SeqIdResolver = CRef< CSeq_id >(*)(const string &, TReaderFlags, bool)
 

Public Member Functions

 CGffBaseColumns ()
 
 CGffBaseColumns (const CGffBaseColumns &rhs)
 
virtual ~CGffBaseColumns ()
 
const stringId () const
 
TSeqPos SeqStart () const
 
TSeqPos SeqStop () const
 
const stringSource () const
 
const stringType () const
 
const stringNormalizedType () const
 
double Score () const
 
ENa_strand Strand () const
 
TFrame Phase () const
 
bool IsSetScore () const
 
bool IsSetStrand () const
 
bool IsSetPhase () const
 
CRef< CSeq_idGetSeqId (TReaderFlags, SeqIdResolver=nullptr) const
 
CRef< CSeq_locGetSeqLoc (TReaderFlags, SeqIdResolver seqidresolve=nullptr) const
 
virtual bool InitializeFeature (TReaderFlags, CRef< CSeq_feat >, SeqIdResolver=nullptr) const
 
virtual void SetExtent (TSeqPos seqStart, TSeqPos seqStop)
 
virtual void SetType (const string &recType)
 
virtual bool xInitFeatureId (TReaderFlags, CRef< CSeq_feat >) const
 
virtual bool xInitFeatureLocation (TReaderFlags, CRef< CSeq_feat >, SeqIdResolver=nullptr) const
 
virtual bool xInitFeatureData (TReaderFlags, CRef< CSeq_feat >) const
 

Static Public Member Functions

static unsigned int NextId ()
 
static void ResetId ()
 

Protected Attributes

string mSeqId
 
TSeqPos m_uSeqStart
 
TSeqPos m_uSeqStop
 
string m_strSource
 
string m_strType
 
string m_strNormalizedType
 
double * m_pdScore
 
ENa_strandm_peStrand
 
TFramem_pePhase
 

Static Protected Attributes

static unsigned int msNextId = 0
 

Detailed Description

Definition at line 42 of file gff_base_columns.hpp.

Member Typedef Documentation

◆ SeqIdResolver

Definition at line 48 of file gff_base_columns.hpp.

◆ TFrame

Definition at line 46 of file gff_base_columns.hpp.

◆ TReaderFlags

Definition at line 47 of file gff_base_columns.hpp.

Constructor & Destructor Documentation

◆ CGffBaseColumns() [1/2]

CGffBaseColumns::CGffBaseColumns ( )

Definition at line 55 of file gff_base_columns.cpp.

◆ CGffBaseColumns() [2/2]

CGffBaseColumns::CGffBaseColumns ( const CGffBaseColumns rhs)

Definition at line 70 of file gff_base_columns.cpp.

References m_pdScore, m_pePhase, m_peStrand, Phase(), Score(), and Strand().

◆ ~CGffBaseColumns()

CGffBaseColumns::~CGffBaseColumns ( )
virtual

Definition at line 95 of file gff_base_columns.cpp.

References m_pdScore, m_pePhase, and m_peStrand.

Member Function Documentation

◆ GetSeqId()

CRef< CSeq_id > CGffBaseColumns::GetSeqId ( TReaderFlags  flags,
SeqIdResolver  seqidresolve = nullptr 
) const

◆ GetSeqLoc()

CRef< CSeq_loc > CGffBaseColumns::GetSeqLoc ( TReaderFlags  flags,
SeqIdResolver  seqidresolve = nullptr 
) const

Definition at line 116 of file gff_base_columns.cpp.

References flags, GetSeqId(), and CSeq_loc::SetInt().

Referenced by CGff3Reader::xVerifyExonLocation().

◆ Id()

const string& CGffBaseColumns::Id ( ) const
inline

◆ InitializeFeature()

bool CGffBaseColumns::InitializeFeature ( TReaderFlags  flags,
CRef< CSeq_feat pFeature,
SeqIdResolver  seqidresolve = nullptr 
) const
virtual

Reimplemented in CGff2Record.

Definition at line 132 of file gff_base_columns.cpp.

References flags.

Referenced by CGff2Record::InitializeFeature().

◆ IsSetPhase()

bool CGffBaseColumns::IsSetPhase ( void  ) const
inline

Definition at line 104 of file gff_base_columns.hpp.

References m_pePhase.

Referenced by Phase().

◆ IsSetScore()

bool CGffBaseColumns::IsSetScore ( void  ) const
inline

Definition at line 96 of file gff_base_columns.hpp.

References m_pdScore.

Referenced by Score(), CGff2Reader::xAlignmentSetScore(), and CGvfReader::xFeatureSetExt().

◆ IsSetStrand()

bool CGffBaseColumns::IsSetStrand ( void  ) const
inline

◆ NextId()

static unsigned int CGffBaseColumns::NextId ( void  )
inlinestatic

Definition at line 149 of file gff_base_columns.hpp.

References msNextId.

◆ NormalizedType()

const string& CGffBaseColumns::NormalizedType ( ) const
inline

◆ Phase()

TFrame CGffBaseColumns::Phase ( ) const
inline

◆ ResetId()

static void CGffBaseColumns::ResetId ( void  )
inlinestatic

Definition at line 153 of file gff_base_columns.hpp.

References msNextId.

Referenced by CGff3Reader::CGff3Reader().

◆ Score()

double CGffBaseColumns::Score ( ) const
inline

◆ SeqStart()

TSeqPos CGffBaseColumns::SeqStart ( ) const
inline

◆ SeqStop()

TSeqPos CGffBaseColumns::SeqStop ( ) const
inline

◆ SetExtent()

virtual void CGffBaseColumns::SetExtent ( TSeqPos  seqStart,
TSeqPos  seqStop 
)
inlinevirtual

Definition at line 122 of file gff_base_columns.hpp.

References m_uSeqStart, and m_uSeqStop.

◆ SetType()

virtual void CGffBaseColumns::SetType ( const string recType)
inlinevirtual

Definition at line 129 of file gff_base_columns.hpp.

References m_strNormalizedType, m_strType, and NStr::ToLower().

Referenced by CGff3ReadRecord::AssignFromGff().

◆ Source()

const string& CGffBaseColumns::Source ( ) const
inline

◆ Strand()

ENa_strand CGffBaseColumns::Strand ( ) const
inline

◆ Type()

const string& CGffBaseColumns::Type ( void  ) const
inline

◆ xInitFeatureData()

bool CGffBaseColumns::xInitFeatureData ( TReaderFlags  flags,
CRef< CSeq_feat pFeature 
) const
virtual

◆ xInitFeatureId()

bool CGffBaseColumns::xInitFeatureId ( TReaderFlags  ,
CRef< CSeq_feat pFeature 
) const
virtual

Definition at line 148 of file gff_base_columns.cpp.

References CObject_id_Base::SetId(), and CFeat_id_Base::SetLocal().

◆ xInitFeatureLocation()

bool CGffBaseColumns::xInitFeatureLocation ( TReaderFlags  flags,
CRef< CSeq_feat pFeature,
SeqIdResolver  seqidresolve = nullptr 
) const
virtual

Definition at line 161 of file gff_base_columns.cpp.

References flags.

Member Data Documentation

◆ m_pdScore

double* CGffBaseColumns::m_pdScore
protected

◆ m_pePhase

TFrame* CGffBaseColumns::m_pePhase
protected

◆ m_peStrand

ENa_strand* CGffBaseColumns::m_peStrand
protected

◆ m_strNormalizedType

string CGffBaseColumns::m_strNormalizedType
protected

Definition at line 164 of file gff_base_columns.hpp.

Referenced by CGff2Record::AssignFromGff(), NormalizedType(), and SetType().

◆ m_strSource

string CGffBaseColumns::m_strSource
protected

Definition at line 162 of file gff_base_columns.hpp.

Referenced by CGff2Record::AssignFromGff(), and Source().

◆ m_strType

string CGffBaseColumns::m_strType
protected

◆ m_uSeqStart

TSeqPos CGffBaseColumns::m_uSeqStart
protected

Definition at line 160 of file gff_base_columns.hpp.

Referenced by CGff2Record::AssignFromGff(), SeqStart(), and SetExtent().

◆ m_uSeqStop

TSeqPos CGffBaseColumns::m_uSeqStop
protected

Definition at line 161 of file gff_base_columns.hpp.

Referenced by CGff2Record::AssignFromGff(), SeqStop(), and SetExtent().

◆ mSeqId

string CGffBaseColumns::mSeqId
protected

Definition at line 159 of file gff_base_columns.hpp.

Referenced by CGff2Record::AssignFromGff(), and Id().

◆ msNextId

unsigned int CGffBaseColumns::msNextId = 0
staticprotected

Definition at line 169 of file gff_base_columns.hpp.

Referenced by NextId(), and ResetId().


The documentation for this class was generated from the following files:
Modified on Wed Jun 19 17:06:28 2024 by modify_doxy.py rev. 669887