CGff3ReadRecord Class Reference

Search Toolkit Book for CGff3ReadRecord

#include <objtools/readers/gff3_reader.hpp>

Inheritance diagram for CGff3ReadRecord:

Collaboration diagram for CGff3ReadRecord:

Public Member Functions
	CGff3ReadRecord ()
	~CGff3ReadRecord ()
bool	AssignFromGff (const string &) override
Public Member Functions inherited from CGff2Record
	CGff2Record ()
	CGff2Record (const CGff2Record &rhs)
virtual	~CGff2Record ()
bool	IsAlignmentRecord () const
const TAttributes &	Attributes () const
bool	GetAttribute (const string &, string &) const
bool	GetAttribute (const string &, list< string > &) const
virtual bool	InitializeFeature (TReaderFlags, CRef< CSeq_feat >, SeqIdResolver=nullptr) const
virtual bool	UpdateFeature (TReaderFlags, CRef< CSeq_feat >, SeqIdResolver=nullptr) const
bool	IsMultiParent () const
Public Member Functions inherited from CGffBaseColumns
	CGffBaseColumns ()
	CGffBaseColumns (const CGffBaseColumns &rhs)
virtual	~CGffBaseColumns ()
const string &	Id () const
TSeqPos	SeqStart () const
TSeqPos	SeqStop () const
const string &	Source () const
const string &	Type () const
const string &	NormalizedType () const
double	Score () const
ENa_strand	Strand () const
TFrame	Phase () const
bool	IsSetScore () const
bool	IsSetStrand () const
bool	IsSetPhase () const
CRef< CSeq_id >	GetSeqId (TReaderFlags, SeqIdResolver=nullptr) const
CRef< CSeq_loc >	GetSeqLoc (TReaderFlags, SeqIdResolver seqidresolve=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

Protected Member Functions
string	x_NormalizedAttributeKey (const string &)
Protected Member Functions inherited from CGff2Record
virtual bool	xAssignAttributesFromGff (const string &, const string &)
bool	xSplitGffAttributes (const string &, vector< string > &) const
virtual bool	xMigrateAttributes (TReaderFlags, CRef< CSeq_feat >) const
virtual bool	xInitFeatureData (TReaderFlags, CRef< CSeq_feat >) const
virtual bool	xUpdateFeatureData (TReaderFlags, CRef< CSeq_feat >, SeqIdResolver=nullptr) const
virtual bool	xMigrateAttributesSubSource (TReaderFlags, CRef< CSeq_feat >, TAttributes &) const
virtual bool	xMigrateAttributesOrgName (TReaderFlags, CRef< CSeq_feat >, TAttributes &) const
virtual bool	xMigrateAttributesGo (TReaderFlags, CRef< CSeq_feat >, TAttributes &) const

Additional Inherited Members
Public Types inherited from CGff2Record
typedef map< string, string >	TAttributes
typedef TAttributes::iterator	TAttrIt
typedef TAttributes::const_iterator	TAttrCit
Public Types inherited from CGffBaseColumns
using	TFrame = CCdregion::EFrame
using	TReaderFlags = long
using	SeqIdResolver = CRef< CSeq_id >(*)(const string &, TReaderFlags, bool)
Static Public Member Functions inherited from CGff2Record
static void	TokenizeGFF (vector< CTempStringEx > &columns, const CTempStringEx &line)
Static Public Member Functions inherited from CGffBaseColumns
static unsigned int	NextId ()
static void	ResetId ()
Static Protected Member Functions inherited from CGff2Record
static string	xNormalizedAttributeKey (const CTempString &)
static string	xNormalizedAttributeValue (const CTempString &)
static bool	xMigrateAttributeDefault (TAttributes &, const string &, CRef< CSeq_feat >, const string &, TReaderFlags)
static bool	xMigrateAttributeSingle (TAttributes &, const string &, CRef< CSeq_feat >, const string &, TReaderFlags)
Protected Attributes inherited from CGff2Record
string	m_strAttributes
TAttributes	m_Attributes
Protected Attributes inherited from CGffBaseColumns
string	mSeqId
TSeqPos	m_uSeqStart
TSeqPos	m_uSeqStop
string	m_strSource
string	m_strType
string	m_strNormalizedType
double *	m_pdScore
ENa_strand *	m_peStrand
TFrame *	m_pePhase
Static Protected Attributes inherited from CGffBaseColumns
static unsigned int	msNextId = 0

Detailed Description

Definition at line 45 of file gff3_reader.hpp.

Constructor & Destructor Documentation

CGff3ReadRecord()

CGff3ReadRecord::CGff3ReadRecord ( )

inline

Definition at line 50 of file gff3_reader.hpp.

~CGff3ReadRecord()

CGff3ReadRecord::~CGff3ReadRecord ( )

inline

Definition at line 51 of file gff3_reader.hpp.

Member Function Documentation

AssignFromGff()

bool CGff3ReadRecord::AssignFromGff ( const string &  strRawInput )

overridevirtual

Reimplemented from CGff2Record.

Reimplemented in CGvfReadRecord.

Definition at line 105 of file gff3_reader.cpp.

References CGff2Record::AssignFromGff(), CGff2Record::GetAttribute(), CGff2Record::m_Attributes, CGffBaseColumns::m_strType, and CGffBaseColumns::SetType().

Referenced by CGvfReadRecord::AssignFromGff().

x_NormalizedAttributeKey()

string CGff3ReadRecord::x_NormalizedAttributeKey ( const string &  strRawKey )

protected

Definition at line 152 of file gff3_reader.cpp.

References NStr::CompareNocase(), and CGff2Record::xNormalizedAttributeKey().

Referenced by CGvfReadRecord::xAssignAttributesFromGff().

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The documentation for this class was generated from the following files:

• include/objtools/readers/gff3_reader.hpp
• src/objtools/readers/gff3_reader.cpp