NCBI C++ ToolKit
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CGff3ReadRecord Class Reference

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#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 TAttributesAttributes () 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 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 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, stringTAttributes
 
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_strandm_peStrand
 
TFramem_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

◆ x_NormalizedAttributeKey()

string CGff3ReadRecord::x_NormalizedAttributeKey ( const string strRawKey)
protected

The documentation for this class was generated from the following files:
Modified on Sat May 25 14:22:16 2024 by modify_doxy.py rev. 669887