NCBI C++ ToolKit
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CGff2Record Class Reference

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#include <objtools/readers/gff2_data.hpp>

+ Inheritance diagram for CGff2Record:
+ Collaboration diagram for CGff2Record:

Public Types

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)
 

Public Member Functions

 CGff2Record ()
 
 CGff2Record (const CGff2Record &rhs)
 
virtual ~CGff2Record ()
 
virtual bool AssignFromGff (const string &)
 
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
 

Static Public Member Functions

static void TokenizeGFF (vector< CTempStringEx > &columns, const CTempStringEx &line)
 
- Static Public Member Functions inherited from CGffBaseColumns
static unsigned int NextId ()
 
static void ResetId ()
 

Protected Member Functions

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
 

Static Protected Member Functions

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

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
 

Additional Inherited Members

- Static Protected Attributes inherited from CGffBaseColumns
static unsigned int msNextId = 0
 

Detailed Description

Definition at line 42 of file gff2_data.hpp.

Member Typedef Documentation

◆ TAttrCit

Definition at line 49 of file gff2_data.hpp.

◆ TAttributes

Definition at line 47 of file gff2_data.hpp.

◆ TAttrIt

Definition at line 48 of file gff2_data.hpp.

Constructor & Destructor Documentation

◆ CGff2Record() [1/2]

CGff2Record::CGff2Record ( )
inline

Definition at line 53 of file gff2_data.hpp.

◆ CGff2Record() [2/2]

CGff2Record::CGff2Record ( const CGff2Record rhs)
inline

◆ ~CGff2Record()

virtual CGff2Record::~CGff2Record ( )
inlinevirtual

Definition at line 61 of file gff2_data.hpp.

Member Function Documentation

◆ AssignFromGff()

bool CGff2Record::AssignFromGff ( const string strRawInput)
virtual

◆ Attributes()

const TAttributes& CGff2Record::Attributes ( void  ) const
inline

Definition at line 80 of file gff2_data.hpp.

References m_Attributes.

Referenced by CGvfReader::xFeatureSetExt(), and CGff3Reader::xInitializeFeature().

◆ GetAttribute() [1/2]

bool CGff2Record::GetAttribute ( const string strKey,
list< string > &  values 
) const

Definition at line 320 of file gff2_data.cpp.

References NStr::Split().

◆ GetAttribute() [2/2]

bool CGff2Record::GetAttribute ( const string strKey,
string strValue 
) const

◆ InitializeFeature()

bool CGff2Record::InitializeFeature ( TReaderFlags  flags,
CRef< CSeq_feat pFeature,
SeqIdResolver  seqidresolve = nullptr 
) const
virtual

◆ IsAlignmentRecord()

bool CGff2Record::IsAlignmentRecord ( ) const
inline

Definition at line 72 of file gff2_data.hpp.

References NStr::EndsWith(), NStr::StartsWith(), and CGffBaseColumns::Type().

◆ IsMultiParent()

bool CGff2Record::IsMultiParent ( ) const

Definition at line 1171 of file gff2_data.cpp.

References GetAttribute().

◆ TokenizeGFF()

void CGff2Record::TokenizeGFF ( vector< CTempStringEx > &  columns,
const CTempStringEx line 
)
static

◆ UpdateFeature()

bool CGff2Record::UpdateFeature ( TReaderFlags  flags,
CRef< CSeq_feat pFeature,
SeqIdResolver  seqidresolve = nullptr 
) const
virtual

◆ xAssignAttributesFromGff()

bool CGff2Record::xAssignAttributesFromGff ( const string strType,
const string strRawAttributes 
)
protectedvirtual

Reimplemented in CGvfReadRecord, and CGtfReadRecord.

Definition at line 452 of file gff2_data.cpp.

References map_checker< Container >::clear(), input(), m_Attributes, next(), and x_GetNextAttribute().

Referenced by AssignFromGff().

◆ xInitFeatureData()

bool CGff2Record::xInitFeatureData ( TReaderFlags  flags,
CRef< CSeq_feat pFeature 
) const
protectedvirtual

◆ xMigrateAttributeDefault()

bool CGff2Record::xMigrateAttributeDefault ( TAttributes attributes,
const string attrKey,
CRef< CSeq_feat pFeature,
const string qualKey,
TReaderFlags  flags 
)
staticprotected

◆ xMigrateAttributes()

bool CGff2Record::xMigrateAttributes ( TReaderFlags  flags,
CRef< CSeq_feat pFeature 
) const
protectedvirtual

◆ xMigrateAttributesGo()

bool CGff2Record::xMigrateAttributesGo ( TReaderFlags  flags,
CRef< CSeq_feat pFeature,
TAttributes attrs 
) const
protectedvirtual

Definition at line 1033 of file gff2_data.cpp.

References CReadUtil::AddGeneOntologyTerm(), and NStr::StartsWith().

◆ xMigrateAttributeSingle()

bool CGff2Record::xMigrateAttributeSingle ( TAttributes attributes,
const string attrKey,
CRef< CSeq_feat pFeature,
const string qualKey,
TReaderFlags  flags 
)
staticprotected

◆ xMigrateAttributesOrgName()

bool CGff2Record::xMigrateAttributesOrgName ( TReaderFlags  flags,
CRef< CSeq_feat pFeature,
TAttributes attrs_left 
) const
protectedvirtual

◆ xMigrateAttributesSubSource()

bool CGff2Record::xMigrateAttributesSubSource ( TReaderFlags  flags,
CRef< CSeq_feat pFeature,
TAttributes attrs_left 
) const
protectedvirtual

Definition at line 1056 of file gff2_data.cpp.

References CSubSource_Base::eSubtype_altitude, CSubSource_Base::eSubtype_cell_line, CSubSource_Base::eSubtype_cell_type, CSubSource_Base::eSubtype_chromosome, CSubSource_Base::eSubtype_clone, CSubSource_Base::eSubtype_clone_lib, CSubSource_Base::eSubtype_collected_by, CSubSource_Base::eSubtype_collection_date, CSubSource_Base::eSubtype_country, CSubSource_Base::eSubtype_dev_stage, CSubSource_Base::eSubtype_endogenous_virus_name, CSubSource_Base::eSubtype_environmental_sample, CSubSource_Base::eSubtype_frequency, CSubSource_Base::eSubtype_fwd_primer_name, CSubSource_Base::eSubtype_fwd_primer_seq, CSubSource_Base::eSubtype_genotype, CSubSource_Base::eSubtype_germline, CSubSource_Base::eSubtype_haplogroup, CSubSource_Base::eSubtype_haplotype, CSubSource_Base::eSubtype_identified_by, CSubSource_Base::eSubtype_insertion_seq_name, CSubSource_Base::eSubtype_isolation_source, CSubSource_Base::eSubtype_lab_host, CSubSource_Base::eSubtype_lat_lon, CSubSource_Base::eSubtype_linkage_group, CSubSource_Base::eSubtype_map, CSubSource_Base::eSubtype_mating_type, CSubSource_Base::eSubtype_metagenomic, CSubSource_Base::eSubtype_other, CSubSource_Base::eSubtype_phenotype, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_plastid_name, CSubSource_Base::eSubtype_pop_variant, CSubSource_Base::eSubtype_rearranged, CSubSource_Base::eSubtype_rev_primer_name, CSubSource_Base::eSubtype_rev_primer_seq, CSubSource_Base::eSubtype_segment, CSubSource_Base::eSubtype_sex, CSubSource_Base::eSubtype_subclone, CSubSource_Base::eSubtype_tissue_lib, CSubSource_Base::eSubtype_tissue_type, CSubSource_Base::eSubtype_transgenic, CSubSource_Base::eSubtype_transposon_name, CSubSource_Base::eSubtype_whole_replicon, CSubSource_Base::SetName(), and CSubSource_Base::SetSubtype().

◆ xNormalizedAttributeKey()

string CGff2Record::xNormalizedAttributeKey ( const CTempString strRawKey)
staticprotected

◆ xNormalizedAttributeValue()

string CGff2Record::xNormalizedAttributeValue ( const CTempString strRawValue)
staticprotected

◆ xSplitGffAttributes()

bool CGff2Record::xSplitGffAttributes ( const string strRawAttributes,
vector< string > &  attributes 
) const
protected

◆ xUpdateFeatureData()

bool CGff2Record::xUpdateFeatureData ( TReaderFlags  flags,
CRef< CSeq_feat pFeature,
SeqIdResolver  seqidresolve = nullptr 
) const
protectedvirtual

Member Data Documentation

◆ m_Attributes

TAttributes CGff2Record::m_Attributes
protected

◆ m_strAttributes

string CGff2Record::m_strAttributes
protected

Definition at line 170 of file gff2_data.hpp.

Referenced by AssignFromGff().


The documentation for this class was generated from the following files:
Modified on Thu Apr 11 15:06:25 2024 by modify_doxy.py rev. 669887