Search Toolkit Book for CSeq_feat_Handle

#include <objmgr/seq_feat_handle.hpp>

Inheritance diagram for CSeq_feat_Handle:

Collaboration diagram for CSeq_feat_Handle:

Public Types
typedef CRange< TSeqPos >	TRange

typedef SSNP_Info::TSNPId	TSNPId

typedef SSNP_Info::TWeight	TWeight

Public Member Functions
	CSeq_feat_Handle (void)

	~CSeq_feat_Handle (void)

void	Reset (void)

	DECLARE_OPERATOR_BOOL (m_Seq_annot &&!IsRemoved())

bool	operator== (const CSeq_feat_Handle &feat) const

bool	operator!= (const CSeq_feat_Handle &feat) const

bool	operator< (const CSeq_feat_Handle &feat) const

CScope &	GetScope (void) const
	Get scope this handle belongs to. More...

const CSeq_annot_Handle &	GetAnnot (void) const
	Get handle to seq-annot for this feature. More...

CConstRef< CSeq_feat >	GetPlainSeq_feat (void) const
	Get current seq-feat. More...

CConstRef< CSeq_feat >	GetOriginalSeq_feat (void) const

virtual CConstRef< CSeq_feat >	GetSeq_feat (void) const

bool	IsPlainFeat (void) const
	Check if this is plain feature. More...

bool	IsTableFeat (void) const
	Check if this is non-SNP table feature. More...

bool	IsSortedTableFeat (void) const
	Check if this is a simple feature from sorted Seq-table. More...

bool	IsTableSNP (void) const
	Check if this is SNP table feature. More...

virtual TRange	GetRange (void) const
	Get range for current seq-feat. More...

virtual CSeq_id_Handle	GetLocationId (void) const

TRange	GetLocationTotalRange (void) const

virtual CSeq_id_Handle	GetProductId (void) const

virtual TRange	GetProductTotalRange (void) const

bool	IsSetId (void) const

const CFeat_id &	GetId (void) const

bool	IsSetData (void) const

const CSeqFeatData &	GetData (void) const

virtual bool	IsSetPartial (void) const

virtual bool	GetPartial (void) const

bool	IsSetExcept (void) const

bool	GetExcept (void) const

bool	IsSetComment (void) const

const string &	GetComment (void) const

bool	IsSetProduct (void) const

virtual const CSeq_loc &	GetProduct (void) const

virtual const CSeq_loc &	GetLocation (void) const

bool	IsSetQual (void) const

const CSeq_feat::TQual &	GetQual (void) const

bool	IsSetTitle (void) const

const string &	GetTitle (void) const

bool	IsSetExt (void) const

const CUser_object &	GetExt (void) const

bool	IsSetCit (void) const

const CPub_set &	GetCit (void) const

bool	IsSetExp_ev (void) const

CSeq_feat::EExp_ev	GetExp_ev (void) const

bool	IsSetXref (void) const

const CSeq_feat::TXref &	GetXref (void) const

bool	IsSetDbxref (void) const

const CSeq_feat::TDbxref &	GetDbxref (void) const

bool	IsSetPseudo (void) const

bool	GetPseudo (void) const

bool	IsSetExcept_text (void) const

const string &	GetExcept_text (void) const

bool	IsSetIds (void) const

const CSeq_feat::TIds &	GetIds (void) const

bool	IsSetExts (void) const

const CSeq_feat::TExts &	GetExts (void) const

CSeqFeatData::E_Choice	GetFeatType (void) const

CSeqFeatData::ESubtype	GetFeatSubtype (void) const

TSNPId	GetSNPId (void) const

const CSeq_id &	GetSNPSeq_id (void) const

CSeq_id::TGi	GetSNPGi (void) const

bool	IsSNPMinusStrand (void) const

TWeight	GetSNPWeight (void) const

size_t	GetSNPAllelesCount (void) const

const string &	GetSNPAllele (size_t index) const

bool	IsSetSNPComment (void) const

const string &	GetSNPComment (void) const

bool	IsSetSNPQualityCode (void) const

CUser_field::TData::E_Choice	GetSNPQualityCodeWhich (void) const

const string &	GetSNPQualityCodeStr (void) const

void	GetSNPQualityCodeOs (vector< char > &os) const

bool	IsSetSNPExtra (void) const

const string &	GetSNPExtra (void) const

bool	IsRemoved (void) const
	Return true if this feature was removed already. More...

void	Remove (void) const
	Remove the feature from Seq-annot. More...

void	Replace (const CSeq_feat &new_feat) const
	Replace the feature with new Seq-feat object. More...

const CGene_ref *	GetGeneXref (void) const
	get gene (if present) from Seq-feat.xref list More...

const CProt_ref *	GetProtXref (void) const
	get protein (if present) from Seq-feat.xref list More...

CConstRef< CDbtag >	GetNamedDbxref (const CTempString &db) const
	Return a specified DB xref. More...

const string &	GetNamedQual (const CTempString &qual_name) const
	Return a named qualifier. More...

Public Member Functions inherited from ISeq_feat
virtual	~ISeq_feat (void)

Protected Types
enum	{ kNoAnnotObjectInfo = 0x80000000 , kFeatIndexMask = 0x7fffffff }

typedef Int4	TFeatIndex

Protected Member Functions
bool	x_HasAnnotObjectInfo () const

TFeatIndex	x_GetFeatIndex () const

const CSeq_annot_Info &	x_GetSeq_annot_Info (void) const

const CSeq_annot_SNP_Info &	x_GetSNP_annot_Info (void) const

const CAnnotObject_Info &	x_GetAnnotObject_InfoAny (void) const

const CAnnotObject_Info &	x_GetAnnotObject_Info (void) const

const CSeq_feat &	x_GetPlainSeq_feat (void) const

const SSNP_Info &	x_GetSNP_InfoAny (void) const

const SSNP_Info &	x_GetSNP_Info (void) const

	CSeq_feat_Handle (const CSeq_annot_Handle &annot, TFeatIndex feat_index)

	CSeq_feat_Handle (const CSeq_annot_Handle &annot, const SSNP_Info &snp_info, CCreatedFeat_Ref &created_ref)

	CSeq_feat_Handle (CScope &scope, CAnnotObject_Info *info)

Private Attributes
CSeq_annot_Handle	m_Seq_annot

TFeatIndex	m_FeatIndex

CConstRef< CSeq_feat >	m_CreatedOriginalFeat

CRef< CCreatedFeat_Ref >	m_CreatedFeat

Friends
class	CMappedFeat

class	CFeat_CI

class	CCreatedFeat_Ref

class	CSeq_annot_Info

class	CSeq_annot_Handle

class	CSeq_annot_ftable_CI

class	CSeq_annot_ftable_I

class	CTSE_Handle

class	CScope_Impl

Detailed Description

CSeq_feat_Handle –.

Proxy to access the seq-feat objects data

Definition at line 75 of file seq_feat_handle.hpp.

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

include/objmgr/seq_feat_handle.hpp
src/objmgr/seq_feat_handle.cpp

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Private Attributes

Friends

Detailed Description