Search Toolkit Book for CSeq_feat_EditHandle

#include <objmgr/seq_feat_handle.hpp>

Inheritance diagram for CSeq_feat_EditHandle:

Collaboration diagram for CSeq_feat_EditHandle:

Public Member Functions
	CSeq_feat_EditHandle (void)

	CSeq_feat_EditHandle (const CSeq_feat_Handle &h)

CSeq_annot_EditHandle	GetAnnot (void) const

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...

void	Update (void) const
	Update index after manual modification of the object. More...

void	SetGeneXref (CGene_ref &value)
	get gene (if present) from Seq-feat.xref list More...

CGene_ref &	SetGeneXref (void)

void	SetProtXref (CProt_ref &value)
	get protein (if present) from Seq-feat.xref list More...

CProt_ref &	SetProtXref (void)

void	AddQualifier (const string &qual_name, const string &qual_val)
	Add a qualifier to this feature. More...

void	RemoveQualifier (const string &qual_name)
	Remove all qualifiers with the given name on this feature. More...

void	AddDbxref (const string &db_name, const string &db_key)
	add a DB xref to this feature More...

void	AddDbxref (const string &db_name, int db_key)

void	AddExceptText (const string &exception_text)
	Add the given exception_text and set the except flag to true. More...

void	RemoveExceptText (const string &exception_text)
	Remove all instances of the given exception text in this feature, and reset the except flag if there are no exception texts left. More...

void	AddFeatId (int id)
	Add feature id. More...

void	AddFeatId (const string &id)

void	AddFeatId (const CObject_id &id)

void	AddFeatXref (int id)

void	AddFeatXref (const string &id)

void	AddFeatXref (const CObject_id &id)

void	RemoveFeatId (int id)
	Remove feature id. More...

void	RemoveFeatId (const string &id)

void	RemoveFeatId (const CObject_id &id)

void	RemoveFeatXref (int id)

void	RemoveFeatXref (const string &id)

void	RemoveFeatXref (const CObject_id &id)

void	ClearFeatIds (void)
	Clear feature ids. More...

void	ClearFeatXrefs (void)

void	SetFeatId (int id)
	Set single feature id. More...

void	SetFeatId (const string &id)

void	SetFeatId (const CObject_id &id)

Public Member Functions inherited from CSeq_feat_Handle
	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 Member Functions
	CSeq_feat_EditHandle (const CSeq_annot_EditHandle &annot, TFeatIndex feat_index)

	CSeq_feat_EditHandle (const CSeq_annot_EditHandle &annot, const SSNP_Info &snp_info, CCreatedFeat_Ref &created_ref)

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

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

Protected Member Functions inherited from CSeq_feat_Handle
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)

Friends
class	CSeq_annot_EditHandle

class	CSeq_annot_Add_EditCommand< CSeq_feat_EditHandle >

class	CSeq_annot_Replace_EditCommand< CSeq_feat_EditHandle >

class	CSeq_annot_Remove_EditCommand< CSeq_feat_EditHandle >

class	CSeq_annot_ftable_I

Additional Inherited Members
Public Types inherited from CSeq_feat_Handle
typedef CRange< TSeqPos >	TRange

typedef SSNP_Info::TSNPId	TSNPId

typedef SSNP_Info::TWeight	TWeight

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

typedef Int4	TFeatIndex

Detailed Description

CSeq_feat_EditHandle –.

Proxy to edit the seq-feat objects data

Definition at line 606 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 Member Functions

Protected Member Functions

Friends

Additional Inherited Members

Detailed Description