CSpliced_exon Class Reference

Search Toolkit Book for CSpliced_exon

#include <objects/seqalign/Spliced_exon.hpp>

Inheritance diagram for CSpliced_exon:

Collaboration diagram for CSpliced_exon:

Public Member Functions
	CSpliced_exon (void)
	~CSpliced_exon (void)
CRef< CSeq_interval >	CreateRowSeq_interval (CSeq_align::TDim row, const CSpliced_seg &seg) const
TSeqRange	GetRowSeq_range (CSeq_align::TDim row, bool always_as_nuc) const
	Return exon's range within this row. More...
CRangeCollection< TSeqPos >	GetRowSeq_insertions (CSeq_align::TDim row, const CSpliced_seg &seg) const
	Return insertions within exon. More...
CRangeCollection< TSeqPos >	GetRowSeq_insertions (CSeq_align::TDim row, const CSpliced_seg &seg, const CRangeCollection< TSeqPos > &within_product_ranges) const
	Return insertions within exon. More...
Public Member Functions inherited from CSpliced_exon_Base
	CSpliced_exon_Base (void)
virtual	~CSpliced_exon_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
bool	IsSetProduct_start (void) const
	product-end >= product-start Check if a value has been assigned to Product_start data member. More...
bool	CanGetProduct_start (void) const
	Check if it is safe to call GetProduct_start method. More...
void	ResetProduct_start (void)
	Reset Product_start data member. More...
const TProduct_start &	GetProduct_start (void) const
	Get the Product_start member data. More...
void	SetProduct_start (TProduct_start &value)
	Assign a value to Product_start data member. More...
TProduct_start &	SetProduct_start (void)
	Assign a value to Product_start data member. More...
bool	IsSetProduct_end (void) const
	Check if a value has been assigned to Product_end data member. More...
bool	CanGetProduct_end (void) const
	Check if it is safe to call GetProduct_end method. More...
void	ResetProduct_end (void)
	Reset Product_end data member. More...
const TProduct_end &	GetProduct_end (void) const
	Get the Product_end member data. More...
void	SetProduct_end (TProduct_end &value)
	Assign a value to Product_end data member. More...
TProduct_end &	SetProduct_end (void)
	Assign a value to Product_end data member. More...
bool	IsSetGenomic_start (void) const
	genomic-end >= genomic-start Check if a value has been assigned to Genomic_start data member. More...
bool	CanGetGenomic_start (void) const
	Check if it is safe to call GetGenomic_start method. More...
void	ResetGenomic_start (void)
	Reset Genomic_start data member. More...
TGenomic_start	GetGenomic_start (void) const
	Get the Genomic_start member data. More...
void	SetGenomic_start (TGenomic_start value)
	Assign a value to Genomic_start data member. More...
TGenomic_start &	SetGenomic_start (void)
	Assign a value to Genomic_start data member. More...
bool	IsSetGenomic_end (void) const
	Check if a value has been assigned to Genomic_end data member. More...
bool	CanGetGenomic_end (void) const
	Check if it is safe to call GetGenomic_end method. More...
void	ResetGenomic_end (void)
	Reset Genomic_end data member. More...
TGenomic_end	GetGenomic_end (void) const
	Get the Genomic_end member data. More...
void	SetGenomic_end (TGenomic_end value)
	Assign a value to Genomic_end data member. More...
TGenomic_end &	SetGenomic_end (void)
	Assign a value to Genomic_end data member. More...
bool	IsSetProduct_id (void) const
	product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data member. More...
bool	CanGetProduct_id (void) const
	Check if it is safe to call GetProduct_id method. More...
void	ResetProduct_id (void)
	Reset Product_id data member. More...
const TProduct_id &	GetProduct_id (void) const
	Get the Product_id member data. More...
void	SetProduct_id (TProduct_id &value)
	Assign a value to Product_id data member. More...
TProduct_id &	SetProduct_id (void)
	Assign a value to Product_id data member. More...
bool	IsSetGenomic_id (void) const
	Check if a value has been assigned to Genomic_id data member. More...
bool	CanGetGenomic_id (void) const
	Check if it is safe to call GetGenomic_id method. More...
void	ResetGenomic_id (void)
	Reset Genomic_id data member. More...
const TGenomic_id &	GetGenomic_id (void) const
	Get the Genomic_id member data. More...
void	SetGenomic_id (TGenomic_id &value)
	Assign a value to Genomic_id data member. More...
TGenomic_id &	SetGenomic_id (void)
	Assign a value to Genomic_id data member. More...
bool	IsSetProduct_strand (void) const
	should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member. More...
bool	CanGetProduct_strand (void) const
	Check if it is safe to call GetProduct_strand method. More...
void	ResetProduct_strand (void)
	Reset Product_strand data member. More...
TProduct_strand	GetProduct_strand (void) const
	Get the Product_strand member data. More...
void	SetProduct_strand (TProduct_strand value)
	Assign a value to Product_strand data member. More...
TProduct_strand &	SetProduct_strand (void)
	Assign a value to Product_strand data member. More...
bool	IsSetGenomic_strand (void) const
	genomic-strand represents the strand of translation Check if a value has been assigned to Genomic_strand data member. More...
bool	CanGetGenomic_strand (void) const
	Check if it is safe to call GetGenomic_strand method. More...
void	ResetGenomic_strand (void)
	Reset Genomic_strand data member. More...
TGenomic_strand	GetGenomic_strand (void) const
	Get the Genomic_strand member data. More...
void	SetGenomic_strand (TGenomic_strand value)
	Assign a value to Genomic_strand data member. More...
TGenomic_strand &	SetGenomic_strand (void)
	Assign a value to Genomic_strand data member. More...
bool	IsSetParts (void) const
	basic seqments always are in biologic order Check if a value has been assigned to Parts data member. More...
bool	CanGetParts (void) const
	Check if it is safe to call GetParts method. More...
void	ResetParts (void)
	Reset Parts data member. More...
const TParts &	GetParts (void) const
	Get the Parts member data. More...
TParts &	SetParts (void)
	Assign a value to Parts data member. More...
bool	IsSetScores (void) const
	scores for this exon Check if a value has been assigned to Scores data member. More...
bool	CanGetScores (void) const
	Check if it is safe to call GetScores method. More...
void	ResetScores (void)
	Reset Scores data member. More...
const TScores &	GetScores (void) const
	Get the Scores member data. More...
void	SetScores (TScores &value)
	Assign a value to Scores data member. More...
TScores &	SetScores (void)
	Assign a value to Scores data member. More...
bool	IsSetAcceptor_before_exon (void) const
	splice sites Check if a value has been assigned to Acceptor_before_exon data member. More...
bool	CanGetAcceptor_before_exon (void) const
	Check if it is safe to call GetAcceptor_before_exon method. More...
void	ResetAcceptor_before_exon (void)
	Reset Acceptor_before_exon data member. More...
const TAcceptor_before_exon &	GetAcceptor_before_exon (void) const
	Get the Acceptor_before_exon member data. More...
void	SetAcceptor_before_exon (TAcceptor_before_exon &value)
	Assign a value to Acceptor_before_exon data member. More...
TAcceptor_before_exon &	SetAcceptor_before_exon (void)
	Assign a value to Acceptor_before_exon data member. More...
bool	IsSetDonor_after_exon (void) const
	Check if a value has been assigned to Donor_after_exon data member. More...
bool	CanGetDonor_after_exon (void) const
	Check if it is safe to call GetDonor_after_exon method. More...
void	ResetDonor_after_exon (void)
	Reset Donor_after_exon data member. More...
const TDonor_after_exon &	GetDonor_after_exon (void) const
	Get the Donor_after_exon member data. More...
void	SetDonor_after_exon (TDonor_after_exon &value)
	Assign a value to Donor_after_exon data member. More...
TDonor_after_exon &	SetDonor_after_exon (void)
	Assign a value to Donor_after_exon data member. More...
bool	IsSetPartial (void) const
	flag: is this exon complete or partial? Check if a value has been assigned to Partial data member. More...
bool	CanGetPartial (void) const
	Check if it is safe to call GetPartial method. More...
void	ResetPartial (void)
	Reset Partial data member. More...
TPartial	GetPartial (void) const
	Get the Partial member data. More...
void	SetPartial (TPartial value)
	Assign a value to Partial data member. More...
TPartial &	SetPartial (void)
	Assign a value to Partial data member. More...
bool	IsSetExt (void) const
	extra info Check if a value has been assigned to Ext data member. More...
bool	CanGetExt (void) const
	Check if it is safe to call GetExt method. More...
void	ResetExt (void)
	Reset Ext data member. More...
const TExt &	GetExt (void) const
	Get the Ext member data. More...
TExt &	SetExt (void)
	Assign a value to Ext data member. More...
virtual void	Reset (void)
	Reset the whole object. More...
Public Member Functions inherited from CSerialObject
	CSerialObject (void)
virtual	~CSerialObject (void)
virtual const CTypeInfo *	GetThisTypeInfo (void) const =0
virtual void	Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
	Set object to copy of another one. More...
virtual bool	Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
	Check if both objects contain the same values. More...
virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...
void	ThrowUnassigned (TMemberIndex index) const
void	ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const
bool	HasNamespaceName (void) const
	Check if object data type has namespace name. More...
const string &	GetNamespaceName (void) const
	Get namespace name. More...
bool	HasNamespacePrefix (void) const
	Check if data type has namespace prefix. More...
const string &	GetNamespacePrefix (void) const
	Get namespace prefix. More...
Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...
	CObject (const CObject &src)
	Copy constructor. More...
virtual	~CObject (void)
	Destructor. More...
CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...
bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...
bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...
bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...
bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...
void	AddReference (void) const
	Add reference to object. More...
void	RemoveReference (void) const
	Remove reference to object. More...
void	ReleaseReference (void) const
	Remove reference without deleting object. More...
virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...
virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...
void *	operator new (size_t size)
	Define new operator for memory allocation. More...
void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...
void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...
void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...
void *	operator new (size_t size, void *place)
	Define new operator. More...
void	operator delete (void *ptr, void *place)
	Define delete operator. More...
void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...
void	operator delete (void *ptr, CObjectMemoryPool *place)
	Define delete operator. More...
Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)
virtual	~CDebugDumpable (void)
void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
void	DumpToConsole (void) const

Private Types
typedef CSpliced_exon_Base	Tparent

Private Member Functions
	CSpliced_exon (const CSpliced_exon &value)
CSpliced_exon &	operator= (const CSpliced_exon &value)

Additional Inherited Members
Public Types inherited from CSpliced_exon_Base
enum class	E_memberIndex {   e__allMandatory = 0 , e_product_start , e_product_end , e_genomic_start ,   e_genomic_end , e_product_id , e_genomic_id , e_product_strand ,   e_genomic_strand , e_parts , e_scores , e_acceptor_before_exon ,   e_donor_after_exon , e_partial , e_ext }
typedef CProduct_pos	TProduct_start
typedef CProduct_pos	TProduct_end
typedef TSeqPos	TGenomic_start
typedef TSeqPos	TGenomic_end
typedef CSeq_id	TProduct_id
typedef CSeq_id	TGenomic_id
typedef ENa_strand	TProduct_strand
typedef ENa_strand	TGenomic_strand
typedef list< CRef< CSpliced_exon_chunk > >	TParts
typedef CScore_set	TScores
typedef CSplice_site	TAcceptor_before_exon
typedef CSplice_site	TDonor_after_exon
typedef bool	TPartial
typedef list< CRef< CUser_object > >	TExt
typedef Tparent::CMemberIndex< E_memberIndex, 15 >	TmemberIndex
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...
typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...
typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...
typedef Uint8	TCount
	Alias for value type of counter. More...
Static Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)
static void	SetVerifyDataGlobal (ESerialVerifyData verify)
static string	UnassignedString (void)
static CStringUTF8	UnassignedStringUTF8 (void)
static char	UnassignedByte (void)
Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)
static EAllocFillMode	GetAllocFillMode (void)
static void	SetAllocFillMode (EAllocFillMode mode)
static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...
Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)
Static Public Attributes inherited from CSerialObject
static const char *	ms_UnassignedStr = "<*unassigned*>"
static const char	ms_UnassignedByte = char(0xcd)
Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...
static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...
static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...
static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...
static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
static const TCount	eCounterStateMask
	Valid object, and object in heap. More...
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 59 of file Spliced_exon.hpp.

Member Typedef Documentation

Tparent

typedef CSpliced_exon_Base CSpliced_exon::Tparent

private

Definition at line 61 of file Spliced_exon.hpp.

Constructor & Destructor Documentation

CSpliced_exon() [1/2]

CSpliced_exon::CSpliced_exon ( void  )

inline

Definition at line 115 of file Spliced_exon.hpp.

~CSpliced_exon()

CSpliced_exon::~CSpliced_exon

(

void

)

Definition at line 50 of file Spliced_exon.cpp.

CSpliced_exon() [2/2]

CSpliced_exon::CSpliced_exon ( const CSpliced_exon &  value )

private

Member Function Documentation

CreateRowSeq_interval()

CRef< CSeq_interval > CSpliced_exon::CreateRowSeq_interval	(	CSeq_align::TDim	row,
		const CSpliced_seg &	seg
	)		const

Definition at line 56 of file Spliced_exon.cpp.

References CSpliced_exon_Base::GetGenomic_id(), CSpliced_seg_Base::GetGenomic_id(), CSpliced_exon_Base::GetGenomic_strand(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_exon_Base::GetProduct_id(), CSpliced_seg_Base::GetProduct_id(), CSpliced_exon_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_strand(), GetRowSeq_range(), CSpliced_exon_Base::IsSetGenomic_id(), CSpliced_seg_Base::IsSetGenomic_id(), CSpliced_exon_Base::IsSetGenomic_strand(), CSpliced_seg_Base::IsSetGenomic_strand(), CSpliced_exon_Base::IsSetProduct_id(), CSpliced_seg_Base::IsSetProduct_id(), CSpliced_exon_Base::IsSetProduct_strand(), CSpliced_seg_Base::IsSetProduct_strand(), NCBI_THROW, compile_time_bits::range(), CRef< C, Locker >::Reset(), row, CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CSeq_interval_Base::SetStrand(), and CSeq_interval_Base::SetTo().

GetRowSeq_insertions() [1/2]

CRangeCollection< TSeqPos > CSpliced_exon::GetRowSeq_insertions	(	CSeq_align::TDim	row,
		const CSpliced_seg &	seg
	)		const

Return insertions within exon.

Parameters

row	return gaps in this row; 0 for product, 1 for genomic
seg	Parent SPliced-seg object

Definition at line 142 of file Spliced_exon.cpp.

References COpenRange< TSeqPos >::GetWhole(), and row.

Referenced by CSeq_align::GapLengthRange().

GetRowSeq_insertions() [2/2]

CRangeCollection< TSeqPos > CSpliced_exon::GetRowSeq_insertions	(	CSeq_align::TDim	row,
		const CSpliced_seg &	seg,
		const CRangeCollection< TSeqPos > &	within_product_ranges
	)		const

Return insertions within exon.

Parameters

row	return gaps in this row; 0 for product, 1 for genomic
seg	Parent SPliced-seg object
within_product_ranges	Only return insertions within these ranges on the product. If row is 1, return genomic insertions aligned to a position within these ranges

Definition at line 149 of file Spliced_exon.cpp.

References CSpliced_exon_chunk_Base::e_Diag, CSpliced_exon_chunk_Base::e_Genomic_ins, CSpliced_exon_chunk_Base::e_Match, CSpliced_exon_chunk_Base::e_Mismatch, CSpliced_exon_chunk_Base::e_Product_ins, eNa_strand_minus, eNa_strand_unknown, CSpliced_exon_chunk_Base::GetDiag(), CSpliced_exon_chunk_Base::GetGenomic_ins(), CSpliced_exon_Base::GetGenomic_strand(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_exon_chunk_Base::GetMatch(), CSpliced_exon_chunk_Base::GetMismatch(), CSpliced_exon_Base::GetParts(), CSpliced_exon_chunk_Base::GetProduct_ins(), CSpliced_exon_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_strand(), GetRowSeq_range(), CRangeCollection< Position >::IntersectingWith(), CSpliced_exon_Base::IsSetGenomic_strand(), CSpliced_seg_Base::IsSetGenomic_strand(), CSpliced_exon_Base::IsSetParts(), CSpliced_exon_Base::IsSetProduct_strand(), CSpliced_seg_Base::IsSetProduct_strand(), ITERATE, row, and CSpliced_exon_chunk_Base::Which().

GetRowSeq_range()

TSeqRange CSpliced_exon::GetRowSeq_range	(	CSeq_align::TDim	row,
		bool	always_as_nuc
	)		const

Return exon's range within this row.

Parameters

row	0 for product, 1 for genomic
always_as_nuc	If true, row is 0 and product is a protein, return range as a nucleic acid sequence; be default for a protein return range over amino acids

Definition at line 106 of file Spliced_exon.cpp.

References _ASSERT, CProduct_pos_Base::e_Nucpos, CProduct_pos_Base::e_Protpos, CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::GetGenomic_start(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_Base::GetProduct_start(), NCBI_THROW, and row.

Referenced by CreateRowSeq_interval(), SAlignmentScoringModel::GetGapLengthOnRow(), GetRowSeq_insertions(), CSpliced_seg::GetSeqStart(), and CSpliced_seg::GetSeqStop().

operator=()

CSpliced_exon& CSpliced_exon::operator= ( const CSpliced_exon &  value )

private

---

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

• include/objects/seqalign/Spliced_exon.hpp
• src/objects/seqalign/Spliced_exon.cpp