#include <objtools/format/items/locus_item.hpp>

Inheritance diagram for CLocusItem:

Collaboration diagram for CLocusItem:

Public Types
typedef CMolInfo::TBiomol	TBiomol

typedef CSeq_inst::TStrand	TStrand

typedef CSeq_inst::TTopology	TTopology

Public Types inherited from IFlatItem
enum	EItem { eItem_None = 0 , eItem_StartSection , eItem_StartItem , eItem_HtmlAnchor , eItem_Head , eItem_Locus , eItem_Date , eItem_Defline , eItem_Accession , eItem_Version , eItem_Project , eItem_GenomeProject , eItem_DbSource , eItem_Keywords , eItem_Segment , eItem_Source , eItem_Reference , eItem_Cache , eItem_Comment , eItem_Primary , eItem_FeatHeader , eItem_SourceFeat , eItem_Feature , eItem_Gap , eItem_BaseCount , eItem_Origin , eItem_Sequence , eItem_Contig , eItem_Wgs , eItem_Tsa , eItem_Alignment , eItem_EndItem , eItem_EndSection , eItem_Slash }

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...

Public Member Functions
	CLocusItem (CBioseqContext &ctx)

void	Format (IFormatter &formatter, IFlatTextOStream &text_os) const override

const string &	GetName (void) const

const string &	GetFullName (void) const

size_t	GetLength (void) const

TStrand	GetStrand (void) const

TBiomol	GetBiomol (void) const

TTopology	GetTopology (void) const

const string &	GetDivision (void) const

const string &	GetDate (void) const

EItem	GetItemType () const override

Public Member Functions inherited from CFlatItem
bool	IsSetObject (void) const

const CSerialObject *	GetObject (void) const

CBioseqContext *	GetContext (void)

CBioseqContext *	GetContext (void) const

bool	Skip (void) const

bool	IsExternal (void) const

	~CFlatItem (void)

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

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...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. 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

Static Public Member Functions
static string	GetDivision (const CBioseq_Handle &bsh, const CBioseqContext *ctx=0)

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)

Private Member Functions
void	x_GatherInfo (CBioseqContext &ctx) override

void	x_SetName (CBioseqContext &ctx)

void	x_SetLength (CBioseqContext &ctx)

void	x_SetStrand (CBioseqContext &ctx)

void	x_SetBiomol (CBioseqContext &ctx)

void	x_SetTopology (CBioseqContext &ctx)

void	x_SetDivision (CBioseqContext &ctx)

void	x_SetDate (CBioseqContext &ctx)

const CDate *	x_GetDateForBioseq (const CBioseq_Handle &bsh) const

const CDate *	x_GetLaterDate (const CDate d1, const CDate d2) const

bool	x_NameHasBadChars (const string &name) const

Private Attributes
string	m_Name

string	m_FullName

size_t	m_Length

TStrand	m_Strand

TBiomol	m_Biomol

TTopology	m_Topology

string	m_Division

string	m_Date

Additional Inherited Members
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 CFlatItem
	CFlatItem (CBioseqContext *ctx=0)

void	x_SetObject (const CSerialObject &obj)

void	x_SetContext (CBioseqContext &ctx)

void	x_SetSkip (void)

void	x_SetExternal (void)

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 57 of file locus_item.hpp.

Member Typedef Documentation

◆ TBiomol

typedef CMolInfo::TBiomol CLocusItem::TBiomol

Definition at line 60 of file locus_item.hpp.

◆ TStrand

typedef CSeq_inst::TStrand CLocusItem::TStrand

Definition at line 61 of file locus_item.hpp.

◆ TTopology

typedef CSeq_inst::TTopology CLocusItem::TTopology

Definition at line 62 of file locus_item.hpp.

Constructor & Destructor Documentation

◆ CLocusItem()

CLocusItem::CLocusItem ( CBioseqContext & ctx )

Definition at line 74 of file locus_item.cpp.

References ctx.

Member Function Documentation

◆ Format()

void CLocusItem::Format	(	IFormatter &	formatter,
		IFlatTextOStream &	text_os
	)		const

overridevirtual

Implements CFlatItem.

Definition at line 86 of file locus_item.cpp.

References IFormatter::FormatLocus().

◆ GetBiomol()

CLocusItem::TBiomol CLocusItem::GetBiomol ( void ) const

inline

Definition at line 141 of file locus_item.hpp.

References m_Biomol.

Referenced by CEmblFormatter::FormatLocus(), CGBSeqFormatter::FormatLocus(), and CGenbankFormatter::FormatLocus().

◆ GetDate()

const string & CLocusItem::GetDate ( void ) const

inline

Definition at line 162 of file locus_item.hpp.

References m_Date.

Referenced by CGenbankFormatter::FormatLocus().

◆ GetDivision() [1/2]

string CLocusItem::GetDivision	(	const CBioseq_Handle &	bsh,
		const CBioseqContext *	ctx = `0`
	)

static

Definition at line 793 of file locus_item.cpp.

References ctx, CSeqdesc_Base::e_Molinfo, CSeq_inst_Base::eRepr_delta, CMolInfo_Base::eTech_unknown, CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CBioseq_Handle::GetInst_Ext(), CBioseq_Handle::GetInst_Repr(), CBioseq_Handle::IsAa(), CSeq_ext_Base::IsDelta(), CBioseq_Handle::IsSetInst_Ext(), CBioseq_Handle::IsSetInst_Repr(), ITERATE, x_GetDivisionProc(), and x_GetDivisionProcIdx().

◆ GetDivision() [2/2]

const string & CLocusItem::GetDivision ( void ) const

inline

Definition at line 155 of file locus_item.hpp.

References m_Division.

Referenced by CEmblFormatter::FormatLocus(), CGBSeqFormatter::FormatLocus(), and CGenbankFormatter::FormatLocus().

◆ GetFullName()

const string & CLocusItem::GetFullName ( void ) const

inline

Definition at line 120 of file locus_item.hpp.

References m_FullName.

Referenced by CFlatFileSequenceListJob::CFlatFileSeqBuilder::AddItem(), CFlatFileLocusItem::CalcSize(), and CGenbankFormatter::FormatLocus().

◆ GetItemType()

IFlatItem::EItem CLocusItem::GetItemType ( void ) const

overridevirtual

Implements IFlatItem.

Definition at line 81 of file locus_item.cpp.

References IFlatItem::eItem_Locus.

◆ GetLength()

size_t CLocusItem::GetLength ( void ) const

inline

Definition at line 127 of file locus_item.hpp.

References m_Length.

Referenced by CEmblFormatter::FormatLocus(), CGBSeqFormatter::FormatLocus(), and CGenbankFormatter::FormatLocus().

◆ GetName()

const string & CLocusItem::GetName ( void ) const

inline

Definition at line 113 of file locus_item.hpp.

References m_Name.

Referenced by CFlatFileFactoryBuilder::AddItem(), CEmblFormatter::FormatLocus(), CGBSeqFormatter::FormatLocus(), CGenbankFormatter::FormatLocus(), and s_GetFirstBioseqName().

◆ GetStrand()

CLocusItem::TStrand CLocusItem::GetStrand ( void ) const

inline

Definition at line 134 of file locus_item.hpp.

References m_Strand.

Referenced by CGBSeqFormatter::FormatLocus(), and CGenbankFormatter::FormatLocus().

◆ GetTopology()

CLocusItem::TTopology CLocusItem::GetTopology ( void ) const

inline

Definition at line 148 of file locus_item.hpp.

References m_Topology.

Referenced by CEmblFormatter::FormatLocus(), CGBSeqFormatter::FormatLocus(), and CGenbankFormatter::FormatLocus().

◆ x_GatherInfo()

void CLocusItem::x_GatherInfo ( CBioseqContext & ctx )

overrideprivatevirtual

Reimplemented from CFlatItem.

Definition at line 105 of file locus_item.cpp.

References ctx, CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::GetMolinfo(), x_SetBiomol(), x_SetDate(), x_SetDivision(), x_SetLength(), x_SetName(), CFlatItem::x_SetObject(), x_SetStrand(), and x_SetTopology().

◆ x_GetDateForBioseq()

const CDate * CLocusItem::x_GetDateForBioseq ( const CBioseq_Handle & bsh ) const

private

Definition at line 895 of file locus_item.cpp.

References CSP_block_Base::CanGetAnnotupd(), CSP_block_Base::CanGetCreated(), CEMBL_block_Base::CanGetCreation_date(), CPDB_replace_Base::CanGetDate(), CPDB_block_Base::CanGetDeposition(), CGB_block_Base::CanGetEntry_date(), CPDB_block_Base::CanGetReplace(), CSP_block_Base::CanGetSequpd(), CEMBL_block_Base::CanGetUpdate_date(), CSeqdesc_Base::e_Create_date, CSeqdesc_Base::e_Embl, CSeqdesc_Base::e_Genbank, CSeqdesc_Base::e_Pdb, CSeqdesc_Base::e_Sp, CSeqdesc_Base::e_Update_date, CSP_block_Base::GetAnnotupd(), CSeqdesc_Base::GetCreate_date(), CSP_block_Base::GetCreated(), CEMBL_block_Base::GetCreation_date(), CPDB_replace_Base::GetDate(), CPDB_block_Base::GetDeposition(), CSeqdesc_Base::GetEmbl(), CGB_block_Base::GetEntry_date(), CSeqdesc_Base::GetGenbank(), CSeqdesc_Base::GetPdb(), CPDB_block_Base::GetReplace(), CSP_block_Base::GetSequpd(), CSeqdesc_Base::GetSp(), CSeqdesc_Base::GetUpdate_date(), CEMBL_block_Base::GetUpdate_date(), CDate_Base::IsStd(), result, and x_GetLaterDate().

Referenced by x_SetDate().

◆ x_GetLaterDate()

const CDate * CLocusItem::x_GetLaterDate	(	const CDate *	d1,
		const CDate *	d2
	)		const

private

Definition at line 973 of file locus_item.cpp.

References CDate::Compare(), CDate_Base::e_Str, CDate::eCompare_after, and CDate_Base::Which().

Referenced by x_GetDateForBioseq().

◆ x_NameHasBadChars()

bool CLocusItem::x_NameHasBadChars ( const string & name ) const

private

Definition at line 327 of file locus_item.cpp.

References isalnum(), and ITERATE.

Referenced by x_SetName().

◆ x_SetBiomol()

void CLocusItem::x_SetBiomol ( CBioseqContext & ctx )

private

Definition at line 385 of file locus_item.cpp.

References ctx, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_other_genetic, CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eBiomol_pre_RNA, CMolInfo_Base::eBiomol_tmRNA, CMolInfo_Base::eBiomol_unknown, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_not_set, CSeq_inst_Base::eMol_rna, CMolInfo_Base::GetBiomol(), CFlatItem::GetObject(), and m_Biomol.

Referenced by x_GatherInfo().

◆ x_SetDate()

void CLocusItem::x_SetDate ( CBioseqContext & ctx )

private

Definition at line 874 of file locus_item.cpp.

References ctx, DateToString(), GetNucleotideParent(), m_Date, and x_GetDateForBioseq().

Referenced by x_GatherInfo().

◆ x_SetDivision()

void CLocusItem::x_SetDivision ( CBioseqContext & ctx )

private

Definition at line 828 of file locus_item.cpp.

References CEMBL_block_Base::CanGetDiv(), ctx, CSeqdesc_Base::e_Embl, CEMBL_block_Base::eDiv_other, CEMBL_block_Base::GetDiv(), CFlatItem::GetObject(), m_Division, s_IsGenomeView(), x_GetDivisionProc(), and x_GetDivisionProcIdx().

Referenced by x_GatherInfo().

◆ x_SetLength()

void CLocusItem::x_SetLength ( CBioseqContext & ctx )

private

Definition at line 341 of file locus_item.cpp.

References ctx, GetLength(), and m_Length.

Referenced by x_GatherInfo().

◆ x_SetName()

void CLocusItem::x_SetName ( CBioseqContext & ctx )

private

Definition at line 244 of file locus_item.cpp.

References basename, ctx, eGetId_Best, CTextseq_id_Base::GetAccession(), GetId(), CTextseq_id_Base::GetName(), NStr::IsBlank(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetName(), m_FullName, m_Name, s_AddLocusSuffix(), s_FastaGetOriginalID(), s_IsGenomeView(), s_ShouldUseOriginalID(), and x_NameHasBadChars().

Referenced by x_GatherInfo().

◆ x_SetStrand()

void CLocusItem::x_SetStrand ( CBioseqContext & ctx )

private

◆ x_SetTopology()

void CLocusItem::x_SetTopology ( CBioseqContext & ctx )

private

Definition at line 422 of file locus_item.cpp.

References CSeq_interval_Base::CanGetStrand(), ctx, eNa_strand_minus, CSeq_inst_Base::eTopology_circular, CSeq_inst_Base::eTopology_linear, CBioseq_Handle::GetBioseqLength(), CSeq_interval_Base::GetFrom(), CBioseq_Handle::GetInst_Topology(), CSeq_loc_Base::GetInt(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), CSeq_loc_Base::IsInt(), CBioseq_Handle::IsSetInst_Length(), CSeq_loc_Base::IsWhole(), and m_Topology.

Referenced by x_GatherInfo().

Member Data Documentation

◆ m_Biomol

TBiomol CLocusItem::m_Biomol

private

Definition at line 101 of file locus_item.hpp.

Referenced by GetBiomol(), x_SetBiomol(), and x_SetStrand().

◆ m_Date

string CLocusItem::m_Date

private

Definition at line 104 of file locus_item.hpp.

Referenced by GetDate(), and x_SetDate().

◆ m_Division

string CLocusItem::m_Division

private

Definition at line 103 of file locus_item.hpp.

Referenced by GetDivision(), and x_SetDivision().

◆ m_FullName

string CLocusItem::m_FullName

private

Definition at line 98 of file locus_item.hpp.

Referenced by GetFullName(), and x_SetName().

◆ m_Length

size_t CLocusItem::m_Length

private

Definition at line 99 of file locus_item.hpp.

Referenced by GetLength(), and x_SetLength().

◆ m_Name

string CLocusItem::m_Name

private

Definition at line 97 of file locus_item.hpp.

Referenced by GetName(), and x_SetName().

◆ m_Strand

TStrand CLocusItem::m_Strand

private

Definition at line 100 of file locus_item.hpp.

Referenced by GetStrand(), and x_SetStrand().

◆ m_Topology

TTopology CLocusItem::m_Topology

private

Definition at line 102 of file locus_item.hpp.

Referenced by GetTopology(), and x_SetTopology().

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

include/objtools/format/items/locus_item.hpp
src/objtools/format/locus_item.cpp

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TBiomol

◆ TStrand

◆ TTopology

Constructor & Destructor Documentation

◆ CLocusItem()

Member Function Documentation

◆ Format()

◆ GetBiomol()

◆ GetDate()

◆ GetDivision() [1/2]

◆ GetDivision() [2/2]

◆ GetFullName()

◆ GetItemType()

◆ GetLength()

◆ GetName()

◆ GetStrand()

◆ GetTopology()

◆ x_GatherInfo()

◆ x_GetDateForBioseq()

◆ x_GetLaterDate()

◆ x_NameHasBadChars()

◆ x_SetBiomol()

◆ x_SetDate()

◆ x_SetDivision()

◆ x_SetLength()

◆ x_SetName()

◆ x_SetStrand()

◆ x_SetTopology()

Member Data Documentation

◆ m_Biomol

◆ m_Date

◆ m_Division

◆ m_FullName

◆ m_Length

◆ m_Name

◆ m_Strand

◆ m_Topology