Search Toolkit Book for CTableDataGCAssembly

Inheritance diagram for CTableDataGCAssembly:

Collaboration diagram for CTableDataGCAssembly:

Public Types
enum	EColType { eSeq_Id = 0 , eRefSeq_Acc , eGenBank_Acc , eChromosome , eRole , eStatus , eParent , eUnit , ePatchType , eMaxColNum }

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 Types inherited from ITableData
enum	ColumnType { kNone , kInt , kReal , kString , kBytes , kCommonString , kCommonBytes , kObject }

Public Member Functions
virtual void	LoadData ()

virtual ColumnType	GetColumnType (size_t col) const

virtual string	GetColumnLabel (size_t col) const

virtual size_t	GetRowsCount () const

virtual size_t	GetColsCount () const

virtual void	GetStringValue (size_t row, size_t col, string &value) const

virtual long	GetIntValue (size_t row, size_t col) const

virtual double	GetRealValue (size_t row, size_t col) const

virtual SConstScopedObject	GetObjectValue (size_t row, size_t col) const

virtual SConstScopedObject	GetRowObject (size_t row) const

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

Public Member Functions inherited from CTableDataBase
virtual string	GetTableTypeId () const

Public Member Functions inherited from ITableData
virtual	~ITableData ()

virtual bool	IsHtmlColumn (size_t col) const

virtual string	GetRowLabel (size_t) const

virtual vector< string >	GetColumnCommonStrings (size_t) const

virtual vector< vector< char > * >	GetColumnCommonBytes (size_t) const

virtual string	GetHtmlValue (size_t, size_t) const

virtual void	SetStringValue (size_t, size_t, const string &)

virtual void	SetIntValue (size_t, size_t, long)

virtual void	SetRealValue (size_t, size_t, double)

virtual void	SetObjectValue (size_t, size_t, SConstScopedObject *)

virtual bool	AllowEdit (size_t)

Static Public Member Functions
static CTableDataGCAssembly *	CreateObject (SConstScopedObject &object, ICreateParams *params)

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	Init ()

Private Attributes
CConstRef< CObject >	m_Object

CRef< objects::CScope >	m_Scope

vector< CConstRef< CGC_Sequence > >	m_Seqs

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 CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 46 of file table_data_gcassembly.cpp.

Member Enumeration Documentation

◆ EColType

enum CTableDataGCAssembly::EColType

Enumerator
eSeq_Id
eRefSeq_Acc
eGenBank_Acc
eChromosome
eRole
eStatus
eParent
eUnit
ePatchType
eMaxColNum

Definition at line 51 of file table_data_gcassembly.cpp.

Member Function Documentation

◆ CreateObject()

CTableDataGCAssembly * CTableDataGCAssembly::CreateObject	(	SConstScopedObject &	object,
		ICreateParams *	params
	)

static

Definition at line 121 of file table_data_gcassembly.cpp.

References Init(), m_Object, and m_Scope.

◆ GetColsCount()

size_t CTableDataGCAssembly::GetColsCount ( ) const

virtual

Implements ITableData.

Definition at line 189 of file table_data_gcassembly.cpp.

References eMaxColNum.

◆ GetColumnLabel()

string CTableDataGCAssembly::GetColumnLabel ( size_t col ) const

virtual

Implements ITableData.

Definition at line 174 of file table_data_gcassembly.cpp.

References eMaxColNum, kEmptyStr, and s_ColNames.

◆ GetColumnType()

ITableData::ColumnType CTableDataGCAssembly::GetColumnType ( size_t col ) const

virtual

Implements ITableData.

Definition at line 165 of file table_data_gcassembly.cpp.

References eMaxColNum, ITableData::kNone, and s_ColTypes.

◆ GetIntValue()

long CTableDataGCAssembly::GetIntValue	(	size_t	row,
		size_t	col
	)		const

virtual

Reimplemented from ITableData.

Definition at line 347 of file table_data_gcassembly.cpp.

References value.

◆ GetObjectValue()

SConstScopedObject CTableDataGCAssembly::GetObjectValue	(	size_t	row,
		size_t	col
	)		const

virtual

Reimplemented from ITableData.

Definition at line 361 of file table_data_gcassembly.cpp.

References CGC_TypedSeqId_Base::e_Genbank, CGC_SeqIdAlias::e_None, CGC_TypedSeqId_Base::e_Private, CGC_SeqIdAlias::e_Public, CGC_TypedSeqId_Base::e_Refseq, eGenBank_Acc, eParent, eRefSeq_Acc, eSeq_Id, CGC_Sequence::GetParent(), CGC_Sequence_Base::GetSeq_id(), CGC_Sequence::GetSynonymSeq_id(), i, CSeq_id_Base::IsLocal(), m_Scope, m_Seqs, CSeq_id::Match(), CConstRef< C, Locker >::Reset(), and value.

◆ GetRealValue()

double CTableDataGCAssembly::GetRealValue	(	size_t	row,
		size_t	col
	)		const

virtual

Reimplemented from ITableData.

Definition at line 354 of file table_data_gcassembly.cpp.

References value.

◆ GetRowObject()

SConstScopedObject CTableDataGCAssembly::GetRowObject ( size_t row ) const

virtual

Reimplemented from ITableData.

Definition at line 423 of file table_data_gcassembly.cpp.

References value.

◆ GetRowsCount()

size_t CTableDataGCAssembly::GetRowsCount ( ) const

virtual

Implements ITableData.

Definition at line 183 of file table_data_gcassembly.cpp.

References m_Seqs.

◆ GetStringValue()

void CTableDataGCAssembly::GetStringValue	(	size_t	row,
		size_t	col,
		string &	value
	)		const

virtual

Implements ITableData.

Definition at line 194 of file table_data_gcassembly.cpp.

References CGC_Sequence_Base::CanGetRoles(), CGC_TypedSeqId_Base::e_Genbank, CGC_SeqIdAlias::e_None, CGC_TypedSeqId_Base::e_Private, CGC_SeqIdAlias::e_Public, CGC_TypedSeqId_Base::e_Refseq, eChromosome, CSeq_id::eContent, eGC_SequenceRole_chromosome, eGC_SequenceRole_component, eGC_SequenceRole_pseudo_scaffold, eGC_SequenceRole_scaffold, eGC_SequenceRole_submitter_pseudo_scaffold, eGenBank_Acc, eGetId_Best, eParent, ePatchType, eRefSeq_Acc, eRole, eSeq_Id, CGC_TaggedSequences_Base::eState_aligned, CGC_TaggedSequences_Base::eState_bits, CGC_TaggedSequences_Base::eState_placed, CGC_TaggedSequences_Base::eState_unlocalized, CGC_TaggedSequences_Base::eState_unplaced, eStatus, eUnit, CGC_Sequence::GetAssemblyUnit(), GetId(), CSeq_id::GetLabel(), CGC_Sequence::GetParent(), CGC_Sequence::GetParentRelation(), CGC_Sequence_Base::GetPatch_type(), CGC_Sequence::GetReplicon(), CGC_Sequence_Base::GetRoles(), CGC_Sequence_Base::GetSeq_id(), CSeq_id_Handle::GetSeqId(), CGC_Sequence::GetSynonymSeq_id(), i, CSeq_id_Base::IsLocal(), CGC_Sequence_Base::IsSetPatch_type(), ITERATE, m_Scope, m_Seqs, CSeq_id::Match(), CConstRef< C, Locker >::Reset(), and value.

◆ Init()

void CTableDataGCAssembly::Init ( void )

private

Definition at line 131 of file table_data_gcassembly.cpp.

References CGC_Assembly::CreateHierarchy(), CGC_Assembly::eChromosome, CGC_Assembly::eTopLevel, CGC_Assembly::GetMolecules(), set< Key, Compare >::insert(), ITERATE, and m_Seqs.

Referenced by CreateObject().

◆ LoadData()

virtual void CTableDataGCAssembly::LoadData ( void )

inlinevirtual

Definition at line 64 of file table_data_gcassembly.cpp.

Member Data Documentation

◆ m_Object

CConstRef<CObject> CTableDataGCAssembly::m_Object

private

Definition at line 80 of file table_data_gcassembly.cpp.

Referenced by CreateObject().

◆ m_Scope

CRef<objects::CScope> CTableDataGCAssembly::m_Scope

mutableprivate

Definition at line 81 of file table_data_gcassembly.cpp.

Referenced by CreateObject(), GetObjectValue(), and GetStringValue().

◆ m_Seqs

vector< CConstRef<CGC_Sequence> > CTableDataGCAssembly::m_Seqs

private

Definition at line 82 of file table_data_gcassembly.cpp.

Referenced by GetObjectValue(), GetRowsCount(), GetStringValue(), and Init().

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

src/gui/objutils/table_data_gcassembly.cpp

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ EColType

Member Function Documentation

◆ CreateObject()

◆ GetColsCount()

◆ GetColumnLabel()

◆ GetColumnType()

◆ GetIntValue()

◆ GetObjectValue()

◆ GetRealValue()

◆ GetRowObject()

◆ GetRowsCount()

◆ GetStringValue()

◆ Init()

◆ LoadData()

Member Data Documentation

◆ m_Object

◆ m_Scope

◆ m_Seqs