Search Toolkit Book for CTableDataBioTreeContainer

Inheritance diagram for CTableDataBioTreeContainer:

Collaboration diagram for CTableDataBioTreeContainer:

Classes
struct	ColInfo

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

CRef< CScope >	GetScope ()

CConstRef< CNode >	GetNode (size_t row) const

int	FindRow (int nodeId) const

void	SelectSeqIds (const CSelectionEvent::TIds &ids, CFeatureDescr::TId seqidFeatId, vector< size_t > &selectedNodes) const

void	SelectTaxIds (const CSelectionEvent::TTaxIds &tids, CFeatureDescr::TId taxidFeatId, vector< size_t > &selectedNodes) const

void	SelectFeatures (const CBioTreeSelection &selection, CFeatureDescr::TId srcFeatId, CFeatureDescr::TId dstFeatId, vector< size_t > &selectedNodes) 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 SConstScopedObject	GetRowObject (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 CTableDataBioTreeContainer *	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 Types
typedef map< CNode::TId, size_t >	TNodeIdRowMap

Private Member Functions
void	Init ()

string	x_GetNodeFeature (int feature_id, const CNode &node) const

Private Attributes
CConstRef< CObject >	m_Object

CRef< objects::CScope >	m_Scope

vector< pair< int, ColInfo > >	m_FeatureDescr

vector< CRef< CNode > >	m_Nodes

TNodeIdRowMap	m_NodeIdRows

Friends
class	CTableSelectionBioTreeContainer

Additional Inherited Members
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 }

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 table_data_biotreecontainer.cpp.

Member Typedef Documentation

◆ TNodeIdRowMap

typedef map<CNode::TId,size_t> CTableDataBioTreeContainer::TNodeIdRowMap

private

Definition at line 104 of file table_data_biotreecontainer.cpp.

Member Function Documentation

◆ CreateObject()

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

static

Definition at line 172 of file table_data_biotreecontainer.cpp.

References Init(), m_Object, and m_Scope.

◆ FindRow()

int CTableDataBioTreeContainer::FindRow ( int nodeId ) const

Definition at line 444 of file table_data_biotreecontainer.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), int, and m_NodeIdRows.

Referenced by CTableSelectionBioTreeContainer::GetRows().

◆ GetColsCount()

size_t CTableDataBioTreeContainer::GetColsCount ( ) const

virtual

Implements ITableData.

Definition at line 280 of file table_data_biotreecontainer.cpp.

References m_FeatureDescr.

◆ GetColumnLabel()

string CTableDataBioTreeContainer::GetColumnLabel ( size_t col ) const

virtual

Implements ITableData.

Definition at line 262 of file table_data_biotreecontainer.cpp.

References m_FeatureDescr.

◆ GetColumnType()

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

virtual

Implements ITableData.

Definition at line 251 of file table_data_biotreecontainer.cpp.

References ITableData::kInt, ITableData::kNone, and m_FeatureDescr.

◆ GetIntValue()

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

virtual

Reimplemented from ITableData.

Definition at line 307 of file table_data_biotreecontainer.cpp.

References CNode_Base::CanGetParent(), Error(), first(), CNode_Base::GetId(), CNode_Base::GetParent(), NStr::IsBlank(), LOG_POST, m_FeatureDescr, m_Nodes, row, NStr::StringToLong(), rapidjson::value, and x_GetNodeFeature().

Referenced by GetStringValue().

◆ GetNode()

CConstRef< CNode > CTableDataBioTreeContainer::GetNode ( size_t row ) const

Definition at line 436 of file table_data_biotreecontainer.cpp.

References m_Nodes, and row.

Referenced by CTableSelectionBioTreeContainer::GetSelection().

◆ GetObjectValue()

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

virtual

Reimplemented from ITableData.

Definition at line 363 of file table_data_biotreecontainer.cpp.

References CSeq_id::Assign(), eGetId_Best, NStr::EqualNocase(), first(), CSeqUtils::GetGIString(), CSeq_id_Handle::GetHandle(), GetId(), CRef< C, Locker >::GetPointer(), CSeq_id_Handle::GetSeqId(), m_FeatureDescr, m_Nodes, m_Scope, row, rapidjson::value, and x_GetNodeFeature().

◆ GetRealValue()

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

virtual

Reimplemented from ITableData.

Definition at line 334 of file table_data_biotreecontainer.cpp.

References Error(), first(), NStr::IsBlank(), LOG_POST, m_FeatureDescr, m_Nodes, row, NStr::StringToDouble(), NStr::StringToDoublePosix(), rapidjson::value, and x_GetNodeFeature().

◆ GetRowsCount()

size_t CTableDataBioTreeContainer::GetRowsCount ( ) const

virtual

Implements ITableData.

Definition at line 275 of file table_data_biotreecontainer.cpp.

References m_Nodes.

◆ GetScope()

CRef<CScope> CTableDataBioTreeContainer::GetScope ( void )

inline

Definition at line 77 of file table_data_biotreecontainer.cpp.

References m_Scope.

◆ GetStringValue()

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

virtual

Implements ITableData.

Definition at line 285 of file table_data_biotreecontainer.cpp.

References Error(), first(), GetIntValue(), LOG_POST, m_FeatureDescr, m_Nodes, row, NStr::SizetToString(), rapidjson::value, and x_GetNodeFeature().

◆ Init()

void CTableDataBioTreeContainer::Init ( void )

private

Definition at line 181 of file table_data_biotreecontainer.cpp.

References NStr::EqualNocase(), first(), CFeatureDictSet_Base::Get(), CNodeSet_Base::Get(), CBioTreeContainer_Base::GetFdict(), CBioTreeContainer_Base::GetNodes(), i, ITERATE, ITableData::kInt, ITableData::kNone, ITableData::kObject, ITableData::kReal, ITableData::kString, m_FeatureDescr, m_NodeIdRows, m_Nodes, NStr::StringToDouble(), NStr::StringToInt(), t, val, and x_GetNodeFeature().

Referenced by CreateObject().

◆ LoadData()

virtual void CTableDataBioTreeContainer::LoadData ( void )

inlinevirtual

Definition at line 66 of file table_data_biotreecontainer.cpp.

◆ SelectFeatures()

void CTableDataBioTreeContainer::SelectFeatures	(	const CBioTreeSelection &	selection,
		CFeatureDescr::TId	srcFeatId,
		CFeatureDescr::TId	dstFeatId,
		vector< size_t > &	selectedNodes
	)		const

Definition at line 491 of file table_data_biotreecontainer.cpp.

References CBioTreeSelection::GetFeatureValue(), CBioTreeSelection::GetNodeIds(), i, ITERATE, m_Nodes, and x_GetNodeFeature().

Referenced by CTableSelectionBioTreeContainer::GetRows().

◆ SelectSeqIds()

void CTableDataBioTreeContainer::SelectSeqIds	(	const CSelectionEvent::TIds &	ids,
		CFeatureDescr::TId	seqidFeatId,
		vector< size_t > &	selectedNodes
	)		const

Definition at line 450 of file table_data_biotreecontainer.cpp.

References Compare(), CSeq_id::e_YES, i, ITERATE, m_Nodes, StringToSeqId(), and x_GetNodeFeature().

Referenced by CTableSelectionBioTreeContainer::GetRows().

◆ SelectTaxIds()

void CTableDataBioTreeContainer::SelectTaxIds	(	const CSelectionEvent::TTaxIds &	tids,
		CFeatureDescr::TId	taxidFeatId,
		vector< size_t > &	selectedNodes
	)		const