Search Toolkit Book for CSeqDB_FilterTree

Tree of nodes describing filtering of database sequences. More...

#include "seqdbfilter.hpp"
(Private to src/objtools/blast/seqdb_reader.)

Inheritance diagram for CSeqDB_FilterTree:

Collaboration diagram for CSeqDB_FilterTree:

Public Types
typedef vector< CRef< CSeqDB_AliasMask > >	TFilters
	Type used to store lists of filters found here. More...

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
	CSeqDB_FilterTree ()
	Construct. More...

void	SetName (string name)
	Set the node name. More...

void	AddFilters (const TFilters &filters)
	Add filters to this node. More...

const TFilters &	GetFilters () const
	Get filters from this node. More...

void	AddNode (CRef< CSeqDB_FilterTree > node)
	Add a child node to this node. More...

void	AddNodes (const vector< CRef< CSeqDB_FilterTree > > &nodes)
	Add several child nodes to this node. More...

const vector< CRef< CSeqDB_FilterTree > > &	GetNodes () const
	Get child nodes attached to this node. More...

void	AddVolume (const CSeqDB_BasePath &vol)
	Attach a volume to this node. More...

void	AddVolumes (const vector< CSeqDB_BasePath > &vols)
	Attach several volumes to this node. More...

const vector< CSeqDB_BasePath > &	GetVolumes () const
	Get volumes attached to this node. More...

void	Print () const
	Print a formatted description of this tree. More...

CRef< CSeqDB_FilterTree >	Specialize (string volname) const
	Specialized this tree for the indicated volume. More...

bool	HasFilter () const
	Check whether this tree represents any volume filtering. 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...

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

Private Member Functions
void	x_Print (int indent) const
	"Pretty-print" this tree in symbolic form. More...

	CSeqDB_FilterTree (CSeqDB_FilterTree &other)
	Prevent copy-construction of this object. More...

CSeqDB_FilterTree &	operator= (CSeqDB_FilterTree &other)
	Prevent assignment of this class. More...

Private Attributes
string	m_Name
	The node name. More...

TFilters	m_Filters
	List of sequence inclusion filters. More...

vector< CRef< CSeqDB_FilterTree > >	m_SubNodes
	Other nodes included by this node. More...

vector< CSeqDB_BasePath >	m_Volumes
	Database volumes attached at this level. More...

Additional Inherited Members
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 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

Tree of nodes describing filtering of database sequences.

Definition at line 207 of file seqdbfilter.hpp.

Member Typedef Documentation

◆ TFilters

typedef vector< CRef<CSeqDB_AliasMask> > CSeqDB_FilterTree::TFilters

Type used to store lists of filters found here.

Definition at line 210 of file seqdbfilter.hpp.

Constructor & Destructor Documentation

◆ CSeqDB_FilterTree() [1/2]

CSeqDB_FilterTree::CSeqDB_FilterTree ( )

inline

Construct.

Definition at line 213 of file seqdbfilter.hpp.

◆ CSeqDB_FilterTree() [2/2]

CSeqDB_FilterTree::CSeqDB_FilterTree ( CSeqDB_FilterTree & other )

private

Prevent copy-construction of this object.

Member Function Documentation

◆ AddFilters()

void CSeqDB_FilterTree::AddFilters ( const TFilters & filters )

inline

Add filters to this node.

Parameters

filters Filters to add here.

Definition at line 226 of file seqdbfilter.hpp.

References m_Filters.

Referenced by CSeqDBAliasNode::BuildFilterTree(), and Specialize().

◆ AddNode()

void CSeqDB_FilterTree::AddNode ( CRef< CSeqDB_FilterTree > node )

inline

Add a child node to this node.

Parameters

node	Child node to add here.

Definition at line 240 of file seqdbfilter.hpp.

References m_SubNodes.

Referenced by CSeqDBAliasNode::BuildFilterTree(), and Specialize().

◆ AddNodes()

void CSeqDB_FilterTree::AddNodes ( const vector< CRef< CSeqDB_FilterTree > > & nodes )

inline

Add several child nodes to this node.

Parameters

node	Child nodes to add here.

Definition at line 247 of file seqdbfilter.hpp.

References m_SubNodes.

Referenced by Specialize().

◆ AddVolume()

void CSeqDB_FilterTree::AddVolume ( const CSeqDB_BasePath & vol )

inline

Attach a volume to this node.

Parameters

vol	Path to new volume.

Definition at line 261 of file seqdbfilter.hpp.

References m_Volumes.

Referenced by CSeqDBAliasNode::BuildFilterTree(), and Specialize().

◆ AddVolumes()

void CSeqDB_FilterTree::AddVolumes ( const vector< CSeqDB_BasePath > & vols )

inline

Attach several volumes to this node.

Parameters

vols	Paths to new volumes.

Definition at line 268 of file seqdbfilter.hpp.

References m_Volumes.

Referenced by Specialize().

◆ GetFilters()

const TFilters& CSeqDB_FilterTree::GetFilters ( void ) const

inline

Get filters from this node.

Returns: Filters attached here.

Definition at line 233 of file seqdbfilter.hpp.

References m_Filters.

Referenced by Specialize(), and CSeqDBOIDList::x_ComputeFilters().

◆ GetNodes()

const vector< CRef<CSeqDB_FilterTree> >& CSeqDB_FilterTree::GetNodes ( void ) const

inline

Get child nodes attached to this node.

Returns: Child nodes attached here.

Definition at line 254 of file seqdbfilter.hpp.

References m_SubNodes.

Referenced by Specialize(), CSeqDBOIDList::x_ComputeFilters(), and CSeqDBImpl::x_GetOidList().

◆ GetVolumes()

const vector<CSeqDB_BasePath>& CSeqDB_FilterTree::GetVolumes ( ) const

inline

Get volumes attached to this node.

Returns: Paths to attached volumes.

Definition at line 275 of file seqdbfilter.hpp.

References m_Volumes.

Referenced by Specialize(), and CSeqDBOIDList::x_ComputeFilters().

◆ HasFilter()

bool CSeqDB_FilterTree::HasFilter ( ) const

Check whether this tree represents any volume filtering.

Returns: True iff any volumes included here are filtered.

Definition at line 81 of file seqdbfilter.cpp.

References ITERATE, m_Filters, and m_SubNodes.

Referenced by CSeqDBOIDList::CSeqDBOIDList(), CSeqDBImpl::x_GetOidList(), and CSeqDBOIDList::x_Setup().

◆ operator=()

CSeqDB_FilterTree& CSeqDB_FilterTree::operator= ( CSeqDB_FilterTree & other )

private

Prevent assignment of this class.

◆ Print()

void CSeqDB_FilterTree::Print ( void ) const

inline

Print a formatted description of this tree.

This is very useful for maintainability, e.g. debugging and for analysis of system behavior. It prints an indented tree of filter tree nodes with volumes and mask information.

Definition at line 285 of file seqdbfilter.hpp.

References indent(), and x_Print().

◆ SetName()

void CSeqDB_FilterTree::SetName ( string name )

inline

Set the node name.

Parameters

name	Name of alias node generating this filter node.

Definition at line 219 of file seqdbfilter.hpp.

References m_Name.

Referenced by CSeqDBAliasNode::BuildFilterTree(), and Specialize().

◆ Specialize()

CRef< CSeqDB_FilterTree > CSeqDB_FilterTree::Specialize ( string volname ) const

Specialized this tree for the indicated volume.

This method returns a copy of this filter tree, specialized on the specified volume. Filter Tree specialization removes all volumes except the one matching the provided name, and cleans up any unnecessary or ineffective elements. This tree is not changed in place, but the new tree will share any subelements of this tree that did not need to change.

Because the OID list is constructed recursively from this tree structure, inefficiencies or redundancies here can result in unnecessary and possibly very expensive extra work. Thus, the goal here is to produce the simplest tree that can correctly represent all filtering for the given volume.

Parameters

volname The name of the volume to specialize on.

Returns: A specialized and simplified tree.

Definition at line 38 of file seqdbfilter.cpp.

References AddFilters(), AddNode(), AddNodes(), AddVolume(), AddVolumes(), GetFilters(), GetNodes(), GetVolumes(), ITERATE, m_Filters, m_Name, m_SubNodes, m_Volumes, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), and SetName().

Referenced by CSeqDBOIDList::x_ComputeFilters().

◆ x_Print()

void CSeqDB_FilterTree::x_Print ( int indent ) const

inlineprivate

"Pretty-print" this tree in symbolic form.

Parameters

indent The amount of spaces to indent each line.

Definition at line 317 of file seqdbfilter.hpp.

References first(), indent(), ITERATE, m_Filters, m_Name, m_SubNodes, and m_Volumes.

Referenced by Print().

Member Data Documentation

◆ m_Filters

TFilters CSeqDB_FilterTree::m_Filters

private

List of sequence inclusion filters.

Definition at line 361 of file seqdbfilter.hpp.

Referenced by AddFilters(), GetFilters(), HasFilter(), Specialize(), and x_Print().

◆ m_Name

string CSeqDB_FilterTree::m_Name

private

The node name.

Definition at line 358 of file seqdbfilter.hpp.

Referenced by SetName(), Specialize(), and x_Print().

◆ m_SubNodes

vector< CRef<CSeqDB_FilterTree> > CSeqDB_FilterTree::m_SubNodes

private

Other nodes included by this node.

Definition at line 364 of file seqdbfilter.hpp.

Referenced by AddNode(), AddNodes(), GetNodes(), HasFilter(), Specialize(), and x_Print().

◆ m_Volumes

vector<CSeqDB_BasePath> CSeqDB_FilterTree::m_Volumes

private

Database volumes attached at this level.

Definition at line 367 of file seqdbfilter.hpp.

Referenced by AddVolume(), AddVolumes(), GetVolumes(), Specialize(), and x_Print().

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

src/objtools/blast/seqdb_reader/seqdbfilter.hpp
src/objtools/blast/seqdb_reader/seqdbfilter.cpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TFilters

Constructor & Destructor Documentation

◆ CSeqDB_FilterTree() [1/2]

◆ CSeqDB_FilterTree() [2/2]

Member Function Documentation

◆ AddFilters()

◆ AddNode()

◆ AddNodes()

◆ AddVolume()

◆ AddVolumes()

◆ GetFilters()

◆ GetNodes()

◆ GetVolumes()

◆ HasFilter()

◆ operator=()

◆ Print()

◆ SetName()

◆ Specialize()

◆ x_Print()

Member Data Documentation

◆ m_Filters

◆ m_Name

◆ m_SubNodes

◆ m_Volumes