Search Toolkit Book for CBlast4_queries_Base

If a PSSM is used (ie. More...

#include <objects/blast/Blast4_queries_.hpp>

Inheritance diagram for CBlast4_queries_Base:

Collaboration diagram for CBlast4_queries_Base:

Public Types
enum	E_Choice { e_not_set = 0 , e_Pssm , e_Seq_loc_list , e_Bioseq_set }
	Choice variants. More...

enum	E_ChoiceStopper { e_MaxChoice = 4 }
	Maximum+1 value of the choice variant enumerator. More...

typedef CPssmWithParameters	TPssm

typedef list< CRef< CSeq_loc > >	TSeq_loc_list

typedef CBioseq_set	TBioseq_set

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
	CBlast4_queries_Base (void)

virtual	~CBlast4_queries_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

virtual void	Reset (void)
	Reset the whole object. More...

virtual void	ResetSelection (void)
	Reset the selection (set it to e_not_set). More...

E_Choice	Which (void) const
	Which variant is currently selected. More...

void	CheckSelected (E_Choice index) const
	Verify selection, throw exception if it differs from the expected. More...

void	ThrowInvalidSelection (E_Choice index) const
	Throw 'InvalidSelection' exception. More...

void	Select (E_Choice index, EResetVariant reset=eDoResetVariant)
	Select the requested variant if needed. More...

void	Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
	Select the requested variant if needed, allocating CObject variants from memory pool. More...

bool	IsPssm (void) const
	Check if variant Pssm is selected. More...

const TPssm &	GetPssm (void) const
	Get the variant data. More...

TPssm &	SetPssm (void)
	Select the variant. More...

void	SetPssm (TPssm &value)
	Select the variant and set its data. More...

bool	IsSeq_loc_list (void) const
	Check if variant Seq_loc_list is selected. More...

const TSeq_loc_list &	GetSeq_loc_list (void) const
	Get the variant data. More...

TSeq_loc_list &	SetSeq_loc_list (void)
	Select the variant. More...

bool	IsBioseq_set (void) const
	Check if variant Bioseq_set is selected. More...

const TBioseq_set &	GetBioseq_set (void) const
	Get the variant data. More...

TBioseq_set &	SetBioseq_set (void)
	Select the variant. More...

void	SetBioseq_set (TBioseq_set &value)
	Select the variant and set its data. 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

Static Public Member Functions
static string	SelectionName (E_Choice index)
	Retrieve selection name (for diagnostic purposes). 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)

Private Types
typedef CSerialObject	Tparent

Private Member Functions
	CBlast4_queries_Base (const CBlast4_queries_Base &)

CBlast4_queries_Base &	operator= (const CBlast4_queries_Base &)

void	DoSelect (E_Choice index, CObjectMemoryPool *pool=0)

Private Attributes
E_Choice	m_choice

union {
NCBI_NS_NCBI::CUnionBuffer< TSeq_loc_list > CBlast4_queries_Base::m_Seq_loc_list

NCBI_NS_NCBI::CSerialObject * CBlast4_queries_Base::m_object

};

Static Private Attributes
static const char *const	sm_SelectionNames []

Additional Inherited Members
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

If a PSSM is used (ie.

for PSI-Blast), it must contain a "query" for formatting purposes. Bioseq-set may contain any number of queries, specified as data. Seq-loc-list may contain only the "whole" or "interval" types. In the case of "whole", any number of queries may be used; in the case of "interval", there should be exactly one query. (This is limited by the BlastObject.)

CBlast4_queries_Base –

Definition at line 84 of file Blast4_queries_.hpp.

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

include/objects/blast/Blast4_queries_.hpp
src/objects/blast/Blast4_queries_.cpp

Public Types

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description