Search Toolkit Book for CBlastDatabaseArgs

Argument class to collect database/subject arguments. More...

#include <algo/blast/blastinput/blast_args.hpp>

Inheritance diagram for CBlastDatabaseArgs:

Collaboration diagram for CBlastDatabaseArgs:

Public Types
typedef CSearchDatabase::EMoleculeType	EMoleculeType
	alias for the database molecule type 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
	CBlastDatabaseArgs (bool request_mol_type=false, bool is_rpsblast=false, bool is_igblast=false, bool is_mapper=false, bool is_kblast=false)
	Constructor. More...

virtual void	SetArgumentDescriptions (CArgDescriptions &arg_desc)
	Interface method,. More...

virtual void	ExtractAlgorithmOptions (const CArgs &args, CBlastOptions &opts)
	Interface method,. More...

void	SetDatabaseMaskingSupport (bool val)
	Turns on/off database masking support. More...

bool	IsProtein () const
	Is the database/subject protein? More...

string	GetDatabaseName () const
	Get the BLAST database name. More...

CRef< CSearchDatabase >	GetSearchDatabase () const
	Retrieve the search database information. More...

void	SetSearchDatabase (CRef< CSearchDatabase > search_db)
	Set the search database information. More...

void	SetSubjects (CRef< IQueryFactory > subjects, CRef< CScope > scope, bool is_protein)
	Sets the subject sequences. More...

CRef< IQueryFactory >	GetSubjects (objects::CScope *scope=NULL)
	Retrieve subject sequences, if provided. More...

void	SetIPGFilteringSupport (bool val)

Public Member Functions inherited from IBlastCmdLineArgs
virtual	~IBlastCmdLineArgs ()
	Our virtual destructor. 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

Static Public Member Functions
static bool	HasBeenSet (const CArgs &args)
	Auxiliary function to determine if the database/subject sequence has been set. More...

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
static const int	kSubjectsDataLoaderPriority = 10
	The default priority for subjects, should be used for subjects/databases. More...

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 Attributes
CRef< CSearchDatabase >	m_SearchDb
	Description of the BLAST database. More...

bool	m_RequestMoleculeType
	Determines whether the database's molecule type should be requested in the command line, true in case of PSI-BLAST. More...

bool	m_IsRpsBlast
	true if the search is RPS-BLAST More...

bool	m_IsIgBlast
	true if the search is Ig-BLAST More...

bool	m_IsProtein
	Is the database/subject(s) protein? More...

bool	m_IsMapper
	true for short read mapper More...

bool	m_IsKBlast
	true for Kblastp More...

CRef< IQueryFactory >	m_Subjects
	The subject sequences. More...

CRef< objects::CScope >	m_Scope
	CScope object in which all subject sequences read are kept. More...

bool	m_SupportsDatabaseMasking
	true if it's supported More...

bool	m_SupportIPGFiltering
	true if IPG filtering is supported More...

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

Detailed Description

Argument class to collect database/subject arguments.

Definition at line 881 of file blast_args.hpp.

Member Typedef Documentation

◆ EMoleculeType

typedef CSearchDatabase::EMoleculeType CBlastDatabaseArgs::EMoleculeType

alias for the database molecule type

Definition at line 889 of file blast_args.hpp.

Constructor & Destructor Documentation

◆ CBlastDatabaseArgs()

CBlastDatabaseArgs::CBlastDatabaseArgs	(	bool	request_mol_type = `false`,
		bool	is_rpsblast = `false`,
		bool	is_igblast = `false`,
		bool	is_mapper = `false`,
		bool	is_kblast = `false`
	)

Constructor.

Parameters

request_mol_type	If true, the command line arguments will include a mandatory option to disambiguate whether a protein or a nucleotide database is searched
is_rpsblast	is it RPS-BLAST?
is_igblast	is it IG-BLAST?
is_deltablast	is it DELTA-BLAST?

Definition at line 2160 of file blast_args.cpp.