CParameters Class Reference

Search Toolkit Book for CParameters

CParameters –. More...

#include <objects/blastxml/Parameters.hpp>

Inheritance diagram for CParameters:

Collaboration diagram for CParameters:

Public Member Functions
	CParameters (void)
	~CParameters (void)
	CParameters (void)
	~CParameters (void)
Public Member Functions inherited from CParameters_Base
	CParameters_Base (void)
virtual	~CParameters_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
bool	IsSetMatrix (void) const
	Matrix used (-M) Check if a value has been assigned to Matrix data member. More...
bool	CanGetMatrix (void) const
	Check if it is safe to call GetMatrix method. More...
void	ResetMatrix (void)
	Reset Matrix data member. More...
const TMatrix &	GetMatrix (void) const
	Get the Matrix member data. More...
void	SetMatrix (const TMatrix &value)
	Assign a value to Matrix data member. More...
void	SetMatrix (TMatrix &&value)
TMatrix &	SetMatrix (void)
	Assign a value to Matrix data member. More...
bool	IsSetExpect (void) const
	Expectation threshold (-e) Check if a value has been assigned to Expect data member. More...
bool	CanGetExpect (void) const
	Check if it is safe to call GetExpect method. More...
void	ResetExpect (void)
	Reset Expect data member. More...
TExpect	GetExpect (void) const
	Get the Expect member data. More...
void	SetExpect (TExpect value)
	Assign a value to Expect data member. More...
TExpect &	SetExpect (void)
	Assign a value to Expect data member. More...
bool	IsSetInclude (void) const
	Inclusion threshold (-h) Check if a value has been assigned to Include data member. More...
bool	CanGetInclude (void) const
	Check if it is safe to call GetInclude method. More...
void	ResetInclude (void)
	Reset Include data member. More...
TInclude	GetInclude (void) const
	Get the Include member data. More...
void	SetInclude (TInclude value)
	Assign a value to Include data member. More...
TInclude &	SetInclude (void)
	Assign a value to Include data member. More...
bool	IsSetSc_match (void) const
	match score for NT (-r) Check if a value has been assigned to Sc_match data member. More...
bool	CanGetSc_match (void) const
	Check if it is safe to call GetSc_match method. More...
void	ResetSc_match (void)
	Reset Sc_match data member. More...
TSc_match	GetSc_match (void) const
	Get the Sc_match member data. More...
void	SetSc_match (TSc_match value)
	Assign a value to Sc_match data member. More...
TSc_match &	SetSc_match (void)
	Assign a value to Sc_match data member. More...
bool	IsSetSc_mismatch (void) const
	mismatch score for NT (-q) Check if a value has been assigned to Sc_mismatch data member. More...
bool	CanGetSc_mismatch (void) const
	Check if it is safe to call GetSc_mismatch method. More...
void	ResetSc_mismatch (void)
	Reset Sc_mismatch data member. More...
TSc_mismatch	GetSc_mismatch (void) const
	Get the Sc_mismatch member data. More...
void	SetSc_mismatch (TSc_mismatch value)
	Assign a value to Sc_mismatch data member. More...
TSc_mismatch &	SetSc_mismatch (void)
	Assign a value to Sc_mismatch data member. More...
bool	IsSetGap_open (void) const
	Gap opening cost (-G) Check if a value has been assigned to Gap_open data member. More...
bool	CanGetGap_open (void) const
	Check if it is safe to call GetGap_open method. More...
void	ResetGap_open (void)
	Reset Gap_open data member. More...
TGap_open	GetGap_open (void) const
	Get the Gap_open member data. More...
void	SetGap_open (TGap_open value)
	Assign a value to Gap_open data member. More...
TGap_open &	SetGap_open (void)
	Assign a value to Gap_open data member. More...
bool	IsSetGap_extend (void) const
	Gap extension cost (-E) Check if a value has been assigned to Gap_extend data member. More...
bool	CanGetGap_extend (void) const
	Check if it is safe to call GetGap_extend method. More...
void	ResetGap_extend (void)
	Reset Gap_extend data member. More...
TGap_extend	GetGap_extend (void) const
	Get the Gap_extend member data. More...
void	SetGap_extend (TGap_extend value)
	Assign a value to Gap_extend data member. More...
TGap_extend &	SetGap_extend (void)
	Assign a value to Gap_extend data member. More...
bool	IsSetFilter (void) const
	Filtering options (-F) Check if a value has been assigned to Filter data member. More...
bool	CanGetFilter (void) const
	Check if it is safe to call GetFilter method. More...
void	ResetFilter (void)
	Reset Filter data member. More...
const TFilter &	GetFilter (void) const
	Get the Filter member data. More...
void	SetFilter (const TFilter &value)
	Assign a value to Filter data member. More...
void	SetFilter (TFilter &&value)
TFilter &	SetFilter (void)
	Assign a value to Filter data member. More...
bool	IsSetPattern (void) const
	PHI-BLAST pattern Check if a value has been assigned to Pattern data member. More...
bool	CanGetPattern (void) const
	Check if it is safe to call GetPattern method. More...
void	ResetPattern (void)
	Reset Pattern data member. More...
const TPattern &	GetPattern (void) const
	Get the Pattern member data. More...
void	SetPattern (const TPattern &value)
	Assign a value to Pattern data member. More...
void	SetPattern (TPattern &&value)
TPattern &	SetPattern (void)
	Assign a value to Pattern data member. More...
bool	IsSetEntrez_query (void) const
	Limit of request to Entrez query Check if a value has been assigned to Entrez_query data member. More...
bool	CanGetEntrez_query (void) const
	Check if it is safe to call GetEntrez_query method. More...
void	ResetEntrez_query (void)
	Reset Entrez_query data member. More...
const TEntrez_query &	GetEntrez_query (void) const
	Get the Entrez_query member data. More...
void	SetEntrez_query (const TEntrez_query &value)
	Assign a value to Entrez_query data member. More...
void	SetEntrez_query (TEntrez_query &&value)
TEntrez_query &	SetEntrez_query (void)
	Assign a value to Entrez_query data member. More...
virtual void	Reset (void)
	Reset the whole object. More...
	CParameters_Base (void)
virtual	~CParameters_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
bool	IsSetMatrix (void) const
	Matrix used (-M) Check if a value has been assigned to Matrix data member. More...
bool	CanGetMatrix (void) const
	Check if it is safe to call GetMatrix method. More...
void	ResetMatrix (void)
	Reset Matrix data member. More...
const TMatrix &	GetMatrix (void) const
	Get the Matrix member data. More...
void	SetMatrix (const TMatrix &value)
	Assign a value to Matrix data member. More...
void	SetMatrix (TMatrix &&value)
TMatrix &	SetMatrix (void)
	Assign a value to Matrix data member. More...
bool	IsSetExpect (void) const
	Expectation threshold (-e) Check if a value has been assigned to Expect data member. More...
bool	CanGetExpect (void) const
	Check if it is safe to call GetExpect method. More...
void	ResetExpect (void)
	Reset Expect data member. More...
TExpect	GetExpect (void) const
	Get the Expect member data. More...
void	SetExpect (TExpect value)
	Assign a value to Expect data member. More...
TExpect &	SetExpect (void)
	Assign a value to Expect data member. More...
bool	IsSetInclude (void) const
	Inclusion threshold (-h) Check if a value has been assigned to Include data member. More...
bool	CanGetInclude (void) const
	Check if it is safe to call GetInclude method. More...
void	ResetInclude (void)
	Reset Include data member. More...
TInclude	GetInclude (void) const
	Get the Include member data. More...
void	SetInclude (TInclude value)
	Assign a value to Include data member. More...
TInclude &	SetInclude (void)
	Assign a value to Include data member. More...
bool	IsSetSc_match (void) const
	match score for NT (-r) Check if a value has been assigned to Sc_match data member. More...
bool	CanGetSc_match (void) const
	Check if it is safe to call GetSc_match method. More...
void	ResetSc_match (void)
	Reset Sc_match data member. More...
TSc_match	GetSc_match (void) const
	Get the Sc_match member data. More...
void	SetSc_match (TSc_match value)
	Assign a value to Sc_match data member. More...
TSc_match &	SetSc_match (void)
	Assign a value to Sc_match data member. More...
bool	IsSetSc_mismatch (void) const
	mismatch score for NT (-q) Check if a value has been assigned to Sc_mismatch data member. More...
bool	CanGetSc_mismatch (void) const
	Check if it is safe to call GetSc_mismatch method. More...
void	ResetSc_mismatch (void)
	Reset Sc_mismatch data member. More...
TSc_mismatch	GetSc_mismatch (void) const
	Get the Sc_mismatch member data. More...
void	SetSc_mismatch (TSc_mismatch value)
	Assign a value to Sc_mismatch data member. More...
TSc_mismatch &	SetSc_mismatch (void)
	Assign a value to Sc_mismatch data member. More...
bool	IsSetGap_open (void) const
	Gap opening cost (-G) Check if a value has been assigned to Gap_open data member. More...
bool	CanGetGap_open (void) const
	Check if it is safe to call GetGap_open method. More...
void	ResetGap_open (void)
	Reset Gap_open data member. More...
TGap_open	GetGap_open (void) const
	Get the Gap_open member data. More...
void	SetGap_open (TGap_open value)
	Assign a value to Gap_open data member. More...
TGap_open &	SetGap_open (void)
	Assign a value to Gap_open data member. More...
bool	IsSetGap_extend (void) const
	Gap extension cost (-E) Check if a value has been assigned to Gap_extend data member. More...
bool	CanGetGap_extend (void) const
	Check if it is safe to call GetGap_extend method. More...
void	ResetGap_extend (void)
	Reset Gap_extend data member. More...
TGap_extend	GetGap_extend (void) const
	Get the Gap_extend member data. More...
void	SetGap_extend (TGap_extend value)
	Assign a value to Gap_extend data member. More...
TGap_extend &	SetGap_extend (void)
	Assign a value to Gap_extend data member. More...
bool	IsSetFilter (void) const
	Filtering options (-F) Check if a value has been assigned to Filter data member. More...
bool	CanGetFilter (void) const
	Check if it is safe to call GetFilter method. More...
void	ResetFilter (void)
	Reset Filter data member. More...
const TFilter &	GetFilter (void) const
	Get the Filter member data. More...
void	SetFilter (const TFilter &value)
	Assign a value to Filter data member. More...
void	SetFilter (TFilter &&value)
TFilter &	SetFilter (void)
	Assign a value to Filter data member. More...
bool	IsSetPattern (void) const
	PHI-BLAST pattern Check if a value has been assigned to Pattern data member. More...
bool	CanGetPattern (void) const
	Check if it is safe to call GetPattern method. More...
void	ResetPattern (void)
	Reset Pattern data member. More...
const TPattern &	GetPattern (void) const
	Get the Pattern member data. More...
void	SetPattern (const TPattern &value)
	Assign a value to Pattern data member. More...
void	SetPattern (TPattern &&value)
TPattern &	SetPattern (void)
	Assign a value to Pattern data member. More...
bool	IsSetEntrez_query (void) const
	Limit of request to Entrez query Check if a value has been assigned to Entrez_query data member. More...
bool	CanGetEntrez_query (void) const
	Check if it is safe to call GetEntrez_query method. More...
void	ResetEntrez_query (void)
	Reset Entrez_query data member. More...
const TEntrez_query &	GetEntrez_query (void) const
	Get the Entrez_query member data. More...
void	SetEntrez_query (const TEntrez_query &value)
	Assign a value to Entrez_query data member. More...
void	SetEntrez_query (TEntrez_query &&value)
TEntrez_query &	SetEntrez_query (void)
	Assign a value to Entrez_query data member. More...
bool	IsSetCbs (void) const
	composition-based stats (numbers correspond to numbering in stand-alone application parameter -comp_based_stats). More...
bool	CanGetCbs (void) const
	Check if it is safe to call GetCbs method. More...
void	ResetCbs (void)
	Reset Cbs data member. More...
TCbs	GetCbs (void) const
	Get the Cbs member data. More...
void	SetCbs (TCbs value)
	Assign a value to Cbs data member. More...
TCbs &	SetCbs (void)
	Assign a value to Cbs data member. More...
bool	IsSetQuery_gencode (void) const
	genetic code for query (blastx or tblastx) Check if a value has been assigned to Query_gencode data member. More...
bool	CanGetQuery_gencode (void) const
	Check if it is safe to call GetQuery_gencode method. More...
void	ResetQuery_gencode (void)
	Reset Query_gencode data member. More...
TQuery_gencode	GetQuery_gencode (void) const
	Get the Query_gencode member data. More...
void	SetQuery_gencode (TQuery_gencode value)
	Assign a value to Query_gencode data member. More...
TQuery_gencode &	SetQuery_gencode (void)
	Assign a value to Query_gencode data member. More...
bool	IsSetDb_gencode (void) const
	genetic code for db or subjects (tblastn or tblastx) Check if a value has been assigned to Db_gencode data member. More...
bool	CanGetDb_gencode (void) const
	Check if it is safe to call GetDb_gencode method. More...
void	ResetDb_gencode (void)
	Reset Db_gencode data member. More...
TDb_gencode	GetDb_gencode (void) const
	Get the Db_gencode member data. More...
void	SetDb_gencode (TDb_gencode value)
	Assign a value to Db_gencode data member. More...
TDb_gencode &	SetDb_gencode (void)
	Assign a value to Db_gencode data member. More...
bool	IsSetBl2seq_mode (void) const
	bl2seq mode Check if a value has been assigned to Bl2seq_mode data member. More...
bool	CanGetBl2seq_mode (void) const
	Check if it is safe to call GetBl2seq_mode method. More...
void	ResetBl2seq_mode (void)
	Reset Bl2seq_mode data member. More...
const TBl2seq_mode &	GetBl2seq_mode (void) const
	Get the Bl2seq_mode member data. More...
void	SetBl2seq_mode (const TBl2seq_mode &value)
	Assign a value to Bl2seq_mode data member. More...
void	SetBl2seq_mode (TBl2seq_mode &&value)
TBl2seq_mode &	SetBl2seq_mode (void)
	Assign a value to Bl2seq_mode data member. More...
virtual void	Reset (void)
	Reset the whole object. 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

Private Types
typedef CParameters_Base	Tparent
typedef CParameters_Base	Tparent

Private Member Functions
	CParameters (const CParameters &value)
CParameters &	operator= (const CParameters &value)
	CParameters (const CParameters &value)
CParameters &	operator= (const CParameters &value)

Additional Inherited Members
Public Types inherited from CParameters_Base
enum class	E_memberIndex {   e__allMandatory = 0 , e_matrix , e_expect , e_include ,   e_sc_match , e_sc_mismatch , e_gap_open , e_gap_extend ,   e_filter , e_pattern , e_entrez_query , e__allMandatory = 0 ,   e_matrix , e_expect , e_include , e_sc_match ,   e_sc_mismatch , e_gap_open , e_gap_extend , e_filter ,   e_pattern , e_entrez_query , e_cbs , e_query_gencode ,   e_db_gencode , e_bl2seq_mode }
enum class	E_memberIndex {   e__allMandatory = 0 , e_matrix , e_expect , e_include ,   e_sc_match , e_sc_mismatch , e_gap_open , e_gap_extend ,   e_filter , e_pattern , e_entrez_query , e__allMandatory = 0 ,   e_matrix , e_expect , e_include , e_sc_match ,   e_sc_mismatch , e_gap_open , e_gap_extend , e_filter ,   e_pattern , e_entrez_query , e_cbs , e_query_gencode ,   e_db_gencode , e_bl2seq_mode }
typedef string	TMatrix
typedef double	TExpect
typedef double	TInclude
typedef int	TSc_match
typedef int	TSc_mismatch
typedef int	TGap_open
typedef int	TGap_extend
typedef string	TFilter
typedef string	TPattern
typedef string	TEntrez_query
typedef Tparent::CMemberIndex< E_memberIndex, 11 >	TmemberIndex
typedef string	TMatrix
typedef double	TExpect
typedef double	TInclude
typedef int	TSc_match
typedef int	TSc_mismatch
typedef int	TGap_open
typedef int	TGap_extend
typedef string	TFilter
typedef string	TPattern
typedef string	TEntrez_query
typedef int	TCbs
typedef int	TQuery_gencode
typedef int	TDb_gencode
typedef string	TBl2seq_mode
typedef Tparent::CMemberIndex< E_memberIndex, 15 >	TmemberIndex
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...
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)
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

CParameters –.

Definition at line 65 of file Parameters.hpp.

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

• include/objects/blastxml/Parameters.hpp
• src/objects/blastxml/Parameters.cpp