CPssm Class Reference

Search Toolkit Book for CPssm

#include <objects/scoremat/Pssm.hpp>

Inheritance diagram for CPssm:

Collaboration diagram for CPssm:

Public Member Functions
	CPssm (void)
	~CPssm (void)
SIZE_TYPE	GetQueryLength () const
	Return the query length or 0 if no query is available. More...
void	GetQuerySequenceData (CNCBIstdaa &sequence) const
	Retrieve the query sequence data in ncbistdaa format. More...
double	GetLambda () const
double	GetKappa () const
double	GetH () const
double	GetLambdaUngapped () const
double	GetKappaUngapped () const
double	GetHUngapped () const
void	SetLambda (double val)
void	SetKappa (double val)
void	SetH (double val)
void	SetLambdaUngapped (double val)
void	SetKappaUngapped (double val)
void	SetHUngapped (double val)
Public Member Functions inherited from CPssm_Base
	CPssm_Base (void)
virtual	~CPssm_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
bool	IsSetIsProtein (void) const
	Is the this a protein or nucleotide scoring matrix? Check if a value has been assigned to IsProtein data member. More...
bool	CanGetIsProtein (void) const
	Check if it is safe to call GetIsProtein method. More...
void	ResetIsProtein (void)
	Reset IsProtein data member. More...
void	SetDefaultIsProtein (void)
	Assign default value to IsProtein data member. More...
TIsProtein	GetIsProtein (void) const
	Get the IsProtein member data. More...
void	SetIsProtein (TIsProtein value)
	Assign a value to IsProtein data member. More...
TIsProtein &	SetIsProtein (void)
	Assign a value to IsProtein data member. More...
bool	IsSetIdentifier (void) const
	PSSM identifier Check if a value has been assigned to Identifier data member. More...
bool	CanGetIdentifier (void) const
	Check if it is safe to call GetIdentifier method. More...
void	ResetIdentifier (void)
	Reset Identifier data member. More...
const TIdentifier &	GetIdentifier (void) const
	Get the Identifier member data. More...
void	SetIdentifier (TIdentifier &value)
	Assign a value to Identifier data member. More...
TIdentifier &	SetIdentifier (void)
	Assign a value to Identifier data member. More...
bool	IsSetNumRows (void) const
	The dimensions of the matrix are returned so the client can verify that all data was received. More...
bool	CanGetNumRows (void) const
	Check if it is safe to call GetNumRows method. More...
void	ResetNumRows (void)
	Reset NumRows data member. More...
TNumRows	GetNumRows (void) const
	Get the NumRows member data. More...
void	SetNumRows (TNumRows value)
	Assign a value to NumRows data member. More...
TNumRows &	SetNumRows (void)
	Assign a value to NumRows data member. More...
bool	IsSetNumColumns (void) const
	number of columns Check if a value has been assigned to NumColumns data member. More...
bool	CanGetNumColumns (void) const
	Check if it is safe to call GetNumColumns method. More...
void	ResetNumColumns (void)
	Reset NumColumns data member. More...
TNumColumns	GetNumColumns (void) const
	Get the NumColumns member data. More...
void	SetNumColumns (TNumColumns value)
	Assign a value to NumColumns data member. More...
TNumColumns &	SetNumColumns (void)
	Assign a value to NumColumns data member. More...
bool	IsSetRowLabels (void) const
	row-labels is given to note the order of residue types so that it can be cross-checked between applications. More...
bool	CanGetRowLabels (void) const
	Check if it is safe to call GetRowLabels method. More...
void	ResetRowLabels (void)
	Reset RowLabels data member. More...
const TRowLabels &	GetRowLabels (void) const
	Get the RowLabels member data. More...
TRowLabels &	SetRowLabels (void)
	Assign a value to RowLabels data member. More...
bool	IsSetByRow (void) const
	are matrices stored row by row? Check if a value has been assigned to ByRow data member. More...
bool	CanGetByRow (void) const
	Check if it is safe to call GetByRow method. More...
void	ResetByRow (void)
	Reset ByRow data member. More...
void	SetDefaultByRow (void)
	Assign default value to ByRow data member. More...
TByRow	GetByRow (void) const
	Get the ByRow member data. More...
void	SetByRow (TByRow value)
	Assign a value to ByRow data member. More...
TByRow &	SetByRow (void)
	Assign a value to ByRow data member. More...
bool	IsSetQuery (void) const
	PSSM representative sequence (master) Check if a value has been assigned to Query data member. More...
bool	CanGetQuery (void) const
	Check if it is safe to call GetQuery method. More...
void	ResetQuery (void)
	Reset Query data member. More...
const TQuery &	GetQuery (void) const
	Get the Query member data. More...
void	SetQuery (TQuery &value)
	Assign a value to Query data member. More...
TQuery &	SetQuery (void)
	Assign a value to Query data member. More...
bool	IsSetIntermediateData (void) const
	both intermediateData and finalData can be provided, but at least one of them must be provided. More...
bool	CanGetIntermediateData (void) const
	Check if it is safe to call GetIntermediateData method. More...
void	ResetIntermediateData (void)
	Reset IntermediateData data member. More...
const TIntermediateData &	GetIntermediateData (void) const
	Get the IntermediateData member data. More...
void	SetIntermediateData (TIntermediateData &value)
	Assign a value to IntermediateData data member. More...
TIntermediateData &	SetIntermediateData (void)
	Assign a value to IntermediateData data member. More...
bool	IsSetFinalData (void) const
	Final representation for the PSSM Check if a value has been assigned to FinalData data member. More...
bool	CanGetFinalData (void) const
	Check if it is safe to call GetFinalData method. More...
void	ResetFinalData (void)
	Reset FinalData data member. More...
const TFinalData &	GetFinalData (void) const
	Get the FinalData member data. More...
void	SetFinalData (TFinalData &value)
	Assign a value to FinalData data member. More...
TFinalData &	SetFinalData (void)
	Assign a value to FinalData 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

Static Public Attributes
static const double	kInvalidStat = 0.0
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...

Private Types
typedef CPssm_Base	Tparent

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

Additional Inherited Members
Public Types inherited from CPssm_Base
enum class	E_memberIndex {   e__allMandatory = 0 , e_isProtein , e_identifier , e_numRows ,   e_numColumns , e_rowLabels , e_byRow , e_query ,   e_intermediateData , e_finalData }
typedef bool	TIsProtein
typedef CObject_id	TIdentifier
typedef int	TNumRows
typedef int	TNumColumns
typedef list< string >	TRowLabels
typedef bool	TByRow
typedef CSeq_entry	TQuery
typedef CPssmIntermediateData	TIntermediateData
typedef CPssmFinalData	TFinalData
typedef Tparent::CMemberIndex< E_memberIndex, 10 >	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)
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 54 of file Pssm.hpp.

Member Typedef Documentation

Tparent

typedef CPssm_Base CPssm::Tparent

private

Definition at line 56 of file Pssm.hpp.

Constructor & Destructor Documentation

CPssm() [1/2]

CPssm::CPssm ( void  )

inline

Definition at line 97 of file Pssm.hpp.

~CPssm()

CPssm::~CPssm

(

void

)

Definition at line 57 of file Pssm.cpp.

CPssm() [2/2]

CPssm::CPssm ( const CPssm &  value )

private

Member Function Documentation

GetH()

double CPssm::GetH

(

void

)

const

Definition at line 120 of file Pssm.cpp.

References CPssm_Base::CanGetFinalData(), CPssm_Base::GetFinalData(), CPssmFinalData_Base::GetH(), and kInvalidStat.

Referenced by ExtractPssmAncillaryData().

GetHUngapped()

double CPssm::GetHUngapped

(

)

const

Definition at line 147 of file Pssm.cpp.

References CPssm_Base::CanGetFinalData(), CPssm_Base::GetFinalData(), CPssmFinalData_Base::GetHUngapped(), and kInvalidStat.

Referenced by ExtractPssmAncillaryData().

GetKappa()

double CPssm::GetKappa

(

void

)

const

Definition at line 111 of file Pssm.cpp.

References CPssm_Base::CanGetFinalData(), CPssm_Base::GetFinalData(), CPssmFinalData_Base::GetKappa(), and kInvalidStat.

Referenced by ExtractPssmAncillaryData().

GetKappaUngapped()

double CPssm::GetKappaUngapped

(

)

const

Definition at line 138 of file Pssm.cpp.

References CPssm_Base::CanGetFinalData(), CPssm_Base::GetFinalData(), CPssmFinalData_Base::GetKappaUngapped(), and kInvalidStat.

Referenced by ExtractPssmAncillaryData().

GetLambda()

double CPssm::GetLambda

(

void

)

const

Definition at line 102 of file Pssm.cpp.

References CPssm_Base::CanGetFinalData(), CPssm_Base::GetFinalData(), CPssmFinalData_Base::GetLambda(), and kInvalidStat.

Referenced by ExtractPssmAncillaryData().

GetLambdaUngapped()

double CPssm::GetLambdaUngapped

(

)

const

Definition at line 129 of file Pssm.cpp.

References CPssm_Base::CanGetFinalData(), CPssm_Base::GetFinalData(), CPssmFinalData_Base::GetLambdaUngapped(), and kInvalidStat.

Referenced by ExtractPssmAncillaryData().

GetQueryLength()

SIZE_TYPE CPssm::GetQueryLength

(

void

)

const

Return the query length or 0 if no query is available.

Definition at line 62 of file Pssm.cpp.

References CPssm_Base::CanGetQuery(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CPssm_Base::GetQuery(), and CSeq_entry_Base::GetSeq().

Referenced by BOOST_AUTO_TEST_CASE(), GetQuerySequenceData(), CMakeProfileDBApp::x_CheckInputScoremat(), CMakeProfileDBApp::x_CreateDeltaList(), CMakeProfileDBApp::x_MakeVol(), CMakeProfileDBApp::x_RPSAddFirstSequence(), and CMakeProfileDBApp::x_UpdateDelta().

GetQuerySequenceData()

void CPssm::GetQuerySequenceData

(

CNCBIstdaa &

sequence

)

const

Retrieve the query sequence data in ncbistdaa format.

Parameters

sequence

object on which to store the sequence, it will be empty if there is no sequence data available [in|out]

Definition at line 77 of file Pssm.cpp.

References CPssm_Base::CanGetQuery(), CSeqportUtil::Convert(), copy(), CSeq_data_Base::e_Ncbistdaa, CAliasBase< TPrim >::Get(), CBioseq_Base::GetInst(), CSeq_data_Base::GetNcbistdaa(), CPssm_Base::GetQuery(), GetQueryLength(), CSeq_entry_Base::GetSeq(), CSeq_inst_Base::GetSeq_data(), CSeq_data_Base::IsNcbistdaa(), and CAliasBase< TPrim >::Set().

Referenced by CMakeProfileDBApp::x_RPSUpdateStatistics().

operator=()

CPssm& CPssm::operator= ( const CPssm &  value )

private

SetH()

void CPssm::SetH

(

double

val

)

Definition at line 170 of file Pssm.cpp.

References CPssm_Base::SetFinalData(), CPssmFinalData_Base::SetH(), and val.

Referenced by CPsiBlastImpl::Run(), and CPssmEngine::x_PSIMatrix2Asn1().

SetHUngapped()

void CPssm::SetHUngapped

(

double

val

)

Definition at line 188 of file Pssm.cpp.

References CPssm_Base::SetFinalData(), CPssmFinalData_Base::SetHUngapped(), and val.

Referenced by CPsiBlastImpl::Run(), and CPssmEngine::x_PSIMatrix2Asn1().

SetKappa()

void CPssm::SetKappa

(

double

val

)

Definition at line 164 of file Pssm.cpp.

References CPssm_Base::SetFinalData(), CPssmFinalData_Base::SetKappa(), and val.

Referenced by CPsiBlastImpl::Run(), and CPssmEngine::x_PSIMatrix2Asn1().

SetKappaUngapped()

void CPssm::SetKappaUngapped

(

double

val

)

Definition at line 182 of file Pssm.cpp.

References CPssm_Base::SetFinalData(), CPssmFinalData_Base::SetKappaUngapped(), and val.

Referenced by CPsiBlastImpl::Run(), and CPssmEngine::x_PSIMatrix2Asn1().

SetLambda()

void CPssm::SetLambda

(

double

val

)

Definition at line 158 of file Pssm.cpp.

References CPssm_Base::SetFinalData(), CPssmFinalData_Base::SetLambda(), and val.

Referenced by CPsiBlastImpl::Run(), and CPssmEngine::x_PSIMatrix2Asn1().

SetLambdaUngapped()

void CPssm::SetLambdaUngapped

(

double

val

)

Definition at line 176 of file Pssm.cpp.

References CPssm_Base::SetFinalData(), CPssmFinalData_Base::SetLambdaUngapped(), and val.

Referenced by CPsiBlastImpl::Run(), and CPssmEngine::x_PSIMatrix2Asn1().

Member Data Documentation

kInvalidStat

const double CPssm::kInvalidStat = 0.0

static

Definition at line 71 of file Pssm.hpp.

Referenced by GetH(), GetHUngapped(), GetKappa(), GetKappaUngapped(), GetLambda(), GetLambdaUngapped(), and PsiBlastSetupScoreBlock().

---

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

• include/objects/scoremat/Pssm.hpp
• src/objects/scoremat/Pssm.cpp