#include "msladder.hpp"
(Private to src/algo/ms/omssa.)

Inheritance diagram for CLadder:

Collaboration diagram for CLadder:

Public Member Functions
	~CLadder ()

	CLadder (void)

	CLadder (int SizeIn)

	CLadder (const CLadder &Old)

int &	operator[] (int n)

int	size (void)

void	clear (void)

const bool	CreateLadder (const int IonType, const int Charge, const char *const Sequence, const int SeqIndex, const int start, const int stop, const int mass, const CMassArray &MassArray, const CAA &AA, const unsigned ModMask, const CMod ModList[], const int NumMod, const CMSSearchSettings &Settings, const bool NoProline)
	make a ladder More...

bool	CalcDelta (const int IntMassArray, const char const AAMap, const char *Sequence, int Offset, int Direction, int NumMod, int &ModIndex, const CMod ModList[], unsigned ModMask, int i, int &ion, const int ChargeIn, EMSSearchType SearchType, double ExactMass)
	calculate the mass difference More...

bool	MaskSet (unsigned ModMask, int ModIndex)

THit *	GetHit (void)

int	GetStart (void)

int	GetStop (void)

int	GetSeqIndex (void)

int	GetType (void)

int	GetMass (void)

int	GetCharge (void)

bool	Contains (int MassIndex, int Tolerance)

bool	ContainsFast (int MassIndex, int Tolerance)

void	Or (CLadder &LadderIn)

int	HitCount (void)

void	ClearHits (void)

const TIntensity &	GetIntensity (void) const
	Get the intensity array. More...

TIntensity &	SetIntensity (void)
	Set the intensity array. More...

const TDelta &	GetDelta (void) const
	Get the mass delta array. More...

TDelta &	SetDelta (void)
	Set the mass delta array. More...

const int	GetM (void) const
	Get the number of matches. More...

int &	SetM (void)
	Set the number of matches. More...

const int	GetSum (void) const
	Get the sum of ranks of matched peaks. More...

int &	SetSum (void)
	Set the sum of ranks of matched peaks. More...

const TLadderNumber &	GetLadderNumber (void) const
	Return the array containing the number of the ions. More...

TLadderNumber &	SetLadderNumber (void)
	Return the array containing the number of the ions. 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 Attributes
int	LadderIndex

AutoPtr< int, ArrayDeleter< int > >	Ladder
	mass ladder More...

AutoPtr< THit, ArrayDeleter< THit > >	Hit
	hit count for a given m/z value More...

TLadderNumber	LadderNumber
	number of ion in the series More...

TIntensity	Intensity
	intensity of matched peaks More...

TDelta	Delta
	mass deltas between theoretical and experimental More...

int	LadderSize

int	Start

int	Stop

int	Index

int	Type

int	Mass

int	Charge

int	M
	number of matched peaks More...

int	Sum
	sum of ranks of matched peaks More...

Additional Inherited Members
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 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

Definition at line 74 of file msladder.hpp.

Constructor & Destructor Documentation

◆ ~CLadder()

CLadder::~CLadder ( )

Definition at line 111 of file msladder.cpp.

◆ CLadder() [1/3]

CLadder::CLadder ( void )

Definition at line 56 of file msladder.cpp.

◆ CLadder() [2/3]

CLadder::CLadder ( int SizeIn )

Definition at line 69 of file msladder.cpp.

◆ CLadder() [3/3]

CLadder::CLadder ( const CLadder & Old )

Definition at line 83 of file msladder.cpp.

References AutoPtr< X, Del >::get(), GetDelta(), GetHit(), GetIntensity(), GetLadderNumber(), Hit, i, Index, Ladder, LadderIndex, M, Mass, SetDelta(), SetIntensity(), SetLadderNumber(), size(), Start, Stop, Sum, and Type.

Member Function Documentation

◆ CalcDelta()

bool CLadder::CalcDelta	(	const int *	IntMassArray,
		const char *const	AAMap,
		const char *	Sequence,
		int	Offset,
		int	Direction,
		int	NumMod,
		int &	ModIndex,
		const CMod	ModList[],
		unsigned	ModMask,
		int	i,
		int &	ion,
		const int	ChargeIn,
		EMSSearchType	SearchType,
		double	ExactMass
	)

inline

calculate the mass difference

Parameters

IntMassArray	amino acid masses
AAMap	convert aa to index
Sequence	the sequence
Offset	start position in the sequence
Direction	the direction of the ion series
NumMod	number of modifications
ModIndex	position of the modifications
ModList	modification info
ModMask	modification mask
i	index into sequence
ion	the ladder
ChargeIn	charge state
SearchType	what type of mass search (exact, ...)
ExactMass	exact mass threshold

Definition at line 271 of file msladder.hpp.

References delta(), eMSSearchType_exact, CMod::GetProductDelta(), i, kNeutron, MaskSet(), MSSCALE2INT, and Offset().

Referenced by CreateLadder().

◆ clear()

void CLadder::clear ( void )

inline

Definition at line 321 of file msladder.hpp.

References LadderIndex.

◆ ClearHits()

void CLadder::ClearHits ( void )

inline

Definition at line 371 of file msladder.hpp.

References Hit, i, LadderIndex, and LadderSize.

◆ Contains()

bool CLadder::Contains	(	int	MassIndex,
		int	Tolerance
	)

Definition at line 235 of file msladder.cpp.

References i, and LadderIndex.

◆ ContainsFast()

bool CLadder::ContainsFast	(	int	MassIndex,
		int	Tolerance
	)

Definition at line 247 of file msladder.cpp.

References LadderIndex, and r().

Referenced by CMSPeak::CompareTop().

◆ CreateLadder()

const bool CLadder::CreateLadder	(	const int	IonType,
		const int	Charge,
		const char *const	Sequence,
		const int	SeqIndex,
		const int	start,
		const int	stop,
		const int	mass,
		const CMassArray &	MassArray,
		const CAA &	AA,
		const unsigned	ModMask,
		const CMod	ModList[],
		const int	NumMod,
		const CMSSearchSettings &	Settings,
		const bool	NoProline
	)

make a ladder

Parameters

IonType	the ion series to create
Charge	the charge of the series
Sequence	the protein sequence
SeqIndex	the position in the blast library
start	start position in the sequence
stop	the stop position in the sequence
MassArray	AA masses
AA	used for mass calculation
ModMask	bit mask of modifications to use
ModList	modification information
NumMod	the total number of mods
Settings	search settings
NoProline	do not create ions nterm to prolines

Returns: false if fails

Definition at line 117 of file msladder.cpp.

References CalcDelta(), Charge, CMSSearchSettings_Base::GetChargehandling(), CMSSearchSettings_Base::GetExactmass(), GetHit(), CMassArray::GetIntMass(), CAA::GetMap(), CMSChargeHandle_Base::GetNegative(), CMSSearchSettings_Base::GetProductsearchtype(), CMSSearchSettings_Base::GetSearchb1(), CMSSearchSettings_Base::GetSearchctermproduct(), i, Index, kIonDirection, kIonTypeMass, kProton, kTermMass, LadderIndex, LadderSize, Mass, MSSCALE2INT, Offset(), SetLadderNumber(), Start, Stop, and Type.

◆ GetCharge()

int CLadder::GetCharge ( void )

inline

Definition at line 356 of file msladder.hpp.

References Charge.

Referenced by CMSHit::RecordMatchesScan().

◆ GetDelta()

const TDelta & CLadder::GetDelta ( void ) const

inline

Get the mass delta array.

Definition at line 396 of file msladder.hpp.

References Delta.

Referenced by CLadder(), and CMSHit::RecordMatchesScan().

◆ GetHit()

THit * CLadder::GetHit ( void )

inline

Definition at line 326 of file msladder.hpp.

References Hit.

Referenced by CLadder(), CMSPeak::Compare(), CMSPeak::CompareSortedRank(), CreateLadder(), Or(), and CMSHit::RecordMatchesScan().

◆ GetIntensity()

const TIntensity & CLadder::GetIntensity ( void ) const

inline

Get the intensity array.

Definition at line 384 of file msladder.hpp.

References Intensity.

Referenced by CLadder(), and CMSHit::RecordMatchesScan().

◆ GetLadderNumber()

const TLadderNumber & CLadder::GetLadderNumber ( void ) const

inline

Return the array containing the number of the ions.

Returns: const TMSNumber

Definition at line 432 of file msladder.hpp.

References LadderNumber.

Referenced by CLadder(), and CMSHit::RecordMatchesScan().

◆ GetM()

const int CLadder::GetM ( void ) const

inline

Get the number of matches.

Definition at line 408 of file msladder.hpp.

References M.

Referenced by CMSHit::RecordMatchesScan().

◆ GetMass()

int CLadder::GetMass ( void )

inline

Definition at line 351 of file msladder.hpp.

References Mass.

◆ GetSeqIndex()

int CLadder::GetSeqIndex ( void )

inline

Definition at line 341 of file msladder.hpp.

References Index.

◆ GetStart()

int CLadder::GetStart ( void )

inline

Definition at line 331 of file msladder.hpp.

References Start.

◆ GetStop()

int CLadder::GetStop ( void )

inline

Definition at line 336 of file msladder.hpp.

References Stop.

◆ GetSum()

const int CLadder::GetSum ( void ) const

inline

Get the sum of ranks of matched peaks.

Definition at line 420 of file msladder.hpp.

References Sum.

Referenced by CMSHit::RecordMatchesScan().

◆ GetType()

int CLadder::GetType ( void )

inline

Definition at line 346 of file msladder.hpp.

References Type.

Referenced by Or(), and CMSHit::RecordMatchesScan().

◆ HitCount()

int CLadder::HitCount ( void )

inline

Definition at line 362 of file msladder.hpp.

References Hit, i, LadderIndex, and LadderSize.

◆ MaskSet()

bool CLadder::MaskSet	(	unsigned	ModMask,
		int	ModIndex
	)

inline

Definition at line 378 of file msladder.hpp.

Referenced by CalcDelta().

◆ operator[]()

int & CLadder::operator[] ( int n )

inline

Definition at line 311 of file msladder.hpp.

References AutoPtr< X, Del >::get(), Ladder, and n.

◆ Or()

void CLadder::Or ( CLadder & LadderIn )

Definition at line 217 of file msladder.cpp.

References GetHit(), GetType(), i, kIonDirection, LadderIndex, LadderSize, size(), Start, Stop, and Type.

◆ SetDelta()

TDelta & CLadder::SetDelta ( void )

inline

Set the mass delta array.

Definition at line 402 of file msladder.hpp.

References Delta.

Referenced by CLadder(), and CMSPeak::CompareSortedRank().

◆ SetIntensity()

TIntensity & CLadder::SetIntensity ( void )

inline

Set the intensity array.

Definition at line 390 of file msladder.hpp.

References Intensity.

Referenced by CLadder(), and CMSPeak::CompareSortedRank().

◆ SetLadderNumber()

TLadderNumber & CLadder::SetLadderNumber ( void )

inline

Return the array containing the number of the ions.

Returns: TMSNumber&

Definition at line 438 of file msladder.hpp.

References LadderNumber.

Referenced by CLadder(), and CreateLadder().

◆ SetM()

int & CLadder::SetM ( void )

inline

Set the number of matches.

Definition at line 414 of file msladder.hpp.

References M.

Referenced by CMSPeak::CompareSortedRank().

◆ SetSum()

int & CLadder::SetSum ( void )

inline

Set the sum of ranks of matched peaks.

Definition at line 426 of file msladder.hpp.

References Sum.

Referenced by CMSPeak::CompareSortedRank().

◆ size()

int CLadder::size ( void )

inline

Definition at line 316 of file msladder.hpp.

References LadderIndex.

Referenced by CLadder(), CMSPeak::Compare(), CMSPeak::CompareSortedRank(), Or(), and CMSHit::RecordMatchesScan().

Member Data Documentation

◆ Charge

int CLadder::Charge

private

Definition at line 260 of file msladder.hpp.

Referenced by CreateLadder(), and GetCharge().

◆ Delta

TDelta CLadder::Delta

private

mass deltas between theoretical and experimental

Definition at line 253 of file msladder.hpp.

Referenced by GetDelta(), and SetDelta().

◆ Hit

AutoPtr<THit, ArrayDeleter<THit> > CLadder::Hit

private

hit count for a given m/z value

Definition at line 244 of file msladder.hpp.

Referenced by CLadder(), ClearHits(), GetHit(), and HitCount().

◆ Index

int CLadder::Index

private

Definition at line 257 of file msladder.hpp.

Referenced by CLadder(), CreateLadder(), and GetSeqIndex().

◆ Intensity

TIntensity CLadder::Intensity

private

intensity of matched peaks

Definition at line 250 of file msladder.hpp.

Referenced by GetIntensity(), and SetIntensity().

◆ Ladder

AutoPtr<int, ArrayDeleter<int> > CLadder::Ladder

private

mass ladder

Definition at line 241 of file msladder.hpp.

Referenced by CLadder(), and operator[]().

◆ LadderIndex

int CLadder::LadderIndex

private

Definition at line 238 of file msladder.hpp.

Referenced by CLadder(), clear(), ClearHits(), Contains(), ContainsFast(), CreateLadder(), HitCount(), Or(), and size().

◆ LadderNumber

TLadderNumber CLadder::LadderNumber

private

number of ion in the series

Definition at line 247 of file msladder.hpp.

Referenced by GetLadderNumber(), and SetLadderNumber().

◆ LadderSize

int CLadder::LadderSize

private

Definition at line 255 of file msladder.hpp.

Referenced by ClearHits(), CreateLadder(), HitCount(), and Or().

◆ M

int CLadder::M

private

number of matched peaks

Definition at line 262 of file msladder.hpp.

Referenced by CLadder(), GetM(), and SetM().

◆ Mass

int CLadder::Mass

private

Definition at line 259 of file msladder.hpp.

Referenced by CLadder(), CreateLadder(), and GetMass().

◆ Start

int CLadder::Start

private

Definition at line 256 of file msladder.hpp.

Referenced by CLadder(), CreateLadder(), GetStart(), and Or().

◆ Stop

int CLadder::Stop

private

Definition at line 256 of file msladder.hpp.

Referenced by CLadder(), CreateLadder(), GetStop(), and Or().

◆ Sum

int CLadder::Sum

private

sum of ranks of matched peaks

Definition at line 264 of file msladder.hpp.

Referenced by CLadder(), GetSum(), and SetSum().

◆ Type

int CLadder::Type

private

Definition at line 258 of file msladder.hpp.

Referenced by CLadder(), CreateLadder(), GetType(), and Or().

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

src/algo/ms/omssa/msladder.hpp
src/algo/ms/omssa/msladder.cpp

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ~CLadder()

◆ CLadder() [1/3]

◆ CLadder() [2/3]

◆ CLadder() [3/3]

Member Function Documentation

◆ CalcDelta()

◆ clear()

◆ ClearHits()

◆ Contains()

◆ ContainsFast()

◆ CreateLadder()

◆ GetCharge()

◆ GetDelta()

◆ GetHit()

◆ GetIntensity()

◆ GetLadderNumber()

◆ GetM()

◆ GetMass()

◆ GetSeqIndex()

◆ GetStart()

◆ GetStop()

◆ GetSum()

◆ GetType()

◆ HitCount()

◆ MaskSet()

◆ operator[]()

◆ Or()

◆ SetDelta()

◆ SetIntensity()

◆ SetLadderNumber()

◆ SetM()

◆ SetSum()

◆ size()

Member Data Documentation

◆ Charge

◆ Delta

◆ Hit

◆ Index

◆ Intensity

◆ Ladder

◆ LadderIndex

◆ LadderNumber

◆ LadderSize

◆ M

◆ Mass

◆ Start

◆ Stop

◆ Sum

◆ Type