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

Inheritance diagram for CCleave:

Collaboration diagram for CCleave:

Public Member Functions
	CCleave (void)

bool	CalcAndCut (const char SeqStart, const char SeqEnd, const char *PepStart, int Masses, int &NumMod, int MaxNumMod, int EndMasses, CMSMod &VariableMods, CMSMod &FixedMods, CMod ModList[], const int IntCalcMass, const int *PrecursorIntCalcMass, CRef< CMSModSpecSet > &Modset, int Maxproductions)
	cleaves the sequence. More...

bool	CheckCleave (const char iPepStart, const char iSeqStart)
	Check to see if we are at a cleavage point Used by CalcAndCut. More...

bool	CheckCleaveChar (const char *iPepStart) const
	is the character given one of the cleavage chars? More...

void	CalcMass (char SeqChar, int Masses, const int IntCalcMass)

void	EndMass (int *Masses)

int	findfirst (char *Seq, int Pos, int SeqLen)

void	CheckNonSpecificMods (EMSModType ModType, CMSMod &VariableMods, int &NumMod, int MaxNumMod, CMod ModList[], const char *iPepStart, bool setfixed, CRef< CMSModSpecSet > &Modset)
	looks for non-specific ptms More...

void	CheckAAMods (EMSModType ModType, CMSMod &VariableMods, int &NumMod, char SeqChar, int MaxNumMod, CMod ModList[], const char *iPepStart, bool setfixed, CRef< CMSModSpecSet > &Modset)
	looks for amino acid specific ptms More...

void	CheckMods (EMSModType NonSpecificIn, EMSModType Specific, CMSMod &VariableMods, CMSMod &FixedMods, int &NumMod, char SeqChar, int MaxNumMod, CMod ModList[], const char *iPepStart, CRef< CMSModSpecSet > &Modset)
	checks all mods for a particular type More...

bool	GetTopDown (void) const
	Is the enzyme really a top-down search? More...

const char *	GetStop (void) const
	Get the enzyme stop value. More...

const char *&	SetStop (void)
	Set the enzyme stop value. More...

bool	GetNonSpecific (void) const
	Is this a non-specific search? More...

int	GetCleaveNum (void) const
	Get the number of cleavage chars. More...

const char *	GetCleaveOffset (void) const
	Get the the cleave offset, 0 = cterm, 1 = nterm. More...

bool	GetNMethionine (void) const
	Is there n-term methionine cleavage? More...

bool &	SetNMethionine (void)
	Set n-term methionine cleavage. More...

const string	GetCleaveAt (void) const
	What are the cleavage chars? More...

bool	GetCheckProline (void) const
	Should we check for proline? More...

const char *	GetCleaveSense (void) const
	Should we check for proline? 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

Protected Attributes
int	ProtonMass

int	TermMass

CAA	ReverseAA

const char *	CleaveAt
	where to cleave. More...

const char *	CleaveOffset
	what is the cleavage offset More...

int	kCleave
	How many cleavage characters. More...

bool	TopDown
	TopDown does this signify a top-down search. More...

const char *	Stop
	Stop Stop position for no-enzyme and semi-tryptic searches. More...

bool	NonSpecific
	Is this a non-specific search? More...

bool	CheckProline
	Should we apply the proline rule (no cleavage before proline) More...

bool	NMethionine
	n-terminal methionine cleavage 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 469 of file msms.hpp.

Constructor & Destructor Documentation

◆ CCleave()

CCleave::CCleave ( void )

Definition at line 74 of file msms.cpp.

References kProton, kWater, MSSCALE2INT, ProtonMass, and TermMass.

Member Function Documentation

◆ CalcAndCut()

bool CCleave::CalcAndCut	(	const char *	SeqStart,
		const char *	SeqEnd,
		const char **	PepStart,
		int *	Masses,
		int &	NumMod,
		int	MaxNumMod,
		int *	EndMasses,
		CMSMod &	VariableMods,
		CMSMod &	FixedMods,
		CMod	ModList[],
		const int *	IntCalcMass,
		const int *	PrecursorIntCalcMass,
		CRef< CMSModSpecSet > &	Modset,
		int	Maxproductions
	)

cleaves the sequence.

Note that output is 0 and the positions of the aa's to be cleaved. Should be interpreted as [0, pos1], (pos1, pos2], ..., (posn, end]. This weirdness is historical – the C++ string class uses an identifier for end-of-string and has no identifier for before start of string.

Parameters

SeqStart	pointer to start of sequence
SeqEnd	pointer to end of sequence
PepStart	** to the start of peptide
Masses	cumulative masses of peptides
NumMod	number of variable mods
MaxNumMod	upper bound on number of variable mods
EndMass	the end masses of the peptides
VariableMods	list of variable mods
FixedMods	list of fixed modifications
ModList	mod site info
IntCalcMass	integer AA masses
PrecursorIntCalcMass	integer precursor masses
Modset	list of possible mods
Maxproductions	max number of product ions to calculate

Returns: are we at the end of the sequence?

Note that output is 0 and the positions of the aa's to be cleaved. Should be interpreted as [0, pos1], (pos1, pos2], ..., (posn, end]. This weirdness is historical – the C++ string class uses an identifier for end-of-string and has no identifier for before start of string.

Parameters

SeqStart	pointer to start of sequence
SeqEnd	pointer to end of sequence
PepStart	** to the start of peptide
Masses	cumulative masses of peptides
NumMod	number of variable mods
MaxNumMod	upper bound on number of variable mods
EndMass	the end masses of the peptides
VariableMods	list of variable mods
FixedMods	list of fixed modifications
ModList	mod site info
IntCalcMass	integer AA masses
PrecursorIntCalcMass	integer precursor masses
Modset	list of possible mods
Maxproductions	max number of product ions to calculate

Returns: true if end of sequence

Definition at line 116 of file msms.cpp.

References CalcMass(), CheckAAMods(), CheckCleave(), CheckMods(), eMSModType_modaa, eMSModType_modc, eMSModType_modcaa, eMSModType_modcp, eMSModType_modcpaa, eMSModType_modn, eMSModType_modnaa, eMSModType_modnp, eMSModType_modnpaa, EndMass(), GetTopDown(), and NMethionine.

Referenced by CSearch< LEGACY, NHITS >::Search().

◆ CalcMass()

void CCleave::CalcMass	(	char	SeqChar,
		int *	Masses,
		const int *	IntCalcMass
	)

inline

Definition at line 762 of file msms.hpp.

References CAA::GetMap(), and ReverseAA.

Referenced by CalcAndCut().

◆ CheckAAMods()

void CCleave::CheckAAMods	(	EMSModType	ModType,
		CMSMod &	VariableMods,
		int &	NumMod,
		char	SeqChar,
		int	MaxNumMod,
		CMod	ModList[],
		const char *	iPepStart,
		bool	setfixed,
		CRef< CMSModSpecSet > &	Modset
	)

inline

looks for amino acid specific ptms

Definition at line 780 of file msms.hpp.

References CMSMod::GetAAMods(), CMSModSpecSet::GetModChar(), CMSModSpecSet::GetModMass(), CMSModSpecSet::GetModNumChars(), CMSModSpecSet::GetNeutralLoss(), CMod::SetEnum(), CMod::SetFixed(), CMod::SetPrecursorDelta(), CMod::SetProductDelta(), CMod::SetSite(), and ncbi::grid::netcache::search::fields::size.

Referenced by CalcAndCut(), and CheckMods().

◆ CheckCleave()

bool CCleave::CheckCleave	(	const char *	iPepStart,
		const char *	iSeqStart
	)

inline

Check to see if we are at a cleavage point Used by CalcAndCut.

Parameters

iPepStart	pointer to location of sequence cursor
iSeqStart	points to start of the sequence
iPepStart	pointer to location of sequence cursor

Definition at line 736 of file msms.hpp.

References CheckCleaveChar(), CheckProline, GetStop(), NMethionine, NonSpecific, and TopDown.

Referenced by CalcAndCut().

◆ CheckCleaveChar()

bool CCleave::CheckCleaveChar ( const char * iPepStart ) const

inline

is the character given one of the cleavage chars?

Parameters

iPepStart position in the sequence

Definition at line 720 of file msms.hpp.

References CleaveAt, CleaveOffset, and kCleave.

Referenced by CheckCleave(), and CSearch< LEGACY, NHITS >::Search().

◆ CheckMods()

void CCleave::CheckMods	(	EMSModType	NonSpecificIn,
		EMSModType	Specific,
		CMSMod &	VariableMods,
		CMSMod &	FixedMods,
		int &	NumMod,
		char	SeqChar,
		int	MaxNumMod,
		CMod	ModList[],
		const char *	iPepStart,
		CRef< CMSModSpecSet > &	Modset
	)

inline

checks all mods for a particular type

Definition at line 833 of file msms.hpp.

References CheckAAMods(), and CheckNonSpecificMods().

Referenced by CalcAndCut().

◆ CheckNonSpecificMods()

void CCleave::CheckNonSpecificMods	(	EMSModType	ModType,
		CMSMod &	VariableMods,
		int &	NumMod,
		int	MaxNumMod,
		CMod	ModList[],
		const char *	iPepStart,
		bool	setfixed,
		CRef< CMSModSpecSet > &	Modset
	)

inline

looks for non-specific ptms

Definition at line 808 of file msms.hpp.

References CMSMod::GetAAMods(), CMSModSpecSet::GetModMass(), CMSModSpecSet::GetNeutralLoss(), CMod::SetEnum(), CMod::SetFixed(), CMod::SetPrecursorDelta(), CMod::SetProductDelta(), CMod::SetSite(), and ncbi::grid::netcache::search::fields::size.

Referenced by CheckMods().

◆ EndMass()

void CCleave::EndMass ( int * Masses )

inline

Definition at line 772 of file msms.hpp.

References TermMass.

Referenced by CalcAndCut().

◆ findfirst()

int CCleave::findfirst	(	char *	Seq,
		int	Pos,
		int	SeqLen
	)

Definition at line 82 of file msms.cpp.

References CleaveAt, i, and kCleave.

◆ GetCheckProline()

bool CCleave::GetCheckProline ( void ) const

inline

Should we check for proline?

Definition at line 696 of file msms.hpp.

References CheckProline.

Referenced by CPepXML::ConvertFromOMSSA().

◆ GetCleaveAt()

const string CCleave::GetCleaveAt ( void ) const

inline

What are the cleavage chars?

Definition at line 684 of file msms.hpp.

References CleaveAt, CSeqConvert::Convert(), CSeqUtil::e_Ncbieaa, CSeqUtil::e_Ncbistdaa, kCleave, and out().

Referenced by CPepXML::ConvertFromOMSSA().

◆ GetCleaveNum()

int CCleave::GetCleaveNum ( void ) const

inline

Get the number of cleavage chars.

Definition at line 878 of file msms.hpp.

References kCleave.

Referenced by CPepXML::ConvertFromOMSSA(), and CSearch< LEGACY, NHITS >::Search().

◆ GetCleaveOffset()

const char * CCleave::GetCleaveOffset ( void ) const

inline

Get the the cleave offset, 0 = cterm, 1 = nterm.

Definition at line 884 of file msms.hpp.

References CleaveOffset.

◆ GetCleaveSense()

const char * CCleave::GetCleaveSense ( void ) const

inline

Should we check for proline?

Definition at line 706 of file msms.hpp.

References CleaveOffset.

Referenced by CPepXML::ConvertFromOMSSA().

◆ GetNMethionine()

bool CCleave::GetNMethionine ( void ) const

inline

Is there n-term methionine cleavage?

Definition at line 890 of file msms.hpp.

References NMethionine.

◆ GetNonSpecific()

bool CCleave::GetNonSpecific ( void ) const

inline

Is this a non-specific search?

Definition at line 860 of file msms.hpp.

References NonSpecific.

Referenced by CSearch< LEGACY, NHITS >::Search().

◆ GetStop()

const char * CCleave::GetStop ( void ) const

inline

Get the enzyme stop value.

Definition at line 866 of file msms.hpp.

References Stop.

Referenced by CheckCleave(), and CSearch< LEGACY, NHITS >::Search().

◆ GetTopDown()

bool CCleave::GetTopDown ( void ) const

inline

Is the enzyme really a top-down search?

Definition at line 854 of file msms.hpp.

References TopDown.

Referenced by CalcAndCut().

◆ SetNMethionine()

bool & CCleave::SetNMethionine ( void )

inline

Set n-term methionine cleavage.

Definition at line 897 of file msms.hpp.

References NMethionine.

Referenced by CSearch< LEGACY, NHITS >::Search().

◆ SetStop()

const char *& CCleave::SetStop ( void )

inline

Set the enzyme stop value.

Definition at line 872 of file msms.hpp.

References Stop.

Referenced by CSearch< LEGACY, NHITS >::Search().

Member Data Documentation

◆ CheckProline

bool CCleave::CheckProline

protected

Should we apply the proline rule (no cleavage before proline)

Definition at line 668 of file msms.hpp.

Referenced by CArgC::CArgC(), CAspN::CAspN(), CAspNDE::CAspNDE(), CChymoP::CChymoP(), CChymotrypsin::CChymotrypsin(), CCNBr::CCNBr(), CFormicAcid::CFormicAcid(), CGluC::CGluC(), CGluCAspN::CGluCAspN(), CGluCDE::CGluCDE(), CheckCleave(), CLysC::CLysC(), CLysCP::CLysCP(), CLysN::CLysN(), CNoEnzyme::CNoEnzyme(), CPepsinA::CPepsinA(), CSemiChymotrypsin::CSemiChymotrypsin(), CSemiGluC::CSemiGluC(), CSemiTryptic::CSemiTryptic(), CThermolysinP::CThermolysinP(), CTopDown::CTopDown(), CTrypChymo::CTrypChymo(), CTrypCNBr::CTrypCNBr(), CTrypsin::CTrypsin(), CTrypsinP::CTrypsinP(), CWholeProtein::CWholeProtein(), and GetCheckProline().

◆ CleaveAt

const char* CCleave::CleaveAt

protected

where to cleave.

last two letters are in readdb format, assuming it uses the UniqueAA alphabet

Definition at line 636 of file msms.hpp.

Referenced by CArgC::CArgC(), CAspN::CAspN(), CAspNDE::CAspNDE(), CChymoP::CChymoP(), CChymotrypsin::CChymotrypsin(), CCNBr::CCNBr(), CFormicAcid::CFormicAcid(), CGluC::CGluC(), CGluCAspN::CGluCAspN(), CGluCDE::CGluCDE(), CheckCleaveChar(), CLysC::CLysC(), CLysCP::CLysCP(), CLysN::CLysN(), CNoEnzyme::CNoEnzyme(), CPepsinA::CPepsinA(), CSemiChymotrypsin::CSemiChymotrypsin(), CSemiGluC::CSemiGluC(), CSemiTryptic::CSemiTryptic(), CThermolysinP::CThermolysinP(), CTopDown::CTopDown(), CTrypChymo::CTrypChymo(), CTrypCNBr::CTrypCNBr(), CTrypsin::CTrypsin(), CTrypsinP::CTrypsinP(), CWholeProtein::CWholeProtein(), findfirst(), and GetCleaveAt().

◆ CleaveOffset

const char* CCleave::CleaveOffset

protected

◆ kCleave

int CCleave::kCleave

protected

◆ NMethionine

bool CCleave::NMethionine

protected

n-terminal methionine cleavage

Definition at line 673 of file msms.hpp.

Referenced by CalcAndCut(), CheckCleave(), GetNMethionine(), and SetNMethionine().

◆ NonSpecific

bool CCleave::NonSpecific

protected

◆ ProtonMass

int CCleave::ProtonMass

protected

Definition at line 628 of file msms.hpp.

Referenced by CCleave().

◆ ReverseAA

CAA CCleave::ReverseAA

protected

Definition at line 630 of file msms.hpp.

Referenced by CalcMass().

◆ Stop

const char* CCleave::Stop

protected

Stop Stop position for no-enzyme and semi-tryptic searches.

Definition at line 658 of file msms.hpp.

Referenced by GetStop(), and SetStop().

◆ TermMass

int CCleave::TermMass

protected

Definition at line 629 of file msms.hpp.

Referenced by CCleave(), and EndMass().

◆ TopDown

bool CCleave::TopDown

protected

TopDown does this signify a top-down search.

Definition at line 652 of file msms.hpp.

Referenced by CArgC::CArgC(), CAspN::CAspN(), CAspNDE::CAspNDE(), CChymoP::CChymoP(), CChymotrypsin::CChymotrypsin(), CCNBr::CCNBr(), CFormicAcid::CFormicAcid(), CGluC::CGluC(), CGluCAspN::CGluCAspN(), CGluCDE::CGluCDE(), CheckCleave(), CLysC::CLysC(), CLysCP::CLysCP(), CLysN::CLysN(), CNoEnzyme::CNoEnzyme(), CPepsinA::CPepsinA(), CSemiChymotrypsin::CSemiChymotrypsin(), CSemiGluC::CSemiGluC(), CSemiTryptic::CSemiTryptic(), CThermolysinP::CThermolysinP(), CTopDown::CTopDown(), CTrypChymo::CTrypChymo(), CTrypCNBr::CTrypCNBr(), CTrypsin::CTrypsin(), CTrypsinP::CTrypsinP(), CWholeProtein::CWholeProtein(), and GetTopDown().

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

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

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CCleave()

Member Function Documentation

◆ CalcAndCut()

◆ CalcMass()

◆ CheckAAMods()

◆ CheckCleave()

◆ CheckCleaveChar()

◆ CheckMods()

◆ CheckNonSpecificMods()

◆ EndMass()

◆ findfirst()

◆ GetCheckProline()

◆ GetCleaveAt()

◆ GetCleaveNum()

◆ GetCleaveOffset()

◆ GetCleaveSense()

◆ GetNMethionine()

◆ GetNonSpecific()

◆ GetStop()

◆ GetTopDown()

◆ SetNMethionine()

◆ SetStop()

Member Data Documentation

◆ CheckProline

◆ CleaveAt

◆ CleaveOffset

◆ kCleave

◆ NMethionine

◆ NonSpecific

◆ ProtonMass

◆ ReverseAA

◆ Stop

◆ TermMass

◆ TopDown