@MSModSpecSet.hpp User-defined methods of the data storage class. More...

#include <objects/omssa/MSModSpecSet.hpp>

Inheritance diagram for CMSModSpecSet:

Collaboration diagram for CMSModSpecSet:

Public Member Functions
	CMSModSpecSet (void)

	~CMSModSpecSet (void)

void	Append (const CMSModSpecSet &ModsIn)
	concatenates in another CMSModSpecSet More...

void	CreateArrays (void)
	creates arrays for the existing set More...

bool	IsArrayed (void)
	Have the arrays been intialized? More...

char	GetModChar (int Mod, int Number) const
	get modification AA's More...

int	GetModNumChars (int Mod) const
	get the number of modification AA's More...

int	GetModMass (int Mod) const
	get modification mass More...

int	GetNeutralLoss (int Mod) const
	get neutral loss More...

const char *	GetModName (int Mod) const
	get modification friendly name More...

const char *	GetUnimodName (int Mod) const
	get unimod name More...

EMSModType	GetModType (int Mod) const
	get modification type More...

Public Member Functions inherited from CMSModSpecSet_Base
	CMSModSpecSet_Base (void)

virtual	~CMSModSpecSet_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSet (void) const
	Check if a value has been assigned to data member. More...

bool	CanGet (void) const
	Check if it is safe to call Get method. More...

void	Reset (void)
	Reset data member. More...

const Tdata &	Get (void) const
	Get the member data. More...

Tdata &	Set (void)
	Assign a value to data member. More...

	operator const Tdata & (void) const
	Conversion operator to 'const Tdata' type. More...

	operator Tdata & (void)
	Conversion operator to 'Tdata' type. 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 int	kMaxNameSize = 128
	the maximum size of an modification friendly name More...

static const int	kMaxAAs = 3
	the maximum number of AA's a modification can affect More...

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 CMSModSpecSet_Base	Tparent

Private Member Functions
	CMSModSpecSet (const CMSModSpecSet &value)

CMSModSpecSet &	operator= (const CMSModSpecSet &value)

Private Attributes
char	ModChar [eMSMod_max][kMaxAAs]
	the AA's affected More...

int	NumModChars [eMSMod_max]
	the number of AA's affected More...

int	ModMass [eMSMod_max]
	the integer scaled mass of the mod More...

int	NeutralLoss [eMSMod_max]
	the integer scaled mass of the neutral loss More...

char	ModNames [eMSMod_max][kMaxNameSize]
	friendly names More...

char	UnimodNames [eMSMod_max][kMaxNameSize]
	friendly names More...

EMSModType	ModTypes [eMSMod_max]
	categorizes existing mods as the types EMSModType More...

bool	isArrayed
	Have the arrays been intialized? More...

Additional Inherited Members
Public Types inherited from CMSModSpecSet_Base
typedef list< CRef< CMSModSpec > >	Tdata

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

@MSModSpecSet.hpp User-defined methods of the data storage class.

This file was originally generated by application DATATOOL using the following specifications: 'omssa.asn'.

New methods or data members can be added to it if needed. See also: MSModSpecSet_.hpp

Definition at line 54 of file MSModSpecSet.hpp.

Member Typedef Documentation

◆ Tparent

typedef CMSModSpecSet_Base CMSModSpecSet::Tparent

private

Definition at line 56 of file MSModSpecSet.hpp.

Constructor & Destructor Documentation

◆ CMSModSpecSet() [1/2]

CMSModSpecSet::CMSModSpecSet ( void )

inline

Definition at line 156 of file MSModSpecSet.hpp.

◆ ~CMSModSpecSet()

CMSModSpecSet::~CMSModSpecSet ( void )

Definition at line 54 of file MSModSpecSet.cpp.

◆ CMSModSpecSet() [2/2]

CMSModSpecSet::CMSModSpecSet ( const CMSModSpecSet & value )

private

Member Function Documentation

◆ Append()

void CMSModSpecSet::Append ( const CMSModSpecSet & ModsIn )

concatenates in another CMSModSpecSet

Definition at line 129 of file MSModSpecSet.cpp.

References CMSModSpecSet_Base::CanGet(), CMSModSpecSet_Base::Get(), i, and CMSModSpecSet_Base::Set().

Referenced by CSearchHelper::ReadModFiles().

◆ CreateArrays()

void CMSModSpecSet::CreateArrays ( void )

creates arrays for the existing set

Definition at line 59 of file MSModSpecSet.cpp.

References eMSMod_max, ERR_POST_X, CMSModSpecSet_Base::Get(), i, isArrayed, kMaxAAs, kMaxNameSize, ModChar, ModMass, ModNames, ModTypes, MSSCALE2INT, NeutralLoss, NumModChars, UnimodNames, UniqueAA, and Warning().

Referenced by COMSSA::Run(), and COmssa2pepxmlApplication::Run().

◆ GetModChar()

char CMSModSpecSet::GetModChar	(	int	Mod,
		int	Number
	)		const

inline

get modification AA's

Parameters

Mod	the modification number
Number	the residue number for the modification type

Definition at line 174 of file MSModSpecSet.hpp.

References ModChar.

Referenced by CCleave::CheckAAMods(), CPepXML::ConvertModSetting(), and CMassArray::Init().

◆ GetModMass()

int CMSModSpecSet::GetModMass ( int Mod ) const

inline

get modification mass

get the number of modification AA's

Parameters

Mod	the modification number

Definition at line 184 of file MSModSpecSet.hpp.

References ModMass.

Referenced by CCleave::CheckAAMods(), CCleave::CheckNonSpecificMods(), CPepXML::ConvertModifications(), CPepXML::ConvertModSetting(), CMassArray::Init(), and COMSSABase::PrintMods().

◆ GetModName()

const char * CMSModSpecSet::GetModName ( int Mod ) const

inline

get modification friendly name

Parameters

Mod	the modification number

Definition at line 210 of file MSModSpecSet.hpp.

References ModNames.

Referenced by CMSHits::MakeModString(), and COMSSABase::PrintMods().

◆ GetModNumChars()

int CMSModSpecSet::GetModNumChars ( int Mod ) const

inline

get the number of modification AA's

get modification mass

Parameters

Mod	the modification number

Definition at line 200 of file MSModSpecSet.hpp.

References NumModChars.

Referenced by CCleave::CheckAAMods(), CPepXML::ConvertModSetting(), and CMassArray::Init().

◆ GetModType()

EMSModType CMSModSpecSet::GetModType ( int Mod ) const

inline

get modification type

Parameters

Mod	the modification number

Definition at line 230 of file MSModSpecSet.hpp.

References ModTypes.

Referenced by CPepXML::ConvertModifications(), CPepXML::ConvertModSetting(), CMSMod::Init(), CSearch< LEGACY, NHITS >::Search(), and CSearch< LEGACY, NHITS >::UpdateWithNewPep().

◆ GetNeutralLoss()

int CMSModSpecSet::GetNeutralLoss ( int Mod ) const

inline

get neutral loss

Parameters

Mod	the modification number

Definition at line 190 of file MSModSpecSet.hpp.

References NeutralLoss.

Referenced by CCleave::CheckAAMods(), and CCleave::CheckNonSpecificMods().

◆ GetUnimodName()

const char * CMSModSpecSet::GetUnimodName ( int Mod ) const

inline

get unimod name

Parameters

Mod	the modification number

Definition at line 220 of file MSModSpecSet.hpp.

References UnimodNames.

Referenced by CPepXML::ConvertModSetting().

◆ IsArrayed()

bool CMSModSpecSet::IsArrayed ( void )

inline

Have the arrays been intialized?

Definition at line 162 of file MSModSpecSet.hpp.

References isArrayed.

Referenced by CMassArray::Init(), and CMSMod::Init().

◆ operator=()

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

private

Member Data Documentation

◆ isArrayed

bool CMSModSpecSet::isArrayed

private

Have the arrays been intialized?

Definition at line 149 of file MSModSpecSet.hpp.

Referenced by CreateArrays(), and IsArrayed().

◆ kMaxAAs

const int CMSModSpecSet::kMaxAAs = 3

static

the maximum number of AA's a modification can affect

Definition at line 120 of file MSModSpecSet.hpp.

Referenced by CreateArrays().

◆ kMaxNameSize

const int CMSModSpecSet::kMaxNameSize = 128

static

the maximum size of an modification friendly name

Definition at line 117 of file MSModSpecSet.hpp.

Referenced by CreateArrays().

◆ ModChar

char CMSModSpecSet::ModChar[eMSMod_max][kMaxAAs]

private

the AA's affected

Definition at line 128 of file MSModSpecSet.hpp.

Referenced by CreateArrays(), and GetModChar().

◆ ModMass

int CMSModSpecSet::ModMass[eMSMod_max]

private

the integer scaled mass of the mod

Definition at line 134 of file MSModSpecSet.hpp.

Referenced by CreateArrays(), and GetModMass().

◆ ModNames

char CMSModSpecSet::ModNames[eMSMod_max][kMaxNameSize]

private

friendly names

Definition at line 140 of file MSModSpecSet.hpp.

Referenced by CreateArrays(), and GetModName().

◆ ModTypes

EMSModType CMSModSpecSet::ModTypes[eMSMod_max]

private

categorizes existing mods as the types EMSModType

Definition at line 146 of file MSModSpecSet.hpp.

Referenced by CreateArrays(), and GetModType().

◆ NeutralLoss

int CMSModSpecSet::NeutralLoss[eMSMod_max]

private

the integer scaled mass of the neutral loss

Definition at line 137 of file MSModSpecSet.hpp.

Referenced by CreateArrays(), and GetNeutralLoss().

◆ NumModChars

int CMSModSpecSet::NumModChars[eMSMod_max]

private

the number of AA's affected

Definition at line 131 of file MSModSpecSet.hpp.

Referenced by CreateArrays(), and GetModNumChars().

◆ UnimodNames

char CMSModSpecSet::UnimodNames[eMSMod_max][kMaxNameSize]

private

friendly names

Definition at line 143 of file MSModSpecSet.hpp.

Referenced by CreateArrays(), and GetUnimodName().

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

include/objects/omssa/MSModSpecSet.hpp
src/objects/omssa/MSModSpecSet.cpp

Public Member Functions

Static Public Attributes

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Tparent

Constructor & Destructor Documentation

◆ CMSModSpecSet() [1/2]

◆ ~CMSModSpecSet()

◆ CMSModSpecSet() [2/2]

Member Function Documentation

◆ Append()

◆ CreateArrays()

◆ GetModChar()

◆ GetModMass()

◆ GetModName()

◆ GetModNumChars()

◆ GetModType()

◆ GetNeutralLoss()

◆ GetUnimodName()

◆ IsArrayed()

◆ operator=()

Member Data Documentation

◆ isArrayed

◆ kMaxAAs

◆ kMaxNameSize

◆ ModChar

◆ ModMass

◆ ModNames

◆ ModTypes

◆ NeutralLoss

◆ NumModChars

◆ UnimodNames