CMod Class Reference

Search Toolkit Book for CMod

#include <Mod.hpp>

List of all members.

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Detailed Description

contains information for a post translational modification at a particular sequence site

Definition at line 55 of file Mod.hpp.

Public Types
typedef const char *	TSite
	type for a site on a sequence
typedef int	TMass
	type for masses
typedef int	TEnum
	what is the type of the mod?
typedef int	TFixed
	is the mod fixed?
Public Member Functions
	CMod (void)
	default constructor
	~CMod (void)
bool	isResidueSubset (const string residues)
size_t	name_distance (const string name)
	CMod (void)
	default constructor
	CMod (const CMod &Old)
	copy constructor
const CMod &	operator= (const CMod &rhs)
	assignment
void	Reset (void)
	reset to default values
TSite	GetSite (void) const
	Get the site position.
TSite &	SetSite (void)
	Set the site postion.
TMass	GetPrecursorDelta (void) const
	Get the mass to be added to the precursor mass.
TMass &	SetPrecursorDelta (void)
	Set the site postion.
TMass	GetProductDelta (void) const
	Get the mass to be added to the product mass.
TMass &	SetProductDelta (void)
	Set the site postion.
TEnum	GetEnum (void) const
	Get mod type.
TEnum &	SetEnum (void)
	Set the mod type.
TFixed	GetFixed (void) const
	Is the mod fixed?
TFixed &	SetFixed (void)
	set mod state (1 = fixed)
Private Types
typedef CMod_Base	Tparent
Private Member Functions
	CMod (const CMod &value)
	copy constructor
CMod &	operator= (const CMod &value)
	assignment
Private Attributes
const char *	Site
	the position within the peptide of a variable modification
int	PrecursorDelta
	the modification mass for the precursor
int	ProductDelta
	the modification mass for the product
int	ModEnum
	the modification type (used for saving for output)
int	IsFixed
	track fixed mods, 1 == fixed

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Member Typedef Documentation

typedef int CMod::TEnum

what is the type of the mod? Definition at line 189 of file msms.hpp.

typedef int CMod::TFixed

is the mod fixed? Definition at line 194 of file msms.hpp.

typedef int CMod::TMass

type for masses Definition at line 184 of file msms.hpp.

typedef CMod_Base CMod::Tparent [private]

Definition at line 57 of file Mod.hpp.

typedef const char* CMod::TSite

type for a site on a sequence Definition at line 179 of file msms.hpp.

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Constructor & Destructor Documentation

CMod::CMod (  void   )  [inline]

default constructor Definition at line 77 of file Mod.hpp.

CMod::~CMod (  void   )

Definition at line 80 of file Mod.cpp.

CMod::CMod (  const CMod &  value  )  [inline, private]

copy constructor Definition at line 319 of file msms.hpp.

CMod::CMod (  void   )

default constructor

CMod::CMod (  const CMod &  Old  )

copy constructor

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Member Function Documentation

CMod::TEnum CMod::GetEnum (  void   )  const [inline]

Get mod type. Definition at line 397 of file msms.hpp. References ModEnum.

CMod::TFixed CMod::GetFixed (  void   )  const [inline]

Is the mod fixed? Definition at line 415 of file msms.hpp. References IsFixed. Referenced by CMSHit::RecordModInfo().

CMod::TMass CMod::GetPrecursorDelta (  void   )  const [inline]

Get the mass to be added to the precursor mass. Definition at line 361 of file msms.hpp. References PrecursorDelta.

CMod::TMass CMod::GetProductDelta (  void   )  const [inline]

Get the mass to be added to the product mass. Definition at line 379 of file msms.hpp. References ProductDelta. Referenced by CLadder::CalcDelta().

CMod::TSite CMod::GetSite (  void   )  const [inline]

Get the site position. Definition at line 343 of file msms.hpp. References Site. Referenced by CSearch< LEGACY, NHITS >::CalcModIndex(), CSearch< LEGACY, NHITS >::CountModSites(), and CMSHit::RecordModInfo().

BEGIN_unimod_SCOPE bool CMod::isResidueSubset (  const string  residues  )

Definition at line 53 of file Mod.cpp. References ITERATE.

size_t CMod::name_distance (  const string  name  )

Definition at line 69 of file Mod.cpp. References CDictionaryUtil::GetEditDistance(), and GetTitle().

const CMod& CMod::operator= (  const CMod &  rhs  )

assignment

const CMod & CMod::operator= (  const CMod &  value  )  [inline, private]

assignment Definition at line 328 of file msms.hpp. References IsFixed, ModEnum, PrecursorDelta, ProductDelta, and Site.

void CMod::Reset (  void   )  [inline]

reset to default values Definition at line 306 of file msms.hpp. References IsFixed, ModEnum, PrecursorDelta, ProductDelta, and Site.

CMod::TEnum & CMod::SetEnum (  void   )  [inline]

Set the mod type. Definition at line 406 of file msms.hpp. References ModEnum. Referenced by CCleave::CheckAAMods(), and CCleave::CheckNonSpecificMods().

CMod::TFixed & CMod::SetFixed (  void   )  [inline]

set mod state (1 = fixed) Definition at line 424 of file msms.hpp. References IsFixed. Referenced by CCleave::CheckAAMods(), and CCleave::CheckNonSpecificMods().

CMod::TMass & CMod::SetPrecursorDelta (  void   )  [inline]

Set the site postion. Definition at line 370 of file msms.hpp. References PrecursorDelta. Referenced by CCleave::CheckAAMods(), and CCleave::CheckNonSpecificMods().

CMod::TMass & CMod::SetProductDelta (  void   )  [inline]

Set the site postion. Definition at line 388 of file msms.hpp. References ProductDelta. Referenced by CCleave::CheckAAMods(), and CCleave::CheckNonSpecificMods().

CMod::TSite & CMod::SetSite (  void   )  [inline]

Set the site postion. Definition at line 352 of file msms.hpp. References Site. Referenced by CCleave::CheckAAMods(), and CCleave::CheckNonSpecificMods().

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Member Data Documentation

int CMod::IsFixed [private]

track fixed mods, 1 == fixed Definition at line 290 of file msms.hpp. Referenced by GetFixed(), operator=(), Reset(), and SetFixed().

int CMod::ModEnum [private]

the modification type (used for saving for output) Definition at line 285 of file msms.hpp. Referenced by GetEnum(), operator=(), Reset(), and SetEnum().

int CMod::PrecursorDelta [private]

the modification mass for the precursor Definition at line 275 of file msms.hpp. Referenced by GetPrecursorDelta(), operator=(), Reset(), and SetPrecursorDelta().

int CMod::ProductDelta [private]

the modification mass for the product Definition at line 280 of file msms.hpp. Referenced by GetProductDelta(), operator=(), Reset(), and SetProductDelta().

const char* CMod::Site [private]

the position within the peptide of a variable modification Definition at line 270 of file msms.hpp. Referenced by GetSite(), operator=(), Reset(), and SetSite().

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

• include/algo/ms/formats/unimod/Mod.hpp
• src/algo/ms/omssa/msms.hpp
• src/algo/ms/formats/unimod/Mod.cpp

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