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CMod Class Reference

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

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

Public Types

typedef const char * TSite
 type for a site on a sequence More...
 
typedef int TMass
 type for masses More...
 
typedef int TEnum
 what is the type of the mod? More...
 
typedef int TFixed
 is the mod fixed? More...
 

Public Member Functions

 CMod (void)
 default constructor More...
 
 CMod (const CMod &Old)
 copy constructor More...
 
const CModoperator= (const CMod &rhs)
 assignment More...
 
void Reset (void)
 reset to default values More...
 
TSite GetSite (void) const
 Get the site position. More...
 
TSiteSetSite (void)
 Set the site postion. More...
 
TMass GetPrecursorDelta (void) const
 Get the mass to be added to the precursor mass. More...
 
TMassSetPrecursorDelta (void)
 Set the site postion. More...
 
TMass GetProductDelta (void) const
 Get the mass to be added to the product mass. More...
 
TMassSetProductDelta (void)
 Set the site postion. More...
 
TEnum GetEnum (void) const
 Get mod type. More...
 
TEnumSetEnum (void)
 Set the mod type. More...
 
TFixed GetFixed (void) const
 Is the mod fixed? More...
 
TFixedSetFixed (void)
 set mod state (1 = fixed) More...
 

Private Attributes

const char * Site
 the position within the peptide of a variable modification More...
 
int PrecursorDelta
 the modification mass for the precursor More...
 
int ProductDelta
 the modification mass for the product More...
 
int ModEnum
 the modification type (used for saving for output) More...
 
int IsFixed
 track fixed mods, 1 == fixed More...
 

Detailed Description

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

Definition at line 172 of file msms.hpp.

Member Typedef Documentation

◆ TEnum

typedef int CMod::TEnum

what is the type of the mod?

Definition at line 189 of file msms.hpp.

◆ TFixed

typedef int CMod::TFixed

is the mod fixed?

Definition at line 194 of file msms.hpp.

◆ TMass

typedef int CMod::TMass

type for masses

Definition at line 184 of file msms.hpp.

◆ TSite

typedef const char* CMod::TSite

type for a site on a sequence

Definition at line 179 of file msms.hpp.

Constructor & Destructor Documentation

◆ CMod() [1/2]

CMod::CMod ( void  )
inline

default constructor

Definition at line 297 of file msms.hpp.

References Reset().

◆ CMod() [2/2]

CMod::CMod ( const CMod Old)
inline

copy constructor

Definition at line 319 of file msms.hpp.

Member Function Documentation

◆ GetEnum()

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

Get mod type.

Definition at line 397 of file msms.hpp.

References ModEnum.

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

◆ GetFixed()

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

◆ GetPrecursorDelta()

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.

◆ GetProductDelta()

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().

◆ GetSite()

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

◆ operator=()

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

assignment

Definition at line 328 of file msms.hpp.

References IsFixed, ModEnum, PrecursorDelta, ProductDelta, and Site.

◆ Reset()

void CMod::Reset ( void  )
inline

reset to default values

Definition at line 306 of file msms.hpp.

References IsFixed, ModEnum, PrecursorDelta, ProductDelta, and Site.

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

◆ SetEnum()

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().

◆ SetFixed()

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(), CCleave::CheckNonSpecificMods(), and CSearch< LEGACY, NHITS >::DeleteVariableOverlap().

◆ SetPrecursorDelta()

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().

◆ SetProductDelta()

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().

◆ SetSite()

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().

Member Data Documentation

◆ IsFixed

int CMod::IsFixed
private

track fixed mods, 1 == fixed

Definition at line 290 of file msms.hpp.

Referenced by GetFixed(), operator=(), Reset(), and SetFixed().

◆ ModEnum

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().

◆ PrecursorDelta

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().

◆ ProductDelta

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().

◆ Site

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().


The documentation for this class was generated from the following file:
Modified on Mon Mar 04 05:14:50 2024 by modify_doxy.py rev. 669887