NCBI C++ ToolKit
Classes | Macros | Typedefs | Enumerations | Variables
msscore.hpp File Reference
#include <vector>
#include <map>
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Classes

class  CMSBasicPeak
 minimal information about a peak More...
 
class  CMSBasicMatchedPeak
 information about a matched peak. More...
 
class  CMSMatchedPeak
 holds match of a spectrum peak to a theoretical m/z value More...
 
class  CMSMatchedPeakSet
 container for a set of matches More...
 
class  CMSMatchedPeakSetMap
 contains a map of charge and series to a set of matches More...
 
class  CMSSpectrumMatch
 container for match between a spectrum and a mass ladder More...
 

Macros

#define NCBI_XOMSSA_EXPORT
 

Typedefs

typedef pair< TMSCharge, EMSIonSeriesTSeriesChargePair
 pair of ion series, charge More...
 
typedef std::vector< EMSIonSeriesTIonSeriesSet
 set of ion series specifiers More...
 
typedef std::vector< CMSMatchedPeak * > TMatchedPeakSet
 container typedef for a set of matches More...
 
typedef std::map< int, CMSMatchedPeakSet * > TIonSeriesMatchMap
 map from an ion series to a set of matched peak sets More...
 

Enumerations

enum  EMSIonSeries {
  eMSIonTypeA , eMSIonTypeB , eMSIonTypeC , eMSIonTypeX ,
  eMSIonTypeY , eMSIonTypeZ , eMSIonParent , eMSIonInternal ,
  eMSIonImmonium , eMSIonTypeUnknown , eMSIonTypeAdot , eMSIonTypeXCO2 ,
  eMSIonTypeACO2 , eMSIonTypeMax
}
 enumeration of ion series More...
 
enum  EMSMatchType {
  eMSMatchTypeUnknown , eMSMatchTypeNotTyped , eMSMatchTypeIndependent , eMSMatchTypeSemiIndependent ,
  eMSMatchTypeDependent , eMSMatchTypeNoSearch , eMSMatchTypeNoMatch , eMSMatchTypeTerminus
}
 enumeration to denote the type of match More...
 
enum  EMSTerminalBias { eMSNoTerminalBias , eMSNTerminalBias , eMSCTerminalBias , eMSBothTerminalBias }
 is the peptide statistically biased in any way on either end? More...
 

Variables

const int kIonDirection [] = { 1, 1, 1, -1, -1, -1, 1, 1, 1, 0, 1 , -1, 1 }
 ion direction. More...
 

Macro Definition Documentation

◆ NCBI_XOMSSA_EXPORT

#define NCBI_XOMSSA_EXPORT

Definition at line 58 of file msscore.hpp.

Typedef Documentation

◆ TIonSeriesMatchMap

map from an ion series to a set of matched peak sets

Definition at line 460 of file msscore.hpp.

◆ TIonSeriesSet

typedef std::vector<EMSIonSeries> TIonSeriesSet

set of ion series specifiers

Definition at line 93 of file msscore.hpp.

◆ TMatchedPeakSet

typedef std::vector<CMSMatchedPeak *> TMatchedPeakSet

container typedef for a set of matches

Definition at line 371 of file msscore.hpp.

◆ TSeriesChargePair

pair of ion series, charge

Definition at line 90 of file msscore.hpp.

Enumeration Type Documentation

◆ EMSIonSeries

enumeration of ion series

should overlap with EMSIonType in omssa object loaders

Enumerator
eMSIonTypeA 
eMSIonTypeB 
eMSIonTypeC 
eMSIonTypeX 
eMSIonTypeY 
eMSIonTypeZ 
eMSIonParent 
eMSIonInternal 
eMSIonImmonium 
eMSIonTypeUnknown 
eMSIonTypeAdot 
eMSIonTypeXCO2 
eMSIonTypeACO2 
eMSIonTypeMax 

Definition at line 68 of file msscore.hpp.

◆ EMSMatchType

enumeration to denote the type of match

Enumerator
eMSMatchTypeUnknown 

unknown if there is a match or not, i.e.

default state

eMSMatchTypeNotTyped 

there is a match but the type is unknown

eMSMatchTypeIndependent 

the match is statistically independent

eMSMatchTypeSemiIndependent 

the match is independent to first order

eMSMatchTypeDependent 

the match is statistically dependent

eMSMatchTypeNoSearch 

the peak was not searched, e.g.

b1

eMSMatchTypeNoMatch 

peak was searched, but no match

eMSMatchTypeTerminus 

statistically biased terminal match

Definition at line 283 of file msscore.hpp.

◆ EMSTerminalBias

is the peptide statistically biased in any way on either end?

Enumerator
eMSNoTerminalBias 
eMSNTerminalBias 
eMSCTerminalBias 
eMSBothTerminalBias 

Definition at line 550 of file msscore.hpp.

Variable Documentation

◆ kIonDirection

const int kIonDirection[] = { 1, 1, 1, -1, -1, -1, 1, 1, 1, 0, 1 , -1, 1 }

ion direction.

1 = N->C, -1 = C->N

Definition at line 86 of file msscore.hpp.

Referenced by CLadder::CreateLadder(), CSearch< LEGACY, NHITS >::MatchAndSort(), and CLadder::Or().

Modified on Fri Apr 12 17:22:16 2024 by modify_doxy.py rev. 669887