Search Toolkit Book for CMSSpectrumMatch

container for match between a spectrum and a mass ladder More...

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

Inheritance diagram for CMSSpectrumMatch:

Collaboration diagram for CMSSpectrumMatch:

Public Member Functions
	CMSSpectrumMatch (void)
	c'tor More...

virtual	~CMSSpectrumMatch ()
	d'tor More...

const TMSMZ	GetExpMass (void) const
	Get the experimental m/z of the spectrum. More...

TMSMZ &	SetExpMass (void)
	Set the experimental mass of the spectrum. More...

const TMSMZ	GetTheoreticalMass (void) const
	return theoretical mass of the hit More...

TMSMZ &	SetTheoreticalMass (void)
	set the theoretical mass of the hit More...

const TMSCharge	GetCharge (void) const
	get the charge More...

TMSCharge &	SetCharge ()
	set the charge More...

const int	GetSum (void) const
	Get the sum of ranks. More...

int &	SetSum (void)
	Set the sum of ranks. More...

const int	GetM (void) const
	Get the number of matched peaks. More...

int &	SetM (void)
	Set the number of matched peaks. More...

const int	GetN (void) const
	Get the number of experimental peaks. More...

int &	SetN (void)
	Set the number of experimental peaks. More...

const int	GetHits (void) const
	return the size of the HitInfo array More...

int &	SetHits (void)
	set the size of the HitInfo array More...

const CMSBasicMatchedPeak &	GetHitInfo (int n) const
	Get the hit info at array position n. More...

CMSBasicMatchedPeak &	SetHitInfo (int n)
	Set the hit info at array position n. More...

void	CreateHitInfo (void)
	initialize the HitInfo array delete any existing array size is determined by GetHits() More...

CMSBasicMatchedPeak *	Find (TMSNumber Number, TMSCharge ChargeIn, TMSIonSeries Series)
	find a peak within HitInfo More...

const CMSMatchedPeakSetMap &	GetIonSeriesMatchMap (void) const
	get map from ion series to CMSMatchedPeakSet * More...

CMSMatchedPeakSetMap &	SetIonSeriesMatchMap (void)
	Set map from ion series to CMSMatchedPeakSet *. More...

void	FillMatchedPeaks (TMSCharge ChargeIn, TMSIonSeries Series, unsigned Size, TMSIntensity MinIntensity, bool Skipb1, EMSTerminalBias TerminalIon, int Maxproductions, string &Sequence, bool NoProline)
	copies hit array into match array fills in missing peaks does not fill in exp peak values. More...

const double	CalcPoissonMean (double ProbTerminal=0.0L, int NumTerminalMasses=2, double ProbDependent=0.0L, int NumUniqueMasses=19, double ToleranceAdjust=1.0L) const
	calculate the mean value of the poisson distribution for this match More...

const double	CalcPoisson (double Mean, int i) const
	calulate the poisson distribution More...

const double	CalcPoissonTopHit (double Mean, int i, double TopHitProb) const
	calculates the poisson times the top n hit probability More...

const double	CalcPvalue (double Mean, int HitsIn) const
	calculate the p-value using poisson distribution More...

const double	CalcNormalTopHit (double Mean, double TopHitProb) const
	integrate CalcPoissonTopHit over all i More...

const double	CalcPvalueTopHit (double Mean, int HitsIn, double Normal, double TopHitProb) const
	calculate the p-value using poisson distribution and the top hit prob More...

const double	CalcRankProb (void) const
	calculate the rank score More...

const TMSMZ	GetMeanDelta (void) const
	Calc mean delta. More...

const TMSMZ	GetStdDevDelta (void) const
	Calc std dev of delta. More...

const TMSMZ	GetMaxDelta (void) const
	calc max abs difference between experimental and theoretical mass values More...

Private Member Functions
	CMSSpectrumMatch (const CMSSpectrumMatch &in)

Private Attributes
CMSBasicMatchedPeak *	HitInfo
	list of matched peaks ideally, this would be an array of pointers to allow each element to be virtual, but efficiency requires that it be an array. More...

int	Hits
	size of HitInfo array More...

TMSMZ	ExpMass
	the experimental mass More...

TMSMZ	TheoreticalMass
	theoretical mass More...

TMSCharge	Charge
	the charge of the hit More...

int	Sum
	Sum of Ranks. More...

int	M
	Number of matched peaks. More...

int	N
	Number of exp peaks. More...

CMSMatchedPeakSetMap	IonSeriesMatchMap
	map from ion series to matched peak sets More...

Detailed Description

container for match between a spectrum and a mass ladder

base class for omssa CMSHit

Definition at line 562 of file msscore.hpp.

Constructor & Destructor Documentation

◆ CMSSpectrumMatch() [1/2]

CMSSpectrumMatch::CMSSpectrumMatch ( void )

c'tor

Definition at line 247 of file msscore.cpp.

◆ ~CMSSpectrumMatch()

CMSSpectrumMatch::~CMSSpectrumMatch ( )

virtual

d'tor

deletes the HitInfo Array

Definition at line 258 of file msscore.cpp.

References HitInfo.

◆ CMSSpectrumMatch() [2/2]

CMSSpectrumMatch::CMSSpectrumMatch ( const CMSSpectrumMatch & in )

inlineprivate

Definition at line 786 of file msscore.hpp.

Member Function Documentation

◆ CalcNormalTopHit()

const double CMSSpectrumMatch::CalcNormalTopHit	(	double	Mean,
		double	TopHitProb
	)		const

integrate CalcPoissonTopHit over all i

Parameters

Mean	mean value of poisson
TopHitProb	probability for top n hits

Returns: integral

Definition at line 509 of file msscore.cpp.

References CalcPoissonTopHit(), and i.

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

◆ CalcPoisson()

const double CMSSpectrumMatch::CalcPoisson	(	double	Mean,
		int	i
	)		const

calulate the poisson distribution

Parameters

Mean	mean value of poisson
i	counts

Returns: value of poisson at i

Definition at line 496 of file msscore.cpp.

References i, and MSLNGAMMA.

Referenced by CalcPvalue().

◆ CalcPoissonMean()

const double CMSSpectrumMatch::CalcPoissonMean	(	double	ProbTerminal = `0.0L`,
		int	NumTerminalMasses = `2`,
		double	ProbDependent = `0.0L`,
		int	NumUniqueMasses = `19`,
		double	ToleranceAdjust = `1.0L`
	)		const

calculate the mean value of the poisson distribution for this match

Parameters

ProbTerminal	the probability of a terminal peak
NumTerminalMasses	the number of terminal masses searched (2 for trypsin)
ProbDependent	the probability of a peak following a peak
NumUniqueMasses	the number of unique masses searched (19 with no modifications)
ToleranceAdjust	the fraction to adjust mass tolerance > 0 and <=1

Returns: mean of poisson

Definition at line 452 of file msscore.cpp.

References _TRACE, eMSMatchTypeDependent, eMSMatchTypeNoSearch, eMSMatchTypeTerminus, CMSMatchedPeak::GetExpIons(), GetIonSeriesMatchMap(), CMSMatchedPeak::GetMassTolerance(), CMSMatchedPeakSet::GetMatchedPeakSet(), CMSMatchedPeakSetMap::GetMatchMap(), CMSMatchedPeak::GetMatchType(), and i.

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

◆ CalcPoissonTopHit()

const double CMSSpectrumMatch::CalcPoissonTopHit	(	double	Mean,
		int	i,
		double	TopHitProb
	)		const

calculates the poisson times the top n hit probability

Parameters

Mean	mean value of poisson
i	counts
TopHitProb	probability for top n hits

Returns: value of poisson times top hit prob at i

Definition at line 501 of file msscore.cpp.

References i, and MSLNGAMMA.

Referenced by CalcNormalTopHit(), and CalcPvalueTopHit().

◆ CalcPvalue()

const double CMSSpectrumMatch::CalcPvalue	(	double	Mean,
		int	HitsIn
	)		const

calculate the p-value using poisson distribution

Parameters

Mean	mean value of poisson
HitsIn	number of hits

Returns: p-value

Definition at line 526 of file msscore.cpp.

References CalcPoisson(), epsilon, i, and MSDOUBLELIMIT.

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

◆ CalcPvalueTopHit()

const double CMSSpectrumMatch::CalcPvalueTopHit	(	double	Mean,
		int	HitsIn,
		double	Normal,
		double	TopHitProb
	)		const

calculate the p-value using poisson distribution and the top hit prob

Parameters

Mean	mean value of poisson
HitsIn	number of hits
Normal	the integral of the distribution, used to normalize
TopHitProb	the probability of a top n hit.

Returns: p-value

Definition at line 554 of file msscore.cpp.

References CalcPoissonTopHit(), epsilon, i, and MSDOUBLELIMIT.

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

◆ CalcRankProb()

const double CMSSpectrumMatch::CalcRankProb ( void ) const

calculate the rank score

Returns: probability of given ranks

Definition at line 585 of file msscore.cpp.

References GetM(), GetN(), GetSum(), and MSERF.

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

◆ CreateHitInfo()

void CMSSpectrumMatch::CreateHitInfo ( void )

initialize the HitInfo array delete any existing array size is determined by GetHits()

Definition at line 263 of file msscore.cpp.

References GetHits(), and HitInfo.

Referenced by CMSHit::RecordMatches().

◆ FillMatchedPeaks()

void CMSSpectrumMatch::FillMatchedPeaks	(	TMSCharge	ChargeIn,
		TMSIonSeries	Series,
		unsigned	Size,
		TMSIntensity	MinIntensity,
		bool	Skipb1,
		EMSTerminalBias	TerminalIon,
		int	Maxproductions,
		string &	Sequence,
		bool	NoProline
	)

copies hit array into match array fills in missing peaks does not fill in exp peak values.

This has to be done by the calling algorithm.

Parameters

ChargeIn	charge of the ion series to fill
Series	ion series
size	length of the ion series
MinIntensity	the minimum intensity of the peak to consider it as a match
Skipb1	should the first forward going ion be ignored?
TerminalIon	is either of the terminal ions statistically biased, e.g. only K or R at Cterm?
Maxproductions	the number of ions in the ions series actually calculated
Sequence	the sequence (used for proline rule)
NoProline	no n term proline cleavage

Definition at line 287 of file msscore.cpp.

References CMSMatchedPeakSetMap::CreateSeries(), eMSBothTerminalBias, eMSCTerminalBias, eMSMatchTypeDependent, eMSMatchTypeIndependent, eMSMatchTypeNoSearch, eMSMatchTypeNotTyped, eMSMatchTypeSemiIndependent, eMSMatchTypeTerminus, eMSMatchTypeUnknown, eMSNTerminalBias, Find(), GetExpMass(), CMSBasicPeak::GetIntensity(), CMSMatchedPeakSet::GetMatchedPeakSet(), i, CMSBasicMatchedPeak::IsForwardSeries(), SetIonSeriesMatchMap(), CMSMatchedPeakSet::SetMatchedPeakSet(), and ncbi::grid::netcache::search::fields::size.

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

◆ Find()

CMSBasicMatchedPeak * CMSSpectrumMatch::Find	(	TMSNumber	Number,
		TMSCharge	ChargeIn,
		TMSIonSeries	Series
	)

find a peak within HitInfo

Parameters

Number	number of the peak, starting with 0
ChargeIn	charge of peak
Series	the series to search

Returns: found peak (0 if not found)

Definition at line 271 of file msscore.cpp.

References CMSBasicMatchedPeak::GetCharge(), GetHitInfo(), GetHits(), CMSBasicMatchedPeak::GetIonSeries(), CMSBasicMatchedPeak::GetNumber(), i, and SetHitInfo().

Referenced by FillMatchedPeaks().

◆ GetCharge()

const TMSCharge CMSSpectrumMatch::GetCharge ( void ) const

inline

get the charge

Definition at line 846 of file msscore.hpp.

References Charge.

Referenced by CSearch< LEGACY, NHITS >::CalcNSort(), CMSHit::RecordMatches(), and CSearch< LEGACY, NHITS >::SetResult().

◆ GetExpMass()

const TMSMZ CMSSpectrumMatch::GetExpMass ( void ) const

inline

Get the experimental m/z of the spectrum.

Definition at line 822 of file msscore.hpp.

References ExpMass.

Referenced by CSearch< LEGACY, NHITS >::CalcNSort(), FillMatchedPeaks(), CSearch< LEGACY, NHITS >::PepCharge(), and CSearch< LEGACY, NHITS >::SetResult().

◆ GetHitInfo()

const CMSBasicMatchedPeak & CMSSpectrumMatch::GetHitInfo ( int n ) const

inline

Get the hit info at array position n.

Parameters

n	array position

Definition at line 906 of file msscore.hpp.

References HitInfo, and n.

Referenced by CSearch< LEGACY, NHITS >::AddIonsToHit(), CMSHit::CountHitsByType(), Find(), GetMaxDelta(), GetMeanDelta(), and GetStdDevDelta().

◆ GetHits()

const int CMSSpectrumMatch::GetHits ( void ) const

inline

return the size of the HitInfo array

Definition at line 894 of file msscore.hpp.

References Hits.

Referenced by CMSPeak::AddHit(), CSearch< LEGACY, NHITS >::AddIonsToHit(), CMSHit::CountHits(), CMSHit::CountHitsByType(), CreateHitInfo(), Find(), GetMaxDelta(), GetMeanDelta(), and GetStdDevDelta().

◆ GetIonSeriesMatchMap()

const CMSMatchedPeakSetMap & CMSSpectrumMatch::GetIonSeriesMatchMap ( void ) const

inline

get map from ion series to CMSMatchedPeakSet *

Definition at line 918 of file msscore.hpp.

References IonSeriesMatchMap.

Referenced by CalcPoissonMean().

◆ GetM()

const int CMSSpectrumMatch::GetM ( void ) const

inline

Get the number of matched peaks.

Definition at line 870 of file msscore.hpp.

References M.

Referenced by CalcRankProb().

◆ GetMaxDelta()

const TMSMZ CMSSpectrumMatch::GetMaxDelta ( void ) const

calc max abs difference between experimental and theoretical mass values

Returns: const TMSMZ

Definition at line 629 of file msscore.cpp.

References abs, CMSBasicMatchedPeak::GetDelta(), GetHitInfo(), GetHits(), and i.

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

◆ GetMeanDelta()

const TMSMZ CMSSpectrumMatch::GetMeanDelta ( void ) const

Calc mean delta.

Definition at line 599 of file msscore.cpp.

References CMSBasicMatchedPeak::GetDelta(), GetHitInfo(), GetHits(), and i.

Referenced by GetStdDevDelta().

◆ GetN()

const int CMSSpectrumMatch::GetN ( void ) const

inline

Get the number of experimental peaks.

Definition at line 882 of file msscore.hpp.

References N.

Referenced by CalcRankProb().

◆ GetStdDevDelta()

const TMSMZ CMSSpectrumMatch::GetStdDevDelta ( void ) const

Calc std dev of delta.

Definition at line 612 of file msscore.cpp.

References GetHitInfo(), GetHits(), GetMeanDelta(), and i.

◆ GetSum()

const int CMSSpectrumMatch::GetSum ( void ) const

inline

Get the sum of ranks.

Definition at line 858 of file msscore.hpp.

References Sum.

Referenced by CalcRankProb().

◆ GetTheoreticalMass()

const TMSMZ CMSSpectrumMatch::GetTheoreticalMass ( void ) const

inline

return theoretical mass of the hit

Definition at line 834 of file msscore.hpp.

References TheoreticalMass.

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

◆ SetCharge()

TMSCharge & CMSSpectrumMatch::SetCharge ( void )

inline

set the charge

Definition at line 852 of file msscore.hpp.

References Charge.

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

◆ SetExpMass()

TMSMZ & CMSSpectrumMatch::SetExpMass ( void )

inline

Set the experimental mass of the spectrum.

Definition at line 828 of file msscore.hpp.

References ExpMass.

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

◆ SetHitInfo()

CMSBasicMatchedPeak & CMSSpectrumMatch::SetHitInfo ( int n )

inline

Set the hit info at array position n.

note: there is an implicit assumption in the scoring code that ions of the same species are grouped together and that the ions within the species are in order

Parameters

n	array position

Definition at line 912 of file msscore.hpp.

References HitInfo, and n.

Referenced by CMSHit::CountHits(), Find(), and CMSHit::RecordMatchesScan().

◆ SetHits()

int & CMSSpectrumMatch::SetHits ( void )

inline

set the size of the HitInfo array

Definition at line 900 of file msscore.hpp.

References Hits.

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

◆ SetIonSeriesMatchMap()

CMSMatchedPeakSetMap & CMSSpectrumMatch::SetIonSeriesMatchMap ( void )

inline

Set map from ion series to CMSMatchedPeakSet *.

Definition at line 924 of file msscore.hpp.

References IonSeriesMatchMap.

Referenced by FillMatchedPeaks(), and CSearch< LEGACY, NHITS >::PepCharge().

◆ SetM()

int & CMSSpectrumMatch::SetM ( void )

inline

Set the number of matched peaks.

Definition at line 876 of file msscore.hpp.

References M.

Referenced by CMSHit::RecordMatches(), and CMSHit::RecordMatchesScan().

◆ SetN()

int & CMSSpectrumMatch::SetN ( void )

inline

Set the number of experimental peaks.

Definition at line 888 of file msscore.hpp.

References N.

Referenced by CMSHit::RecordMatches().

◆ SetSum()

int & CMSSpectrumMatch::SetSum ( void )

inline

Set the sum of ranks.

Definition at line 864 of file msscore.hpp.

References Sum.

Referenced by CMSHit::RecordMatches(), and CMSHit::RecordMatchesScan().

◆ SetTheoreticalMass()

TMSMZ & CMSSpectrumMatch::SetTheoreticalMass ( void )

inline

set the theoretical mass of the hit

Definition at line 840 of file msscore.hpp.

References TheoreticalMass.

Referenced by CMSHit::RecordMatches().

Member Data Documentation

◆ Charge

TMSCharge CMSSpectrumMatch::Charge

private

the charge of the hit

Definition at line 806 of file msscore.hpp.

Referenced by GetCharge(), and SetCharge().

◆ ExpMass

TMSMZ CMSSpectrumMatch::ExpMass

private

the experimental mass

Definition at line 800 of file msscore.hpp.

Referenced by GetExpMass(), and SetExpMass().

◆ HitInfo

CMSBasicMatchedPeak* CMSSpectrumMatch::HitInfo

private

list of matched peaks ideally, this would be an array of pointers to allow each element to be virtual, but efficiency requires that it be an array.

this assertion should be tested.

Definition at line 794 of file msscore.hpp.

Referenced by CreateHitInfo(), GetHitInfo(), SetHitInfo(), and ~CMSSpectrumMatch().

◆ Hits

int CMSSpectrumMatch::Hits

private

size of HitInfo array

Definition at line 797 of file msscore.hpp.

Referenced by GetHits(), and SetHits().

◆ IonSeriesMatchMap

CMSMatchedPeakSetMap CMSSpectrumMatch::IonSeriesMatchMap

private

map from ion series to matched peak sets

Definition at line 818 of file msscore.hpp.

Referenced by GetIonSeriesMatchMap(), and SetIonSeriesMatchMap().

◆ M

int CMSSpectrumMatch::M

private

Number of matched peaks.

Definition at line 812 of file msscore.hpp.

Referenced by GetM(), and SetM().

◆ N

int CMSSpectrumMatch::N

private

Number of exp peaks.

Definition at line 815 of file msscore.hpp.

Referenced by GetN(), and SetN().

◆ Sum

int CMSSpectrumMatch::Sum

private

Sum of Ranks.

Definition at line 809 of file msscore.hpp.

Referenced by GetSum(), and SetSum().

◆ TheoreticalMass

TMSMZ CMSSpectrumMatch::TheoreticalMass

private

theoretical mass

Definition at line 803 of file msscore.hpp.

Referenced by GetTheoreticalMass(), and SetTheoreticalMass().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CMSSpectrumMatch() [1/2]

◆ ~CMSSpectrumMatch()

◆ CMSSpectrumMatch() [2/2]

Member Function Documentation

◆ CalcNormalTopHit()

◆ CalcPoisson()

◆ CalcPoissonMean()

◆ CalcPoissonTopHit()

◆ CalcPvalue()

◆ CalcPvalueTopHit()

◆ CalcRankProb()

◆ CreateHitInfo()

◆ FillMatchedPeaks()

◆ Find()

◆ GetCharge()

◆ GetExpMass()

◆ GetHitInfo()

◆ GetHits()

◆ GetIonSeriesMatchMap()

◆ GetM()

◆ GetMaxDelta()

◆ GetMeanDelta()

◆ GetN()

◆ GetStdDevDelta()

◆ GetSum()

◆ GetTheoreticalMass()

◆ SetCharge()

◆ SetExpMass()

◆ SetHitInfo()

◆ SetHits()

◆ SetIonSeriesMatchMap()

◆ SetM()

◆ SetN()

◆ SetSum()

◆ SetTheoreticalMass()

Member Data Documentation

◆ Charge

◆ ExpMass

◆ HitInfo

◆ Hits

◆ IonSeriesMatchMap

◆ M

◆ N

◆ Sum

◆ TheoreticalMass