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NCBI C++ ToolKit: src/algo/ms/omssa/msscore.cpp Source File

(!

||

==

)

;

(!

||

==

)

;

(

= 0;

< SizeIn; ++

)

(SameDirection) j =

;

j = Other->

() -

- 1;

TIonSeriesMatchMap::iterator

;

Realsize =

(Size, Maxproductions);

().insert(std::pair <int, CMSMatchedPeakSet * > (Key, retval));

(FoundPeak && FoundPeak->

() > MinIntensity) {

LastIndex(

);

(

!= LastIndex) {

(j = LastIndex+1; j <

; j++) {

(

- LastIndex )) * (j - LastIndex) ;

MassIncrement = (

()/ChargeIn)/(Size+1);

StartMass = (

()/ChargeIn)/(Size+1);

StartIndex = LastIndex + 1;

StartMass + MassIncrement * (j - StartIndex);

NumTerminalMasses,

ProbDependent,

ToleranceAdjust

TIonSeriesMatchMap::const_iterator

;

TMatchedPeakSet::const_iterator j;

Mean += ProbDependent / NumUniqueMasses;

(

<< Mean <<

<< ProbDependent <<

<< NumUniqueMasses);

Mean += ProbTerminal / NumTerminalMasses;

exp(-Mean) * pow(Mean,

) / exp(

(

+1));

retval = exp(-Mean) * pow(Mean,

) / exp(

(

+1));

(TopHitProb != 1.0L) retval *= 1.0L - pow((1.0L-TopHitProb),

);

retval(0.0L), before(-1.0L), increment;

(

= 1;

< 1000;

++) {

(increment <= MSDOUBLELIMIT && i > 10)

;

(retval == before)

;

(HitsIn <= 0)

1.0L;

retval(0.0L), increment, beforeincrement(0.0L);

(

= 0;

< HitsIn;

++) {

(retval == 1.0L)

;

beforeincrement = increment;

retval -= beforeincrement;

retval = 1.0L - retval;

(HitsIn <= 0)

1.0L;

retval(0.0L), increment, beforeretval(-1.0), beforeincrement(0.0L);

(

= 1;

< HitsIn;

++) {

(retval == beforeretval)

;

beforeretval = retval;

beforeincrement = increment;

(retval == Normal) retval -= beforeincrement;

retval = 1.0L - retval;

Average, StdDev, Perf(1.0L);

(

() != 0.0) {

Average = (

() *(

()+1))/2.0;

StdDev = sqrt(Average * (

() -

()) / 6.0);

Perf = 0.5*(1.0 +

((

() - Average)/(StdDev*sqrt(2.0))));

(Mean/(

(

())));

StdDev += pow((

)

(

).GetDelta() - Mean, 2.0);

StdDev = pow((

)StdDev/

(), 0.5);

(

)StdDev;

information about a matched peak.

TMSNumber & SetNumber(void)

Set the ion series number.

const TMSNumber GetNumber(void) const

Get the ion series number.

const TMSMZ GetDelta(void) const

Get the mass delta.

const TMSIonSeries GetIonSeries(void) const

Get the ion type.

const TMSCharge GetCharge(void) const

Get the ion charge.

TMSCharge & SetCharge(void)

Set the ion charge.

TMSIonSeries & SetIonSeries(void)

Set the ion type.

static const int IsForwardSeries(EMSIonSeries Series)

is a particular series forward going?

const TMSIntensity GetIntensity(void) const

return the intensity of the peak

TMSMZ & SetMZ(void)

set the m/z value of the peak

TMSIntensity & SetIntensity(void)

set the intensity of the peak

static const int ChargeSeries2Key(TMSCharge Charge, TMSIonSeries Series)

convert a charge and series to a map key

const TIonSeriesMatchMap & GetMatchMap(void) const

Get the Map.

~CMSMatchedPeakSetMap()

d'tor

CMSMatchedPeakSet * CreateSeries(TMSCharge Charge, TMSIonSeries Series, int Size, int Maxproductions)

create a new ion series if the series exists and is the same size, it will reuse old array

CMSMatchedPeakSetMap(void)

c'tor

static const TMSIonSeries Key2Series(int Key)

convert a key into a series type

TIonSeriesMatchMap & SetMatchMap(void)

Set the Map.

static const TMSCharge Key2Charge(int Key)

convert a key into a charge

CMSMatchedPeakSet * SetSeries(TMSCharge Charge, TMSIonSeries Series)

get a series for modification

container for a set of matches

int & SetSize(void)

Set Size of ion series.

TMatchedPeakSet & SetMatchedPeakSet(void)

Set the match info.

virtual ~CMSMatchedPeakSet()

void Compare(CMSMatchedPeakSet *Other, bool SameDirection)

compare to another CMSMatchedPeakSet and set MatchType accordingly if there is a correlation

const int GetSize(void) const

Get Size of ion series.

const TMatchedPeakSet & GetMatchedPeakSet(void) const

Get the match info.

void DeleteMatchedPeakSet(void)

delete the MatchInfo array

virtual void CreateMatchedPeakSet(int SizeIn)

initialize the MatchInfo array delete any existing array

holds match of a spectrum peak to a theoretical m/z value

const EMSMatchType GetMatchType(void) const

Get the type of match.

const TMSExpIons GetExpIons() const

Get the exp ions per unit mass.

TMSMZ & SetMassTolerance(void)

Set the experimental mass tolerance of the peak.

const TMSMZ GetMassTolerance(void) const

Get the experimental mass tolerance of the peak.

TMSExpIons & SetExpIons()

Set the exp ions per unit mass.

virtual void Assign(CMSMatchedPeak *in)

virtual assignment operator

EMSMatchType & SetMatchType(void)

Set the type of match.

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

CMSBasicMatchedPeak & SetHitInfo(int n)

Set the hit info at array position n.

const int GetN(void) const

Get the number of experimental peaks.

const double CalcPoisson(double Mean, int i) const

calulate the poisson distribution

const TMSMZ GetExpMass(void) const

Get the experimental m/z of the spectrum.

CMSBasicMatchedPeak * HitInfo

list of matched peaks ideally, this would be an array of pointers to allow each element to be virtual...

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.

const int GetSum(void) const

Get the sum of ranks.

virtual ~CMSSpectrumMatch()

d'tor

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

calculates the poisson times the top n hit probability

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

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

const CMSMatchedPeakSetMap & GetIonSeriesMatchMap(void) const

get map from ion series to CMSMatchedPeakSet *

CMSMatchedPeakSetMap & SetIonSeriesMatchMap(void)

Set map from ion series to CMSMatchedPeakSet *.

const TMSMZ GetMeanDelta(void) const

Calc mean delta.

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

find a peak within HitInfo

const TMSMZ GetStdDevDelta(void) const

Calc std dev of delta.

const int GetM(void) const

Get the number of matched peaks.

const CMSBasicMatchedPeak & GetHitInfo(int n) const

Get the hit info at array position n.

const int GetHits(void) const

return the size of the HitInfo array

const TMSMZ GetMaxDelta(void) const

calc max abs difference between experimental and theoretical mass values

const double CalcNormalTopHit(double Mean, double TopHitProb) const

integrate CalcPoissonTopHit over all i

void CreateHitInfo(void)

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

const double CalcRankProb(void) const

calculate the rank score

CMSSpectrumMatch(void)

c'tor

const double CalcPvalue(double Mean, int HitsIn) const

calculate the p-value using poisson distribution

EMSTerminalBias

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

EMSIonSeries

enumeration of ion series

@ eMSMatchTypeTerminus

statistically biased terminal match

@ eMSMatchTypeIndependent

the match is statistically independent

@ eMSMatchTypeDependent

the match is statistically dependent

@ eMSMatchTypeSemiIndependent

the match is independent to first order

@ eMSMatchTypeNoSearch

the peak was not searched, e.g.

@ eMSMatchTypeUnknown

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

@ eMSMatchTypeNotTyped

there is a match but the type is unknown

constexpr bool empty(list< Ts... >) noexcept

const struct ncbi::grid::netcache::search::fields::SIZE size

std::istream & in(std::istream &in_, double &x_)

signed char TMSCharge

charge type

#define USING_OMSSA_SCOPE

short TMSNumber

ion sequence number, starting from 0.

signed char TMSIonSeries

ion type, e.g.

unsigned TMSIntensity

intensity type

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