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

(

= 0;

< Ladder.

();

++) {

(Ladder.

()[

] > 0) {

}

(NCBI_NS_STD::exception& e) {

(

<<

<< e.what());

(

= 0;

< NumMod;

++)

(ModMask & (1 <<

)) retval++;

(

= 0;

< NumMod;

++) {

(ModMask & (1 <<

)) {

*PepStart,

Searchctermproduct,

TheoreticalMassIn

LadderContainer.

(Iter, ChargeLimit, ChargeLimit);

(*((*(Iter->second))[iMod]),iHitInfo, Peaks, Which, Searchb1, Searchctermproduct);

LadderContainer.

(Iter, ChargeLimit, ChargeLimit);

Independent = Dependent = 0;

LastIon(-1), LastCharge(-1), LastNumber(-1);

(

)(retval+0.5);

Index =

.GetCharge() -

[0];

(

.GetHits() <=

[Index])

;

= PeakList->GetNum() - 1;

(PeakList->GetMZI()[x].GetMZ() <

-

)

(PeakList->GetMZI()[x].GetMZ() >

+

)

(x < PeakList->GetNum() - 1 &&

PeakList->GetMZI()[x+1].GetMZ() <

+

&&

PeakList->GetMZI()[x+1].GetMZ() >

-

)

vector<bool>& usedPeaks)

(Ladder.

() == 0 || PeakList->GetNum() == 0)

0;

(PeakList->GetMZI()[j].GetMZ() < Ladder[

] -

) {

(j >= PeakList->GetNum())

;

}

(PeakList->GetMZI()[j].GetMZ() > Ladder[

] +

) {

(

>= Ladder.

())

;

usedPeaks[j] =

;

Ladder.

() += PeakList->GetMZI()[j].GetRank();

Ladder.

()[

] = PeakList->GetMZI()[j].GetIntensity();

Ladder.

()[

] = PeakList->GetMZI()[j].GetMZ() - Ladder[

];

(j >= PeakList->GetNum())

;

(

>= Ladder.

())

;

(

= 0;

< Ladder.

();

++) {

(

= 0;

< PeakList->GetNum();

++) {

(Ladder.

(PeakList->GetMZI()[

].GetMZ(),

))

;

(NCBI_NS_STD::exception& e) {

(

<<

<< e.what());

(

(Spectrum, Settings) != 0) {

(

<<

);

(

<<

);

StopFraction)

Start.

() =

(StartFraction * Precursor);

Stop.

() =

(StopFraction * Precursor);

*HiHit = upper_bound(

HiHit - LoHit;

MinIntensity,

Which)

Start.

() = StartIn;

Stop.

() = StopIn;

*LoHit = lower_bound(

*HiHit = upper_bound(

(; LoHit != HiHit; ++LoHit)

*Hit = upper_bound(

Stop)

(

)Lo/Hi;

}

(

(1.0, 1.5, 2.0) > 1.25) {

(iCharges = 0; iCharges <

(); iCharges++) {

(

= 0;

< Num;

++) {

(Intensity == 0.0) Intensity = 1;

(double)MZISort[

].GetIntensity()/MZISort[0].

() > Threshold;

++);

(iMZI = 0; iMZI < TempLen && Temp[iMZI].

() > Threshold * Temp[0].GetIntensity(); iMZI++);

(iMZI = 0; iMZI < TempLen; iMZI++) {

(Temp[iMZI].GetMZ() > Precursor - 5*

/Charge &&

Temp[iMZI].GetMZ() < Precursor + 5*

/Charge)

;

(Temp[iMZI].GetMZ() > Precursor - 19*

/Charge &&

Temp[iMZI].GetMZ() < Precursor + 5*

/Charge)

;

(Temp[iMZI].GetMZ() > Precursor/2 - 10 *

/Charge &&

Temp[iMZI].GetMZ() < Precursor/2 + 3*

/Charge)

;

(Temp[iMZI].GetMZ() > Precursor/3 - 7*

/Charge &&

Temp[iMZI].GetMZ() < Precursor/3 + 2*

/Charge)

;

(Temp[iMZI].GetMZ() > Precursor/4 - 5*

/Charge &&

Temp[iMZI].GetMZ() < Precursor/4 + 1*

/Charge)

;

(Temp[iMZI].GetMZ() > Precursor - 12*

/Charge &&

Temp[iMZI].GetMZ() < Precursor + 12*

/Charge)

;

Temp[iMZI].GetMZ() < Precursor/2 +

(1) * PrecursorSign +

+ Precursor/500/2 )

;

Temp[iMZI].GetMZ() < Precursor/3 +

(1) * PrecursorSign +

+ Precursor/500/3 && Charge>=3)

;

Temp[iMZI].GetMZ() < Precursor/4 +

(1) * PrecursorSign +

+ Precursor/500/4 && Charge>=4)

;

Temp[iMZI].GetMZ() < Precursor/5 +

(1) * PrecursorSign +

+ Precursor/500/5 && Charge>=5)

;

Temp[iMZI].GetMZ() < Precursor/6 +

(1) * PrecursorSign +

+ Precursor/500/6 && Charge>=6)

;

Temp[iTemp] = Temp[iMZI];

iTemp(0), iMZI, jMZI;

(iMZI = 0; iMZI < TempLen - 1; iMZI++) {

(Deleted.

(iMZI) != Deleted.

())

;

(jMZI = iMZI + 1; jMZI < TempLen; jMZI++) {

((*FCN)(Temp[iMZI], Temp[jMZI],

)) {

(iMZI = 0; iMZI < TempLen; iMZI++) {

(Deleted.count(iMZI) == 0) {

Temp[iTemp] = Temp[iMZI];

ConsiderMultProduct(

);

ofstream FileOut(

);

(FileOut, Temp, TempLen);

Temp, TempLen, ConsiderMultProduct);

tolin)

(TestMZ < BigMZ -

(Diff) + tolin &&

tolin)

(

(BigMZ, TestMZ, 1, tolin) ||

(BigMZ, TestMZ, 16, tolin) ||

(BigMZ, TestMZ, 17, tolin) ||

(BigMZ, TestMZ, 18, tolin))

;

ConsiderMultProduct)

ofstream FileOut(

);

(FileOut, Temp, TempLen);

ofstream FileOut(

);

(FileOut, Temp, TempLen);

(iMZI = 0; iMZI < TempLen - 1; iMZI++) {

(Deleted.count(iMZI) != 0)

;

(!ConsiderMultProduct ||

Temp[iMZI].GetMZ() >

(jMZI = iMZI + 1; jMZI < TempLen; jMZI++) {

(Temp[jMZI].GetMZ() < Temp[iMZI].GetMZ() +

(Window) +

&&

Temp[jMZI].GetMZ() > Temp[iMZI].GetMZ() -

(Window) -

&&

Deleted.

(jMZI) == Deleted.

()) {

(

(Temp[iMZI].GetMZ(), Temp[jMZI].GetMZ(),

)) {

MajorPeak[jMZI] = iMZI;

(MajorPeak.

(jMZI) != MajorPeak.

()) {

(Considered.

(jMZI) != Considered.

())

Considered.

(jMZI);

(HitCount <= HitsAllowed)

;

(HitCount <= HitsAllowed)

;

(iMZI = 0; iMZI < TempLen; iMZI++) {

(Deleted.count(iMZI) == 0) {

Temp[iTemp] = Temp[iMZI];

ofstream FileOut(

);

(FileOut, Temp, TempLen);

Charge,

Threshold,

& NumLo,

& NumHi)

NumPeaks = NumLo = NumHi = 0;

Low = PrecursorMass;

(iMZI = 0; iMZI <

()[Which]->GetNum(); iMZI++) {

(

()[Which]->GetMZI()[iMZI].GetIntensity() > Threshold*MaxI &&

()[Which]->GetMZI()[iMZI].GetMZ() <= PrecursorMass) {

(

()[Which]->GetMZI()[iMZI].GetMZ() > High) {

(

()[Which]->GetMZI()[iMZI].GetMZ() < Low) {

(

()[Which]->GetMZI()[iMZI].GetMZ() < PrecursorMass/2.0) NumLo++;

*IntMassArray = MassArray.

();

(ipeaks = 0 ; ipeaks <

()[Which]->GetNum() - 1; ipeaks++) {

(; low <

()[Which]->GetNum(); low++) {

(IntMassArray[

] == 0)

;

(Nodup)

newpeak;

Intensity(0);

(Intensity <

()[Which]->GetMZI()[

].GetIntensity())

Intensity =

()[Which]->GetMZI()[

].GetIntensity();

TPeakSet::iterator iPeakSet;

(iPeakSet =

().begin();

(iCharges = 0; iCharges < Peaks->

(); iCharges++) {

ptol = (Zdep * (Peaks->

()[iCharges] - 1) + 1);

ptol = (Zdep * (Peaks->

()[iCharges] - 1) + 1) * Peptol;

(iIsotopes = 0; iIsotopes <= Numisotopes; ++iIsotopes) {

temp->

= CalcMass;

temp->

= Peaks;

ncbi::CConstRef<ncbi::CObject> myobject(

*

(temp));

const int kNumUniqueAA

@MSMod.hpp User-defined methods of the data storage class.

void Next(TLadderMap::iterator &Iter, TMSCharge BeginCharge=0, TMSCharge EndCharge=0, TMSIonSeries SeriesType=eMSIonTypeUnknown)

iterate over the ladder map over the charge range and series type indicated

void Begin(TLadderMap::iterator &Iter, TMSCharge BeginCharge=0, TMSCharge EndCharge=0, TMSIonSeries SeriesType=eMSIonTypeUnknown)

TLadderMap & SetLadderMap(void)

returns the laddermap (maps key based on charge and series type to a vector of CLadder)

TIntensity & SetIntensity(void)

Set the intensity array.

const TDelta & GetDelta(void) const

Get the mass delta array.

int & SetSum(void)

Set the sum of ranks of matched peaks.

const TIntensity & GetIntensity(void) const

Get the intensity array.

const int GetSum(void) const

Get the sum of ranks of matched peaks.

int & SetM(void)

Set the number of matches.

bool ContainsFast(int MassIndex, int Tolerance)

TDelta & SetDelta(void)

Set the mass delta array.

const int GetM(void) const

Get the number of matches.

const TLadderNumber & GetLadderNumber(void) const

Return the array containing the number of the ions.

TMSNumber & SetNumber(void)

Set the ion series number.

const TMSNumber GetNumber(void) const

Get the ion series number.

TMSMZ & SetDelta(void)

Set 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.

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

const TMSMZ GetMZ(void) const

get the m/z value of the peak

class to contain preliminary hits.

TModInfo ModInfo

modification information array

void RecordMatches(CLadderContainer &LadderContainer, int iMod, CMSPeak *Peaks, unsigned ModMask, CMod ModList[], int NumMod, const char *PepStart, int Searchctermproduct, int Searchb1, int TheoreticalMassIn)

Make a record of the hits to the mass ladders.

CMSModInfo & SetModInfo(int n)

set modification info

void RecordMatchesScan(CLadder &Ladder, int &iHitInfo, CMSPeak *Peaks, EMSPeakListTypes Which, int NOffset, int COffset)

helper function for RecordHits that scans thru a single ladder

void CountHitsByType(int &Independent, int &Dependent, double Threshold, int MaxI) const

count hits into two categories: independent hits and hits that are dependent on others

int CountMods(unsigned ModMask, int NumMod)

Count Modifications in Mask.

int CountHits(double Threshold, int MaxI)

return number of hits above threshold

void RecordModInfo(unsigned ModMask, CMod ModList[], int NumMod, const char *PepStart)

Record the modifications used in the hit Note that fixed aa modifications are *not* recorded as these...

int NumModInfo

size of ModInfo

Class to hold mod information for a hit.

class for holding a set of peaks

EMSPeakListSort & SetSorted(void)

CMZI *const GetMZI(void) const

void Rank(void)

Rank the given spectrum by intensity.

const int GetNum(void) const

const EMSPeakListSort GetSorted(void) const

void Sort(EMSPeakListSort SortType)

sort the peak by sort type

void CreateLists(int Size)

fill out the arrays and set defaults

int SortPeaks(int Peptol, int Zdep, int Numisotopes, bool Pepppm, int ChargeSign)

put the pointers into an array sorted by mass

TPeakSet & GetPeaks(void)

CIntervalTree MassIntervals

class to hold spectral data for filtering and statistical characterization

void CullBaseLine(const double Threshold, CMZI *Temp, int &TempLen)

take out peaks below a threshold

int CompareSortedRank(CLadder &Ladder, EMSPeakListTypes Which, vector< bool > &usedPeaks)

Compare the ladder and peaks and return back rank statistics.

int tol

product error tolerance of peptide

const EMSHitError GetError(void) const

return any errors in computing on peaks

void SetPrecursorTol(double tolin)

set the precursor mass tolerance in Daltons.

void CullChargeAndWhich(const CMSSearchSettings &Settings)

Performs culling based on whether to consider multiply charged ions or not.

const int CountRange(const double StartFraction, const double StopFraction) const

return the number of peaks in a range.

const bool CompareTop(CLadder &Ladder)

compares only the top hits

void CullIsotope(CMZI *Temp, int &TempLen)

cull isotopes using the Markey Method

int & SetNumber(void)

set the spectrum number

const bool Contains(const int value, const EMSPeakListTypes Which) const

see if value is contained in peaks

const int GetMaxI(const EMSPeakListTypes Which) const

Get Maximum intensity.

const bool ContainsFast(const int value, const EMSPeakListTypes Which) const

see if value is contained in peaks using binary search

TMSHitList HitList[eMSPeakListChargeMax - eMSPeakListCharge1]

int * GetCharges(void)

return allowed computed charges

void SetError(const EMSHitError ErrorIn)

set any errors in computing on peaks

void SmartCull(const CMSSearchSettings &Settings, CMZI *Temp, int &TempLen, const bool ConsiderMultProduct)

recursively culls the peaks

const int GetPrecursormz(void) const

get precursor m/z

int LastHitNum[eMSPeakListChargeMax - eMSPeakListCharge1]

int Read(const CMSSpectrum &Spectrum, const CMSSearchSettings &Settings)

Read a spectrum set into a CMSPeak.

void ReadAndProcess(const CMSSpectrum &Spectrum, const CMSSearchSettings &Settings)

Read and process a spectrum set into a CMSPeak.

CMSSpectrum::TIds & SetName(void)

set the names of the spectrum

const bool IsMajorPeak(const int BigMZ, const int TestMZ, const int tolin) const

see if TestMZ can be associated with BigMZ, e.g.

const int CountAAIntervals(const CMassArray &MassArray, const bool Nodup, const EMSPeakListTypes Which) const

count number of AA intervals in spectrum.

void InitHitList(const int Minhitin)

initializes arrays used to track hits

CMSPeak(void)

CMSPeak ctor.

void HighLow(int &High, int &Low, int &NumPeaks, const int PrecursorMass, const int Charge, const double Threshold, int &NumLo, int &NumHi)

return the lowest culled peak and the highest culled peak less than the precursor mass passed in

void xCMSPeak(void)

shared c'tor code

void SetComputedCharge(const CMSChargeHandle &ChargeHandle, const CMSSpectrum &Spectrum)

calculates charge based on threshold and sets charge value

const int CalcPrecursorMass(const int PrecursorCharge) const

calculates neutral mass

void CullPrecursor(CMZI *Temp, int &TempLen, const int Precursor, const int Charge, bool PrecursorCull, int PrecursorSign)

cull precursors

int PeptidesExamined[eMSPeakListChargeMax - eMSPeakListCharge1]

int Charges[eMSPeakListChargeMax - eMSPeakListCharge1]

TPeakLists & SetPeakLists(void)

set the peak lists

const bool AddHit(CMSHit &in, CMSHit *&out)

add hit to hitlist.

const bool IsAtMZ(const int BigMZ, const int TestMZ, const int Diff, const int tolin) const

check to see if TestMZ is Diff away from BigMZ

int HitListIndex[eMSPeakListChargeMax - eMSPeakListCharge1]

const int GetMinhit() const

Get minimum hit.

const int CountMZRange(const int StartIn, const int StopIn, const double MinIntensity, const int Which) const

return the number of peaks in a range

const bool IsPlus1(const double PercentBelowIn) const

is the data charge +1?

const int GetNumCharges(void) const

return number of allowed computed charges

EChargeState ComputedCharge

void CullH20NH3(CMZI *Temp, int &TempLen)

cull peaks that are water or ammonia loss note that this only culls the water or ammonia loss if thes...

const TPeakLists & GetPeakLists(void) const

get the peak lists

const int Compare(CLadder &Ladder, const EMSPeakListTypes Which) const

compare peaks to ladder using ContainsFast

void xWrite(std::ostream &FileOut, const CMZI *const Temp, const int Num) const

writes out dta format

const double RangeRatio(const double Start, const double Middle, const double Stop) const

takes the ratio, low/high, of two ranges in the spectrum

void CullIterate(CMZI *Temp, int &TempLen, const TMZIbool FCN)

iterate thru peaks, deleting ones that pass the test

void SetTolerance(const double tolin)

set the product mass tolerance in Daltons.

void CullAll(const CMSSearchSettings &Settings)

use smartcull on all charge states

const int AboveThresh(const double Threshold, const EMSPeakListTypes Which) const

counts the number of peaks above % of maximum peak

const EMSPeakListTypes GetWhich(const int Charge) const

returns the cull array index

const int GetConsiderMult(void) const

gets min precursor charge to consider multiply charged product ions

const int PercentBelow(void) const

the number of peaks at and below the precursor ion

void Write(std::ostream &FileOut, const EMSSpectrumFileType FileType, const EMSPeakListTypes Which) const

Write out a CMSPeak in dta format (useful for debugging)

int & SetMinhit(void)

Set minimum hit.

@MSSearchSettings.hpp User-defined methods of the data storage class.

CMSBasicMatchedPeak & SetHitInfo(int n)

Set the hit info at array position n.

int & SetM(void)

Set the number of matched peaks.

TMSMZ & SetTheoreticalMass(void)

set the theoretical mass of the hit

int & SetSum(void)

Set the sum of ranks.

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

int & SetN(void)

Set the number of experimental peaks.

void CreateHitInfo(void)

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

const TMSCharge GetCharge(void) const

get the charge

a class for holding an m/z value, intensity, and rank

TMSRank & SetRank(void)

set the peak rank

const int *const GetIntMass(void) const

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

TSite GetSite(void) const

Get the site position.

TEnum GetEnum(void) const

Get mod type.

TFixed GetFixed(void) const

Is the mod fixed?

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

Include a standard set of the NCBI C++ Toolkit most basic headers.

std::ofstream out("events_result.xml")

main entry point for tests

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Fatal(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

iterator Insert(const interval_type &interval, const mapped_type &value)

TNegative GetNegative(void) const

Get the Negative member data.

const TMz & GetMz(void) const

Get the Mz member data.

TTophitnum GetTophitnum(void) const

Get the Tophitnum member data.

TPeptol GetPeptol(void) const

Get the Peptol member data.

TMincharge GetMincharge(void) const

Get the Mincharge member data.

TMinspectra GetMinspectra(void) const

Get the Minspectra member data.

const TAbundance & GetAbundance(void) const

Get the Abundance member data.

TMaxcharge GetMaxcharge(void) const

Get the Maxcharge member data.

TDoublewin GetDoublewin(void) const

Get the Doublewin member data.

const TChargehandling & GetChargehandling(void) const

Get the Chargehandling member data.

bool CanGetIds(void) const

Check if it is safe to call GetIds method.

TPlusone GetPlusone(void) const

Get the Plusone member data.

TConsidermult GetConsidermult(void) const

Get the Considermult member data.

TDoublenum GetDoublenum(void) const

Get the Doublenum member data.

bool CanGetNumber(void) const

Check if it is safe to call GetNumber method.

const TCharge & GetCharge(void) const

Get the Charge member data.

TCalccharge GetCalccharge(void) const

Get the Calccharge member data.

TMsmstol GetMsmstol(void) const

Get the Msmstol member data.

TCalcplusone GetCalcplusone(void) const

Get the Calcplusone member data.

const TIds & GetIds(void) const

Get the Ids member data.

EMSSpectrumFileType

Access to EMSSpectrumFileType's attributes (values, names) as defined in spec.

TNumber GetNumber(void) const

Get the Number member data.

TCutlo GetCutlo(void) const

Get the Cutlo member data.

TMinhit GetMinhit(void) const

Get the Minhit member data.

TPrecursorcull GetPrecursorcull(void) const

Get the Precursorcull member data.

TSinglenum GetSinglenum(void) const

Get the Singlenum member data.

TPrecursormz GetPrecursormz(void) const

Get the Precursormz member data.

TSinglewin GetSinglewin(void) const

Get the Singlewin member data.

@ eMSCalcPlusOne_calc

guess charge one

@ eMSHitError_notenuffpeaks

not enough peaks to search

@ eMSSpectrumFileType_dta

const double kNeutron

neutron mass

static bool FCompareIsotope(const CMZI &x, const CMZI &y, int tol)

static bool FCompareH2ONH3(const CMZI &x, const CMZI &y, int tol)

EMSPeakListSort

enumeration of peak sort order

@ eMSPeakListSortIntensity

bool(* TMZIbool)(const CMZI &, const CMZI &, int tol)

function object for cull iterate

EMSPeakListTypes

enum that describes type of peak list

constexpr auto sort(_Init &&init)

const GenericPointer< typename T::ValueType > T2 value

Int minimum(Int i, Int j)

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

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

bool operator()(CMZI x, CMZI y)

bool operator()(CMZI x, CMZI y)

bool operator()(CMZI x, CMZI y)

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