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

& UserModFileName,

(ModFileName ==

)

FileName = DirEntry.

() + ModFileName;

FileName = ModFileName;

unique_ptr<CObjectIStream>

(

<<

<<

}

(NCBI_NS_STD::exception& e) {

FileName <<

<< e.what());

(UserModFileName !=

) {

FileName = DirEntry.

() + UserModFileName;

FileName = UserModFileName;

unique_ptr<CObjectIStream>

(usermodsin->fail()) {

(

<<

<<

Modset->

(*UserModset);

}

(NCBI_NS_STD::exception& e) {

(

<<

<<

FileName <<

<< e.what());

ifstream taxnames(Filename.c_str());

list<string> linelist;

list<string>::iterator ilist;

(taxnames && !taxnames.eof()) {

getline(taxnames, line);

(!linelist.empty()) {

ilist = linelist.begin();

(!xml_out)

;

(

<<

<<

(*MySearch.

().begin())->SetSpectra(*SpectrumSet);

SpectrumSet->LoadFile(FileType, PeakFile);

unique_ptr<CObjectIStream>

->Open(Filename.c_str(), DataFormat);

unique_ptr <CNcbiIfstream> raw_in;

unique_ptr <CCompressionIStream> compress_in;

unique_ptr <CObjectIStream>

;

* SearchEngineIterative)

Filename(InFile->GetInfile());

(DataFormat) {

(SearchEngineIterative) *SearchEngineIterative =

;

(SearchEngineIterative) *SearchEngineIterative =

;

Filename,

unique_ptr <CNcbiOfstream> raw_out;

unique_ptr <CCompressionOStream> compress_out;

unique_ptr <CObjectOStream> txt_out;

CMSSearchSettings::TOutfiles::const_iterator iOutFile;

(iOutFile = OutFiles.begin(); iOutFile != OutFiles.end(); ++iOutFile) {

Filename((*iOutFile)->GetOutfile());

unique_ptr <CObjectOStream> txt_out;

(DataFormat) {

(*iOutFile)->GetIncluderequest(),

(*iOutFile)->GetIncluderequest(),

*file_out << outPepXML;

oscsv.open(Filename.c_str());

(*MySearch.

().begin())->PrintCSV(oscsv, Modset);

(

<<

<< DataFormat);

list <string> ValidError;

(Settings->

(ValidError) != 0) {

list <string>::iterator iErr;

(iErr = ValidError.begin(); iErr != ValidError.end(); iErr++)

(FileName !=

) {

unique_ptr<CObjectIStream>

(paramsin->fail()) {

(

<<

<<

}

(NCBI_NS_STD::exception& e) {

FileName <<

<< e.what());

UseRankScore(

),

RestrictedSearch(

)

(!blastdb)

0;

NoProline = find(

()->GetNoprolineions().begin(),

(!(*(Iter->second))[iMod]->

ChargeLimitLo(0), ChargeLimitHi(0);

vector<bool> usedPeaks(Peaks->

()[Which]->GetNum(),

);

ChargeLimitLo(0), ChargeLimitHi(0);

(Peaks->

(*((*(Iter->second))[iMod])))

;

(

()->GetIterativesettings().GetResearchthresh() != 0.0) {

(HitSet.

())

;

(HitSet->GetHits().empty())

;

((*HitSet->GetHits().begin())->GetEvalue() <=

()->GetIterativesettings().GetResearchthresh())

CSpectrumSet::Tdata::const_iterator iSpectrum;

iSpectrum =

()->GetSpectra().Get().begin();

(; iSpectrum !=

()->GetSpectra().Get().end(); iSpectrum++) {

(Spectrum->SetCharge().begin(), Spectrum->SetCharge().end(), Spectrum->SetCharge().begin(),

);

ofstream os(

);

Pepppm(

);

Numisotopes, Pepppm,

()->GetChargehandling().GetNegative());

(x.

< y.

)

;

(

= 0;

< NumMod;

++) {

(ModList[

].GetFixed() != 1) {

(j = 0; j < NumMod; j++) {

(ModList[j].GetFixed() == 1 &&

ModList[

].GetSite() == ModList[j].GetSite()) {

(

= 0;

< NumMod;) {

(ModList[

].GetFixed() == -1) {

(

== NumMod)

;

(j=

; j < NumMod; ++j) {

ModList[j] = ModList[j+1];

*PepStart[],

*PepEnd[],

(iMissed = 0; iMissed < Missed - 1; iMissed++) {

(PepStart[iMissed] == (

*)-1)

;

PepEnd[iMissed] = PepEnd[Missed - 1];

*OldSite(0);

NumModSitesCount(0), NumModCount(0);

(iMod = 0; iMod < NumMod[Missed-1]; iMod++) {

(NumModCount + NumMod[iMissed] >=

)

;

PepStart[iMissed] != ModList[Missed-1][iMod].GetSite()) {

ModList[iMissed][NumModCount + NumMod[iMissed]] =

ModList[Missed-1][iMod];

(OldSite != ModList[iMissed][NumModCount + NumMod[iMissed]].GetSite() &&

ModList[iMissed][NumModCount + NumMod[iMissed]].GetFixed() != 1) {

OldSite = ModList[iMissed][NumModCount + NumMod[iMissed]].GetSite();

Masses[iMissed] += Masses[Missed - 1];

EndMasses[iMissed] = EndMasses[Missed - 1];

NumMod[iMissed] += NumModCount;

NumModSites[iMissed] += NumModSitesCount;

*OldSite(0);

(

= 0;

< NumMod;

++) {

(ModList[

].GetSite() != OldSite && ModList[

].GetFixed() != 1 ) {

*PepStart[],

NumMassAndMask[],

Mask, MassOfMask;

(iMissed = 0; iMissed < Missed; iMissed++) {

(PepStart[iMissed] == (

*)-1)

;

Masses[iMissed] + EndMasses[iMissed];

NumVariable(NumMod[iMissed]);

(iMod = 0; iMod < NumMod[iMissed]; iMod++) {

(ModList[iMissed][iMod].GetFixed()) {

(iMissed, iModCount).

+= ModList[iMissed][iMod].GetPrecursorDelta();

NumFixed = NumMod[iMissed] - NumVariable;

(iMod = 0; iMod < NumModSites[iMissed] && iModCount <

; iMod++) {

NumModSites[iMissed], ModList[iMissed]);

(iiMod = 0; iiMod <= iMod; iiMod++ )

MassOfMask += ModList[iMissed][ModIndex[iiMod + NumFixed]].GetPrecursorDelta();

printf(

, NumMod[iMissed], iMod);

(iii=NumMod[iMissed]-1; iii >= 0; iii--) {

(Mask & 1 << iii) printf(

);

(ModIndex, iMod, NumMod[iMissed], NumFixed,

NumModSites[iMissed], ModList[iMissed]));

(ii = 0; ii < iModCount; ++ii) {

NumMassAndMask[iMissed] = iModCount;

(

<<

);

CMSSearchSettings::TIonstosearch::const_iterator

;

(;

!=

()->GetIonstosearch().end(); ++

) {

MaxLadderSize =

()->GetMaxproductions();

list <EMSIonSeries> ::const_iterator iIons;

(iIons = Ions.begin(); iIons != Ions.end(); ++iIons) {

(

= 1;

<=

()->GetChargehandling().GetMaxproductcharge(); ++

) {

(

()->GetIterativesettings().GetSubsetthresh() != 0.0) {

GetOidsBelowThreshold(

()->GetIterativesettings().GetSubsetthresh());

(

);

);

list <EMSIonSeries> Ions;

(

()->GetNonSpecific()) Missed = 1;

Missed =

()->GetMissedcleave()+1;

endposition, position;

()->GetPrecursorsearchtype(), Modset);

CMSSearchSettings::TTaxids::const_iterator iTax;

vector <int> taxids;

vector <int>::iterator itaxids;

TaxInfo(

);

iSearchNotDone(

);

(iSearchNotDone) {

iSearchNotDone =

;

(iSearch % 10000 == 0) {

(Callback) Callback(

(), iSearch, CallbackData);

(itaxids = taxids.begin(); itaxids != taxids.end(); ++itaxids) {

(*itaxids == 0)

;

(iTax = Tax.begin(); iTax != Tax.end(); ++iTax) {

(*itaxids == *iTax)

TaxContinue;

SequenceDone =

;

(iMissed = 0; iMissed < Missed; iMissed++) {

PepStart[iMissed] = (

*)-1;

PepEnd[iMissed] =

.GetData();

Masses[iMissed] = 0;

EndMasses[iMissed] = 0;

NumMod[iMissed] = 0;

NumModSites[iMissed] = 0;

ModList[iMissed][0].

();

PepStart[Missed - 1] =

.GetData();

(!SequenceDone) {

Masses[Missed - 1] = 0;

EndMasses[Missed - 1] = 0;

NumMod[Missed - 1] = 0;

NumModSites[Missed - 1] = 0;

ModList[Missed - 1][0].

();

&(PepEnd[Missed - 1]),

&(Masses[Missed - 1]),

&(EndMasses[Missed - 1]),

ModList[Missed - 1],

PrecursorIntMassArray,

ModList[Missed - 1]);

ModList[Missed - 1]);

Masses, EndMasses, NumModSites, Modset);

EndMasses, NumMod, NumMassAndMask,

NumModSites, ModList);

(iMissed = 0; iMissed < Missed; iMissed++) {

(PepStart[iMissed] == (

*)-1)

;

position = PepStart[iMissed] -

.GetData();

endposition = PepEnd[iMissed] -

.GetData();

NoMassMatch =

;

(iMod = 0; iMod < NumMassAndMask[iMissed]; iMod++) {

NoMassMatch)

;

NoMassMatch =

;

MassPeak =

*

(im.

().GetPointerOrNull());

Peaks = MassPeak->

;

NoMassMatch =

;

NumMod[iMissed]) != 0)

;

(*(Iter->second))[iMod]->ClearHits();

hits += (*(Iter->second))[iMod]->HitCount();

(Peaks->

(NewHit, NewHitOut)) {

NewHitOut->

() = position;

NewHitOut->

() = endposition;

NonSpecificMass(Masses[0] + EndMasses[0]);

(NonSpecificMass <

&&

NonSpecificMass = 0;

*iSeqChar;

(iSeqChar = PepStart[0]; iSeqChar <=

()->

(); iSeqChar++)

NonSpecificMass += PrecursorIntMassArray[AA.

()[*iSeqChar]];

SequenceDone =

;

SequenceDone =

;

PepStart[0] !=

.GetData() &&

PepEnd[0] = PepStart[0];

(!SequenceDone) {

*OldSite;

NumModSitesCount;

(iMissed = 0; iMissed < Missed - 1; iMissed++) {

Masses[iMissed] = Masses[iMissed + 1];

NumModSitesCount = 0;

(iMod = 0; iMod < NumMod[iMissed + 1]; iMod++) {

ModList[iMissed][NumModCount] = ModList[iMissed + 1][iMod];

(OldSite != ModList[iMissed + 1][iMod].GetSite() &&

ModList[iMissed + 1][iMod].

() != 1) {

OldSite = ModList[iMissed + 1][iMod].

();

NumMod[iMissed] = NumModCount;

NumModSites[iMissed] = NumModSitesCount;

PepStart[iMissed] = PepStart[iMissed + 1];

PepEnd[Missed-1] += 1;

PepStart[Missed-1] = PepEnd[Missed-1];

);

(NCBI_NS_STD::exception& e) {

(

<<

<< e.what());

Hit->

().push_back(ModHit);

modseqstring = seqstring;

(iseq = Start; iseq <= Stop; iseq++) {

(!PeakSet->

().empty()) {

Peaks = *(PeakSet->

().begin());

HitSet->SetNumber(Peaks->

());

HitSet->SetIds() = Peaks->

();

HitSet->SetSettingid() =

()->GetSettingid();

ScoreList.

();

*(PeakSet->

().begin());

Threshold, MinThreshold(ThreshStart), MinEval(1000000.0L);

(Threshold = ThreshStart; Threshold <= ThreshEnd;

Threshold += ThreshInc) {

(ScoreList, Threshold, Peaks);

(!ScoreList.

()) {

(

<< Threshold <<

<< ScoreList.

()->first);

(!ScoreList.

() && ScoreList.

()->first < MinEval) {

MinEval = ScoreList.

()->first;

MinThreshold = Threshold;

ScoreList.

();

(

<< MinThreshold);

((

()->GetIterativesettings().GetReplacethresh() == 0.0 &&

(HitSet->GetHits().empty() ||

ScoreList.

()->first <= (*HitSet->GetHits().begin())->GetEvalue())) ||

(

()->GetIterativesettings().GetReplacethresh() != 0.0 &&

ScoreList.

()->first <=

()->GetIterativesettings().GetReplacethresh())) {

HitSet->SetHits().clear();

ScoreList.

();

*(PeakSet->

().begin());

CMSSearchSettings::TTaxids::const_iterator iTax;

(iScoreList = ScoreList.

();

iScoreList != ScoreList.

();

++iScoreList,++HitNum) {

Score = iScoreList->first;

(Score > Evalcutoff)

MSHit = iScoreList->second;

CBlast_def_line_set::Tdata::const_iterator iDefLine;

(iDefLine = Hdr->

().begin();

iDefLine != Hdr->

().end();

(iTax = Tax.begin(); iTax != Tax.end(); iTax++) {

((*iDefLine)->GetTaxid() == *iTax)

TaxContinue2;

seqstring, modseqstring;

tempstartstop;

(PepDone.

(modseqstring) != PepDone.

()) {

Hit = PepDone[modseqstring];

(

(Score)) {

HitSet->GetNumber() <<

<< modseqstring);

(!

(Score)) {

HitSet->GetNumber() <<

<< modseqstring);

GetPeptidesExamined(MSHit->

HitSet->SetHits().push_back(hitref);

PepDone[modseqstring] = Hit;

((*iDefLine)->CanGetSeqid()) {

((**seqid).IsGi()) {

Pephit->

((**seqid).GetGi());

Pephit->

((*iDefLine)->GetTitle());

ScoreList.

();

*(PeakSet->

().begin());

MSBioseq->SetOid() = *iOids;

lowmz(0), highmz;

(Maxproductions == 0) Maxproductions =

;

(iii = 0; iii <

()->GetCleaveNum(); ++iii) {

(

()->GetCleaveOffset()[iii] == 1 ) {

(

()->GetCleaveOffset()[iii] == 0 ) {

NoProline = find(

()->GetNoprolineions().begin(),

SeriesCharge*Maxproductions

TMatchedPeakSet::iterator bin,

,

;

lowmz = ((*bin)->GetMZ() + (*prev)->GetMZ())/2;

highmz = ((*bin)->GetMZ() + (*next)->GetMZ())/2;

highmz = Hit.

()/SeriesCharge;

(*bin)->SetExpIons() =

(double)(highmz - lowmz);

(*bin)->SetMassTolerance() = (Peaks->

())/SeriesCharge;

MatchPeakSet;

TSeriesChargePairList::const_iterator &iPairList,

list<CMSMatchedPeakSet *> &Forward,

list<CMSMatchedPeakSet *> &Backward)

Forward.push_back(current);

Backward.push_back(current);

list<CMSMatchedPeakSet *> &SingleBackward,

list<CMSMatchedPeakSet *> &Double,

list<CMSMatchedPeakSet *>::iterator iDouble, iFront, iBack;

(iDouble = Double.begin(); iDouble != Double.end(); ++iDouble) {

(iFront = SingleForward.begin(); iFront != SingleForward.end(); ++iFront) {

(*iDouble)->Compare(*iFront, DoubleForward);

(iBack = SingleBackward.begin(); iBack != SingleBackward.end(); ++iBack) {

(*iDouble)->Compare(*iBack, !DoubleForward);

(iCharges = 0; iCharges < Peaks->

(); iCharges++) {

tempMass = HitList[iHitList].

();

Charge = HitList[iHitList].

();

minintensity =

(Threshold * Peaks->

(Which));

TSeriesChargePairList::const_iterator iPairList;

list <CMSMatchedPeakSet *> SingleForward, SingleBackward, DoubleForward, DoubleBackward;

(iPairList->first == 1) {

(Peaks, HitList[iHitList], Which, minintensity,

iPairList, SingleForward, SingleBackward);

(Peaks, HitList[iHitList], Which, minintensity,

iPairList, DoubleForward, DoubleBackward);

list <CMSMatchedPeakSet *> ::iterator iFront, iBack, iDouble;

(

()->GetNocorrelationscore() == 0) {

(iFront = SingleForward.begin(); iFront != SingleForward.end(); ++iFront) {

(iBack = SingleBackward.begin(); iBack != SingleBackward.end(); ++iBack) {

(*iFront)->Compare(*iBack,

);

(SingleForward, SingleBackward, DoubleForward,

);

(SingleForward, SingleBackward, DoubleBackward,

);

adjust = HitList[iHitList].

() /

(

);

(

<<

);

(HitList[iHitList].

() <

)

;

High, Low, NumPeaks, NumLo, NumHi;

Peaks->

(High, Low, NumPeaks, tempMass, Charge, Threshold, NumLo, NumHi);

TopHitProb = ((double)Tophitnum)/NumPeaks;

(TopHitProb > 1.0) TopHitProb = 1.0;

numhits = HitList[iHitList].

(Threshold, Peaks->

(Which));

pval = HitList[iHitList].

(

, HitList[iHitList].CountHits(Threshold, Peaks->

(Which)));

(HitList[iHitList].GetM() != 0.0) {

(

<< Perf <<

<< pval <<

<<

);

eval = 3e3 * pval *

;

ScoreList.

(pair<const double, CMSHit *>

(eval, &(HitList[iHitList])));

const char *const UniqueAA

void transform(Container &c, UnaryFunction *op)

const char *const GetMap(void) const

return the map for translating AA char to AA number

CBZip2StreamCompressor – bzip2 based compression stream processor.

CBZip2StreamDecompressor – bzip2 based decompression stream processor.

static CRef< CCleave > CleaveFactory(const EMSEnzymes enzyme)

Simple factory to return back object for enzyme.

const char *& SetStop(void)

Set the enzyme stop value.

bool GetNonSpecific(void) const

Is this a non-specific search?

bool CalcAndCut(const char *SeqStart, const char *SeqEnd, const char **PepStart, int *Masses, int &NumMod, int MaxNumMod, int *EndMasses, CMSMod &VariableMods, CMSMod &FixedMods, CMod ModList[], const int *IntCalcMass, const int *PrecursorIntCalcMass, CRef< CMSModSpecSet > &Modset, int Maxproductions)

cleaves the sequence.

bool & SetNMethionine(void)

Set n-term methionine cleavage.

const char * GetStop(void) const

Get the enzyme stop value.

bool CheckCleaveChar(const char *iPepStart) const

is the character given one of the cleavage chars?

int GetCleaveNum(void) const

Get the number of cleavage chars.

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

TSeriesChargePairList & SetSeriesChargePairList(void)

return the list of charge, series type pairs that are used to initialize the maps

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

void CreateLadderArrays(int MaxModPerPep, int MaxLadderSize)

populate the Ladder Map with arrays based on the ladder

const TSeriesChargePairList & GetSeriesChargePairList(void) const

return the list of charge, series type pairs that are used to initialize the maps

const TMSNumber GetNumber(void) const

Get the ion series number.

const TMSIonSeries GetIonSeries(void) const

Get the ion type.

const TMSCharge GetCharge(void) const

Get the ion charge.

const TMSMZ GetMZ(void) const

get the m/z value of the peak

class to contain preliminary hits.

const int GetSeqIndex(void) const

get blast oid

int & SetStart()

set sequence start

int & SetSeqIndex(void)

set blast oid

const int GetStart(void) const

get sequence start

int CountHits(double Threshold, int MaxI)

return number of hits above threshold

const CMSModInfo & GetModInfo(int n) const

get modification info

const int GetStop(void) const

get sequence stop

int & SetStop(void)

set sequence stop

const int GetNumModInfo(void) const

get size of modification info array

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

static const TMSIonSeries Key2Series(int Key)

convert a key into a series type

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

TMatchedPeakSet & SetMatchedPeakSet(void)

Set the match info.

const int GetModEnum(void) const

const int GetIsFixed(void) const

const int GetSite(void) const

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

void Append(const CMSModSpecSet &ModsIn)

concatenates in another CMSModSpecSet

EMSModType GetModType(int Mod) const

get modification type

bool Init(const CMSSearchSettings::TVariable &Mods, CRef< CMSModSpecSet > Modset)

initialize variable mod type array

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

put the pointers into an array sorted by mass

CIntervalTree & SetIntervalTree(void)

void AddPeak(CMSPeak *PeakIn)

TPeakSet & GetPeaks(void)

class to hold spectral data for filtering and statistical characterization

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

Compare the ladder and peaks and return back rank statistics.

const EMSHitError GetError(void) const

return any errors in computing on peaks

const bool CompareTop(CLadder &Ladder)

compares only the top hits

const int GetMaxI(const EMSPeakListTypes Which) const

Get Maximum intensity.

TMSHitList & GetHitList(const int Index)

Get a hit list.

const int GetPeptidesExamined(const int ChargeIn) const

return number of peptides examine for each charge state

const int GetNumber(void) const

get the spectrum number

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

Read and process a spectrum set into a CMSPeak.

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

TPeakLists & SetPeakLists(void)

set the peak lists

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

add hit to hitlist.

const int GetTol(void) const

get the product mass tolerance in Daltons.

int & SetPeptidesExamined(const int ChargeIn)

set the number of peptides examine for each charge state

const CMSSpectrum::TIds & GetName(void) const

get the names of the spectrum

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 int GetNumCharges(void) const

return number of allowed computed charges

const int GetHitListIndex(const int Index) const

Get size of hit list.

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

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

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

CRef< CMSHitSet > FindHitSet(const int Number) const

Find hitset with given number.

int Validate(std::list< std::string > &Error) const

Validate Search Settings returns 0 if OK, 1 if not Error contains explanations.

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

const TMSMZ GetExpMass(void) const

Get the experimental m/z of the spectrum.

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

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

CMSMatchedPeakSetMap & SetIonSeriesMatchMap(void)

Set map from ion series to CMSMatchedPeakSet *.

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 TMSMZ GetTheoreticalMass(void) const

return theoretical mass of the hit

TMSCharge & SetCharge()

set the charge

const double CalcNormalTopHit(double Mean, double TopHitProb) const

integrate CalcPoissonTopHit over all i

TMSMZ & SetExpMass(void)

Set the experimental mass of the spectrum.

int & SetHits(void)

set the size of the HitInfo array

const double CalcRankProb(void) const

calculate the rank score

const TMSCharge GetCharge(void) const

get the charge

const double CalcPvalue(double Mean, int HitsIn) const

calculate the p-value using poisson distribution

const int *const GetIntMass(void) const

void Init(const CMSSearchSettings::TProductsearchtype &SearchType)

initialize mass arrays with fixed mods

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

TSite GetSite(void) const

Get the site position.

TFixed & SetFixed(void)

set mod state (1 = fixed)

TEnum GetEnum(void) const

Get mod type.

void Reset(void)

reset to default values

TFixed GetFixed(void) const

Is the mod fixed?

void ConvertFromOMSSA(CMSSearch &inOMSSA, CRef< CMSModSpecSet > Modset, string basename, string newname)

convert OMSSA to PepXML

static int SaveAnyFile(CMSSearch &MySearch, CMSSearchSettings::TOutfiles OutFiles, CRef< CMSModSpecSet > Modset)

Write out a complete search.

static void ConditionXMLStream(CObjectOStreamXml *xml_out)

correctly set up xml stream

static void SaveOneFile(CMSSearch &MySearch, const string Filename, ESerialDataFormat FileFormat, bool IncludeRequest, bool bz2)

static int ReadCompleteSearch(const string &Filename, const ESerialDataFormat DataFormat, bool bz2, CMSSearch &MySearch)

Read in a complete search (typically for an iterative search)

static void ReadTaxFile(string &Filename, TTaxNameMap &TaxNameMap)

static int ReadSearchRequest(const string &Filename, const ESerialDataFormat DataFormat, CMSSearch &MySearch)

Read in an MSRequest.

static void ValidateSearchSettings(CRef< CMSSearchSettings > &Settings)

Validates Search Settings.

static void CreateSearchSettings(string FileName, CRef< CMSSearchSettings > &Settings)

create search setting object from file or brand new

static int ReadFile(const string &Filename, const EMSSpectrumFileType FileType, CMSSearch &MySearch)

Read in a spectrum file.

static int LoadAnyFile(CMSSearch &MySearch, CConstRef< CMSInFile > InFile, bool *SearchEngineIterative=0)

Read in any input file.

static int ReadModFiles(const string &ModFileName, const string &UserModFileName, const string &Path, CRef< CMSModSpecSet > Modset)

read in modification files.

unsigned MakeBoolMask(int *ModIndex, int iMod)

CMSResponse::TOidSet & SetOidSet(void)

get the oidset

void SetResult(CRef< CMSPeakSet > PeakSet)

void DeleteVariableOverlap(int &NumMod, CMod ModList[])

delete variable mods that overlap with fixed mods

void UpdateWithNewPep(int Missed, const char *PepStart[], const char *PepEnd[], int NumMod[], CMod ModList[][32], int Masses[], int EndMasses[], int NumModSites[], CRef< CMSModSpecSet > &Modset)

update sites and masses for new peptide

const bool GetIterative(void) const

Gets iterate search.

Int1 & SetLadderCalc(int i)

Set the bit that indicates whether a ladder was calculated.

AutoPtr< Int1, ArrayDeleter< Int1 > > LadderCalc

bool array that indicates if the ladders been calculated

void AddModsToHit(CMSHits *Hit, CMSHit *MSHit)

Adds modification information to hitset.

CLadderContainer & SetLadderContainer(void)

set the ladder container

bool CalcModIndex(int *ModIndex, int &iMod, int &NumMod, int NumFixed, int NumModSites, CMod CModList[])

CRef< CMSResponse > & SetResponse(void)

Set search response.

void Spectrum2Peak(CRef< CMSPeakSet > PeakSet)

CRef< CSeqDB > rdfp

blast library

bool UseRankScore

boolean to turn on rank scoring

CConstRef< CMSRequest > GetRequest(void) const

Get search request.

virtual void OnExit(void)

Override this to execute finalization code.

void WriteBioseqs(void)

write oidset to result

Int1 GetLadderCalc(int i) const

Get the bit that indicates whether a ladder was calculated.

int InitBlast(const char *blastdb, bool use_mmap=false)

init blast databases.

void CreateModCombinations(int Missed, const char *PepStart[], int Masses[], int EndMasses[], int NumMod[], int NumMassAndMask[], int NumModSites[], CMod ModList[][32])

void MatchAndSort(CMSPeak *Peaks, CMSHit &Hit, EMSPeakListTypes Which, int minintensity, const TSeriesChargePairList::const_iterator &iPairList, list< CMSMatchedPeakSet * > &SingleForward, list< CMSMatchedPeakSet * > &SingleBackward)

Creates match ion match lists.

int CompareLadders(int iMod, CMSPeak *Peaks, bool OrLadders, const TMassPeak *MassPeak)

compare ladders to experiment

void CopySettings(CRef< CSearch > fromObj)

TMassMask & SetMassAndMask(int i, int j)

Set the mask and mass of mod bit array.

void Search(CRef< CMSRequest > MyRequestIn, CRef< CMSResponse > MyResponseIn, CRef< CMSModSpecSet > Modset, CRef< CMSSearchSettings > SettingsIn, TOMSSACallback Callback=0, void *CallbackData=0)

Performs the ms/ms search.

void ClearLadderCalc(int Max)

Clear the ladder calc array up to max index.

CMassArray PrecursorMassArray

CConstRef< CCleave > GetEnzyme(void) const

Get search enzyme.

bool & SetRestrictedSearch(void)

is this search restricted to the oid set?

CRef< CMSRequest > & SetRequest(void)

Set search request.

void InitModIndex(int *ModIndex, int &iMod, int NumMod, int NumModSites, CMod ModList[])

CConstRef< CMSSearchSettings > GetSettings(void) const

Get search settings.

CConstRef< CMSResponse > GetResponse(void) const

Get search response.

void AddIonsToHit(CMSHits *Hit, CMSHit *MSHit)

Adds ion information to hitset.

void DoubleCompare(list< CMSMatchedPeakSet * > &SingleForward, list< CMSMatchedPeakSet * > &SingleBackward, list< CMSMatchedPeakSet * > &Double, bool DoubleForward)

CMSMatchedPeakSet * PepCharge(CMSHit &Hit, int SeriesCharge, int Ion, int MinIntensity, int Which, CMSPeak *Peaks, int Maxproductions)

fill out MatchedPeakSet

static void MakeModString(string &seqstring, string &modseqstring, CMSHit *MSHit)

Makes a string hashed out of the sequence plus mods.

const bool GetPoissonOnly(void) const

Gets the scoring to use rank statistics only with Poisson.

const CMSResponse::TOidSet & GetOidSet(void) const

get the oidset

const bool GetRestrictedSearch(void) const

is this search restricted to the oid set?

static int iSearchGlobal

Tracks the iSearch number for all search threads.

CRef< CCleave > & SetEnzyme(void)

Set search enzyme.

void CountModSites(int &NumModSites, int NumMod, CMod ModList[])

count the number of unique sites modified

bool CompareLaddersTop(int iMod, CMSPeak *Peaks, const TMassPeak *MassPeak)

void InitLadders(std::list< EMSIonSeries > &Ions)

initialize mass ladders

int CreateLadders(const char *Sequence, int iSearch, int position, int endposition, int *Masses, int iMissed, CAA &AA, int iMod, CMod ModList[], int NumMod)

create the ladders from sequence

void SetIons(list< EMSIonSeries > &Ions)

set up the ions to use

void SetupSearch(CRef< CMSRequest > MyRequestIn, CRef< CMSResponse > MyResponseIn, CRef< CMSModSpecSet > Modset, CRef< CMSSearchSettings > SettingsIn, TOMSSACallback Callback=0, void *CallbackData=0)

Setup the ms/ms search.

void CreateSequence(int Start, int Stop, string &seqstring, CSeqDBSequence &Sequence)

Generate a peptide sequence.

virtual void * Main(void)

Derived (user-created) class must provide a real thread function.

CRef< CMSSearchSettings > & SetSettings(void)

Set search settings.

CRef< CMSModSpecSet > initModset

void CalcNSort(TScoreList &ScoreList, double Threshold, CMSPeak *Peaks)

calculate the evalues of the top hits and sort

void MakeOidSet(void)

makes map of oid from previous search used in iterative searching

static void ResetGlobals(void)

Reset global parameters used in threaded search.

TOMSSACallback initCallback

const int Getnumseq(void) const

CRef< CMSRequest > initRequestIn

These are so CSearch::Main() can call CSearch::Search() in a threaded run, this requires CSearch::Set...

CRef< CMSResponse > initResponseIn

int MaxModPerPep

maximum number of mod combinations per peptide

bool Iterative

boolean to turn on iterative search

AutoPtr< TMassMask, ArrayDeleter< TMassMask > > MassAndMask

contains bit mask of modifications and resulting mass

const bool ReSearch(const int Number) const

examines a hitset to see if any good hits

static int MaxMZ

maximum m/z value of all spectra precursors used to bound non-specific cleavage searches

static CRef< CMSPeakSet > SharedPeakSet

CRef< CMSSearchSettings > initSettingsIn

int ThreadNum

The threadid number.

int GetNumOIDs() const

Returns the size of the (possibly sparse) OID range.

CRef< CBioseq > GetBioseq(int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_seq_id=NULL) const

Get a CBioseq for a sequence.

void GetTaxIDs(int oid, map< TGi, TTaxId > &gi_to_taxid, bool persist=false) const

Get taxid for an OID.

bool CheckOrFindOID(int &next_oid) const

Find an included OID, incrementing next_oid if necessary.

CRef< CBlast_def_line_set > GetHdr(int oid) const

Get the ASN.1 header for the sequence.

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

const_iterator end() const

iterator insert(const value_type &val)

const_iterator begin() const

container_type::iterator iterator

iterator_bool insert(const value_type &val)

string GetSeqIdString(const CSeq_id &id)

string Path(const string &dir, const string &file)

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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 ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

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

void Critical(CExceptionArgs_Base &args)

void Error(CExceptionArgs_Base &args)

void Warning(CExceptionArgs_Base &args)

void Fatal(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

#define finite

Define value of finite (Is Finite).

string GetDir(EIfEmptyPath mode=eIfEmptyPath_Current) const

Get the directory component for this directory entry.

static bool IsAbsolutePath(const string &path)

Check if a "path" is absolute for the current OS.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

const_iterator AllIntervals(void) const

const_iterator IntervalsContaining(coordinate_type point) const

reference GetValue(void) const

static int Score(const CRef< CSeq_id > &id)

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

pair< TObjectPtr, TTypeInfo > ObjectInfo(C &obj)

void SetReferenceSchema(bool use_schema=true)

Make generated XML document reference XML schema.

void SetWriteNamedIntegersByValue(bool set)

Set up writing named integers (in ANS.1 sense) by value only.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

int8_t Int1

1-byte (8-bit) signed integer

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

const Tdata & Get(void) const

Get the member data.

const THits & GetHits(void) const

Get the Hits member data.

void SetMass(TMass value)

Assign a value to Mass data member.

TMods & SetMods(void)

Assign a value to Mods data member.

void SetStop(TStop value)

Assign a value to Stop data member.

void SetPvalue(TPvalue value)

Assign a value to Pvalue data member.

void SetProtlength(TProtlength value)

Assign a value to Protlength data member.

void SetOid(TOid value)

Assign a value to Oid data member.

TMinnoenzyme GetMinnoenzyme(void) const

Get the Minnoenzyme member data.

void SetGi(TGi value)

Assign a value to Gi data member.

void SetAccession(const TAccession &value)

Assign a value to Accession data member.

void SetSinglenum(TSinglenum value)

Assign a value to Singlenum data member.

void SetCharge(TCharge value)

Assign a value to Charge data member.

void SetTheomass(TTheomass value)

Assign a value to Theomass data member.

void SetEvalue(TEvalue value)

Assign a value to Evalue data member.

EMSSerialDataFormat

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

void SetDefline(const TDefline &value)

Assign a value to Defline data member.

void SetPepstring(const TPepstring &value)

Assign a value to Pepstring data member.

void SetPepstop(const TPepstop &value)

Assign a value to Pepstop data member.

void SetStart(TStart value)

Assign a value to Start data member.

void SetBioseqs(TBioseqs &value)

Assign a value to Bioseqs data member.

list< CRef< CMSOutFile > > TOutfiles

TResponse & SetResponse(void)

Assign a value to Response data member.

TMzhits & SetMzhits(void)

Assign a value to Mzhits data member.

TNmethionine GetNmethionine(void) const

Get the Nmethionine member data.

void SetDoublenum(TDoublenum value)

Assign a value to Doublenum data member.

TRequest & SetRequest(void)

Assign a value to Request data member.

EMSEnzymes

enumerate enzymes

void SetDbversion(TDbversion value)

Assign a value to Dbversion data member.

EMSSpectrumFileType

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

void SetPepstart(const TPepstart &value)

Assign a value to Pepstart data member.

void SetScale(TScale value)

Assign a value to Scale data member.

THitsets & SetHitsets(void)

Assign a value to Hitsets data member.

TPephits & SetPephits(void)

Assign a value to Pephits data member.

void SetScale(TScale value)

Assign a value to Scale data member.

@ eMSSerialDataFormat_csv

csv (excel)

@ eMSSerialDataFormat_none

@ eMSSerialDataFormat_xml

open XML format

@ eMSSerialDataFormat_asnbinary

open ASN.1 binary format

@ eMSSerialDataFormat_pepxml

pepXML format

@ eMSSerialDataFormat_asntext

open ASN.1 text format

@ eMSSerialDataFormat_xmlbz2

bzip2 XML format

@ eMSModType_modn

at the N terminus of a protein

@ eMSModType_modnpaa

at the N terminus of a peptide at particular amino acids

@ eMSModType_modcpaa

at the C terminus of a peptide at particular amino acids

@ eMSModType_modnp

at the N terminus of a peptide

@ eMSModType_modcp

at the C terminus of a peptide

@ eMSModType_modnaa

at the N terminus of a protein at particular amino acids

@ eMSHitError_notenuffpeaks

not enough peaks to search

@ eMSSpectrumFileType_pks

@ eMSSpectrumFileType_mgf

@ eMSSpectrumFileType_sciex

@ eMSSpectrumFileType_omxbz2

bzip2 omx file

@ eMSSpectrumFileType_dtablank

@ eMSSpectrumFileType_pkl

@ eMSSpectrumFileType_omx

xml for iterative search

@ eMSSpectrumFileType_dtaxml

@ eMSSpectrumFileType_dta

@ eMSSpectrumFileType_unknown

@ eMSSpectrumFileType_asc

@ eMSSpectrumFileType_xml

xml MSRequest

@ eMSSpectrumFileType_oms

asn.1 binary for iterative search

const double kNeutron

neutron mass

EMSPeakListTypes

enum that describes type of peak list

EMSTerminalBias

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

const int kIonDirection[]

ion direction.

EMSIonSeries

enumeration of ion series

constexpr auto sort(_Init &&init)

double value_type

The numeric datatype used by the parser.

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

Prototypes for portable math library (ported from C Toolkit)

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

int PositiveSign(int input)

DEFINE_STATIC_FAST_MUTEX(iSearchMutex)

void(* TOMSSACallback)(int TotalSeq, int Completed, void *Anything)

progress callback for CSearch

bool operator()(const TMassMask &x, const TMassMask &y)

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