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

pep = msHits->GetPepstring();

pos = (*iMod)->GetSite();

num = (*iMod)->GetModtype();

mass = aaMass + mdiff;

modaaMass->SetAttlist().SetPosition(pos+1);

modaaMass->SetAttlist().SetMass(mass);

modInfo->

().SetMod_nterm_mass(mass);

modInfo->

().SetMod_cterm_mass(mass);

(

=0;

<pep.length();

++) {

it = modMap.

(

);

(it != modMap.

()) {

modPep.append(it->second);

modaaMass->SetAttlist().SetPosition(

+1);

modaaMass->SetAttlist().SetMass(staticMass);

CMSSearchSettings::TFixed::const_iterator iterF;

(iterF = inOMSSA.

().front()->GetSettings().GetFixed().begin();

iterF != inOMSSA.

().front()->GetSettings().GetFixed().end(); ++iterF) {

(

% 2 != 0) {

(!hasMod)

;

modInfo->

().SetModified_peptide(modPep);

(

% 2 == 0) {

aaMod->SetAttlist().SetAminoacid(aaStr);

mass = aaMass + mdiff;

aaMod->SetAttlist().SetMass(mass);

aaMod->SetAttlist().SetVariable(

);

aaMod->SetAttlist().SetVariable(

);

aaMod->SetAttlist().SetDescription(Modset->

(modnum));

sSum->SetAminoacid_modification().push_back(aaMod);

termMod->SetAttlist().SetVariable(

);

termMod->SetAttlist().SetVariable(

);

termMod->SetAttlist().SetDescription(Modset->

(modnum));

termMod->SetAttlist().SetTerminus(

);

termMod->SetAttlist().SetProtein_terminus(

);

termMod->SetAttlist().SetTerminus(

);

termMod->SetAttlist().SetProtein_terminus(

);

termMod->SetAttlist().SetTerminus(

);

termMod->SetAttlist().SetProtein_terminus(

);

termMod->SetAttlist().SetMass(mass +

);

termMod->SetAttlist().SetTerminus(

);

termMod->SetAttlist().SetProtein_terminus(

);

termMod->SetAttlist().SetMass(mass +

);

sSum->SetTerminal_modification().push_back(termMod);

specFile, startScan, stopScan, dtaCharge;

(RxpLocus.

(SpecID)) {

stopScan = startScan;

specFile = RxpParse.

(SpecID, 0, 1);

(specFile ==

) {

startScan= RxpParse.

(SpecID, 0, 2);

(startScan ==

) {

stopScan = startScan;

stopScan = RxpParse.

(SpecID, 0, 3);

(stopScan ==

) {

stopScan = startScan;

sQuery->SetAttlist().SetSpectrum(specFile +

+ startScan +

+ stopScan +

+ dtaCharge);

(pHit->CanGetAccession()) {

pHit->GetAccession();

}

(pHit->CanGetGi()) {

pHit->GetDefline();

(pHitSet->GetHits().empty())

CMSHitSet::THits::const_iterator iHit;

(iHit = pHitSet->GetHits().begin(); iHit != pHitSet->GetHits().end(); iHit++) {

charges.

((*iHit)->GetCharge());

iHit = pHitSet->GetHits().begin();

charge = (*iHit)->GetCharge();

( charge != *iCharge ) {

charge = (*iHit)->GetCharge();

(!(pHitSet->GetIds().empty())) {

spectrumID = *(pHitSet->GetIds().begin());

(sQuery, spectrumID, pHitSet->GetNumber(), charge);

neutral_precursor_mass = (*iHit)->GetMass()/

;

sQuery->SetAttlist().SetPrecursor_neutral_mass(neutral_precursor_mass);

sQuery->SetAttlist().SetAssumed_charge(charge);

sQuery->SetAttlist().SetIndex(

++);

CMSHits::TPephits::const_iterator iPephit;

( ; iHit != pHitSet->GetHits().end(); iHit++) {

charge = (*iHit)->GetCharge();

( charge != *iCharge ) {

iPephit = (*iHit)->GetPephits().begin();

sHit->SetAttlist().SetHit_rank(hitRank);

sHit->SetAttlist().SetPeptide((*iHit)->GetPepstring());

((*iHit)->CanGetPepstart())

sHit->SetAttlist().SetPeptide_prev_aa((*iHit)->GetPepstart());

((*iHit)->CanGetPepstop())

sHit->SetAttlist().SetPeptide_next_aa((*iHit)->GetPepstop());

sHit->SetAttlist().SetNum_tot_proteins((*iHit)->GetPephits().size());

sHit->SetAttlist().SetNum_matched_ions((*iHit)->GetMzhits().size());

tot_num_ions = ((*iHit)->GetPepstring().length()-1) * 2;

sHit->SetAttlist().SetTot_num_ions(tot_num_ions);

sHit->SetAttlist().SetCalc_neutral_pep_mass((*iHit)->GetTheomass()/

);

sHit->SetAttlist().SetMassdiff(

(neutral_precursor_mass - ((*iHit)->GetTheomass())/

));

sHit->SetAttlist().SetProtein_descr((*iPephit)->GetDefline());

pValue->SetAttlist().SetName(

);

pValue->SetAttlist().SetValue(

((*iHit)->GetPvalue()));

eValue->SetAttlist().SetName(

);

eValue->SetAttlist().SetValue(

((*iHit)->GetEvalue()));

sHit->SetSearch_score().push_back(pValue);

sHit->SetSearch_score().push_back(eValue);

((*iHit)->CanGetScores()) {

score->SetAttlist().SetName((*iScore)->GetName());

score->SetAttlist().SetValue(

((*iScore)->GetValue()));

sHit->SetSearch_score().push_back(score);

(iPephit++ ; iPephit != (*iHit)->GetPephits().end(); iPephit++) {

altPro->SetAttlist().SetProtein_descr((*iPephit)->GetDefline());

sHit->SetAlternative_protein().push_back(altPro);

(modInfo) sHit->SetModification_info(*modInfo);

sResult->SetSearch_hit().push_back(sHit);

sQuery->SetSearch_result().push_back(sResult);

sQueries.push_back(sQuery);

=

(inOMSSA.

().front()->GetSettings().GetScale());

(

modchar=0; modchar < 29; modchar++) {

rSum->SetAttlist().SetBase_name(

);

rSum->SetAttlist().SetRaw_data_type(

);

rSum->SetAttlist().SetRaw_data(

);

rSum->SetSample_enzyme().SetAttlist().SetName(enzymeName);

specificity->SetAttlist().SetCut(cleave->

());

cerr <<

<< endl;

specificity->SetAttlist().SetNo_cut(

);

rSum->SetSample_enzyme().SetSpecificity().push_back(specificity);

sSum->SetAttlist().SetBase_name(

);

sSum->SetAttlist().SetSearch_engine(

);

sSum->SetAttlist().SetOut_data_type(

);

sSum->SetAttlist().SetOut_data(

);

(searchType) {

cerr <<

<< endl;

searchType =

(inOMSSA.

().front()->GetSettings().GetProductsearchtype());

(searchType) {

cerr <<

<< endl;

sSum->SetAttlist().SetSearch_id(1);

sSum->SetSearch_database().SetAttlist().SetLocal_path(

);

(inOMSSA.

().front()->IsSetBioseqs() && inOMSSA.

().front()->GetBioseqs().Get().size() > 0)

dbtype = inOMSSA.

().front()->GetBioseqs().Get().front()->GetSeq().GetInst().GetMol();

sSum->SetSearch_database().SetAttlist().SetSize_in_db_entries(inOMSSA.

().front()->GetDbversion());

sSum->SetEnzymatic_search_constraint().SetAttlist().SetEnzyme(enzymeName);

sSum->SetEnzymatic_search_constraint().SetAttlist().SetMax_num_internal_cleavages(inOMSSA.

().front()->GetSettings().GetMissedcleave());

sSum->SetEnzymatic_search_constraint().SetAttlist().SetMin_number_termini(cleave->

());

CMSSearchSettings::TFixed::const_iterator iterF;

(iterF = inOMSSA.

().front()->GetSettings().GetFixed().begin();

iterF != inOMSSA.

().front()->GetSettings().GetFixed().end(); ++iterF) {

CMSSearchSettings::TVariable::const_iterator iterV;

(iterV = inOMSSA.

().front()->GetSettings().GetVariable().begin();

iterV != inOMSSA.

().front()->GetSettings().GetVariable().end(); ++iterV) {

variableMods.

(*iterV);

CMSResponse::THitsets::const_iterator iHits;

(iHits = inOMSSA.

().front()->GetHitsets().begin();

iHits != inOMSSA.

().front()->GetHitsets().end(); iHits++) {

(*iHits, rSum->SetSpectrum_query(), Modset, variableMods, inOMSSA);

rSum->SetSearch_summary().push_back(sSum);

char const *const kEnzymeNames[eMSEnzymes_max]

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

CAlternative_protein –.

CAminoacid_modification –.

static CRef< CCleave > CleaveFactory(const EMSEnzymes enzyme)

Simple factory to return back object for enzyme.

bool GetCheckProline(void) const

Should we check for proline?

const string GetCleaveAt(void) const

What are the cleavage chars?

const char * GetCleaveSense(void) const

Should we check for proline?

int GetCleaveNum(void) const

Get the number of cleavage chars.

const char * GetUnimodName(int Mod) const

get unimod name

int GetModNumChars(int Mod) const

get the number of modification AA's

char GetModChar(int Mod, int Number) const

get modification AA's

EMSModType GetModType(int Mod) const

get modification type

int GetModMass(int Mod) const

get modification mass

TAminoAcidMassMap m_aaMassMap

CRef< CModification_info > ConvertModifications(CRef< CMSHits > msHits, CRef< CMSModSpecSet > Modset, set< int > &vModSet, CMSSearch &inOMSSA)

void ConvertModSetting(CRef< CSearch_summary > sSum, CRef< CMSModSpecSet > Modset, int modnum, bool fixed)

string ConvertDouble(double n)

string GetProteinName(CRef< CMSPepHit > pHit)

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

convert OMSSA to PepXML

pair< char, double > TAminoAcidMassPair

set< char > m_staticModSet

void ConvertMSHitSet(CRef< CMSHitSet > pHitSet, CMsms_run_summary::TSpectrum_query &sQueries, CRef< CMSModSpecSet > Modset, set< int > &variableMods, CMSSearch &inOMSSA)

void ConvertScanID(CRef< CSpectrum_query > sQuery, string SpecID, int query, int charge)

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

CTerminal_modification –.

container_type::iterator iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

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

main entry point for tests

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

bool IsMatch(CTempString str, TMatch flags=fMatch_default)

Check existence substring which match a specified pattern.

CTempString GetMatch(CTempString str, size_t offset=0, size_t idx=0, TMatch flags=fMatch_default, bool noreturn=false)

Get matching pattern and subpatterns.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

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

Convert string to int.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

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

Convert int to string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static void SetFormat(const CTimeFormat &fmt)

Set the current time format.

string AsString(const CTimeFormat &format=kEmptyStr, TSeconds out_tz=eCurrentTimeZone) const

Transform time to string.

@ eCurrent

Use current time. See also CCurrentTime.

list< CRef< CMSScoreSet > > TScores

const TRequest & GetRequest(void) const

Get the Request member data.

EMSSearchType

what type of atomic mass to use

list< CRef< CMSModHit > > TMods

const TResponse & GetResponse(void) const

Get the Response member data.

EMSModType

enumerate modification types

EMSEnzymes

enumerate enzymes

@ eMSSearchType_multiisotope

@ eMSSearchType_monoisotopic

@ eMSModType_modn

at the N terminus of a protein

@ eMSModType_modc

at the C 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_modaa

at particular amino acids

@ eMSModType_modcaa

at the C terminus of a protein at particular amino acids

@ eMSModType_modcp

at the C terminus of a peptide

@ eMSModType_modnaa

at the N terminus of a protein at particular amino acids

TAttlist & SetAttlist(void)

Assign a value to Attlist data member.

TMod_aminoacid_mass & SetMod_aminoacid_mass(void)

Assign a value to Mod_aminoacid_mass data member.

void SetDate(const TDate &value)

Assign a value to Date data member.

void SetAttlist(TAttlist &value)

Assign a value to Attlist data member.

void SetSummary_xml(const TSummary_xml &value)

Assign a value to Summary_xml data member.

list< CRef< CSpectrum_query > > TSpectrum_query

TMsms_run_summary & SetMsms_run_summary(void)

Assign a value to Msms_run_summary data member.

@ eAttlist_fragment_mass_type_average

@ eAttlist_fragment_mass_type_monoisotopic

@ eAttlist_precursor_mass_type_average

@ eAttlist_precursor_mass_type_monoisotopic

char * dbname(DBPROCESS *dbproc)

Get name of current database.

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

const double HYDROGEN_MASS

map< int, string > TAAModMap

pair< int, string > TAAModPair

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

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