cTheoreticalSpectrum Class Reference

The class representing a theoretical mass spectrum. More...

#include <cTheoreticalSpectrum.h>

Public Member Functions
	cTheoreticalSpectrum ()
	The constructor.
	cTheoreticalSpectrum (cParameters *parameters, cCandidate &candidate)
	The constructor. More...
void	clear (bool clearpeaklist=true)
	Clear the spectrum. More...
cCandidate &	getCandidate ()
	Get the peptide spectrum candidate. More...
void	setCandidate (cCandidate &candidate)
	Set a peptide spectrum candidate. More...
int	getNumberOfPeaks ()
	Get the number of peaks in the spectrum. More...
int	compareBranched (cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid)
	Compare the theoretical spectrum of a branched peptide with an experimental spectrum. More...
int	compareLinear (cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid)
	Compare the theoretical spectrum of a linear peptide with an experimental spectrum. More...
int	compareCyclic (cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid)
	Compare the theoretical spectrum of a cyclic peptide with an experimental spectrum. More...
int	compareBranchCyclic (cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid)
	Compare the theoretical spectrum of a branch-cyclic peptide with an experimental spectrum. More...
int	compareLinearPolyketide (cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid)
	Compare the theoretical spectrum of a linear polyketide with an experimental spectrum. More...
int	compareCyclicPolyketide (cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid)
	Compare the theoretical spectrum of a cyclic polyketide with an experimental spectrum. More...
int	compareOther (cPeaksList &sortedpeaklist, bool writedescription, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid)
	Compare the theoretical spectrum of a metabolite with an experimental spectrum. More...
void	generateMSSpectrum (int sequencestart, int sequencestop, bool &terminatecomputation, bool writedescription)
	Generate a simple mass spectrum. More...
void	generateFineMSSpectrum (int sequencestart, int sequencestop, bool &terminatecomputation)
	Generate a simple mass spectrum with fine isotopic patterns. More...
void	getHintsIndex (int id, int peaklistseriesvectorid, cTheoreticalSpectrum &tsfull, cPeaksList &unmatchedpeaksinmatchedpatterns, vector< vector< int > > &hintsindex, bool lcmsrt, bool skipcomparison)
	Get a map of search hints to identify features in LC-MS data. More...
void	compareMSSpectrum (int id, int peaklistseriesvectorid, cTheoreticalSpectrum &tsfull, cPeaksList &unmatchedpeaksinmatchedpatterns, vector< vector< int > > &hintsindex, bool lcmsrt, bool skipcomparison)
	Compare theoretical peaks with an experimental spectrum. More...
void	compareAverageMSSpectrum (cPeaksList &averagespectrum, cTheoreticalSpectrum &tsfull, cPeaksList &unmatchedpeaksinmatchedpatterns)
	Compare theoretical peaks with an average spectrum. More...
void	finalizeMSSpectrum (cPeaksList &unmatchedpeaksinmatchedpatterns, bool writedescription)
	Finalize MS spectrum after comparison. More...
int	getNumberOfMatchedPeaks () const
	Get the number of matched peaks between an experimental and a theoretical spectrum. More...
int	getNumberOfScrambledPeaks ()
	Get the number of matched scrambled peaks between an experimental and a theoretical spectrum. More...
int	getNumberOfMatchedPeaks (eFragmentIonType iontype, int neutrallosstype) const
	Get the number of matched peaks between an experimental and a theoretical spectrum of a specified fragment ion type. More...
int	getNumberOfMatchedPeaksB () const
	Get the number of matched B ions between an experimental and a theoretical spectrum. More...
int	getNumberOfMatchedPeaksY () const
	Get the number of matched Y ions between an experimental and a theoretical spectrum. More...
int	getNumberOfMatchedPeaksYB () const
	Get the number of matched Y and B ions between an experimental and a theoretical spectrum. More...
double	getRatioOfMatchedPeaks ()
	Get a ratio of matched peaks. More...
double	getWeightedRatioOfMatchedPeaks () const
	Get weighted ratio of matched peaks. More...
double	getCosineSimilarity () const
	Get cosine similarity. More...
void	generateNTerminalFragmentIons (int maxcharge, int &peaklistrealsize, vector< int > &intcomposition, eFragmentIonType fragmentiontype, int neutrallosstype, cBricksDatabase &bricksdatabase, bool writedescription, int rotationid, vector< splitSite > &splittingsites, vector< cFragmentIonType > &searchedmodifications, ePeptideType peptidetype, bool regularblocksorder, TRotationInfo *trotation=0, eResidueLossType leftresiduelosstype=h2o_loss, bool hasfirstblockartificial=false)
	Generate a N-terminal fragment ion series. More...
void	generateCTerminalFragmentIons (int maxcharge, int &peaklistrealsize, vector< int > &intcomposition, eFragmentIonType fragmentiontype, int neutrallosstype, cBricksDatabase &bricksdatabase, bool writedescription, int rotationid, vector< splitSite > &splittingsites, vector< cFragmentIonType > &searchedmodifications, ePeptideType peptidetype, bool regularblocksorder, TRotationInfo *trotation=0, eResidueLossType rightresiduelosstype=h2o_loss, bool haslastblockartificial=false)
	Generate a C-terminal fragment ion series. More...
void	sortByMass (int limit=-1)
	Sort peaks by mass. More...
void	resizePeakList (int size)
	Resize the list of peaks. More...
double	getSumOfRelativeIntensities () const
	Get the sum of relative intensities of matched peaks. More...
cPeak &	operator[] (int position)
	Overloaded operator []. More...
cPeaksList &	getExperimentalSpectrum ()
	Get an experimental spectrum which has been compared with the theoretical spectrum. More...
void	setExperimentalSpectrum (cPeaksList &experimentalspectrum)
	Set the experimental spectrum. More...
set< int > &	getExperimentalMatches (int peakid)
	Get ids of theoretical peaks which hit an experimental peak. More...
string	getCoverageBySeries ()
	Get coverage of series of fragment ions. More...
int	getUnmatchedExperimentalPeaksCount ()
	Get the number of unmatched experimental peaks. More...
cPeaksList *	getTheoreticalPeaks ()
	Get a list of theoretical peaks. More...
bool	isValid ()
	Check if the candidate sequence corresponds to the searched sequence. More...
int	getValidPosition ()
	Get a position of a rotation of a cyclic peptide sequence corresponding to searched sequence. More...
int	getReverseValidPosition ()
	Get a reverted position of a rotation of a cyclic peptide sequence corresponding to searched sequence. More...
void	setValidSequence (regex &searchedsequence)
	Set a flag determining if the candidate sequence corresponds to the searched sequence. More...
vector< string > &	getLabelsOfRotations ()
	Get the labels of cyclic rotations. More...
int	getNumberOfCompletedSeries ()
	Get a number of series which identify the peptide. More...
void	setNumberOfCompletedSeries (int numberofcompletedseries)
	Set a number of series which identify the peptide. More...
void	setPathId (int pathid)
	Set path id. More...
int	getPathId () const
	Get path id. More...
void	setParameters (cParameters *parameters)
	Set a pointer to the parameters of the application. More...
double	getTargetPatternScore (int groupid)
	Get target pattern score. More...
double	getTargetPatternFDR (int groupid)
	Get target pattern FDR. More...
map< int, double > &	getTargetScores ()
	Get map of target scores. More...
map< int, double > &	getDecoyScores ()
	Get map of decoy scores. More...
void	setFDRs (vector< double > &targetscoresvector, vector< double > &fdrs, cPeaksList &unmatchedpeaksinmatchedpatterns)
	Set false discovery rates to peak groups. More...
void	store (ofstream &os)
	Store the structure into an output stream. More...
void	load (ifstream &is, int fileversionpart1, int fileversionpart2, int fileversionpart3)
	Load the structure from an input stream. More...
bool	equals (cTheoreticalSpectrum &secondtheoreticalspectrum)
	Check if the object equals to another object. More...
void	attach (cTheoreticalSpectrum &secondtheoreticalspectrum)
	Attach another spectrum. More...

Detailed Description

The class representing a theoretical mass spectrum.

Constructor & Destructor Documentation

cTheoreticalSpectrum()

cTheoreticalSpectrum::cTheoreticalSpectrum	(	cParameters *	parameters,
		cCandidate &	candidate
	)

The constructor.

Parameters

parameters	a pointer to the parameters of the application
candidate	reference to a peptide sequence candidate

Member Function Documentation

attach()

void cTheoreticalSpectrum::attach

(

cTheoreticalSpectrum &

secondtheoreticalspectrum

)

Attach another spectrum.

Parameters

secondtheoreticalspectrum

spectrum to be attached

clear()

void cTheoreticalSpectrum::clear

(

bool

clearpeaklist = true

)

Clear the spectrum.

Parameters

clearpeaklist

if true then all variables including the list of theoretical peaks are cleared else the list of theoretical peaks is not cleared

compareAverageMSSpectrum()

void cTheoreticalSpectrum::compareAverageMSSpectrum	(	cPeaksList &	averagespectrum,
		cTheoreticalSpectrum &	tsfull,
		cPeaksList &	unmatchedpeaksinmatchedpatterns
	)

Compare theoretical peaks with an average spectrum.

Parameters

averagespectrum	average experimental spectrum
tsfull	theoretical spectrum with descriptions of peaks
unmatchedpeaksinmatchedpatterns	unmatched peaks in matched isotope patterns

compareBranchCyclic()

int cTheoreticalSpectrum::compareBranchCyclic	(	cPeaksList &	sortedpeaklist,
		cBricksDatabase &	bricksdatabasewithcombinations,
		bool	writedescription,
		regex &	sequencetag,
		regex &	searchedsequence,
		cPeaksList &	unmatchedpeaksinmatchedpatterns,
		unordered_map< string, int > *	isotopeformuladesctoid
	)

Compare the theoretical spectrum of a branch-cyclic peptide with an experimental spectrum.

Parameters

sortedpeaklist	reference to an experimental peaklist
bricksdatabasewithcombinations	reference to a database of bricks with combinations of bricks
writedescription	if true then string descriptions of peaks are filled
sequencetag	reference to a regex of a sequence tag
searchedsequence	reference to a regex of a searched sequence
unmatchedpeaksinmatchedpatterns	unmatched peaks in matched isotope patterns
isotopeformuladesctoid	a map of isotope descriptions

Return values

int	number theoretical peaks generated; -2 when the sequence tag does not match the peptide sequence candidate

compareBranched()

int cTheoreticalSpectrum::compareBranched	(	cPeaksList &	sortedpeaklist,
		cBricksDatabase &	bricksdatabasewithcombinations,
		bool	writedescription,
		regex &	sequencetag,
		regex &	searchedsequence,
		cPeaksList &	unmatchedpeaksinmatchedpatterns,
		unordered_map< string, int > *	isotopeformuladesctoid
	)

Compare the theoretical spectrum of a branched peptide with an experimental spectrum.

Parameters

sortedpeaklist	reference to an experimental peaklist
bricksdatabasewithcombinations	reference to a database of bricks with combinations of bricks
writedescription	if true then string descriptions of peaks are filled
sequencetag	reference to a regex of a sequence tag
searchedsequence	reference to a regex of a searched sequence
unmatchedpeaksinmatchedpatterns	unmatched peaks in matched isotope patterns
isotopeformuladesctoid	a map of isotope descriptions

Return values

int	number theoretical peaks generated; -2 when the sequence tag does not match the peptide sequence candidate

compareCyclic()

int cTheoreticalSpectrum::compareCyclic	(	cPeaksList &	sortedpeaklist,
		cBricksDatabase &	bricksdatabasewithcombinations,
		bool	writedescription,
		regex &	sequencetag,
		regex &	searchedsequence,
		cPeaksList &	unmatchedpeaksinmatchedpatterns,
		unordered_map< string, int > *	isotopeformuladesctoid
	)

Compare the theoretical spectrum of a cyclic peptide with an experimental spectrum.

Parameters

sortedpeaklist	reference to an experimental peaklist
bricksdatabasewithcombinations	reference to a database of bricks with combinations of bricks
writedescription	if true then string descriptions of peaks are filled
sequencetag	reference to a regex of a sequence tag
searchedsequence	reference to a regex of a searched sequence
unmatchedpeaksinmatchedpatterns	unmatched peaks in matched isotope patterns
isotopeformuladesctoid	a map of isotope descriptions

Return values

int	number theoretical peaks generated; -2 when the sequence tag does not match the peptide sequence candidate

compareCyclicPolyketide()

int cTheoreticalSpectrum::compareCyclicPolyketide	(	cPeaksList &	sortedpeaklist,
		cBricksDatabase &	bricksdatabasewithcombinations,
		bool	writedescription,
		regex &	sequencetag,
		regex &	searchedsequence,
		cPeaksList &	unmatchedpeaksinmatchedpatterns,
		unordered_map< string, int > *	isotopeformuladesctoid
	)

Compare the theoretical spectrum of a cyclic polyketide with an experimental spectrum.

Parameters

sortedpeaklist	reference to an experimental peaklist
bricksdatabasewithcombinations	reference to a database of bricks with combinations of bricks
writedescription	if true then string descriptions of peaks are filled
sequencetag	reference to a regex of a sequence tag
searchedsequence	reference to a regex of a searched sequence
unmatchedpeaksinmatchedpatterns	unmatched peaks in matched isotope patterns
isotopeformuladesctoid	a map of isotope descriptions

Return values

int	number theoretical peaks generated; -2 when the sequence tag does not match the peptide sequence candidate

compareLinear()

int cTheoreticalSpectrum::compareLinear	(	cPeaksList &	sortedpeaklist,
		cBricksDatabase &	bricksdatabasewithcombinations,
		bool	writedescription,
		regex &	sequencetag,
		regex &	searchedsequence,
		cPeaksList &	unmatchedpeaksinmatchedpatterns,
		unordered_map< string, int > *	isotopeformuladesctoid
	)

Compare the theoretical spectrum of a linear peptide with an experimental spectrum.

Parameters

sortedpeaklist	reference to an experimental peaklist
bricksdatabasewithcombinations	reference to a database of bricks with combinations of bricks
writedescription	if true then string descriptions of peaks are filled
sequencetag	reference to a regex of a sequence tag
searchedsequence	reference to a regex of a searched sequence
unmatchedpeaksinmatchedpatterns	unmatched peaks in matched isotope patterns
isotopeformuladesctoid	a map of isotope descriptions

Return values

int	number theoretical peaks generated; -2 when the sequence tag does not match the peptide sequence candidate

compareLinearPolyketide()

int cTheoreticalSpectrum::compareLinearPolyketide	(	cPeaksList &	sortedpeaklist,
		cBricksDatabase &	bricksdatabasewithcombinations,
		bool	writedescription,
		regex &	sequencetag,
		regex &	searchedsequence,
		cPeaksList &	unmatchedpeaksinmatchedpatterns,
		unordered_map< string, int > *	isotopeformuladesctoid
	)

Compare the theoretical spectrum of a linear polyketide with an experimental spectrum.

Parameters

sortedpeaklist	reference to an experimental peaklist
bricksdatabasewithcombinations	reference to a database of bricks with combinations of bricks
writedescription	if true then string descriptions of peaks are filled
sequencetag	reference to a regex of a sequence tag
searchedsequence	reference to a regex of a searched sequence
unmatchedpeaksinmatchedpatterns	unmatched peaks in matched isotope patterns
isotopeformuladesctoid	a map of isotope descriptions

Return values

int	number theoretical peaks generated; -2 when the sequence tag does not match the peptide sequence candidate

compareMSSpectrum()

void cTheoreticalSpectrum::compareMSSpectrum	(	int	id,
		int	peaklistseriesvectorid,
		cTheoreticalSpectrum &	tsfull,
		cPeaksList &	unmatchedpeaksinmatchedpatterns,
		vector< vector< int > > &	hintsindex,
		bool	lcmsrt,
		bool	skipcomparison
	)

Compare theoretical peaks with an experimental spectrum.

Parameters

id	identifier of an experimental spectrum
peaklistseriesvectorid	id of a peaklistseriesvector
tsfull	theoretical spectrum with descriptions of peaks
unmatchedpeaksinmatchedpatterns	unmatched peaks in matched isotope patterns
hintsindex	index of experimental spectra for every matched theoretical peak
lcmsrt	true if LC-MS data are processed and retention time is available
skipcomparison	if true, the peak comparison is skipped

compareOther()

int cTheoreticalSpectrum::compareOther	(	cPeaksList &	sortedpeaklist,
		bool	writedescription,
		cPeaksList &	unmatchedpeaksinmatchedpatterns,
		unordered_map< string, int > *	isotopeformuladesctoid
	)

Compare the theoretical spectrum of a metabolite with an experimental spectrum.

Parameters

sortedpeaklist	reference to an experimental peaklist
writedescription	if true then string descriptions of peaks are filled
unmatchedpeaksinmatchedpatterns	unmatched peaks in matched isotope patterns
isotopeformuladesctoid	a map of isotope descriptions

Return values

int	number theoretical peaks generated

equals()

bool cTheoreticalSpectrum::equals

(

cTheoreticalSpectrum &

secondtheoreticalspectrum

)

Check if the object equals to another object.

Parameters

secondtheoreticalspectrum

object for comparison

Return values

bool	true if the objects are equals

finalizeMSSpectrum()

void cTheoreticalSpectrum::finalizeMSSpectrum	(	cPeaksList &	unmatchedpeaksinmatchedpatterns,
		bool	writedescription
	)

Finalize MS spectrum after comparison.

Parameters

unmatchedpeaksinmatchedpatterns	unmatched peaks in matched isotope patterns
writedescription	if true then string descriptions of fragment ions are generated

generateCTerminalFragmentIons()

void cTheoreticalSpectrum::generateCTerminalFragmentIons	(	int	maxcharge,
		int &	peaklistrealsize,
		vector< int > &	intcomposition,
		eFragmentIonType	fragmentiontype,
		int	neutrallosstype,
		cBricksDatabase &	bricksdatabase,
		bool	writedescription,
		int	rotationid,
		vector< splitSite > &	splittingsites,
		vector< cFragmentIonType > &	searchedmodifications,
		ePeptideType	peptidetype,
		bool	regularblocksorder,
		TRotationInfo *	trotation = 0,
		eResidueLossType	rightresiduelosstype = h2o_loss,
		bool	haslastblockartificial = false
	)

Generate a C-terminal fragment ion series.

Parameters

maxcharge	a charge of precursor ion
peaklistrealsize	real size of the peak list
intcomposition	reference to a vector of ids of bricks as integers
fragmentiontype	fragment ion type to be generated
neutrallosstype	neutral loss type to be generated
bricksdatabase	reference to a database of building blocks
writedescription	if true then string descriptions of fragment ions are generated
rotationid	id of a cyclic peptide
splittingsites	reference to a vector of splitting sites of a cyclic peptide
searchedmodifications	reference to a vector of searched modifications
peptidetype	the type of searched peptide
regularblocksorder	check regular order of ketide blocks
trotation	a pointer to a T-permutation of a branched peptide
rightresiduelosstype	a residue type of the rightmost building block
haslastblockartificial	true when the last block is artificial, false otherwise

generateFineMSSpectrum()

void cTheoreticalSpectrum::generateFineMSSpectrum	(	int	sequencestart,
		int	sequencestop,
		bool &	terminatecomputation
	)

Generate a simple mass spectrum with fine isotopic patterns.

Parameters

sequencestart	index of the first item to be processed
sequencestop	index of the last item to be processed (excluding the last item)
terminatecomputation	reference to a variable determining that the computation must be stopped

generateMSSpectrum()

void cTheoreticalSpectrum::generateMSSpectrum	(	int	sequencestart,
		int	sequencestop,
		bool &	terminatecomputation,
		bool	writedescription
	)

Generate a simple mass spectrum.

Parameters

sequencestart	index of the first item to be processed
sequencestop	index of the last item to be processed (excluding the last item)
terminatecomputation	reference to a variable determining that the computation must be stopped
writedescription	if true then string descriptions of peaks are filled

generateNTerminalFragmentIons()

void cTheoreticalSpectrum::generateNTerminalFragmentIons	(	int	maxcharge,
		int &	peaklistrealsize,
		vector< int > &	intcomposition,
		eFragmentIonType	fragmentiontype,
		int	neutrallosstype,
		cBricksDatabase &	bricksdatabase,
		bool	writedescription,
		int	rotationid,
		vector< splitSite > &	splittingsites,
		vector< cFragmentIonType > &	searchedmodifications,
		ePeptideType	peptidetype,
		bool	regularblocksorder,
		TRotationInfo *	trotation = 0,
		eResidueLossType	leftresiduelosstype = h2o_loss,
		bool	hasfirstblockartificial = false
	)

Generate a N-terminal fragment ion series.

Parameters

maxcharge	a charge of precursor ion
peaklistrealsize	real size of the peak list
intcomposition	reference to a vector of ids of bricks as integers
fragmentiontype	fragment ion type to be generated
neutrallosstype	neutral loss type to be generated
bricksdatabase	reference to a database of building blocks
writedescription	if true then string descriptions of fragment ions are generated
rotationid	id of a cyclic peptide
splittingsites	reference to a vector of splitting sites of a cyclic peptide
searchedmodifications	reference to a vector of searched modifications
peptidetype	the type of searched peptide
regularblocksorder	check regular order of ketide blocks
trotation	a pointer to a T-permutation of a branched peptide
leftresiduelosstype	a residue type of the leftmost building block
hasfirstblockartificial	true when the first block is artificial, false otherwise

getCandidate()

cCandidate & cTheoreticalSpectrum::getCandidate

(

)

Get the peptide spectrum candidate.

Return values

cCandidate

reference to the peptide sequence candidate

getCosineSimilarity()

double cTheoreticalSpectrum::getCosineSimilarity

(

)

const

Get cosine similarity.

Return values

double

cosine similarity

getCoverageBySeries()

string cTheoreticalSpectrum::getCoverageBySeries

(

)

Get coverage of series of fragment ions.

Return values

string

coverage of the series of fragment ions

getDecoyScores()

map< int, double > & cTheoreticalSpectrum::getDecoyScores

(

)

Get map of decoy scores.

Return values

map<int,double>

map of decoy scores

getExperimentalMatches()

set< int > & cTheoreticalSpectrum::getExperimentalMatches

(

int

peakid

)

Get ids of theoretical peaks which hit an experimental peak.

Return values

set<int>

set of ids of theoretical peaks

getExperimentalSpectrum()

cPeaksList & cTheoreticalSpectrum::getExperimentalSpectrum

(

)

Get an experimental spectrum which has been compared with the theoretical spectrum.

Return values

cPeaksList

reference to an experimental spectrum

getHintsIndex()

void cTheoreticalSpectrum::getHintsIndex	(	int	id,
		int	peaklistseriesvectorid,
		cTheoreticalSpectrum &	tsfull,
		cPeaksList &	unmatchedpeaksinmatchedpatterns,
		vector< vector< int > > &	hintsindex,
		bool	lcmsrt,
		bool	skipcomparison
	)

Get a map of search hints to identify features in LC-MS data.

Parameters

id	identifier of an experimental spectrum
peaklistseriesvectorid	id of a peaklistseriesvector
tsfull	theoretical spectrum
unmatchedpeaksinmatchedpatterns	unmatched peaks in matched isotope patterns
hintsindex	index of experimental spectra for every matched theoretical peak
lcmsrt	true if LC-MS data are processed and retention time is available
skipcomparison	if true, the peak comparison is skipped

getLabelsOfRotations()

vector< string > & cTheoreticalSpectrum::getLabelsOfRotations

(

)

Get the labels of cyclic rotations.

Return values

vector<string>

a vector of labels

getNumberOfCompletedSeries()

int cTheoreticalSpectrum::getNumberOfCompletedSeries

(

)

Get a number of series which identify the peptide.

Return values

int	number of completed series

getNumberOfMatchedPeaks() [1/2]

int cTheoreticalSpectrum::getNumberOfMatchedPeaks

(

)

const

Get the number of matched peaks between an experimental and a theoretical spectrum.

Return values

int	number of matched peaks

getNumberOfMatchedPeaks() [2/2]

int cTheoreticalSpectrum::getNumberOfMatchedPeaks	(	eFragmentIonType	iontype,
		int	neutrallosstype
	)		const

Get the number of matched peaks between an experimental and a theoretical spectrum of a specified fragment ion type.

Parameters

iontype	a fragment ion type
neutrallosstype	a neutral loss type

Return values

int	number of matched peaks

getNumberOfMatchedPeaksB()

int cTheoreticalSpectrum::getNumberOfMatchedPeaksB

(

)

const

Get the number of matched B ions between an experimental and a theoretical spectrum.

Return values

int	number of matched peaks

getNumberOfMatchedPeaksY()

int cTheoreticalSpectrum::getNumberOfMatchedPeaksY

(

)

const

Get the number of matched Y ions between an experimental and a theoretical spectrum.

Return values

int	number of matched peaks

getNumberOfMatchedPeaksYB()

int cTheoreticalSpectrum::getNumberOfMatchedPeaksYB

(

)

const

Get the number of matched Y and B ions between an experimental and a theoretical spectrum.

Return values

int	number of matched peaks

getNumberOfPeaks()

int cTheoreticalSpectrum::getNumberOfPeaks

(

)

Get the number of peaks in the spectrum.

Return values

int	the number of peaks

getNumberOfScrambledPeaks()

int cTheoreticalSpectrum::getNumberOfScrambledPeaks

(

)

Get the number of matched scrambled peaks between an experimental and a theoretical spectrum.

Return values

int	number of matched scrambled peaks

getPathId()

int cTheoreticalSpectrum::getPathId

(

)

const

Get path id.

Return values

int	id of a path

getRatioOfMatchedPeaks()

double cTheoreticalSpectrum::getRatioOfMatchedPeaks

(

)

Get a ratio of matched peaks.

Return values

double

ratio of matched peaks

getReverseValidPosition()

int cTheoreticalSpectrum::getReverseValidPosition

(

)

Get a reverted position of a rotation of a cyclic peptide sequence corresponding to searched sequence.

Return values

int	reverted position of sequence

getSumOfRelativeIntensities()

double cTheoreticalSpectrum::getSumOfRelativeIntensities

(

)

const

Get the sum of relative intensities of matched peaks.

Return values

double

sum of relative intensities of matched peaks

getTargetPatternFDR()

double cTheoreticalSpectrum::getTargetPatternFDR

(

int

groupid

)

Get target pattern FDR.

Parameters

groupid

id of a group of peaks forming a target pattern

Return values

double

target pattern FDR

getTargetPatternScore()

double cTheoreticalSpectrum::getTargetPatternScore

(

int

groupid

)

Get target pattern score.

Parameters

groupid

id of a group of peaks forming a target pattern

Return values

double

target pattern score

getTargetScores()

map< int, double > & cTheoreticalSpectrum::getTargetScores

(

)

Get map of target scores.

Return values

map<int,double>

map of target scores

getTheoreticalPeaks()

cPeaksList * cTheoreticalSpectrum::getTheoreticalPeaks

(

)

Get a list of theoretical peaks.

Return values

cPeaksList

a pointer to a list of theoretical peaks

getUnmatchedExperimentalPeaksCount()

int cTheoreticalSpectrum::getUnmatchedExperimentalPeaksCount

(

)

Get the number of unmatched experimental peaks.

Return values

number

of unmatched experimental peaks

getValidPosition()

int cTheoreticalSpectrum::getValidPosition

(

)

Get a position of a rotation of a cyclic peptide sequence corresponding to searched sequence.

Return values

int	position of sequence

getWeightedRatioOfMatchedPeaks()

double cTheoreticalSpectrum::getWeightedRatioOfMatchedPeaks

(

)

const

Get weighted ratio of matched peaks.

Return values

double

weighted ratio of matched peaks

isValid()

bool cTheoreticalSpectrum::isValid

(

)

Check if the candidate sequence corresponds to the searched sequence.

Return values

bool	if true then the theoretical spectrum corresponds to a searched sequence

load()

void cTheoreticalSpectrum::load	(	ifstream &	is,
		int	fileversionpart1,
		int	fileversionpart2,
		int	fileversionpart3
	)

Load the structure from an input stream.

Parameters

is	an input stream
fileversionpart1	first number of .res the file version
fileversionpart2	second number of .res the file version
fileversionpart3	third number of .res the file version

operator[]()

cPeak & cTheoreticalSpectrum::operator[]

(

int

position

)

Overloaded operator [].

Parameters

position

position of a peak in the peak list

Return values

cPeak

reference to the peak

resizePeakList()

void cTheoreticalSpectrum::resizePeakList

(

int

size

)

Resize the list of peaks.

Parameters

size	the number of peaks

setCandidate()

void cTheoreticalSpectrum::setCandidate

(

cCandidate &

candidate

)

Set a peptide spectrum candidate.

Parameters

candidate

reference to the peptide sequence candidate

setExperimentalSpectrum()

void cTheoreticalSpectrum::setExperimentalSpectrum

(

cPeaksList &

experimentalspectrum

)

Set the experimental spectrum.

Parameters

experimentalspectrum

an experimental spectrum

setFDRs()

void cTheoreticalSpectrum::setFDRs	(	vector< double > &	targetscoresvector,
		vector< double > &	fdrs,
		cPeaksList &	unmatchedpeaksinmatchedpatterns
	)

Set false discovery rates to peak groups.

Parameters

targetscoresvector	vector of target scores
fdrs	vector of FDRs
unmatchedpeaksinmatchedpatterns	unmatched peaks in matched isotope patterns

setNumberOfCompletedSeries()

void cTheoreticalSpectrum::setNumberOfCompletedSeries

(

int

numberofcompletedseries

)

Set a number of series which identify the peptide.

Parameters

numberofcompletedseries

number of completed series

setParameters()

void cTheoreticalSpectrum::setParameters

(

cParameters *

parameters

)

Set a pointer to the parameters of the application.

Parameters

parameters

the pointer to the parameters of the application

setPathId()

void cTheoreticalSpectrum::setPathId

(

int

pathid

)

Set path id.

Parameters

pathid

id of a path

setValidSequence()

void cTheoreticalSpectrum::setValidSequence

(

regex &

searchedsequence

)

Set a flag determining if the candidate sequence corresponds to the searched sequence.

Parameters

searchedsequence

searched sequence

sortByMass()

void cTheoreticalSpectrum::sortByMass

(

int

limit = -1

)

Sort peaks by mass.

Parameters

limit

sort first limit peaks only; if limit == -1 then all peaks are sorted

store()

void cTheoreticalSpectrum::store

(

ofstream &

os

)

Store the structure into an output stream.

Parameters

os	an output stream

---

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

• core/cTheoreticalSpectrum.h
• core/cTheoreticalSpectrum.cpp