cTheoreticalSpectrumList Class Reference

The class representing lists of theoretical spectra. More...

#include <cTheoreticalSpectrumList.h>

Public Member Functions
	cTheoreticalSpectrumList ()
	The constructor.
void	clear ()
	Clear the class.
void	clear (int fileid)
	Clear a specified file id. More...
void	initialize (cMainThread &os, cParameters &parameters, cDeNovoGraph *graph)
	Initialize the list. More...
void	add (int fileid, cTheoreticalSpectrum &theoreticalspectrum)
	Add a spectrum to the list. More...
cTheoreticalSpectrum &	get (int fileid, int order)
	Get a reference to a spectrum. More...
int	size ()
	Get the number of files. More...
int	size (int fileid)
	Get the number of spectra in a file. More...
void	resize (int size)
	Resize the vector of files. More...
void	resize (int fileid, int size)
	Resize a file id vector. More...
int	parallelCompareAndStore (int fileid, cCandidateSet &candidates, bool &terminatecomputation)
	Parallel comparison of theoretical spectra with an experimental spectrum. More...
double	updatekNNList (cTheoreticalSpectrum &theoreticalspectrum, int theoreticalpeaksrealsize, double score, regex *rxsearchedsequence)
	Update the kNN list of peptide sequence candidates (thread-safe). More...
void	sortAndFitSize (int fileid)
	Sort the list according to a score defined by cParameters::scoretype and crop the list according cParameters::hitsreported. More...

Detailed Description

The class representing lists of theoretical spectra.

Member Function Documentation

add()

void cTheoreticalSpectrumList::add	(	int	fileid,
		cTheoreticalSpectrum &	theoreticalspectrum
	)

Add a spectrum to the list.

Parameters

fileid	file id
theoreticalspectrum	reference to a spectrum

clear()

void cTheoreticalSpectrumList::clear

(

int

fileid

)

Clear a specified file id.

Parameters

fileid

file id

get()

cTheoreticalSpectrum & cTheoreticalSpectrumList::get	(	int	fileid,
		int	order
	)

Get a reference to a spectrum.

Parameters

fileid	file id
order	id of a spectrum

Return values

cTheoreticalSpectrum

reference to a spectrum

initialize()

void cTheoreticalSpectrumList::initialize	(	cMainThread &	os,
		cParameters &	parameters,
		cDeNovoGraph *	graph
	)

Initialize the list.

Parameters

os	reference to the main thread of the application
parameters	reference to the parameters of the application
graph	pointer to the de novo graph

parallelCompareAndStore()

int cTheoreticalSpectrumList::parallelCompareAndStore	(	int	fileid,
		cCandidateSet &	candidates,
		bool &	terminatecomputation
	)

Parallel comparison of theoretical spectra with an experimental spectrum.

Parameters

fileid	file id
candidates	reference to a set of peptide sequence candidates
terminatecomputation	reference to a variable determining that the computation must be stopped

Return values

int	0 when successfully finished; -1 when an error occurred

resize() [1/2]

void cTheoreticalSpectrumList::resize	(	int	fileid,
		int	size
	)

Resize a file id vector.

Parameters

fileid	file id
size	size

resize() [2/2]

void cTheoreticalSpectrumList::resize

(

int

size

)

Resize the vector of files.

Parameters

size

size

size() [1/2]

int cTheoreticalSpectrumList::size

(

)

Get the number of files.

Return values

int	number of files

size() [2/2]

int cTheoreticalSpectrumList::size

(

int

fileid

)

Get the number of spectra in a file.

Parameters

fileid

file id

Return values

int	number of spectra

sortAndFitSize()

void cTheoreticalSpectrumList::sortAndFitSize

(

int

fileid

)

Sort the list according to a score defined by cParameters::scoretype and crop the list according cParameters::hitsreported.

Parameters

fileid

file id

updatekNNList()

double cTheoreticalSpectrumList::updatekNNList	(	cTheoreticalSpectrum &	theoreticalspectrum,
		int	theoreticalpeaksrealsize,
		double	score,
		regex *	rxsearchedsequence
	)

Update the kNN list of peptide sequence candidates (thread-safe).

Parameters

theoreticalspectrum	reference to the newly added spectrum
theoreticalpeaksrealsize	the number of peaks in the newly added spectrum (required because of a performance improvement)
score	score of the candidate to be inserted
rxsearchedsequence	regular expression corresponding to searched sequence

Return values

double

current value of the worst score in the list of candidates

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

• core/cTheoreticalSpectrumList.h
• core/cTheoreticalSpectrumList.cpp