cParameters Class Reference

The class storing parameters of the application. More...

#include <cParameters.h>

Public Member Functions
	cParameters ()
	The constructor.
void	clear ()
	Clear the structure.
int	checkAndPrepare (bool &terminatecomputation)
	Test restrictions of parameters and prepare some internal parameters. More...
int	prepareLossesAndCompounds (bool &terminatecomputation)
	Prepare neutral losses and compounds. More...
bool	checkModifications (cSequence &sequence, int &startmodifid, int &endmodifid, int &middlemodifid, string &errormessage)
	Check if the names of modifications used in a sequence are correct. More...
string	printToString ()
	Print parameters to a string. More...
void	setOutputStream (cMainThread &os)
	Set the ouput stream. More...
void	updateFragmentDefinitions ()
	Update definitions of fragment ions when cyclicnterminus, cycliccterminus or precursoradduct have been changed.
int	calculateNeutralLosses (bool &terminatecomputation, string &errormessage)
	Calculate a list of neutral losses. More...
int	generateCompounds (bool &terminatecomputation, string &errormessage)
	Generate compounds. 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...

Public Attributes
cFragmentIons	iondefinitions
	Definitions of ion types.
ePeptideType	peptidetype
	The type of analyzed peptide.
vector< string >	peaklistfilenames
	The filenames of peaklists.
string	originalpeaklistfilenames
	Original input line with peaklist(s).
bool	useprofiledata
	Use profile data.
bool	convertprofiledata
	Convert profile data.
string	profiledatafilename
	Profile data file name.
int	linebafprocessing
	Line spectra processing method (baf).
vector< ePeakListFileFormat >	peaklistfileformats
	The file formats of peaklists.
vector< cPeakListSeries >	peaklistseriesvector
	A structure representing a vector of series of peaklists.
int	scannumber
	Scan number.
double	precursormass
	Precursor mass of the peptide.
string	precursoradduct
	An adduct of a precursor ion.
vector< string >	metaladducts
	A list of parsed metal adducts from precursoradduct.
double	precursormasserrortolerance
	Precursor mass error tolerance (ppm).
int	precursorcharge
	The charge of the precursor ion.
double	fragmentmasserrortolerance
	Fragment mass error tolerance (ppm).
double	minimumrelativeintensitythreshold
	Minimum relative intensity threshold.
unsigned	minimumabsoluteintensitythreshold
	Minimum absolute intensity threshold.
double	minimummz
	Minimum m/z ratio.
double	maximummz
	Maximum m/z ratio.
double	minimumrt
	Minimum retention time.
double	maximumrt
	Maximum retention time.
double	fwhm
	FWHM.
bool	enableratio54Fe56Fe
	Enable 54Fe/56Fe ratio.
double	minratio54Fe56Fe
	Minimum ratio 54Fe/56Fe.
double	maxratio54Fe56Fe
	Maximum ratio 54Fe/56Fe.
bool	enableratio60Ni58Ni
	Enable 60Ni/58Ni ratio.
double	minratio60Ni58Ni
	Minimum ratio 60Ni/58Ni.
double	maxratio60Ni58Ni
	Maximum ratio 60Ni/58Ni.
bool	enableratio62Ni58Ni
	Enable 62Ni/58Ni ratio.
double	minratio62Ni58Ni
	Minimum ratio 62Ni/58Ni.
double	maxratio62Ni58Ni
	Maximum ratio 62Ni/58Ni.
bool	enableratio65Cu63Cu
	Enable 65Cu/63Cu ratio.
double	minratio65Cu63Cu
	Minimum ratio 65Cu/63Cu.
double	maxratio65Cu63Cu
	Maximum ratio 65Cu/63Cu.
bool	enableratio66Zn64Zn
	Enable 66Zn/64Zn ratio.
double	minratio66Zn64Zn
	Minimum ratio 66Zn/64Zn.
double	maxratio66Zn64Zn
	Maximum ratio 66Zn/64Zn.
bool	enableratio67Zn64Zn
	Enable 67Zn/64Zn ratio.
double	minratio67Zn64Zn
	Minimum ratio 67Zn/64Zn.
double	maxratio67Zn64Zn
	Maximum ratio 67Zn/64Zn.
bool	enableratio68Zn64Zn
	Enable 68Zn/64Zn ratio.
double	minratio68Zn64Zn
	Minimum ratio 68Zn/64Zn.
double	maxratio68Zn64Zn
	Maximum ratio 68Zn/64Zn.
string	bricksdatabasefilename
	A file name of a bricks database.
cBricksDatabase	bricksdatabase
	A structure representing a database of bricks.
int	maximumbricksincombinationbegin
	The maximum number of bricks in combination (at the beginning of a spectrum).
int	maximumbricksincombinationmiddle
	The maximum number of bricks in combination (in the middle of a spectrum).
int	maximumbricksincombinationend
	The maximum number of bricks in combination (at the end of a spectrum).
int	maximumbricksincombination
	The global maximum number of bricks in combination (maximum from maximumbricksincombinationbegin, maximumbricksincombinationmiddle and maximumbricksincombinationend).
double	maximumcumulativemass
	The maximum cummulative mass of bricks.
string	modificationsfilename
	A file with modifications.
int	maximumnumberofthreads
	Maximum number of threads.
eModeType	mode
	Program mode.
eScoreType	scoretype
	A type of score.
int	maximumcombinedlosses
	Maximum number of combined neutral losses.
int	maximumcombinedelements
	Maximum number of combined chemical elements.
bool	reportunmatchedtheoreticalpeaks
	True when matches of peaks which do not have parent peaks are removed. More...
bool	generateisotopepattern
	True when complete isotope pattern is generated.
int	minimumpatternsize
	The minimum number of peaks in a matched pattern.
int	minimumfeaturesize
	The minimum number of consecutive scans in which a compound must be identified to be reported (LC-MS data only).
int	minimumiontypes
	The minimum number of ion types which must be matched to report a given compound.
bool	basicformulacheck
	Apply Senior's filtering rules.
bool	advancedformulacheck
	Advanced filtering rules are aplied if compounds are generated in MS mode.
bool	noratiocheck
	Check N/O ratio.
bool	calculatefdrs
	Calculate FDRs.
double	minimumannotationintensityrelative
	Minimum relative intensity of the most intense peak in an isotopic pattern.
unsigned	minimumannotationintensityabsolute
	Minimum absolute intensity of the most intense peak in an isotopic pattern.
double	mzdifftolerance
	Maximum m/z tolerance of matched isotopes.
double	intensitytolerance
	Maximum tolerance of intensities of matched isotopes.
bool	cyclicnterminus
	True if the N-terminus of a linear peptide is cyclized.
bool	cycliccterminus
	True if the C-terminus of a linear peptide is cyclized.
bool	internalfragments
	True if the internal fragments are generated.
bool	enablescrambling
	True if the detection of scrambled ions is enabled.
bool	similaritysearch
	True if the similarity search is enabled.
bool	regularblocksorder
	True if the order of polyketide blocks is regularly changed.
int	hitsreported
	Maximum number of reported hits.
string	sequencetag
	A sequence tag.
string	originalsequencetag
	A copy of sequence tag.
string	searchedsequence
	A searched sequence.
string	originalsearchedsequence
	A copy of searched sequence.
string	searchedsequenceNtermmodif
	N-terminal modification of a searched peptide.
string	searchedsequenceCtermmodif
	C-terminal modification of a searched peptide.
string	searchedsequenceTmodif
	Terminal modification of a branch of searched branched peptide.
string	searchedsequenceformula
	Formula of searched sequence.
int	maximumnumberofcandidates
	Maximum number of peptide sequence candidates.
int	blindedges
	The identifier of an action with edges forming incomplete paths.
string	sequencedatabasefilename
	A file name of a sequence database.
cSequenceDatabase	sequencedatabase
	A structure representing a database of sequences.
vector< cFragmentIonType >	searchedmodifications
	A vector of searched N-terminal and C-terminal modifications.
vector< eFragmentIonType >	fragmentionsfordenovograph
	A vector of fragment ion types generated in the de novo graph.
vector< cIonType >	ionsfortheoreticalspectraMS1
	A vector of ion types generated in theoretical conventional mass spectra.
vector< eFragmentIonType >	ionsfortheoreticalspectraMS2
	A vector of ion types generated in theoretical fragment ion spectra.
vector< neutralLoss >	neutrallossesdefinitions
	A vector of all neutral losses.
vector< neutralLoss >	originalneutrallossesdefinitions
	A vector of all neutral losses (without combinations of losses).
vector< int >	neutrallossesfortheoreticalspectra
	A vector of neutral losses generated in theoretical spectra.
int	numberofgeneratedneutrallosses
	A number of generated combinations of neutral losses.
vector< int >	originalneutrallossesfortheoreticalspectra
	A vector of neutral losses generated in theoretical spectra (without combinations).
vector< neutralLoss >	originalelementsdefinitions
	A vector of all elements (without combinations).
vector< int >	originalelementsfortheoreticalspectra
	A vector of elements used when generating compounds (without combinations).
vector< string >	peakidtodesc
	A vector of peak descriptions.
vector< string >	isotopeformulaidtodesc
	A vector of isotope formula descriptions.
map< string, int >	pchemresults
	An auxiliary map to store search results from PubChem in Compound Search mode.
int	defaultmaxx
	Max count of pixel x - parsed from imzML file.
int	defaultmaxy
	Max count of pixel y - parsed from imzML file.
int	defaultpixelsizex
	Pixel size x - parsed from imzML file.
int	defaultpixelsizey
	Pixel size y - parsed from imzML file.
eVendorType	vendor
	Vendor type.

Detailed Description

The class storing parameters of the application.

Member Function Documentation

calculateNeutralLosses()

int cParameters::calculateNeutralLosses	(	bool &	terminatecomputation,
		string &	errormessage
	)

Calculate a list of neutral losses.

Parameters

terminatecomputation	reference to a variable determining that the computation must be stopped
errormessage	an error message if failed

Return values

int	-1 when an error occurred, 0 otherwise

checkAndPrepare()

int cParameters::checkAndPrepare

(

bool &

terminatecomputation

)

Test restrictions of parameters and prepare some internal parameters.

Parameters

terminatecomputation

reference to a variable determining that the computation must be stopped

Return values

int	-1 when an error occurred, 0 otherwise

checkModifications()

bool cParameters::checkModifications	(	cSequence &	sequence,
		int &	startmodifid,
		int &	endmodifid,
		int &	middlemodifid,
		string &	errormessage
	)

Check if the names of modifications used in a sequence are correct.

Parameters

sequence	an input sequence
startmodifid	an output identifier of a start modification
endmodifid	an output identifier of an end modification
middlemodifid	an output identifier of a branch modification
errormessage	an output error message if failed

Return values

bool	true if success

generateCompounds()

int cParameters::generateCompounds	(	bool &	terminatecomputation,
		string &	errormessage
	)

Generate compounds.

Parameters

terminatecomputation	reference to a variable determining that the computation must be stopped
errormessage	an error message if failed

Return values

int	-1 when an error occurred, 0 otherwise

load()

void cParameters::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

prepareLossesAndCompounds()

int cParameters::prepareLossesAndCompounds

(

bool &

terminatecomputation

)

Prepare neutral losses and compounds.

Parameters

terminatecomputation

reference to a variable determining that the computation must be stopped

Return values

int	-1 when an error occurred, 0 otherwise

printToString()

string cParameters::printToString

(

)

Print parameters to a string.

Return values

string

string with parameters

setOutputStream()

void cParameters::setOutputStream

(

cMainThread &

os

)

Set the ouput stream.

Parameters

os	reference to the main thread of the application (output stream)

store()

void cParameters::store

(

ofstream &

os

)

Store the structure into an output stream.

Parameters

os	an output stream

Member Data Documentation

reportunmatchedtheoreticalpeaks

bool cParameters::reportunmatchedtheoreticalpeaks

True when matches of peaks which do not have parent peaks are removed.

Report unmatched theoretical peaks.

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

• core/cParameters.h
• core/cParameters.cpp