The class representing a peak list. More...

#include <cPeaksList.h>

Public Member Functions
	cPeaksList ()
	The constructor.

	cPeaksList (const cPeaksList &peakslist)
	The copy constructor. More...

cPeaksList &	operator= (const cPeaksList &peakslist)
	Overloaded operator=. More...

void	clear ()
	Clear the peak list.

void	attach (cPeaksList &peaklist)
	Attach a peak list. More...

void	add (cPeak &peak)
	Add a peak. More...

void	loadFromPlainTextStream (ifstream &stream)
	Load the spectrum from a plain text stream (tab separated values m/z ratio and intensity). More...

void	loadFromBAFStream (ifstream &stream)
	Load the spectrum from a .csv file converted from a .baf file by CompassXport. More...

void	loadFromIBDStream (cImzMLItem &imzmlitem, ifstream &ibdstream, bool use_64bit_float_mz_precision, bool use_64bit_float_intensity_precision)
	Load the spectrum from .ibd file. More...

void	storeToIBDStream (ofstream &ibdstream, bool use_64bit_float_mz_precision, bool use_64bit_float_intensity_precision)
	Store the spectrum into .ibd file. More...

void	loadFromMGFStream (ifstream &stream, int timeunit)
	Load the spectrum from a .mgf file. More...

int	size ()
	The number of peaks. More...

string	print (bool htmlterminatelines=false, bool printgroupid=false)
	Print the spectrum. More...

void	sortbyMass (int limit=-1)
	Sort the peaks by mass. More...

void	sortbyRelativeIntensityDesc ()
	Sort the peaks by relative intensity in the descending order.

void	sortbyAbsoluteIntensityDesc ()
	Sort the peaks by absolute intensity in the descending order.

void	sortbyGroupId ()
	Sort the peaks by group id.

void	sortbyOrderId ()
	Sort the peaks by order id.

int	normalizeIntenzity ()
	Normalize intensities of peaks. More...

void	normalizeIntenzityByValue (double value)
	Normalize intensities of peaks using a value. More...

void	cropRelativeIntenzity (double minimumrelativeintensitythreshold)
	Remove peaks with relative intensities lower than the threshold. More...

void	cropAbsoluteIntenzity (unsigned minimumabsoluteintensitythreshold)
	Remove peaks with absolute intensities lower than the threshold. More...

void	cropMinimumMZRatio (double minimummz, double errortolerance)
	Crop mz ratio lower than a threshold. More...

void	cropMaximumMZRatio (double maximummz, double errortolerance)
	Crop mz ratio bigger than a threshold. More...

cPeak &	operator[] (int position)
	Overloaded operator []. More...

void	resize (int size)
	Resize the peak list. More...

double	getMinimumMZRatio ()
	Get the minimum mz ratio. More...

double	getMaximumMZRatio ()
	Get the maximum mz ratio. More...

void	removeIsotopes (int maximumcharge, double fragmentmasserrortolerance, cMainThread *os=0)
	Remove isotopic peaks. More...

int	find (double mzratio, double fragmentmasserrortolerance)
	Get a position of a peak with specified mzratio. More...

void	remove (int position)
	Remove a peak. More...

void	removeChargeVariants (int maximumcharge, double fragmentmasserrortolerance)
	Perform a deconvolution. More...

void	removeNeutralLoss (double loss, int maximumcharge, double fragmentmasserrortolerance)
	Remove neutral losses. More...

void	removeObsolete ()
	Remove peaks having set up the flag removeme == true.

void	maxHighestPeaksInWindow (int maximumnumberofpeaksinwindow, double windowsize)
	Keep only n highest peaks in a window of a specified size. More...

double	getMaximumRelativeIntensityFromMZInterval (double minmz, double maxmz, bool hidematched, bool hideunmatched, ePeptideType peptidetype, bool hidescrambled)
	Get the maximum relative intensity from an m/z interval. More...

double	getMaximumAbsoluteIntensityFromMZInterval (double minmz, double maxmz, bool hidematched, bool hideunmatched, ePeptideType peptidetype, bool hidescrambled)
	Get the maximum absolute intensity from an m/z interval. More...

double	getMaximumRelativeIntensity ()
	Get the maximum relative intensity. More...

double	getMaximumAbsoluteIntensity ()
	Get the maximum absolute intensity. More...

void	setRetentionTime (double rt)
	Set the retention time. More...

double	getRetentionTime ()
	Get the retention time. More...

void	setRetentionTimeUnit (int unit)
	Set the retention time unit. More...

int	getRetentionTimeUnit ()
	Get the retention time unit. More...

void	setCoordinates (int x, int y)
	Set the coordinates. More...

int	getCoordinateX ()
	Get the X coordinate. More...

int	getCoordinateY ()
	Get the Y coordinate. 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...

string &	getTitle ()
	Get the title. More...

void	setTitle (string &title)
	Set the title. More...

void	reducePeakDescriptions (unordered_map< string, int > &peakdesctoid)
	Reduce redundant descriptions of peaks. More...

void	reduceIsotopeFormulaDescriptions (unordered_map< string, int > &isotopeformuladesctoid)
	Reduce redundant descriptions of isotope formulas. More...

void	fillOrderIDs ()
	Define order ids of peaks.

void	setIsotopeFlags (bool value)
	Set isotope flags. More...

void	markIsotopes ()
	Mark isotopic peaks in isotopic patterns.

bool	equals (cPeaksList &secondpeaklist)
	Check if the object equals to another object. More...

Detailed Description

The class representing a peak list.

Constructor & Destructor Documentation

◆ cPeaksList()

cPeaksList::cPeaksList ( const cPeaksList & peakslist )

The copy constructor.

Parameters

peakslist reference to a cPeaksList

Member Function Documentation

◆ add()

void cPeaksList::add ( cPeak & peak )

Add a peak.

Parameters

peak	peak which will be added

◆ attach()

void cPeaksList::attach ( cPeaksList & peaklist )

Attach a peak list.

Parameters

peaklist peaklist which will be attached

◆ cropAbsoluteIntenzity()

void cPeaksList::cropAbsoluteIntenzity ( unsigned minimumabsoluteintensitythreshold )

Remove peaks with absolute intensities lower than the threshold.

Parameters

minimumabsoluteintensitythreshold minimum threshold of absolute intensity

◆ cropMaximumMZRatio()

void cPeaksList::cropMaximumMZRatio	(	double	maximummz,
		double	errortolerance
	)

Crop mz ratio bigger than a threshold.

Parameters

maximummz	maximum threshold of mz ratio
errortolerance	mz error tolerance in ppm

◆ cropMinimumMZRatio()

void cPeaksList::cropMinimumMZRatio	(	double	minimummz,
		double	errortolerance
	)

Crop mz ratio lower than a threshold.

Parameters

minimummz	minimum threshold of mz ratio
errortolerance	mz error tolerance in ppm

◆ cropRelativeIntenzity()

void cPeaksList::cropRelativeIntenzity ( double minimumrelativeintensitythreshold )

Remove peaks with relative intensities lower than the threshold.

Parameters

minimumrelativeintensitythreshold minimum threshold of relative intensity

◆ equals()

bool cPeaksList::equals ( cPeaksList & secondpeaklist )

Check if the object equals to another object.

Parameters

secondpeaklist object for comparison

Return values

bool	true if the objects are equals

◆ find()

int cPeaksList::find	(	double	mzratio,
		double	fragmentmasserrortolerance
	)

Get a position of a peak with specified mzratio.

Parameters

mzratio	of searched peak
fragmentmasserrortolerance	mz error tolerance

Return values

int	position; -1 when the peak is not found

◆ getCoordinateX()

int cPeaksList::getCoordinateX ( )

Get the X coordinate.

Return values

int	X coordinate

◆ getCoordinateY()

int cPeaksList::getCoordinateY ( )

Get the Y coordinate.

Return values

int	Y coordinate

◆ getMaximumAbsoluteIntensity()

double cPeaksList::getMaximumAbsoluteIntensity ( )

Get the maximum absolute intensity.

Return values

double maximum absolute intensity

◆ getMaximumAbsoluteIntensityFromMZInterval()

double cPeaksList::getMaximumAbsoluteIntensityFromMZInterval	(	double	minmz,
		double	maxmz,
		bool	hidematched,
		bool	hideunmatched,
		ePeptideType	peptidetype,
		bool	hidescrambled
	)

Get the maximum absolute intensity from an m/z interval.

Parameters

minmz	minimum mz ratio
maxmz	maximum mz ratio
hidematched	true, if matched peaks are hidden
hideunmatched	true, if unmatched peaks are hidden
peptidetype	the type of peptide
hidescrambled	true, if scrambled peaks are hidden

Return values

double maximum absolute intensity

◆ getMaximumMZRatio()

double cPeaksList::getMaximumMZRatio ( )

Get the maximum mz ratio.

Return values

double maximum mz ratio

◆ getMaximumRelativeIntensity()

double cPeaksList::getMaximumRelativeIntensity ( )

Get the maximum relative intensity.

Return values

double maximum relative intensity

◆ getMaximumRelativeIntensityFromMZInterval()

double cPeaksList::getMaximumRelativeIntensityFromMZInterval	(	double	minmz,
		double	maxmz,
		bool	hidematched,
		bool	hideunmatched,
		ePeptideType	peptidetype,
		bool	hidescrambled
	)

Get the maximum relative intensity from an m/z interval.

Parameters

minmz	minimum mz ratio
maxmz	maximum mz ratio
hidematched	true, if matched peaks are hidden
hideunmatched	true, if unmatched peaks are hidden
peptidetype	the type of peptide
hidescrambled	true, if scrambled peaks are hidden

Return values

double maximum relative intensity

◆ getMinimumMZRatio()

double cPeaksList::getMinimumMZRatio ( )

Get the minimum mz ratio.

Return values

double minimum mz ratio

◆ getRetentionTime()

double cPeaksList::getRetentionTime ( )

Get the retention time.

Return values

double retention time

◆ getRetentionTimeUnit()

int cPeaksList::getRetentionTimeUnit ( )

Get the retention time unit.

Return values

int	0 == second, 1 == minute

◆ getTitle()

string & cPeaksList::getTitle ( )

Get the title.

Return values

string title

◆ load()

void cPeaksList::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

◆ loadFromBAFStream()

void cPeaksList::loadFromBAFStream ( ifstream & stream )

Load the spectrum from a .csv file converted from a .baf file by CompassXport.

Parameters

stream source stream

◆ loadFromIBDStream()

void cPeaksList::loadFromIBDStream	(	cImzMLItem &	imzmlitem,
		ifstream &	ibdstream,
		bool	use_64bit_float_mz_precision,
		bool	use_64bit_float_intensity_precision
	)

Load the spectrum from .ibd file.

Parameters

imzmlitem	cImzML containing the offset in the ibd file
ibdstream	an input binary file stream
use_64bit_float_mz_precision	if true, 64bit mz precision is used; if false, 32bit precision is used
use_64bit_float_intensity_precision	if true, 64bit intensity precision is used; if false, 32bit precision is used

◆ loadFromMGFStream()

void cPeaksList::loadFromMGFStream	(	ifstream &	stream,
		int	timeunit
	)

Load the spectrum from a .mgf file.

Parameters

stream	source stream
timeunit	rt unit

◆ loadFromPlainTextStream()

void cPeaksList::loadFromPlainTextStream ( ifstream & stream )

Load the spectrum from a plain text stream (tab separated values m/z ratio and intensity).

Parameters

stream source stream

◆ maxHighestPeaksInWindow()

void cPeaksList::maxHighestPeaksInWindow	(	int	maximumnumberofpeaksinwindow,
		double	windowsize
	)

Keep only n highest peaks in a window of a specified size.

Parameters

maximumnumberofpeaksinwindow	maximum number of peaks in a window
windowsize	size of a window

◆ normalizeIntenzity()

int cPeaksList::normalizeIntenzity ( )

Normalize intensities of peaks.

Return values

int	0 == success, -1 == maximum intensity <= 0

◆ normalizeIntenzityByValue()

void cPeaksList::normalizeIntenzityByValue ( double value )

Normalize intensities of peaks using a value.

Parameters

value normalization value

◆ operator=()

cPeaksList & cPeaksList::operator= ( const cPeaksList & peakslist )

Overloaded operator=.

Parameters

peakslist reference to a cPeaksList

◆ operator[]()

cPeak & cPeaksList::operator[] ( int position )

Overloaded operator [].

Parameters

position position of a peak in the peak list

Return values

cPeak reference to the peak

◆ print()

string cPeaksList::print	(	bool	htmlterminatelines = `false`,
		bool	printgroupid = `false`
	)

Print the spectrum.

Parameters

htmlterminatelines	true if the html line endings should be used
printgroupid	true if the groupid should be printed

Return values

string string with a printed spectrum

◆ reduceIsotopeFormulaDescriptions()

void cPeaksList::reduceIsotopeFormulaDescriptions ( unordered_map< string, int > & isotopeformuladesctoid )

Reduce redundant descriptions of isotope formulas.

Parameters

isotopeformuladesctoid map of isotope formula descriptions to ids

◆ reducePeakDescriptions()

void cPeaksList::reducePeakDescriptions ( unordered_map< string, int > & peakdesctoid )

Reduce redundant descriptions of peaks.

Parameters

peakdesctoid map of peak descriptions to ids

◆ remove()

void cPeaksList::remove ( int position )

Remove a peak.

Parameters

position position of a peak

◆ removeChargeVariants()

void cPeaksList::removeChargeVariants	(	int	maximumcharge,
		double	fragmentmasserrortolerance
	)

Perform a deconvolution.

Parameters

maximumcharge	charge of the precursor
fragmentmasserrortolerance	mz error tolerance

◆ removeIsotopes()

void cPeaksList::removeIsotopes	(	int	maximumcharge,
		double	fragmentmasserrortolerance,
		cMainThread *	os = `0`
	)

Remove isotopic peaks.

Parameters

maximumcharge	charge of the precursor
fragmentmasserrortolerance	mz error tolerance
os	reference to a main thread of the application (stream, respectively)

◆ removeNeutralLoss()

void cPeaksList::removeNeutralLoss	(	double	loss,
		int	maximumcharge,
		double	fragmentmasserrortolerance
	)

Remove neutral losses.

Parameters

loss	mass change
maximumcharge	charge of the precursor
fragmentmasserrortolerance	mz error tolerance

◆ resize()

void cPeaksList::resize ( int size )

Resize the peak list.

Parameters

size	number of peaks

◆ setCoordinates()

void cPeaksList::setCoordinates	(	int	x,
		int	y
	)

Set the coordinates.

Parameters

x	X coordinate
y	Y coordinate

◆ setIsotopeFlags()

void cPeaksList::setIsotopeFlags ( bool value )

Set isotope flags.

Parameters

value flag value

◆ setRetentionTime()

void cPeaksList::setRetentionTime ( double rt )

Set the retention time.

Parameters

rt	retention time

◆ setRetentionTimeUnit()

void cPeaksList::setRetentionTimeUnit ( int unit )

Set the retention time unit.

Parameters

unit	0 == second, 1 == minute

◆ setTitle()

void cPeaksList::setTitle ( string & title )

Set the title.

Parameters

title title

◆ size()

int cPeaksList::size ( )

The number of peaks.

Return values

int	number of peaks

◆ sortbyMass()

void cPeaksList::sortbyMass ( int limit = -1 )

Sort the peaks by mass.

Parameters

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

◆ store()

void cPeaksList::store ( ofstream & os )

Store the structure into an output stream.

Parameters

os	an output stream

◆ storeToIBDStream()

void cPeaksList::storeToIBDStream	(	ofstream &	ibdstream,
		bool	use_64bit_float_mz_precision,
		bool	use_64bit_float_intensity_precision
	)

Store the spectrum into .ibd file.

Parameters

ibdstream	an output binary file stream
use_64bit_float_mz_precision	if true, 64bit mz precision is used; if false, 32bit precision is used
use_64bit_float_intensity_precision	if true, 64bit intensity precision is used; if false, 32bit precision is used

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

core/cPeaksList.h
core/cPeaksList.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ cPeaksList()

Member Function Documentation

◆ add()

◆ attach()

◆ cropAbsoluteIntenzity()

◆ cropMaximumMZRatio()

◆ cropMinimumMZRatio()

◆ cropRelativeIntenzity()

◆ equals()

◆ find()

◆ getCoordinateX()

◆ getCoordinateY()

◆ getMaximumAbsoluteIntensity()

◆ getMaximumAbsoluteIntensityFromMZInterval()

◆ getMaximumMZRatio()

◆ getMaximumRelativeIntensity()

◆ getMaximumRelativeIntensityFromMZInterval()

◆ getMinimumMZRatio()

◆ getRetentionTime()

◆ getRetentionTimeUnit()

◆ getTitle()

◆ load()

◆ loadFromBAFStream()

◆ loadFromIBDStream()

◆ loadFromMGFStream()

◆ loadFromPlainTextStream()

◆ maxHighestPeaksInWindow()

◆ normalizeIntenzity()

◆ normalizeIntenzityByValue()

◆ operator=()

◆ operator[]()

◆ print()

◆ reduceIsotopeFormulaDescriptions()

◆ reducePeakDescriptions()

◆ remove()

◆ removeChargeVariants()

◆ removeIsotopes()

◆ removeNeutralLoss()

◆ resize()

◆ setCoordinates()

◆ setIsotopeFlags()

◆ setRetentionTime()

◆ setRetentionTimeUnit()

◆ setTitle()

◆ size()

◆ sortbyMass()

◆ store()

◆ storeToIBDStream()