Implements the isotope wavelet function. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/IsotopeWavelet.h>

Classes
union	fi_
	Internal union for fast computation of the power function. More...

Static Public Member Functions
static IsotopeWavelet *	init (const double max_m, const UInt max_charge)

static IsotopeWavelet *	getInstance ()

static void	destroy ()

static double	getValueByMass (const double t, const double m, const UInt z, const Int mode=+1)
	Returns the value of the isotope wavelet at position `t`. Usually, you do not need to call this function. Please use. More...

static double	getValueByLambda (const double lambda, const double tz1)
	Returns the value of the isotope wavelet at position `t` via a fast table lookup. Usually, you do not need to call this function. Please use. More...

static double	getValueByLambdaExtrapol (const double lambda, const double tz1)
	Returns the value of the isotope wavelet at position `t`. This function is usually significantly slower than the table lookup performed in. More...

static double	getValueByLambdaExact (const double lambda, const double tz1)

static UInt	getMaxCharge ()
	Returns the largest charge state we will consider. More...

static void	setMaxCharge (const UInt max_charge)
	Sets the `max_charge` parameter. More...

static double	getTableSteps ()
	Returns the table_steps_ parameter. More...

static double	getInvTableSteps ()
	Returns the inv_table_steps_ parameter. More...

static void	setTableSteps (const double table_steps)
	Sets the `table_steps` parameter. More...

static double	getLambdaL (const double m)
	Returns the mass-parameter lambda (linear fit). More...

static const IsotopeDistribution::ContainerType &	getAveragine (const double m, UInt *size=nullptr)
	Computes the averagine isotopic distribution we would expect at the de-convoluted mass. More...

static Size	getGammaTableMaxIndex ()
	Returns the largest possible index for the pre-sampled gamma table. More...

static Size	getExpTableMaxIndex ()
	Returns the largest possible index for the pre-sampled exp table. More...

static float	myPow (float a, float b)
	Internally used function; uses register shifts for fast computation of the power function. More...

static UInt	getMzPeakCutOffAtMonoPos (const double mass, const UInt z)

static UInt	getNumPeakCutOff (const double mass, const UInt z)

static UInt	getNumPeakCutOff (const double mz)

Protected Member Functions
	IsotopeWavelet ()
	Default Constructor. More...

	IsotopeWavelet (const double max_m, const UInt max_charge)
	Constructor. More...

virtual	~IsotopeWavelet ()
	Destructor. More...

Static Protected Member Functions
static void	preComputeExpensiveFunctions_ (const double max_m)
	Should be called once before values are drawn from the isotope wavelet function. The function is automatically called by the public constructor. More...

static void	computeIsotopeDistributionSize_ (const double max_m)
	Initializes the internally used averagine model; automatically called by the public constructor. More...

static float	myPow2_ (float i)
	Internally used function; uses register shifts for fast computation of the power function. The function follows http://www.dctsystems.co.uk/Software/power.html , code by Ian Stephenson, DCT Systems, NCCA Bournemouth University. More...

static float	myLog2_ (float i)
	Internally used function uses register shifts for fast computation of the power function. The function follows http://www.dctsystems.co.uk/Software/power.html , code by Ian Stephenson, DCT Systems, NCCA Bournemouth University. More...

Static Protected Attributes
static IsotopeWavelet *	me_

static UInt	max_charge_

static double	table_steps_

static double	inv_table_steps_

static std::vector< double >	gamma_table_

static std::vector< double >	gamma_table_new_

static std::vector< double >	exp_table_

static std::vector< double >	sine_table_

static CoarseIsotopePatternGenerator	solver_

static IsotopeDistribution	averagine_

static Size	gamma_table_max_index_

static Size	exp_table_max_index_

Detailed Description

Implements the isotope wavelet function.

The IsotopeWavelet class implements the isotope wavelet as described by R. Hussong, A. Tholey, A. Hildebrandt: Efficient Analysis of Mass Spectrometry Data Using the Isotope Wavelet. Proceedings of the 3rd international Symposium in Computational Life Sciences (Complife07). American Institute of Physics (AIP) Proceedings (2007).

Note: This class features a singleton design pattern.

Constructor & Destructor Documentation

◆ IsotopeWavelet() [1/2]

IsotopeWavelet ( )

protected

Default Constructor.

◆ IsotopeWavelet() [2/2]

IsotopeWavelet	(	const double	max_m,
		const UInt	max_charge
	)

protected

Constructor.

Parameters

max_m	The maximal de-convoluted mass that occurs in the current data set.
max_charge	The maximal charge state we would like to analyze.

◆ ~IsotopeWavelet()

virtual ~IsotopeWavelet ( )

protectedvirtual

Destructor.

Member Function Documentation

◆ computeIsotopeDistributionSize_()

static void computeIsotopeDistributionSize_ ( const double max_m )

staticprotected

Initializes the internally used averagine model; automatically called by the public constructor.

Parameters

max_m The maximal de-convoluted mass that occurs in the current data set.

◆ destroy()

static void destroy ( )

static

Deletes the singleton instance.

◆ getAveragine()

static const IsotopeDistribution::ContainerType& getAveragine	(	const double	m,
		UInt *	size = `nullptr`
	)

static

Computes the averagine isotopic distribution we would expect at the de-convoluted mass.

Parameters

m	The de-convoluted mass m.
size	Returns the number of significant peaks within a pattern occurring at mass `m`.

Returns: The isotopic distribution.

◆ getExpTableMaxIndex()

static Size getExpTableMaxIndex ( )

inlinestatic

Returns the largest possible index for the pre-sampled exp table.

◆ getGammaTableMaxIndex()

static Size getGammaTableMaxIndex ( )

inlinestatic

Returns the largest possible index for the pre-sampled gamma table.

◆ getInstance()

static IsotopeWavelet* getInstance ( )

inlinestatic

Returns an pointer to the current instance of the class.

◆ getInvTableSteps()

static double getInvTableSteps ( )

inlinestatic

Returns the inv_table_steps_ parameter.

This is an internally used parameter controlling the precision of several pre-sampling steps. Normally, this parameter can be left unchanged.

◆ getLambdaL()

static double getLambdaL ( const double m )

static

Returns the mass-parameter lambda (linear fit).

Referenced by IsotopeWaveletTransform< PeakType >::getTransform(), IsotopeWaveletTransform< PeakType >::getTransformHighRes(), and IsotopeWaveletTransform< PeakType >::mapSeeds2Features().

◆ getMaxCharge()

static UInt getMaxCharge ( )

inlinestatic

Returns the largest charge state we will consider.

◆ getMzPeakCutOffAtMonoPos()

static UInt getMzPeakCutOffAtMonoPos	(	const double	mass,
		const UInt	z
	)

static

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::getTransform(), IsotopeWaveletTransform< PeakType >::getTransformHighRes(), IsotopeWaveletTransform< PeakType >::identifyCharge(), IsotopeWaveletTransform< PeakType >::initializeScan(), IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform(), and IsotopeWaveletTransform< PeakType >::mapSeeds2Features().

◆ getNumPeakCutOff() [1/2]

static UInt getNumPeakCutOff	(	const double	mass,
		const UInt	z
	)

static

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::identifyCharge(), and IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().

◆ getNumPeakCutOff() [2/2]

static UInt getNumPeakCutOff ( const double mz )

static

◆ getTableSteps()

static double getTableSteps ( )

inlinestatic

Returns the table_steps_ parameter.

This is an internally used parameter controlling the precision of several pre-sampling steps. Normally, this parameter can be left unchanged.

◆ getValueByLambda()

static double getValueByLambda	(	const double	lambda,
		const double	tz1
	)

static

Returns the value of the isotope wavelet at position t via a fast table lookup. Usually, you do not need to call this function. Please use.

See also: sampleTheWavelet instead.

Note that this functions returns the pure function value of psi and not the normalized (average=0) value given by Psi.

Parameters

lambda	The mass-parameter lambda.
tz1	t (the position) times the charge (z) plus 1.

Referenced by IsotopeWaveletTransform< PeakType >::getTransform(), and IsotopeWaveletTransform< PeakType >::getTransformHighRes().

◆ getValueByLambdaExact()

static double getValueByLambdaExact	(	const double	lambda,
		const double	tz1
	)

static

◆ getValueByLambdaExtrapol()

static double getValueByLambdaExtrapol	(	const double	lambda,
		const double	tz1
	)

static

Returns the value of the isotope wavelet at position t. This function is usually significantly slower than the table lookup performed in.

See also: getValueByLambda. Nevertheless, it might be necessary to call this function due to extrapolating reasons caused by the alignment of the wavelet.

Usually, you do not need to call this function. Please use

See also: sampleTheWavelet instead.

Note that this functions returns the pure function value of psi and not the normalized (average=0) value given by Psi.

Parameters

lambda	The mass-parameter lambda.
tz1	t (the position) times the charge (z) plus 1.

◆ getValueByMass()

static double getValueByMass	(	const double	t,
		const double	m,
		const UInt	z,
		const Int	mode = `+1`
	)

inlinestatic

Returns the value of the isotope wavelet at position t. Usually, you do not need to call this function. Please use.

See also: sampleTheWavelet instead.

Note that this functions returns the pure function value of psi and not the normalized (average=0) value given by Psi.

Parameters

t	The position at which the wavelet has to be drawn (within the coordinate system of the wavelet).
m	The m/z position within the signal (i.e. the mass not de-charged) within the signal.
z	The charge `z` we want to detect.
mode	Indicates whether positive mode (+1) or negative mode (-1) has been used for ionization.

References OpenMS::Constants::IW_PROTON_MASS.

◆ init()

static IsotopeWavelet* init	(	const double	max_m,
		const UInt	max_charge
	)

static

The init function; creates an instance of this singleton class.

Referenced by IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().

◆ myLog2_()

static float myLog2_ ( float i )

staticprotected

Internally used function uses register shifts for fast computation of the power function. The function follows http://www.dctsystems.co.uk/Software/power.html , code by Ian Stephenson, DCT Systems, NCCA Bournemouth University.

Note: Please, do not modify this function.

◆ myPow()

static float myPow	(	float	a,
		float	b
	)

static

Internally used function; uses register shifts for fast computation of the power function.

Note: Please, do not modify this function.

◆ myPow2_()

static float myPow2_ ( float i )

staticprotected

Internally used function; uses register shifts for fast computation of the power function. The function follows http://www.dctsystems.co.uk/Software/power.html , code by Ian Stephenson, DCT Systems, NCCA Bournemouth University.

Note: Please, do not modify this function.

◆ preComputeExpensiveFunctions_()

static void preComputeExpensiveFunctions_ ( const double max_m )

staticprotected

Should be called once before values are drawn from the isotope wavelet function. The function is automatically called by the public constructor.

The function pre-computes the expensive gamma function. Parameters related to this function are:

See also: max_charge_ and; peak_cutoff_. If both of these are set correctly; getValue will never compute the gamma function online.

Parameters

max_m The maximal de-convoluted mass that occurs in the current data set.

◆ setMaxCharge()

static void setMaxCharge ( const UInt max_charge )

inlinestatic

Sets the max_charge parameter.

◆ setTableSteps()

static void setTableSteps ( const double table_steps )

inlinestatic

Sets the table_steps parameter.

Member Data Documentation

◆ averagine_

IsotopeDistribution averagine_

staticprotected

◆ exp_table_

std::vector<double> exp_table_

staticprotected

Internal table for the precomputed values of the exponential function.

◆ exp_table_max_index_

Size exp_table_max_index_

staticprotected

◆ gamma_table_

std::vector<double> gamma_table_

staticprotected

Internal table for the precomputed values of the gamma function.

◆ gamma_table_max_index_

Size gamma_table_max_index_

staticprotected

◆ gamma_table_new_

std::vector<double> gamma_table_new_

staticprotected

◆ inv_table_steps_

double inv_table_steps_

staticprotected

◆ max_charge_

UInt max_charge_

staticprotected

This parameter determines the maximal charge state we will consider.

◆ me_

IsotopeWavelet* me_

staticprotected

The singleton pointer.

◆ sine_table_

std::vector<double> sine_table_

staticprotected

Internal table for the precomputed values of the exponential function.

◆ solver_

CoarseIsotopePatternGenerator solver_

staticprotected

Internally used averagine model.

◆ table_steps_

double table_steps_

staticprotected

This parameter determines the sample rate for the pre-computation of the gamma function.

Classes

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ IsotopeWavelet() [1/2]

◆ IsotopeWavelet() [2/2]

◆ ~IsotopeWavelet()

Member Function Documentation

◆ computeIsotopeDistributionSize_()

◆ destroy()

◆ getAveragine()

◆ getExpTableMaxIndex()

◆ getGammaTableMaxIndex()

◆ getInstance()

◆ getInvTableSteps()

◆ getLambdaL()

◆ getMaxCharge()

◆ getMzPeakCutOffAtMonoPos()

◆ getNumPeakCutOff() [1/2]

◆ getNumPeakCutOff() [2/2]

◆ getTableSteps()

◆ getValueByLambda()

◆ getValueByLambdaExact()

◆ getValueByLambdaExtrapol()

◆ getValueByMass()

◆ init()

◆ myLog2_()

◆ myPow()

◆ myPow2_()

◆ preComputeExpensiveFunctions_()

◆ setMaxCharge()

◆ setTableSteps()

Member Data Documentation

◆ averagine_

◆ exp_table_

◆ exp_table_max_index_

◆ gamma_table_

◆ gamma_table_max_index_

◆ gamma_table_new_

◆ inv_table_steps_

◆ max_charge_

◆ me_

◆ sine_table_

◆ solver_

◆ table_steps_