SpectrumAccessQuadMZTransforming Class Reference

A transforming m/z wrapper around spectrum access using a quadratic equation. More...

#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessQuadMZTransforming.h>

Inheritance diagram for SpectrumAccessQuadMZTransforming:

Collaboration diagram for SpectrumAccessQuadMZTransforming:

Public Member Functions
	SpectrumAccessQuadMZTransforming (OpenSwath::SpectrumAccessPtr sptr, double a, double b, double c, bool ppm)
	Constructor. More...
	~SpectrumAccessQuadMZTransforming () override
boost::shared_ptr< OpenSwath::ISpectrumAccess >	lightClone () const override
	Light clone operator to produce a copy for concurrent read access. More...
OpenSwath::SpectrumPtr	getSpectrumById (int id) override
	Return a pointer to a spectrum at the given id. More...
Public Member Functions inherited from SpectrumAccessTransforming
	SpectrumAccessTransforming (OpenSwath::SpectrumAccessPtr sptr)
	~SpectrumAccessTransforming () override=0
OpenSwath::SpectrumPtr	getSpectrumById (int id) override
	Return a pointer to a spectrum at the given id. More...
OpenSwath::SpectrumMeta	getSpectrumMetaById (int id) const override
	Returns the meta information for a spectrum. More...
std::vector< std::size_t >	getSpectraByRT (double RT, double deltaRT) const override
	Return a vector of ids of spectra that are within RT +/- deltaRT. More...
size_t	getNrSpectra () const override
	Returns the number of spectra available. More...
OpenSwath::ChromatogramPtr	getChromatogramById (int id) override
	Return a pointer to a chromatogram at the given id. More...
size_t	getNrChromatograms () const override
	Returns the number of chromatograms available. More...
std::string	getChromatogramNativeID (int id) const override
	Returns the native id of the chromatogram at the given id. More...
Public Member Functions inherited from ISpectrumAccess
virtual	~ISpectrumAccess ()
	Destructor. More...
SpectrumPtr	getSpectrumById (int id, double drift_start, double drift_end)
	Return pointer to a spectrum at the given id, the spectrum will be filtered by drift time. More...
SpectrumSequence	getMultipleSpectra (double RT, int nr_spectra_to_fetch)
SpectrumSequence	getMultipleSpectra (double RT, int nr_spectra_to_fetch, double drift_start, double drift_end)

Private Attributes
double	a_
double	b_
double	c_
bool	ppm_

Additional Inherited Members
Static Public Member Functions inherited from ISpectrumAccess
static SpectrumPtr	filterByDrift (const SpectrumPtr &input, double drift_start, double drift_end)
	filters a spectrum by drift time, spectrum pointer returned is a copy More...
Protected Attributes inherited from SpectrumAccessTransforming
OpenSwath::SpectrumAccessPtr	sptr_

Detailed Description

A transforming m/z wrapper around spectrum access using a quadratic equation.

For each spectrum access, each m/z value is transformed using the equation mz = a + b * mz + c * mz^2

This can be used to implement an on-line mass correction for TOF instruments (for example).

Constructor & Destructor Documentation

SpectrumAccessQuadMZTransforming()

SpectrumAccessQuadMZTransforming ( OpenSwath::SpectrumAccessPtr  sptr, double  a, double  b, double  c, bool  ppm  )

explicit

Constructor.

Parameters

sptr	The spectrum to work on
a	Regression parameter 0
b	Regression parameter 1
c	Regression parameter 2
ppm	Whether the transformation should be applied in ppm domain (if false, it is applied directly in m/z domain)

~SpectrumAccessQuadMZTransforming()

~SpectrumAccessQuadMZTransforming ( )

override

Member Function Documentation

getSpectrumById()

OpenSwath::SpectrumPtr getSpectrumById ( int  id )

overridevirtual

Return a pointer to a spectrum at the given id.

Implements ISpectrumAccess.

lightClone()

boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone ( ) const

overridevirtual

Light clone operator to produce a copy for concurrent read access.

This function guarantees to produce a copy of the underlying object that provides thread-safe concurrent read access to the underlying data. It should be implemented with minimal copy-overhead to make this operation as fast as possible.

To use this function, each thread should call this function to produce an individual copy on which it can operate.

Implements SpectrumAccessTransforming.

Member Data Documentation

a_

double a_

private

b_

double b_

private

c_

double c_

private

ppm_

bool ppm_

private