IsoSpecTotalProbGeneratorWrapper Class Reference

Generate a p-set of configurations for a given p (that is, a set of configurations such that their probabilities sum up to p). The p in normal usage will usually be close to 1 (e.g. 0.99). More...

#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsoSpecWrapper.h>

Inheritance diagram for IsoSpecTotalProbGeneratorWrapper:

Public Member Functions
	IsoSpecTotalProbGeneratorWrapper (const std::vector< int > &isotopeNumbers, const std::vector< int > &atomCounts, const std::vector< std::vector< double > > &isotopeMasses, const std::vector< std::vector< double > > &isotopeProbabilities, double p, bool do_p_trim=false)
	Constructor. More...
	IsoSpecTotalProbGeneratorWrapper (const EmpiricalFormula &formula, double p, bool do_p_trim=false)
	Setup the algorithm to run on an EmpiricalFormula. More...
virtual bool	nextConf () override final
	Move the generator to a next isotopologue. More...
virtual Peak1D	getConf () override final
	Obtain the current isotopologue. More...
virtual double	getMass () override final
	Obtain the mass of the current isotopologue. More...
virtual double	getIntensity () override final
	Obtain the intensity (probability, relative peak height) of the current configuration. More...
virtual double	getLogIntensity () override final
	Obtain the natural logarithm of the intensity (probability, relative peak height) of the current configuration. More...
Public Member Functions inherited from IsoSpecGeneratorWrapper
virtual	~IsoSpecGeneratorWrapper ()
	Destructor. More...

Protected Attributes
IsoSpec::IsoLayeredGenerator	ILG

Detailed Description

Generate a p-set of configurations for a given p (that is, a set of configurations such that their probabilities sum up to p). The p in normal usage will usually be close to 1 (e.g. 0.99).

An optimal p-set of isotopologues is the smallest set of isotopologues that, taken together, cover at least p of the probability space (that is, their probabilities sum up to at least p). This means that the computed spectrum is accurate to at least degree p, and that the L1 distance between the computed spectrum and the true spectrum is less than 1-p. The optimality of the p-set means that it contains the most probable configurations - any isotopologues outside of the returned p-set have lower intensity than the configurations in the p-set.

This is the method most users will want: the p parameter directly controls the accuracy of results.

Advanced usage note: The algorithm works by computing an optimal p'-set for a p' slightly larger than the requested p. By default these extra isotopologues are returned too (as they have to be computed anyway). It is possible to request that the extra configurations be discarded, using the do_p_trim parameter. This will *increase* the runtime and especially the memory usage of the algorithm, and should not be done unless there is a good reason to.

Note

The eligible configurations are NOT guaranteed to be returned in any particular order.

Constructor & Destructor Documentation

IsoSpecTotalProbGeneratorWrapper() [1/2]

IsoSpecTotalProbGeneratorWrapper	(	const std::vector< int > &	isotopeNumbers,
		const std::vector< int > &	atomCounts,
		const std::vector< std::vector< double > > &	isotopeMasses,
		const std::vector< std::vector< double > > &	isotopeProbabilities,
		double	p,
		bool	do_p_trim = false
	)

Constructor.

Parameters

isotopeNumbers	A vector of how many isotopes each element has, e.g. [2, 2, 3])
atomCounts	How many atoms of each we have [e.g. 12, 6, 6 for Glucose]
isotopeMasses	Array with the individual elements isotopic masses
isotopeProbabilities	Array with the individual elements isotopic probabilities
p	Total coverage of probability space desired, usually close to 1 (e.g. 0.99)
do_p_trim	Whether to discard extra configurations that have been computed

Note

This constructor is only useful if you need to define non-standard abundances of isotopes, for other uses the one accepting EmpiricalFormula is easier to use.

IsoSpecTotalProbGeneratorWrapper() [2/2]

IsoSpecTotalProbGeneratorWrapper	(	const EmpiricalFormula &	formula,
		double	p,
		bool	do_p_trim = false
	)

Setup the algorithm to run on an EmpiricalFormula.

Member Function Documentation

getConf()

virtual Peak1D getConf ( )

inlinefinaloverridevirtual

Obtain the current isotopologue.

Returns

The current isotopologue as a Peak1D

Note

It is invalid (undefined results) to call this method before the first call to nextConf(), or after it returns false

Implements IsoSpecGeneratorWrapper.

getIntensity()

virtual double getIntensity ( )

inlinefinaloverridevirtual

Obtain the intensity (probability, relative peak height) of the current configuration.

Returns

The intensity (probability) of the current isotopologue

Note

It is invalid (undefined results) to call this method before the first call to nextConf(), or after it returns false

Implements IsoSpecGeneratorWrapper.

getLogIntensity()

virtual double getLogIntensity ( )

inlinefinaloverridevirtual

Obtain the natural logarithm of the intensity (probability, relative peak height) of the current configuration.

This will be more precise (and faster) than just calling std::log(getIntensity()) - it will produce correct results even for configurations so unlikely that the double-precision floating point number returned from getIntensity() underflows to zero.

Returns

The natural logarithm of intensity (probability) of the current isotopologue

Note

It is invalid (undefined results) to call this method before the first call to nextConf(), or after it returns false

Implements IsoSpecGeneratorWrapper.

getMass()

virtual double getMass ( )

inlinefinaloverridevirtual

Obtain the mass of the current isotopologue.

Returns

The mass of the current isotopologue

Note

It is invalid (undefined results) to call this method before the first call to nextConf(), or after it returns false

Implements IsoSpecGeneratorWrapper.

nextConf()

virtual bool nextConf ( )

inlinefinaloverridevirtual

Move the generator to a next isotopologue.

Advance the internal generator to the next isotopologue. The value returned determines whether the generator has been exhausted (that is, all eligible configurations have already been visited). It is invalid to call any other generator methods before the first call to nextConf(), as well as after this method returns false.

Returns

A boolean value stating whether the generator has been exhausted.

Implements IsoSpecGeneratorWrapper.

Member Data Documentation

ILG

IsoSpec::IsoLayeredGenerator ILG

protected