Provides a threshold-based generator of isotopologues: generates all isotopologues more probable than a given probability threshold. More...

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

Inheritance diagram for IsoSpecThresholdGeneratorWrapper:

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Public Member Functions
	IsoSpecThresholdGeneratorWrapper (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 threshold, bool absolute)
	Constructor. More...

	IsoSpecThresholdGeneratorWrapper (const IsoSpecThresholdGeneratorWrapper &)=delete

	IsoSpecThresholdGeneratorWrapper (const EmpiricalFormula &formula, double threshold, bool absolute)
	Setup the algorithm to run on an EmpiricalFormula. More...

	~IsoSpecThresholdGeneratorWrapper ()

bool	nextConf () final
	Move the generator to a next isotopologue. More...

Peak1D	getConf () final
	Obtain the current isotopologue. More...

double	getMass () final
	Obtain the mass of the current isotopologue. More...

double	getIntensity () final
	Obtain the intensity (probability, relative peak height) of the current configuration. More...

double	getLogIntensity () 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 ()=default
	Destructor. More...

Protected Attributes
std::unique_ptr< IsoSpec::IsoThresholdGenerator >	ITG

Detailed Description

Provides a threshold-based generator of isotopologues: generates all isotopologues more probable than a given probability threshold.

This is the simplest generator - most users will however want to use IsoSpecTotalProbGeneratorWrapper. The reason for it is that when thresholding by peak intensity one has no idea how far the obtained spectrum is from a real spectrum. For example, consider human insulin: if the threshold is set at 0.1 of the most intense peak, then the peaks above the threshold account for 99.7% of total probability for water, 82% for substance P, only 60% for human insulin, and 23% for titin. For a threshold of 0.01, the numbers will be: still 99.7% for water, 96% for substance P, 88% for human insulin and 72% for titin (it also took 5 minutes on an average notebook computer to process the 17 billion configurations involved).

As you can see the threshold does not have a straightforward correlation to the accuracy of the final spectrum obtained - and accuracy of final spectrum is often what the user is interested in. The IsoSpecTotalProbGeneratorWrapper provides a way to directly parameterize based on the desired accuracy of the final spectrum - and should be used instead in most cases. The trade-off is that it's (slightly, though much less than it used to be) slower than Threshold algorithm.

Note: The eligible isotopologues are NOT guaranteed to be generated in any particular order.

Constructor & Destructor Documentation

◆ IsoSpecThresholdGeneratorWrapper() [1/3]

IsoSpecThresholdGeneratorWrapper	(	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	threshold,
		bool	absolute
	)

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
threshold	Intensity threshold: will only compute peaks above this threshold
absolute	Whether the threshold is absolute or relative (relative to the most intense peak)

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.

◆ IsoSpecThresholdGeneratorWrapper() [2/3]

IsoSpecThresholdGeneratorWrapper ( const IsoSpecThresholdGeneratorWrapper & )

delete

◆ IsoSpecThresholdGeneratorWrapper() [3/3]

IsoSpecThresholdGeneratorWrapper	(	const EmpiricalFormula &	formula,
		double	threshold,
		bool	absolute
	)

Setup the algorithm to run on an EmpiricalFormula.

◆ ~IsoSpecThresholdGeneratorWrapper()

~IsoSpecThresholdGeneratorWrapper ( )

Member Function Documentation

◆ getConf()

Peak1D getConf ( )

finalvirtual

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()

double getIntensity ( )

finalvirtual

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()

double getLogIntensity ( )

finalvirtual

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()

double getMass ( )

finalvirtual

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()

bool nextConf ( )

finalvirtual

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

◆ ITG

std::unique_ptr<IsoSpec::IsoThresholdGenerator> ITG

protected

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ IsoSpecThresholdGeneratorWrapper() [1/3]

◆ IsoSpecThresholdGeneratorWrapper() [2/3]

◆ IsoSpecThresholdGeneratorWrapper() [3/3]

◆ ~IsoSpecThresholdGeneratorWrapper()

Member Function Documentation

◆ getConf()

◆ getIntensity()

◆ getLogIntensity()

◆ getMass()

◆ nextConf()

Member Data Documentation

◆ ITG