#include <marginalTrek++.h>

Inheritance diagram for IsoSpec::LayeredMarginal:

Public Member Functions
	LayeredMarginal (Marginal &&m, int tabSize=1000, int hashSize=1000)
	Move constructor: specializes the Marginal class.
	LayeredMarginal (const LayeredMarginal &other)=delete
LayeredMarginal &	operator= (const LayeredMarginal &other)=delete
bool	extend (double new_threshold, bool do_sort=true)
	Extend the set of computed subisotopologues to those above the new threshold.
double	get_lProb (int idx) const
	get the log-probability of the idx-th subisotopologue, see details in PrecalculatedMarginal::get_lProb.
double	get_prob (int idx) const
	get the probability of the idx-th subisotopologue, see details in PrecalculatedMarginal::get_eProb.
double	get_mass (int idx) const
	get the mass of the idx-th subisotopologue, see details in PrecalculatedMarginal::get_mass.
const double *	get_lProbs_ptr () const
	get the pointer to lProbs array. Accessing index -1 is legal and returns a guardian of -inf. Warning: The pointer gets invalidated on calls to extend()
const Conf &	get_conf (int idx) const
	get the counts of isotopes that define the subisotopologue, see details in PrecalculatedMarginal::get_conf.
unsigned int	get_no_confs () const
	Get the number of precomputed subisotopologues, see details in PrecalculatedMarginal::get_no_confs.
double	get_min_mass () const
	Get the minimal mass in current layer.
double	get_max_mass () const
	Get the maximal mass in current layer.
double	getModeLProb () const
	Get the log-probability of the mode subisotopologue.
const pod_vector< double > &	conf_lprobs () const
const pod_vector< double > &	conf_masses () const
Public Member Functions inherited from IsoSpec::Marginal
	Marginal (const double _masses, const double _probs, int _isotopeNo, int _atomCnt)
	Class constructor.
Marginal &	operator= (const Marginal &other)=delete
	Marginal (const Marginal &other)
	Copy constructor.
	Marginal (Marginal &&other)
	Move constructor.
virtual	~Marginal ()
	Destructor.
int	get_isotopeNo () const
	Get the number of isotopes of the investigated element.
const double *	get_lProbs () const
double	getLightestConfMass () const
	Get the mass of the lightest subisotopologue.
double	getHeaviestConfMass () const
	Get the mass of the heaviest subisotopologue.
double	getMonoisotopicConfMass () const
	Get the mass of the monoisotopic subisotopologue.
size_t	getMonoisotopicAtomIndex () const
	Get the index of the monoisotopic (most probable) atom.
double	getModeMass ()
	The the mass of the mode subisotopologue.
double	getModeLProb ()
	Get the log-probability of the mode subisotopologue.
double	fastGetModeLProb ()
	Get the log-probability of the mode subisotopologue. Results undefined if ensureModeConf() wasn't called before.
Conf	computeModeConf () const
	The the probability of the mode subisotopologue.
double	getSmallestLProb () const
	The the log-probability of the lightest subisotopologue.
double	getAtomAverageMass () const
	The average mass of a single atom.
double	getTheoreticalAverageMass () const
	The theoretical average mass of the molecule.
double	variance () const
	Calculate the variance of the theoretical distribution describing the subisotopologue.
double	getLogSizeEstimate (double logEllipsoidRadius) const
	Return estimated logarithm of size of the marginal at a given ellipsoid radius.
void	ensureModeConf ()

Additional Inherited Members
Protected Member Functions inherited from IsoSpec::Marginal
ISOSPEC_FORCE_INLINE double	unnormalized_logProb (Conf conf) const
	Calculate the log-probability of a given subisotopologue.
ISOSPEC_FORCE_INLINE double	logProb (Conf conf) const
Protected Attributes inherited from IsoSpec::Marginal
const unsigned int	isotopeNo
const unsigned int	atomCnt
const double *const	atom_lProbs
const double *const	atom_masses
const double	loggamma_nominator
Conf	mode_conf
double	mode_lprob

Detailed Description

LayeredMarginal class.

An extendable version of the PrecalculatedMarginal, where you can extend the threshold at will.

Definition at line 358 of file marginalTrek++.h.

Constructor & Destructor Documentation

◆ LayeredMarginal()

IsoSpec::LayeredMarginal::LayeredMarginal	(	Marginal &&	m,
		int	tabSize = 1000,
		int	hashSize = 1000 )

Move constructor: specializes the Marginal class.

Parameters

tabSize	The size of the table used to store configurations in the allocator.
hashSize	The size of the hash table used to store visited subisotopologues.

Definition at line 562 of file marginalTrek++.cpp.

Member Function Documentation

◆ conf_lprobs()

const pod_vector< double > & IsoSpec::LayeredMarginal::conf_lprobs ( ) const

inline

Definition at line 420 of file marginalTrek++.h.

◆ conf_masses()

const pod_vector< double > & IsoSpec::LayeredMarginal::conf_masses ( ) const

inline

Definition at line 421 of file marginalTrek++.h.

◆ extend()

bool IsoSpec::LayeredMarginal::extend	(	double	new_threshold,
		bool	do_sort = true )

Extend the set of computed subisotopologues to those above the new threshold.

Parameters

new_threshold The new log-probability limiting the subisotopologues from below.

Returns: Returns false, if there are no fringe-subisotopologues (subisotopologues that were neighbours of the previously calculated subisotopologues, with log-probability below the previous threshold).

Definition at line 573 of file marginalTrek++.cpp.

◆ get_conf()

const Conf & IsoSpec::LayeredMarginal::get_conf ( int idx ) const

inline

get the counts of isotopes that define the subisotopologue, see details in PrecalculatedMarginal::get_conf.

Definition at line 404 of file marginalTrek++.h.

◆ get_lProb()

double IsoSpec::LayeredMarginal::get_lProb ( int idx ) const

inline

get the log-probability of the idx-th subisotopologue, see details in PrecalculatedMarginal::get_lProb.

Definition at line 392 of file marginalTrek++.h.

◆ get_lProbs_ptr()

const double * IsoSpec::LayeredMarginal::get_lProbs_ptr ( ) const

inline

get the pointer to lProbs array. Accessing index -1 is legal and returns a guardian of -inf. Warning: The pointer gets invalidated on calls to extend()

Definition at line 401 of file marginalTrek++.h.

◆ get_mass()

double IsoSpec::LayeredMarginal::get_mass ( int idx ) const

inline

get the mass of the idx-th subisotopologue, see details in PrecalculatedMarginal::get_mass.

Definition at line 398 of file marginalTrek++.h.

◆ get_max_mass()

double IsoSpec::LayeredMarginal::get_max_mass ( ) const

Get the maximal mass in current layer.

Definition at line 695 of file marginalTrek++.cpp.

◆ get_min_mass()

double IsoSpec::LayeredMarginal::get_min_mass ( ) const

Get the minimal mass in current layer.

Definition at line 685 of file marginalTrek++.cpp.

◆ get_no_confs()

unsigned int IsoSpec::LayeredMarginal::get_no_confs ( ) const

inline

Get the number of precomputed subisotopologues, see details in PrecalculatedMarginal::get_no_confs.

Definition at line 407 of file marginalTrek++.h.

◆ get_prob()

double IsoSpec::LayeredMarginal::get_prob ( int idx ) const

inline

get the probability of the idx-th subisotopologue, see details in PrecalculatedMarginal::get_eProb.

Definition at line 395 of file marginalTrek++.h.

◆ getModeLProb()

double IsoSpec::LayeredMarginal::getModeLProb ( ) const

inline

Get the log-probability of the mode subisotopologue.

Returns: The log-probability of a/the most probable subisotopologue.

Definition at line 419 of file marginalTrek++.h.

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

/build/reproducible-path/isospec-2.3.2/src/IsoSpec++/marginalTrek++.h
/build/reproducible-path/isospec-2.3.2/src/IsoSpec++/marginalTrek++.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ LayeredMarginal()

Member Function Documentation

◆ conf_lprobs()

◆ conf_masses()

◆ extend()

◆ get_conf()

◆ get_lProb()

◆ get_lProbs_ptr()

◆ get_mass()

◆ get_max_mass()

◆ get_min_mass()

◆ get_no_confs()

◆ get_prob()

◆ getModeLProb()