IsoSpec  2.1.2
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
IsoSpec::Marginal Class Reference

The marginal distribution class (a subisotopologue). More...

#include <marginalTrek++.h>

Inheritance diagram for IsoSpec::Marginal:
IsoSpec::LayeredMarginal IsoSpec::MarginalTrek IsoSpec::PrecalculatedMarginal

Public Member Functions

 Marginal (const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)
 Class constructor. More...
 
Marginaloperator= (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. More...
 
const double * get_lProbs () const
 
double getLightestConfMass () const
 Get the mass of the lightest subisotopologue. More...
 
double getHeaviestConfMass () const
 Get the mass of the heaviest subisotopologue. More...
 
double getMonoisotopicConfMass () const
 Get the mass of the monoisotopic subisotopologue. More...
 
double getModeMass ()
 The the mass of the mode subisotopologue. More...
 
double getModeLProb ()
 Get the log-probability of the mode subisotopologue. More...
 
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. More...
 
double getSmallestLProb () const
 The the log-probability of the lightest subisotopologue. More...
 
double getAtomAverageMass () const
 The average mass of a single atom. More...
 
double getTheoreticalAverageMass () const
 The theoretical average mass of the molecule. More...
 
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 ()
 

Protected Member Functions

ISOSPEC_FORCE_INLINE double unnormalized_logProb (Conf conf) const
 Calculate the log-probability of a given subisotopologue. More...
 
ISOSPEC_FORCE_INLINE double logProb (Conf conf) const
 

Protected Attributes

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

The marginal distribution class (a subisotopologue).

This class mostly provides some basic common API for subclasses, but itself is not abstract. This class represents the probability distribution generated by one element only – a subisotopologue. For instance, it might be the distribution of C200, that might be part of, say, C200H402. It corresponds to the multinomial distribution, where each configuration can also be attributed a precise mass. The constructor method perform initial hill-climbing to find the most probable sub-isotopologue (the mode).

Definition at line 42 of file marginalTrek++.h.

Constructor & Destructor Documentation

◆ Marginal()

IsoSpec::Marginal::Marginal ( const double *  _masses,
const double *  _probs,
int  _isotopeNo,
int  _atomCnt 
)

Class constructor.

Parameters
_massesA table of masses of the stable isotopes of the investigated element, e.g. for C10 it is 2: C12 and C13.
_probsA table of natural frequencies of the stable isotopes of the investigated element, see IUPAC at https://iupac.org/isotopesmatter/
_isotopeNoNumber of isotopes of a given element.
_atomCntThe number of atoms of the given element, e.g. 10 for C10.
Returns
An instance of the Marginal class.

Definition at line 165 of file marginalTrek++.cpp.

Member Function Documentation

◆ computeModeConf()

Conf IsoSpec::Marginal::computeModeConf ( ) const

The the probability of the mode subisotopologue.

Returns
The probability of a/the most probable subisotopologue. Computes and returns the mode configuration, a isotopeNo-large array that the caller is responsible for delete[]-ing.

Definition at line 235 of file marginalTrek++.cpp.

◆ get_isotopeNo()

int IsoSpec::Marginal::get_isotopeNo ( ) const
inline

Get the number of isotopes of the investigated element.

Returns
The integer number of isotopes of the investigated element.

Definition at line 88 of file marginalTrek++.h.

◆ getAtomAverageMass()

double IsoSpec::Marginal::getAtomAverageMass ( ) const

The average mass of a single atom.

Returns
The average mass of a single atom.

Definition at line 281 of file marginalTrek++.cpp.

◆ getHeaviestConfMass()

double IsoSpec::Marginal::getHeaviestConfMass ( ) const

Get the mass of the heaviest subisotopologue.

This is trivially obtained by considering all atomNo atoms to be the heaviest isotope possible.

Returns
The mass of the heaviest subisotopologue.

Definition at line 259 of file marginalTrek++.cpp.

◆ getLightestConfMass()

double IsoSpec::Marginal::getLightestConfMass ( ) const

Get the mass of the lightest subisotopologue.

This is trivially obtained by considering all atomNo atoms to be the lightest isotope possible.

Returns
The mass of the lightiest subisotopologue.

Definition at line 250 of file marginalTrek++.cpp.

◆ getModeLProb()

double IsoSpec::Marginal::getModeLProb ( )
inline

Get the log-probability of the mode subisotopologue.

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

Definition at line 121 of file marginalTrek++.h.

◆ getModeMass()

double IsoSpec::Marginal::getModeMass ( )
inline

The the mass of the mode subisotopologue.

Returns
The mass of one of the most probable subisotopologues.

Definition at line 115 of file marginalTrek++.h.

◆ getMonoisotopicConfMass()

double IsoSpec::Marginal::getMonoisotopicConfMass ( ) const

Get the mass of the monoisotopic subisotopologue.

The monoisotopic subisotopologue is defined as the molecule consiting only of the most likely isotope. This is frequently the lightest subisotopologue, making this frequently (but not always) equal to getLightestConfMass()

Definition at line 268 of file marginalTrek++.cpp.

◆ getSmallestLProb()

double IsoSpec::Marginal::getSmallestLProb ( ) const
inline

The the log-probability of the lightest subisotopologue.

Returns
The logarithm of the smallest non-zero probability of a subisotopologue.

Definition at line 139 of file marginalTrek++.h.

◆ getTheoreticalAverageMass()

double IsoSpec::Marginal::getTheoreticalAverageMass ( ) const
inline

The theoretical average mass of the molecule.

Returns
The theoretical average mass of the molecule.

Definition at line 151 of file marginalTrek++.h.

◆ unnormalized_logProb()

ISOSPEC_FORCE_INLINE double IsoSpec::Marginal::unnormalized_logProb ( Conf  conf) const
inlineprotected

Calculate the log-probability of a given subisotopologue.

Parameters
confA subisotopologue (a table of integers describing subsequent isotope-counts).
Returns
The log-probability of the input subisotopologue.

Definition at line 159 of file marginalTrek++.h.

Member Data Documentation

◆ atom_lProbs

const double* const IsoSpec::Marginal::atom_lProbs
protected

Table of log-probabilities of all the isotopeNo isotopes.

Definition at line 49 of file marginalTrek++.h.

◆ atom_masses

const double* const IsoSpec::Marginal::atom_masses
protected

Table of atomic masses of all the isotopeNo isotopes.

Definition at line 50 of file marginalTrek++.h.

◆ atomCnt

const unsigned int IsoSpec::Marginal::atomCnt
protected

The number of atoms of the given element.

Definition at line 48 of file marginalTrek++.h.

◆ isotopeNo

const unsigned int IsoSpec::Marginal::isotopeNo
protected

The number of isotopes of the given element.

Definition at line 47 of file marginalTrek++.h.

◆ loggamma_nominator

const double IsoSpec::Marginal::loggamma_nominator
protected

The constant nominator that appears in the expressions for the multinomial probabilities.

Definition at line 51 of file marginalTrek++.h.

◆ mode_conf

Conf IsoSpec::Marginal::mode_conf
protected

A subisotopologue with most probability. If not unique, one of the representatives of that class of subisotopologues.

Definition at line 52 of file marginalTrek++.h.

◆ mode_lprob

double IsoSpec::Marginal::mode_lprob
protected

The log-probability of the mode subisotopologue.

Definition at line 53 of file marginalTrek++.h.


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