Man page - isospec_precalculatedmarginal(3)

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Manual

IsoSpec::PrecalculatedMarginal

NAME

IsoSpec::PrecalculatedMarginal - Precalculated Marginal class.

SYNOPSIS

#include <marginalTrek++.h>

Inherits IsoSpec::Marginal .

Public Member Functions

PrecalculatedMarginal ( Marginal &&m, double lCutOff, bool sort=true, int tabSize=1000, int hashSize=1000)
The move constructor (disowns the Marginal ).
PrecalculatedMarginal (const PrecalculatedMarginal &other)=delete
PrecalculatedMarginal & operator= (const PrecalculatedMarginal &other)=delete
virtual ˜PrecalculatedMarginal ()
Destructor.
bool inRange (unsigned int idx) const
Is there a subisotopologue with a given number?
const double & get_lProb (int idx) const
Get the log-probability of the idx-th subisotopologue.
const double & get_prob (int idx) const
Get the probability of the idx-th subisotopologue.
const double & get_mass (int idx) const
Get the mass of the idx-th subisotopologue.
const double * get_lProbs_ptr () const
Get the table of the log-probabilities of subisotopologues.
const double * get_masses_ptr () const
Get the table of the masses of subisotopologues.
const Conf & get_conf (int idx) const
Get the counts of isotopes that define the subisotopologue.
unsigned int get_no_confs () const
Get the number of precomputed subisotopologues.
double getModeLProb () const
Get the log-probability of the mode subisotopologue.

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.
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 ()

Protected Attributes

pod_vector < Conf > configurations
Conf * confs
unsigned int no_confs
double * masses
pod_vector < double > lProbs
double * probs
Allocator < int > allocator

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

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

Detailed Description

Precalculated Marginal class.

This class serves to calculate a set of isotopologues that is defined by the minimal probability threshold.

This works faster than if you did not know the threshold. If you have no idea about the threshold, you would need to call us, to change encode the layered version of the marginal.

Definition at line 251 of file marginalTrek++.h .

Constructor & Destructor Documentation

IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal (Marginal && m,double lCutOff, bool sort = true, int tabSize = 1000, int hashSize =1000)

The move constructor (disowns the Marginal ). This constructor memoizes all subisotopologues with log-probability above the provided threshold lCutOff

Parameters

Marginal An instance of the Marginal class this class is about to disown.
lCutOff The lower limit on the log-probability of the precomputed subisotopologues.
sort Should the subisotopologues be stored with descending probability ?

Returns

An instance of the PrecalculatedMarginal class.

Definition at line 443 of file marginalTrek++.cpp .

IsoSpec::PrecalculatedMarginal::˜PrecalculatedMarginal () [virtual]

Destructor.

Definition at line 542 of file marginalTrek++.cpp .

Member Function Documentation

const Conf & IsoSpec::PrecalculatedMarginal::get_conf (int idx) const[inline]

Get the counts of isotopes that define the subisotopologue.

Parameters

idx The number of the considered subisotopologue.

Returns

The counts of isotopes that define the subisotopologue.

Definition at line 329 of file marginalTrek++.h .

const double & IsoSpec::PrecalculatedMarginal::get_lProb (int idx) const[inline]

Get the log-probability of the idx-th subisotopologue.

Parameters

idx The number of the considered subisotopologue.

Returns

The log-probability of the idx-th subisotopologue.

Definition at line 295 of file marginalTrek++.h .

const double * IsoSpec::PrecalculatedMarginal::get_lProbs_ptr () const[inline]

Get the table of the log-probabilities of subisotopologues.

Returns

Pointer to the first element in the table storing log-probabilities of subisotopologues.

Definition at line 315 of file marginalTrek++.h .

const double & IsoSpec::PrecalculatedMarginal::get_mass (int idx) const[inline]

Get the mass of the idx-th subisotopologue.

Parameters

idx The number of the considered subisotopologue.

Returns

The mass of the idx-th subisotopologue.

Definition at line 309 of file marginalTrek++.h .

const double * IsoSpec::PrecalculatedMarginal::get_masses_ptr () const[inline]

Get the table of the masses of subisotopologues.

Returns

Pointer to the first element in the table storing masses of subisotopologues.

Definition at line 321 of file marginalTrek++.h .

unsigned int IsoSpec::PrecalculatedMarginal::get_no_confs () const [inline]

Get the number of precomputed subisotopologues.

Returns

The number of precomputed subisotopologues.

Definition at line 335 of file marginalTrek++.h .

const double & IsoSpec::PrecalculatedMarginal::get_prob (int idx) const[inline]

Get the probability of the idx-th subisotopologue.

Parameters

idx The number of the considered subisotopologue.

Returns

The probability of the idx-th subisotopologue.

Definition at line 302 of file marginalTrek++.h .

double IsoSpec::PrecalculatedMarginal::getModeLProb () const [inline]

Get the log-probability of the mode subisotopologue.

Returns

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

Definition at line 341 of file marginalTrek++.h .

bool IsoSpec::PrecalculatedMarginal::inRange (unsigned int idx) const[inline]

Is there a subisotopologue with a given number?

Returns

Returns true if idx does not exceed the number of pre-computed configurations.

Definition at line 288 of file marginalTrek++.h .

Member Data Documentation

Allocator<int> IsoSpec::PrecalculatedMarginal::allocator [protected]

Definition at line 260 of file marginalTrek++.h .

pod_vector<Conf> IsoSpec::PrecalculatedMarginal::configurations [protected]

Definition at line 254 of file marginalTrek++.h .

Conf* IsoSpec::PrecalculatedMarginal::confs [protected]

Definition at line 255 of file marginalTrek++.h .

pod_vector<double> IsoSpec::PrecalculatedMarginal::lProbs [protected]

Definition at line 258 of file marginalTrek++.h .

double* IsoSpec::PrecalculatedMarginal::masses [protected]

Definition at line 257 of file marginalTrek++.h .

unsigned int IsoSpec::PrecalculatedMarginal::no_confs [protected]

Definition at line 256 of file marginalTrek++.h .

double* IsoSpec::PrecalculatedMarginal::probs [protected]

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

Author

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