Man page - isospec_layeredmarginal(3)

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Manual

IsoSpec::LayeredMarginal

NAME

IsoSpec::LayeredMarginal - LayeredMarginal class.

SYNOPSIS

#include <marginalTrek++.h>

Inherits IsoSpec::Marginal .

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.

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 ()

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 350 of file marginalTrek++.h .

Constructor & Destructor Documentation

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 556 of file marginalTrek++.cpp .

Member Function Documentation

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 567 of file marginalTrek++.cpp .

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 396 of file marginalTrek++.h .

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 384 of file marginalTrek++.h .

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 393 of file marginalTrek++.h .

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 390 of file marginalTrek++.h .

double IsoSpec::LayeredMarginal::get_max_mass () const

Get the maximal mass in current layer.

Definition at line 689 of file marginalTrek++.cpp .

double IsoSpec::LayeredMarginal::get_min_mass () const

Get the minimal mass in current layer.

Definition at line 679 of file marginalTrek++.cpp .

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 399 of file marginalTrek++.h .

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 387 of file marginalTrek++.h .

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 411 of file marginalTrek++.h .

Author

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