ISOSPEC_LAYEREDMARGINAL(3)

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version 2.3.2 · 4 versions
, in ubuntu resolute, ubuntu stonking

✨ IsoSpec::LayeredMarginal 💅

okay bestie, welcome to the manual page for IsoSpec::LayeredMarginal — the LayeredMarginal class, living its best life in the IsoSpec library. it's a library functions manual, it's giving very C++ and very iconic. let's get into it 🫶

🎀 NAME 🎀

IsoSpec::LayeredMarginal — the LayeredMarginal class. that's it, that's the name, periodt. ✨

🌸 SYNOPSIS 🌸

#include <marginalTrek++.h>

Inherits IsoSpec::Marginal. yes bestie, she's a subclass, she got it from her mama 💅

👑 Public Member Functions

  • LayeredMarginal (Marginal &&m, int tabSize=1000, int hashSize=1000) — move constructor: specializes the Marginal class. no cap.
  • LayeredMarginal (const LayeredMarginal &other)=delete — deleted, don't even try it bestie 🚫
  • LayeredMarginal & operator= (const LayeredMarginal &other)=delete — also deleted. she said no 💀
  • 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 the 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 the current layer.
  • double get_max_mass () const — get the maximal mass in the current layer.
  • double getModeLProb () const — get the log-probability of the mode subisotopologue.
  • const pod_vector< double > & conf_lprobs () const — no description, she's mysterious like that 🙈
  • const pod_vector< double > & conf_masses () const — also mysterious, also valid 🎀

🌈 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 — deleted, sorry babes.
  • Marginal (const Marginal &other) — copy constructor.
  • Marginal (Marginal &&other) — move constructor.
  • virtual ~Marginal () — destructor. rip 💀
  • int get_isotopeNo () const — get the number of isotopes of the investigated element.
  • const double * get_lProbs () const — no description given, keep it moving.
  • 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. (yes, "the the" — i'm keeping it exactly as written, bestie, that's the lore 💖)
  • 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 — so call it first or perish fr fr.
  • 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 the estimated logarithm of size of the marginal at a given ellipsoid radius.
  • void ensureModeConf () — no description, but she's important, remember her name.

🦋 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 — no description, still valid, still slaying.

🌸 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. she's flexible like that, main character energy fr 💅

Definition at line 358 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 562 of file marginalTrek++.cpp.

🔥 Member Function Documentation 🔥

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

[inline]

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

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

[inline]

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

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

Extend the set of computed subisotopologues to those above the new threshold. glow up time ✨

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.

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.

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.

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

[inline]

Get the pointer to the lProbs array. Accessing index -1 is legal and returns a guardian of -inf.

Warning: the pointer gets invalidated on calls to extend() — do not hold onto it like it's your emotional support pointer bestie, it WILL ghost you 😭

Definition at line 401 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 398 of file marginalTrek++.h.

double IsoSpec::LayeredMarginal::get_max_mass () const

Get the maximal mass in the current layer.

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

double IsoSpec::LayeredMarginal::get_min_mass () const

Get the minimal mass in the current layer.

Definition at line 685 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 407 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 395 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 419 of file marginalTrek++.h.

💖 Author 💖

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and that's a wrap!! 🎀 this page is IsoSpec::LayeredMarginal(3), part of the IsoSpec library's Library Functions Manual — no date on this footer, so we're just vibing with the source and the page name. go forth and extend those thresholds, queen 👑🦋🌸

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