ISOSPEC_ISOLAYEREDGENERATORTEMPLATE(3)

📦 version 2.3.2, in ubuntu resolute, ubuntu stonking

🌸 IsoSpec::IsoLayeredGeneratorTemplate< MarginalType > 🌸

okay bestie, welcome to the IsoSpec Library Functions Manual 💖 this whole page is about one absolute icon of a class template, and yes she is very good at her job. grab a boba, we're going in 🧋✨

✨ NAME ✨

IsoSpec::IsoLayeredGeneratorTemplate< MarginalType > — that's her. that's the whole name. no cap 🎀

🦋 SYNOPSIS 🦋

she Inherits IsoSpec::IsoGenerator. so everything IsoGenerator can do, she can do too (and honestly, she does it cuter 💅).

💖 Public Member Functions 💖

IsoLayeredGeneratorTemplate(const IsoLayeredGeneratorTemplate &other)=delete — nope, deleted, we do not copy her, she's one of a kind 🙈
IsoLayeredGeneratorTemplate & operator=(const IsoLayeredGeneratorTemplate &other)=delete — also deleted. no assignment. she doesn't do duplicates, periodt ✨
void get_conf_signature(int *space) const override final — Write the signature of configuration into target memory location. It must be large enough to accomodate it. (translating: bestie, YOU gotta make sure space is big enough, she will not check for you 😭)
double get_currentLThreshold() const — hands you the current L-threshold, fr fr
IsoLayeredGeneratorTemplate(Iso &&iso, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true, double t_prob_hint=0.99) — the main constructor, and look at those defaults, she comes pre-styled 👑
ISOSPEC_FORCE_INLINE bool advanceToNextConfiguration() override final — Advance to the next, not yet visited, most probable isotopologue.
ISOSPEC_FORCE_INLINE bool advanceToNextConfigurationWithinLayer() — same vibe but she stays inside the layer 🦋
ISOSPEC_FORCE_INLINE double lprob() const override final — Get the log-probability of the current isotopologue.
ISOSPEC_FORCE_INLINE double mass() const override final — Get the mass of the current isotopologue.
ISOSPEC_FORCE_INLINE double prob() const override final — Get the probability of the current isotopologue.
void terminate_search() — Block the subsequent search of isotopologues. she said enough. 💀
ISOSPEC_FORCE_INLINE void recalc(int idx) — Recalculate the current partial log-probabilities, masses, and probabilities.
bool nextLayer(double offset) — hop to the next layer, with an offset
void get_conf_by_indexes(int *space) const — grab the configuration by its indexes ✨

💜 Public Member Functions inherited from IsoSpec::IsoGenerator 💜

IsoGenerator(Iso &&iso, bool alloc_partials=true) — Move constructor.
virtual ~IsoGenerator() — Destructor.

🌈 Public Member Functions inherited from IsoSpec::Iso 🌈

Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *_isotopeMasses, const double *_isotopeProbabilities) — General constructror.
Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) — the pointer-to-const-pointer glow-up version of the same thing
Iso(const char *formula, bool use_nominal_masses=false) — Constructor from the formula object.
Iso(const std::string &formula, bool use_nominal_masses=false) — Constructor from C++ std::string chemical formula.
Iso(Iso &&other) — The move constructor.
Iso & operator=(const Iso &other)=delete — deleted. no copy-assign. she's not sharing 😤
Iso(const Iso &other, bool fullcopy) — The copy constructor.
virtual ~Iso() — Destructor.
double getLightestPeakMass() const — Get the mass of the lightest peak in the isotopic distribution.
double getHeaviestPeakMass() const — Get the mass of the heaviest peak in the isotopic distribution.
double getMonoisotopicPeakMass() const — the monoisotopic one. the main character 👑
double getModeLProb() const — Get the log-probability of the mode-configuration (if there are many modes, they share this value).
double getUnlikeliestPeakLProb() const — Get the logprobability of the least probable subisotopologue. (yes she said logprobability, one word, she's confident, let her live 💅)
double getModeMass() const — Get the mass of the mode-configuration (if there are many modes, it is undefined which one will be selected). undefined!! so don't come for her if you get a different mode 💀
double getTheoreticalAverageMass() const — Get the theoretical average mass of the molecule.
double variance() const — Get the theoretical variance of the distribution.
double stddev() const — Get the standard deviation of the theoretical distribution.
int getDimNumber() const — Get the number of elements in the chemical formula of the molecule.
int getAllDim() const — Get the total number of isotopes of elements present in a chemical formula.
void addElement(int atomCount, int noIsotopes, const double *isotopeMasses, const double *isotopeProbabilities) — Add an element to the molecule. Note: this method can only be used BEFORE Iso is used to construct an IsoGenerator instance. like, BEFORE. that's a hard rule, not a suggestion 🚨
void saveMarginalLogSizeEstimates(double *priorities, double target_total_prob) const — Save estimates of logarithms of target sizes of marginals using Gaussian approximation into argument array. Array priorities must have length equal to dimNumber.

🎀 Additional Inherited Members 🎀

⭐ Static Public Member Functions inherited from IsoSpec::Iso ⭐

static Iso FromFASTA(const char *fasta, bool use_nominal_masses=false, bool add_water=true) — Constructor (named) from aminoacid FASTA sequence as C string.
static Iso FromFASTA(const std::string &fasta, bool use_nominal_masses=false, bool add_water=true) — Constructor (named) from aminoacid FASTA sequence as C++ std::string. See above for details.

🫶 Public Attributes inherited from IsoSpec::IsoGenerator 🫶

const double mode_lprob — it's const. don't touch. 🛑

🧚 Protected Member Functions inherited from IsoSpec::Iso 🧚

bool doMarginalsNeedSorting() const — protected, so it's between her and her subclasses, mind your business 🙈

🌸 Protected Attributes inherited from IsoSpec::IsoGenerator 🌸

double * partialLProbs
double * partialMasses
double * partialProbs

💜 Protected Attributes inherited from IsoSpec::Iso 💜

int dimNumber
int * isotopeNumbers
int * atomCounts
unsigned int confSize
int allDim
Marginal ** marginals

📖 Detailed Description 📖

template<typename MarginalType>
class IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >"

Definition at line 460 of file isoSpec++.h. ✨

🔧 Constructor & Destructor Documentation 🔧

`template<typename MarginalType> IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::IsoLayeredGeneratorTemplate(Iso && iso, int _tabSize = 1000, int _hashSize = 1000, bool reorder_marginals = true, double t_prob_hint = 0.99)`

Definition at line 654 of file isoSpec++.cpp. 💖

`template<typename MarginalType> IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::~IsoLayeredGeneratorTemplate()`

Definition at line 799 of file isoSpec++.cpp. 🥺 she said goodbye

💅 Member Function Documentation 💅

`template<typename MarginalType> ISOSPEC_FORCE_INLINE bool IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::advanceToNextConfiguration() [inline], [final], [override], [virtual]`

Advance to the next, not yet visited, most probable isotopologue.

Returns: Return false if it is not possible to advance.

Implements IsoSpec::IsoGenerator.

Definition at line 510 of file isoSpec++.h. 🔥

`template<typename MarginalType> ISOSPEC_FORCE_INLINE bool IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::advanceToNextConfigurationWithinLayer() [inline]`

Definition at line 520 of file isoSpec++.h. 🦋

`template<typename MarginalType> void IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::get_conf_by_indexes(int * space) const [inline]`

Definition at line 557 of file isoSpec++.h. ✨

`template<typename MarginalType> void IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::get_conf_signature(int * space) const [inline], [final], [override], [virtual]`

Write the signature of configuration into target memory location. It must be large enough to accomodate it. (again bestie: YOUR job to size it right 😭)

Implements IsoSpec::IsoGenerator.

Definition at line 482 of file isoSpec++.h. 💖

`template<typename MarginalType> double IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::get_currentLThreshold() const [inline]`

Definition at line 504 of file isoSpec++.h. 🎀

`template<typename MarginalType> ISOSPEC_FORCE_INLINE double IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::lprob() const [inline], [final], [override], [virtual]`

Get the log-probability of the current isotopologue.

Returns: The log-probability of the current isotopologue.

Reimplemented from IsoSpec::IsoGenerator.

Definition at line 532 of file isoSpec++.h. 🌈

`template<typename MarginalType> ISOSPEC_FORCE_INLINE double IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::mass() const [inline], [final], [override], [virtual]`

Get the mass of the current isotopologue.

Returns: The mass of the current isotopologue.

Reimplemented from IsoSpec::IsoGenerator.

Definition at line 533 of file isoSpec++.h. ⭐

`template<typename MarginalType> bool IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::nextLayer(double offset)`

Definition at line 722 of file isoSpec++.cpp. 🍓

`template<typename MarginalType> ISOSPEC_FORCE_INLINE double IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::prob() const [inline], [final], [override], [virtual]`

Get the probability of the current isotopologue.

Returns: The probability of the current isotopologue.

Reimplemented from IsoSpec::IsoGenerator.

Definition at line 534 of file isoSpec++.h. 💜

`template<typename MarginalType> ISOSPEC_FORCE_INLINE void IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::recalc(int idx) [inline]`

Recalculate the current partial log-probabilities, masses, and probabilities.

Definition at line 541 of file isoSpec++.h. 🧚

`template<typename MarginalType> void IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::terminate_search()`

Block the subsequent search of isotopologues.

Definition at line 787 of file isoSpec++.cpp. 💀 she's done, she's going home

👑 Author 👑

Generated automatically by Doxygen for IsoSpec from the source code.

and that's the whole page bestie, no cap, every last line accounted for 🫶✨ this one came off the IsoSpec manual (Library Functions Manual vibe, you know the one) — no date on this footer, it just says IsoSpec on both sides, and the source is Doxygen-generated from the IsoSpec source code, so go thank the robots 🤖💖 bye bye, slay responsibly 💅🌸

📦 where this page comes from

ubuntu resolute: libisospec++-dev 2.3.2-1build1 · BSD-2-Clause
ubuntu stonking: libisospec++-dev 2.3.2-2 · BSD-2-Clause
💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on 2026-10-14: a language model's rewrite of the original, under its terms