Inheritance diagram for IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >:

Public Member Functions
	IsoLayeredGeneratorTemplate (const IsoLayeredGeneratorTemplate &other)=delete
IsoLayeredGeneratorTemplate &	operator= (const IsoLayeredGeneratorTemplate &other)=delete
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.
double	get_currentLThreshold () const
	IsoLayeredGeneratorTemplate (Iso &&iso, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true, double t_prob_hint=0.99)
ISOSPEC_FORCE_INLINE bool	advanceToNextConfiguration () override final
	Advance to the next, not yet visited, most probable isotopologue.
ISOSPEC_FORCE_INLINE bool	advanceToNextConfigurationWithinLayer ()
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.
ISOSPEC_FORCE_INLINE void	recalc (int idx)
	Recalculate the current partial log-probabilities, masses, and probabilities.
bool	nextLayer (double offset)
void	get_conf_by_indexes (int *space) const
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)
	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
	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
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.
double	getModeMass () const
	Get the mass of the mode-configuration (if there are many modes, it is undefined which one will be selected).
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.
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
Protected Member Functions inherited from IsoSpec::Iso
bool	doMarginalsNeedSorting () const
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

◆ IsoLayeredGeneratorTemplate()

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.

◆ ~IsoLayeredGeneratorTemplate()

template<typename MarginalType>

IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::~IsoLayeredGeneratorTemplate ( )

Definition at line 799 of file isoSpec++.cpp.

Member Function Documentation

◆ advanceToNextConfiguration()

template<typename MarginalType>

ISOSPEC_FORCE_INLINE bool IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::advanceToNextConfiguration ( )

inlinefinaloverridevirtual

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.

◆ advanceToNextConfigurationWithinLayer()

template<typename MarginalType>

ISOSPEC_FORCE_INLINE bool IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::advanceToNextConfigurationWithinLayer ( )

inline

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

◆ get_conf_by_indexes()

template<typename MarginalType>

void IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::get_conf_by_indexes ( int * space ) const

inline

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

◆ get_conf_signature()

template<typename MarginalType>

void IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::get_conf_signature ( int * space ) const

inlinefinaloverridevirtual

Write the signature of configuration into target memory location. It must be large enough to accomodate it.

Implements IsoSpec::IsoGenerator.

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

◆ get_currentLThreshold()

template<typename MarginalType>

double IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::get_currentLThreshold ( ) const

inline

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

◆ lprob()

template<typename MarginalType>

ISOSPEC_FORCE_INLINE double IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::lprob ( ) const

inlinefinaloverridevirtual

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.

◆ mass()

template<typename MarginalType>

ISOSPEC_FORCE_INLINE double IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::mass ( ) const

inlinefinaloverridevirtual

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.

◆ nextLayer()

template<typename MarginalType>

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

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

◆ prob()

template<typename MarginalType>

ISOSPEC_FORCE_INLINE double IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::prob ( ) const

inlinefinaloverridevirtual

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.

◆ recalc()

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.

◆ terminate_search()

template<typename MarginalType>

void IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::terminate_search ( )

Block the subsequent search of isotopologues.

Definition at line 787 of file isoSpec++.cpp.

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

/build/isospec-8QB56o/isospec-2.3.2/src/IsoSpec++/isoSpec++.h
/build/isospec-8QB56o/isospec-2.3.2/src/IsoSpec++/isoSpec++.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ IsoLayeredGeneratorTemplate()

◆ ~IsoLayeredGeneratorTemplate()

Member Function Documentation

◆ advanceToNextConfiguration()

◆ advanceToNextConfigurationWithinLayer()

◆ get_conf_by_indexes()

◆ get_conf_signature()

◆ get_currentLThreshold()

◆ lprob()

◆ mass()

◆ nextLayer()

◆ prob()

◆ recalc()

◆ terminate_search()