IsoSpec  2.1.2
Public Member Functions | List of all members
IsoSpec::IsoLayeredGenerator Class Reference
Inheritance diagram for IsoSpec::IsoLayeredGenerator:
IsoSpec::IsoGenerator IsoSpec::Iso

Public Member Functions

 IsoLayeredGenerator (const IsoLayeredGenerator &other)=delete
 
IsoLayeredGeneratoroperator= (const IsoLayeredGenerator &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
 
 IsoLayeredGenerator (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. More...
 
ISOSPEC_FORCE_INLINE bool advanceToNextConfigurationWithinLayer ()
 
ISOSPEC_FORCE_INLINE double lprob () const override final
 Get the log-probability of the current isotopologue. More...
 
ISOSPEC_FORCE_INLINE double mass () const override final
 Get the mass of the current isotopologue. More...
 
ISOSPEC_FORCE_INLINE double prob () const override final
 Get the probability of the current isotopologue. More...
 
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)
 
- 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. More...
 
 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.
 
Isooperator= (const Iso &other)=delete
 
 Iso (const Iso &other, bool fullcopy)
 The copy constructor. More...
 
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. More...
 
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

Definition at line 439 of file isoSpec++.h.

Member Function Documentation

◆ advanceToNextConfiguration()

ISOSPEC_FORCE_INLINE bool IsoSpec::IsoLayeredGenerator::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 489 of file isoSpec++.h.

◆ lprob()

ISOSPEC_FORCE_INLINE double IsoSpec::IsoLayeredGenerator::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 511 of file isoSpec++.h.

◆ mass()

ISOSPEC_FORCE_INLINE double IsoSpec::IsoLayeredGenerator::mass ( ) const
inlinefinaloverridevirtual

Get the mass of the current isotopologue.

Returns
The mass of the current isotopologue.

Reimplemented from IsoSpec::IsoGenerator.

Definition at line 512 of file isoSpec++.h.

◆ prob()

ISOSPEC_FORCE_INLINE double IsoSpec::IsoLayeredGenerator::prob ( ) const
inlinefinaloverridevirtual

Get the probability of the current isotopologue.

Returns
The probability of the current isotopologue.

Reimplemented from IsoSpec::IsoGenerator.

Definition at line 513 of file isoSpec++.h.


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