NAME

       IsoSpec::IsoStochasticGenerator

SYNOPSIS

       Inherits IsoSpec::IsoGenerator.

   Public Member Functions
       IsoStochasticGenerator (Iso &&iso, size_t no_molecules, double precision=0.9999, double
           beta_bias=5.0)
       ISOSPEC_FORCE_INLINE size_t count () const
       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.
       ISOSPEC_FORCE_INLINE double lprob () const override final
           Get the log-probability of the current isotopologue.
       ISOSPEC_FORCE_INLINE 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.
       ISOSPEC_FORCE_INLINE bool advanceToNextConfiguration () override final
           Advance to the next, not yet visited, most probable isotopologue.

       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

       Definition at line 542 of file isoSpec++.h.

Constructor & Destructor Documentation

   IsoSpec::IsoStochasticGenerator::IsoStochasticGenerator (Iso && iso, size_t no_molecules,
       double precision = 0.9999, double beta_bias = 5.0)
       Definition at line 923 of file isoSpec++.cpp.

Member Function Documentation

   ISOSPEC_FORCE_INLINE bool IsoSpec::IsoStochasticGenerator::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 565 of file isoSpec++.h.

   ISOSPEC_FORCE_INLINE size_t IsoSpec::IsoStochasticGenerator::count () const [inline]
       Definition at line 555 of file isoSpec++.h.

   ISOSPEC_FORCE_INLINE void IsoSpec::IsoStochasticGenerator::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.

       Implements IsoSpec::IsoGenerator.

       Definition at line 563 of file isoSpec++.h.

   ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::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 561 of file isoSpec++.h.

   ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::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 557 of file isoSpec++.h.

   ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::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 559 of file isoSpec++.h.

Author

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