NAME

       IsoSpec::IsoGenerator - The generator of isotopologues.

SYNOPSIS

       #include <isoSpec++.h>

       Inherits IsoSpec::Iso.

       Inherited by IsoSpec::IsoLayeredGenerator, IsoSpec::IsoOrderedGenerator,
       IsoSpec::IsoStochasticGenerator, and IsoSpec::IsoThresholdGenerator.

   Public Member Functions
       virtual bool advanceToNextConfiguration ()=0
           Advance to the next, not yet visited, most probable isotopologue.
       virtual double lprob () const
           Get the log-probability of the current isotopologue.
       virtual double mass () const
           Get the mass of the current isotopologue.
       virtual double prob () const
           Get the probability of the current isotopologue.
       virtual void get_conf_signature (int *space) const =0
           Write the signature of configuration into target memory location. It must be large
           enough to accomodate it.
       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.

   Public Attributes
       const double mode_lprob

   Protected Attributes
       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

   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.

       Protected Member Functions inherited from IsoSpec::Iso
       bool doMarginalsNeedSorting () const

Detailed Description

       The generator of isotopologues.

       This class provides the common interface for all isotopic generators.

       Definition at line 183 of file isoSpec++.h.

Constructor & Destructor Documentation

   IsoSpec::IsoGenerator::IsoGenerator (Iso && iso, bool alloc_partials = true)
       Move constructor.

       Definition at line 442 of file isoSpec++.cpp.

   IsoSpec::IsoGenerator::~IsoGenerator () [virtual]
       Destructor.

       Definition at line 460 of file isoSpec++.cpp.

Member Function Documentation

   virtual bool IsoSpec::IsoGenerator::advanceToNextConfiguration () [pure virtual]
       Advance to the next, not yet visited, most probable isotopologue.

       Returns
           Return false if it is not possible to advance.

       Implemented in IsoSpec::IsoOrderedGenerator, IsoSpec::IsoThresholdGenerator,
       IsoSpec::IsoLayeredGenerator, and IsoSpec::IsoStochasticGenerator.

   virtual void IsoSpec::IsoGenerator::get_conf_signature (int * space) const [pure virtual]
       Write the signature of configuration into target memory location. It must be large enough
       to accomodate it.

       Implemented in IsoSpec::IsoOrderedGenerator, IsoSpec::IsoThresholdGenerator,
       IsoSpec::IsoLayeredGenerator, and IsoSpec::IsoStochasticGenerator.

   virtual double IsoSpec::IsoGenerator::lprob () const [inline],  [virtual]
       Get the log-probability of the current isotopologue.

       Returns
           The log-probability of the current isotopologue.

       Reimplemented in IsoSpec::IsoThresholdGenerator, IsoSpec::IsoLayeredGenerator, and
       IsoSpec::IsoStochasticGenerator.

       Definition at line 204 of file isoSpec++.h.

   virtual double IsoSpec::IsoGenerator::mass () const [inline],  [virtual]
       Get the mass of the current isotopologue.

       Returns
           The mass of the current isotopologue.

       Reimplemented in IsoSpec::IsoThresholdGenerator, IsoSpec::IsoLayeredGenerator, and
       IsoSpec::IsoStochasticGenerator.

       Definition at line 210 of file isoSpec++.h.

   virtual double IsoSpec::IsoGenerator::prob () const [inline],  [virtual]
       Get the probability of the current isotopologue.

       Returns
           The probability of the current isotopologue.

       Reimplemented in IsoSpec::IsoThresholdGenerator, IsoSpec::IsoLayeredGenerator, and
       IsoSpec::IsoStochasticGenerator.

       Definition at line 216 of file isoSpec++.h.

Member Data Documentation

   const double IsoSpec::IsoGenerator::mode_lprob
       Definition at line 186 of file isoSpec++.h.

   double* IsoSpec::IsoGenerator::partialLProbs [protected]
       The prefix sum of the log-probabilities of the current isotopologue.

       Definition at line 189 of file isoSpec++.h.

   double* IsoSpec::IsoGenerator::partialMasses [protected]
       The prefix sum of the masses of the current isotopologue.

       Definition at line 190 of file isoSpec++.h.

   double* IsoSpec::IsoGenerator::partialProbs [protected]
       The prefix product of the probabilities of the current isotopologue.

       Definition at line 191 of file isoSpec++.h.

Author

       Generated automatically by Doxygen for IsoSpec from the source code.