NAME

       IsoSpec::IsoOrderedGenerator - The generator of isotopologues sorted by their probability
       of occurrence.

SYNOPSIS

       #include <isoSpec++.h>

       Inherits IsoSpec::IsoGenerator.

   Public Member Functions
       IsoOrderedGenerator (const IsoOrderedGenerator &other)=delete
       IsoOrderedGenerator & operator= (const IsoOrderedGenerator &other)=delete
       bool advanceToNextConfiguration () override final
           Advance to the next, not yet visited, most probable isotopologue.
       void get_conf_signature (int *space) const override final
           Save the counts of isotopes in the space.
       IsoOrderedGenerator (Iso &&iso, int _tabSize=1000, int _hashSize=1000)
           The move-contstructor.
       virtual ~IsoOrderedGenerator ()
           Destructor.

       Public Member Functions inherited from IsoSpec::IsoGenerator
       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.
       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

       The generator of isotopologues sorted by their probability of occurrence.

       The subsequent isotopologues are generated with diminishing probability, starting from the
       mode. This algorithm take O(N*log(N)) to compute the N isotopologues because of using the
       Priority Queue data structure. Obtaining the N isotopologues can be achieved in O(N) if
       they are not required to be spit out in the descending order.

       Definition at line 236 of file isoSpec++.h.

Constructor & Destructor Documentation

   IsoSpec::IsoOrderedGenerator::IsoOrderedGenerator (Iso && iso, int _tabSize = 1000, int
       _hashSize = 1000)
       The move-contstructor.

       Definition at line 814 of file isoSpec++.cpp.

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

       Definition at line 855 of file isoSpec++.cpp.

Member Function Documentation

   bool IsoSpec::IsoOrderedGenerator::advanceToNextConfiguration () [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 867 of file isoSpec++.cpp.

   void IsoSpec::IsoOrderedGenerator::get_conf_signature (int * space) const [inline],  [final],
       [override],  [virtual]
       Save the counts of isotopes in the space.

       Parameters
           space An array where counts of isotopes shall be written. Must be as big as the
           overall number of isotopes.

       Implements IsoSpec::IsoGenerator.

       Definition at line 262 of file isoSpec++.h.

Author

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