NAME

       IsoSpec::IsoThresholdGenerator - The generator of isotopologues above a given threshold
       value.

SYNOPSIS

       #include <isoSpec++.h>

       Inherits IsoSpec::IsoGenerator.

   Public Member Functions
       IsoThresholdGenerator (const IsoThresholdGenerator &other)=delete
       IsoThresholdGenerator & operator= (const IsoThresholdGenerator &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.
       IsoThresholdGenerator (Iso &&iso, double _threshold, bool _absolute=true, int
           _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true)
           The move-constructor.
       ISOSPEC_FORCE_INLINE bool advanceToNextConfiguration () override final
           Advance to the next, not yet visited, most probable isotopologue.
       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.
       void reset ()
       size_t count_confs ()

       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

       The generator of isotopologues above a given threshold value.

       Attention: the calculated configurations are only partially ordeded and the user should
       not assume they will be ordered. This algorithm computes N isotopologues in O(N). It is a
       considerable advantage w.r.t. the IsoOrderedGenerator.

       Definition at line 295 of file isoSpec++.h.

Constructor & Destructor Documentation

   IsoSpec::IsoThresholdGenerator::IsoThresholdGenerator (Iso && iso, double _threshold, bool
       _absolute = true, int _tabSize = 1000, int _hashSize = 1000, bool reorder_marginals =
       true)
       The move-constructor.

       Parameters
           iso An instance of the Iso class.
           _threshold The threshold value.
           _absolute If true, the _threshold is interpreted as the absolute minimal peak height
           for the isotopologues. If false, the _threshold is the fraction of the heighest peak's
           probability.
           tabSize The size of the extension of the table with configurations.
           hashSize The size of the hash-table used to store subisotopologues and check if they
           have been already calculated.

       Definition at line 478 of file isoSpec++.cpp.

   IsoSpec::IsoThresholdGenerator::~IsoThresholdGenerator ()
       Definition at line 637 of file isoSpec++.cpp.

Member Function Documentation

   ISOSPEC_FORCE_INLINE bool IsoSpec::IsoThresholdGenerator::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 352 of file isoSpec++.h.

   size_t IsoSpec::IsoThresholdGenerator::count_confs ()
       Count the number of configurations in the distribution. This can be used to pre-allocate
       enough memory to store it (e.g. std::vector's reserve() method - this is faster than
       depending on the vector's dynamic resizing, even though it means that the configuration
       space is walked through twice. This method has to be called before the first call to
       advanceToNextConfiguration and has undefined results (incl. segfaults) otherwise.

       Definition at line 566 of file isoSpec++.cpp.

   void IsoSpec::IsoThresholdGenerator::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 315 of file isoSpec++.h.

   ISOSPEC_FORCE_INLINE double IsoSpec::IsoThresholdGenerator::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 391 of file isoSpec++.h.

   ISOSPEC_FORCE_INLINE double IsoSpec::IsoThresholdGenerator::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 392 of file isoSpec++.h.

   ISOSPEC_FORCE_INLINE double IsoSpec::IsoThresholdGenerator::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 393 of file isoSpec++.h.

   void IsoSpec::IsoThresholdGenerator::reset ()
       Reset the generator to the beginning of the sequence. Allows it to be reused, eg. to go
       through the conf space once, calculate the amount of space needed to store configurations,
       then to allocate that memory, and go through it again, this time saving configurations
       (and is in fact faster than allocating a std::vector and depending on it to grow as
       needed. This is cheaper than throwing away the generator and making a new one too:
       marginal distributions don't need to be recalculated.

       Definition at line 620 of file isoSpec++.cpp.

   void IsoSpec::IsoThresholdGenerator::terminate_search ()
       Block the subsequent search of isotopologues.

       Definition at line 555 of file isoSpec++.cpp.

Author

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