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 ()

   Additional Inherited Members

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.

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.

   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.

Author

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