NAME

       IsoSpec::LayeredMarginal - LayeredMarginal class.

SYNOPSIS

       #include <marginalTrek++.h>

       Inherits IsoSpec::Marginal.

   Public Member Functions
       LayeredMarginal (Marginal &&m, int tabSize=1000, int hashSize=1000)
           Move constructor: specializes the Marginal class.
       LayeredMarginal (const LayeredMarginal &other)=delete
       LayeredMarginal & operator= (const LayeredMarginal &other)=delete
       bool extend (double new_threshold, bool do_sort=true)
           Extend the set of computed subisotopologues to those above the new threshold.
       double get_lProb (int idx) const
           get the log-probability of the idx-th subisotopologue, see details in
           PrecalculatedMarginal::get_lProb.
       double get_prob (int idx) const
           get the probability of the idx-th subisotopologue, see details in
           PrecalculatedMarginal::get_eProb.
       double get_mass (int idx) const
           get the mass of the idx-th subisotopologue, see details in
           PrecalculatedMarginal::get_mass.
       const double * get_lProbs_ptr () const
           get the pointer to lProbs array. Accessing index -1 is legal and returns a guardian of
           -inf. Warning: The pointer gets invalidated on calls to extend()
       const Conf & get_conf (int idx) const
           get the counts of isotopes that define the subisotopologue, see details in
           PrecalculatedMarginal::get_conf.
       unsigned int get_no_confs () const
           Get the number of precomputed subisotopologues, see details in
           PrecalculatedMarginal::get_no_confs.
       double get_min_mass () const
           Get the minimal mass in current layer.
       double get_max_mass () const
           Get the maximal mass in current layer.
       double getModeLProb () const
           Get the log-probability of the mode subisotopologue.

       Public Member Functions inherited from IsoSpec::Marginal
       Marginal (const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)
           Class constructor.
       Marginal & operator= (const Marginal &other)=delete
       Marginal (const Marginal &other)
           Copy constructor.
       Marginal (Marginal &&other)
           Move constructor.
       virtual ~Marginal ()
           Destructor.
       int get_isotopeNo () const
           Get the number of isotopes of the investigated element.
       const double * get_lProbs () const
       double getLightestConfMass () const
           Get the mass of the lightest subisotopologue.
       double getHeaviestConfMass () const
           Get the mass of the heaviest subisotopologue.
       double getMonoisotopicConfMass () const
           Get the mass of the monoisotopic subisotopologue.
       double getModeMass ()
           The the mass of the mode subisotopologue.
       double getModeLProb ()
           Get the log-probability of the mode subisotopologue.
       double fastGetModeLProb ()
           Get the log-probability of the mode subisotopologue. Results undefined if
           ensureModeConf() wasn't called before.
       Conf computeModeConf () const
           The the probability of the mode subisotopologue.
       double getSmallestLProb () const
           The the log-probability of the lightest subisotopologue.
       double getAtomAverageMass () const
           The average mass of a single atom.
       double getTheoreticalAverageMass () const
           The theoretical average mass of the molecule.
       double variance () const
           Calculate the variance of the theoretical distribution describing the subisotopologue.
       double getLogSizeEstimate (double logEllipsoidRadius) const
           Return estimated logarithm of size of the marginal at a given ellipsoid radius.
       void ensureModeConf ()

   Additional Inherited Members
       Protected Member Functions inherited from IsoSpec::Marginal
       ISOSPEC_FORCE_INLINE double unnormalized_logProb (Conf conf) const
           Calculate the log-probability of a given subisotopologue.
       ISOSPEC_FORCE_INLINE double logProb (Conf conf) const

       Protected Attributes inherited from IsoSpec::Marginal
       const unsigned int isotopeNo
       const unsigned int atomCnt
       const double *const atom_lProbs
       const double *const atom_masses
       const double loggamma_nominator
       Conf mode_conf
       double mode_lprob

Detailed Description

       LayeredMarginal class.

       An extendable version of the PrecalculatedMarginal, where you can extend the threshold at
       will.

       Definition at line 350 of file marginalTrek++.h.

Constructor & Destructor Documentation

   IsoSpec::LayeredMarginal::LayeredMarginal (Marginal && m, int tabSize = 1000, int hashSize =
       1000)
       Move constructor: specializes the Marginal class.

       Parameters
           tabSize The size of the table used to store configurations in the allocator.
           hashSize The size of the hash table used to store visited subisotopologues.

       Definition at line 556 of file marginalTrek++.cpp.

Member Function Documentation

   bool IsoSpec::LayeredMarginal::extend (double new_threshold, bool do_sort = true)
       Extend the set of computed subisotopologues to those above the new threshold.

       Parameters
           new_threshold The new log-probability limiting the subisotopologues from below.

       Returns
           Returns false, if there are no fringe-subisotopologues (subisotopologues that were
           neighbours of the previously calculated subisotopologues, with log-probability below
           the previous threshold).

       Definition at line 567 of file marginalTrek++.cpp.

   const Conf & IsoSpec::LayeredMarginal::get_conf (int idx) const [inline]
       get the counts of isotopes that define the subisotopologue, see details in
       PrecalculatedMarginal::get_conf.

       Definition at line 396 of file marginalTrek++.h.

   double IsoSpec::LayeredMarginal::get_lProb (int idx) const [inline]
       get the log-probability of the idx-th subisotopologue, see details in
       PrecalculatedMarginal::get_lProb.

       Definition at line 384 of file marginalTrek++.h.

   const double * IsoSpec::LayeredMarginal::get_lProbs_ptr () const [inline]
       get the pointer to lProbs array. Accessing index -1 is legal and returns a guardian of
       -inf. Warning: The pointer gets invalidated on calls to extend()

       Definition at line 393 of file marginalTrek++.h.

   double IsoSpec::LayeredMarginal::get_mass (int idx) const [inline]
       get the mass of the idx-th subisotopologue, see details in
       PrecalculatedMarginal::get_mass.

       Definition at line 390 of file marginalTrek++.h.

   double IsoSpec::LayeredMarginal::get_max_mass () const
       Get the maximal mass in current layer.

       Definition at line 689 of file marginalTrek++.cpp.

   double IsoSpec::LayeredMarginal::get_min_mass () const
       Get the minimal mass in current layer.

       Definition at line 679 of file marginalTrek++.cpp.

   unsigned int IsoSpec::LayeredMarginal::get_no_confs () const [inline]
       Get the number of precomputed subisotopologues, see details in
       PrecalculatedMarginal::get_no_confs.

       Definition at line 399 of file marginalTrek++.h.

   double IsoSpec::LayeredMarginal::get_prob (int idx) const [inline]
       get the probability of the idx-th subisotopologue, see details in
       PrecalculatedMarginal::get_eProb.

       Definition at line 387 of file marginalTrek++.h.

   double IsoSpec::LayeredMarginal::getModeLProb () const [inline]
       Get the log-probability of the mode subisotopologue.

       Returns
           The log-probability of a/the most probable subisotopologue.

       Definition at line 411 of file marginalTrek++.h.

Author

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