IsoSpec::PrecalculatedMarginal - Precalculated Marginal class.

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IsoSpec                                           Version 2.2.1                IsoSpec::PrecalculatedMarginal(3)

Constructor & Destructor Documentation

IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal(Marginal&&m,doublelCutOff,boolsort=true,inttabSize=1000,inthashSize=1000)
       The move constructor (disowns the Marginal). This constructor memoizes all subisotopologues with log-
       probability above the provided threshold lCutOff

       ParametersMarginalAninstanceoftheMarginalclassthisclassisabouttodisown.lCutOffThelowerlimitonthelog-probabilityoftheprecomputedsubisotopologues.sortShouldthesubisotopologuesbestoredwithdescendingprobability?Returns
           An instance of the PrecalculatedMarginal class.

       Definition at line 443 of file marginalTrek++.cpp.

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

       Definition at line 542 of file marginalTrek++.cpp.

Detailed Description

       Precalculated Marginal class.

       This class serves to calculate a set of isotopologues that is defined by the minimal probability
       threshold.

       This works faster than if you did not know the threshold. If you have no idea about the threshold, you
       would need to call us, to change encode the layered version of the marginal.

       Definition at line 251 of file marginalTrek++.h.

Member Data Documentation

Allocator<int>IsoSpec::PrecalculatedMarginal::allocator[protected]
       Definition at line 260 of file marginalTrek++.h.

   pod_vector<Conf>IsoSpec::PrecalculatedMarginal::configurations[protected]
       Definition at line 254 of file marginalTrek++.h.

   Conf*IsoSpec::PrecalculatedMarginal::confs[protected]
       Definition at line 255 of file marginalTrek++.h.

   pod_vector<double>IsoSpec::PrecalculatedMarginal::lProbs[protected]
       Definition at line 258 of file marginalTrek++.h.

   double*IsoSpec::PrecalculatedMarginal::masses[protected]
       Definition at line 257 of file marginalTrek++.h.

   unsignedintIsoSpec::PrecalculatedMarginal::no_confs[protected]
       Definition at line 256 of file marginalTrek++.h.

   double*IsoSpec::PrecalculatedMarginal::probs[protected]
       Definition at line 259 of file marginalTrek++.h.

Member Function Documentation

constConf&IsoSpec::PrecalculatedMarginal::get_conf(intidx)const[inline]
Get the counts of isotopes that define the subisotopologue.

Parametersidx The number of the considered subisotopologue.

Returns
The counts of isotopes that define the subisotopologue.

Definition at line 329 of file marginalTrek++.h.

constdouble&IsoSpec::PrecalculatedMarginal::get_lProb(intidx)const[inline]
Get the log-probability of the idx-th subisotopologue.

Parametersidx The number of the considered subisotopologue.

Returns
The log-probability of the idx-th subisotopologue.

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

constdouble*IsoSpec::PrecalculatedMarginal::get_lProbs_ptr()const[inline]
Get the table of the log-probabilities of subisotopologues.

Returns
Pointer to the first element in the table storing log-probabilities of subisotopologues.

Definition at line 315 of file marginalTrek++.h.

constdouble&IsoSpec::PrecalculatedMarginal::get_mass(intidx)const[inline]
Get the mass of the idx-th subisotopologue.

Parametersidx The number of the considered subisotopologue.

Returns
The mass of the idx-th subisotopologue.

Definition at line 309 of file marginalTrek++.h.

constdouble*IsoSpec::PrecalculatedMarginal::get_masses_ptr()const[inline]
Get the table of the masses of subisotopologues.

Returns
Pointer to the first element in the table storing masses of subisotopologues.

Definition at line 321 of file marginalTrek++.h.

unsignedintIsoSpec::PrecalculatedMarginal::get_no_confs()const[inline]
Get the number of precomputed subisotopologues.

Returns
The number of precomputed subisotopologues.

Definition at line 335 of file marginalTrek++.h.

constdouble&IsoSpec::PrecalculatedMarginal::get_prob(intidx)const[inline]
Get the probability of the idx-th subisotopologue.

Parametersidx The number of the considered subisotopologue.

Returns
The probability of the idx-th subisotopologue.

Definition at line 302 of file marginalTrek++.h.

doubleIsoSpec::PrecalculatedMarginal::getModeLProb()const[inline]
Get the log-probability of the mode subisotopologue.

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

Definition at line 341 of file marginalTrek++.h.

boolIsoSpec::PrecalculatedMarginal::inRange(unsignedintidx)const[inline]
Is there a subisotopologue with a given number?

Returns
Returns true if idx does not exceed the number of pre-computed configurations.

Definition at line 288 of file marginalTrek++.h.

Name

       IsoSpec::PrecalculatedMarginal - Precalculated Marginal class.

Synopsis

       #include <marginalTrek++.h>

       Inherits IsoSpec::Marginal.

   PublicMemberFunctionsPrecalculatedMarginal (Marginal &&m, double lCutOff, bool sort=true, int tabSize=1000, int hashSize=1000)
           The move constructor (disowns the Marginal).
       PrecalculatedMarginal (const PrecalculatedMarginal &other)=delete
       PrecalculatedMarginal & operator= (const PrecalculatedMarginal &other)=delete
       virtual ~PrecalculatedMarginal ()
           Destructor.
       bool inRange (unsigned int idx) const
           Is there a subisotopologue with a given number?
       const double & get_lProb (int idx) const
           Get the log-probability of the idx-th subisotopologue.
       const double & get_prob (int idx) const
           Get the probability of the idx-th subisotopologue.
       const double & get_mass (int idx) const
           Get the mass of the idx-th subisotopologue.
       const double * get_lProbs_ptr () const
           Get the table of the log-probabilities of subisotopologues.
       const double * get_masses_ptr () const
           Get the table of the masses of subisotopologues.
       const Conf & get_conf (int idx) const
           Get the counts of isotopes that define the subisotopologue.
       unsigned int get_no_confs () const
           Get the number of precomputed subisotopologues.
       double getModeLProb () const
           Get the log-probability of the mode subisotopologue.

       Public Member Functions inherited from IsoSpec::MarginalMarginal (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 ()

   ProtectedAttributespod_vector< Conf > configurations
       Conf * confs
       unsigned int no_confs
       double * massespod_vector< double > lProbs
       double * probsAllocator< int > allocator

       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_lprobAdditionalInheritedMembers
       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

IsoSpec::PrecalculatedMarginal - Precalculated Marginal class.

Contents

Author

Constructor & Destructor Documentation

Detailed Description

Member Data Documentation

Member Function Documentation

Name

Synopsis

See Also