Provided by: libisospec++-dev_2.2.1-4.1build1_amd64 
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
Generated automatically by Doxygen for IsoSpec from the source code.
IsoSpec Version 2.2.1 IsoSpec::IsoOrderedGenerator(3)