.TH "IsoSpec::IsoStochasticGenerator" 3 "Version 2.2.1" "IsoSpec" \" -*- nroff -*-
.ad l
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.SH NAME
IsoSpec::IsoStochasticGenerator
.SH SYNOPSIS
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.PP
.PP
Inherits \fBIsoSpec::IsoGenerator\fP\&.
.SS "Public Member Functions"

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.RI "\fBIsoStochasticGenerator\fP (\fBIso\fP &&iso, size_t no_molecules, double precision=0\&.9999, double beta_bias=5\&.0)"
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.RI "ISOSPEC_FORCE_INLINE size_t \fBcount\fP () const"
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.RI "ISOSPEC_FORCE_INLINE double \fBmass\fP () const override final"
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.RI "Get the mass of the current isotopologue\&. "
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.RI "ISOSPEC_FORCE_INLINE double \fBprob\fP () const override final"
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.RI "Get the probability of the current isotopologue\&. "
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.RI "ISOSPEC_FORCE_INLINE double \fBlprob\fP () const override final"
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.RI "Get the log-probability of the current isotopologue\&. "
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.RI "ISOSPEC_FORCE_INLINE void \fBget_conf_signature\fP (int *space) const override final"
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.RI "Write the signature of configuration into target memory location\&. It must be large enough to accomodate it\&. "
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.RI "ISOSPEC_FORCE_INLINE bool \fBadvanceToNextConfiguration\fP () override final"
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.RI "Advance to the next, not yet visited, most probable isotopologue\&. "
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Public Member Functions inherited from \fBIsoSpec::IsoGenerator\fP
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.RI "\fBIsoGenerator\fP (\fBIso\fP &&iso, bool alloc_partials=true)"
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.RI "Move constructor\&. "
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.RI "virtual \fB~IsoGenerator\fP ()"
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.RI "Destructor\&. "
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Public Member Functions inherited from \fBIsoSpec::Iso\fP
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.RI "\fBIso\fP (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *_isotopeMasses, const double *_isotopeProbabilities)"
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.RI "General constructror\&. "
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.RI "\fBIso\fP (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)"
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.RI "\fBIso\fP (const char *formula, bool use_nominal_masses=false)"
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.RI "Constructor from the formula object\&. "
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.RI "\fBIso\fP (const std::string &formula, bool use_nominal_masses=false)"
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.RI "Constructor from C++ std::string chemical formula\&. "
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.RI "\fBIso\fP (\fBIso\fP &&other)"
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.RI "The move constructor\&. "
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.RI "\fBIso\fP & \fBoperator=\fP (const \fBIso\fP &other)=delete"
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.RI "\fBIso\fP (const \fBIso\fP &other, bool fullcopy)"
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.RI "The copy constructor\&. "
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.RI "virtual \fB~Iso\fP ()"
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.RI "Destructor\&. "
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.RI "double \fBgetLightestPeakMass\fP () const"
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.RI "Get the mass of the lightest peak in the isotopic distribution\&. "
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.RI "double \fBgetHeaviestPeakMass\fP () const"
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.RI "Get the mass of the heaviest peak in the isotopic distribution\&. "
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.RI "double \fBgetMonoisotopicPeakMass\fP () const"
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.RI "double \fBgetModeLProb\fP () const"
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.RI "Get the log-probability of the mode-configuration (if there are many modes, they share this value)\&. "
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.RI "double \fBgetUnlikeliestPeakLProb\fP () const"
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.RI "Get the logprobability of the least probable subisotopologue\&. "
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.RI "double \fBgetModeMass\fP () const"
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.RI "Get the mass of the mode-configuration (if there are many modes, it is undefined which one will be selected)\&. "
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.RI "double \fBgetTheoreticalAverageMass\fP () const"
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.RI "Get the theoretical average mass of the molecule\&. "
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.RI "double \fBvariance\fP () const"
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.RI "Get the theoretical variance of the distribution\&. "
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.RI "double \fBstddev\fP () const"
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.RI "Get the standard deviation of the theoretical distribution\&. "
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.RI "int \fBgetDimNumber\fP () const"
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.RI "Get the number of elements in the chemical formula of the molecule\&. "
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.RI "int \fBgetAllDim\fP () const"
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.RI "Get the total number of isotopes of elements present in a chemical formula\&. "
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.RI "void \fBaddElement\fP (int atomCount, int noIsotopes, const double *isotopeMasses, const double *isotopeProbabilities)"
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.RI "Add an element to the molecule\&. Note: this method can only be used BEFORE \fBIso\fP is used to construct an \fBIsoGenerator\fP instance\&. "
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.RI "void \fBsaveMarginalLogSizeEstimates\fP (double *priorities, double target_total_prob) const"
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.RI "Save estimates of logarithms of target sizes of marginals using Gaussian approximation into argument array\&. Array priorities must have length equal to dimNumber\&. "
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.SS "Additional Inherited Members"


Static Public Member Functions inherited from \fBIsoSpec::Iso\fP
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.RI "static \fBIso\fP \fBFromFASTA\fP (const char *fasta, bool use_nominal_masses=false, bool add_water=true)"
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.RI "Constructor (named) from aminoacid FASTA sequence as C string\&. "
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.RI "static \fBIso\fP \fBFromFASTA\fP (const std::string &fasta, bool use_nominal_masses=false, bool add_water=true)"
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.RI "Constructor (named) from aminoacid FASTA sequence as C++ std::string\&. See above for details\&. "
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Public Attributes inherited from \fBIsoSpec::IsoGenerator\fP
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.RI "const double \fBmode_lprob\fP"
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Protected Member Functions inherited from \fBIsoSpec::Iso\fP
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.RI "bool \fBdoMarginalsNeedSorting\fP () const"
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Protected Attributes inherited from \fBIsoSpec::IsoGenerator\fP
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.RI "double * \fBpartialLProbs\fP"
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.RI "double * \fBpartialMasses\fP"
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.RI "double * \fBpartialProbs\fP"
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Protected Attributes inherited from \fBIsoSpec::Iso\fP
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.RI "int \fBdimNumber\fP"
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.RI "int * \fBisotopeNumbers\fP"
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.RI "int * \fBatomCounts\fP"
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.RI "unsigned int \fBconfSize\fP"
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.RI "int \fBallDim\fP"
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.RI "\fBMarginal\fP ** \fBmarginals\fP"
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.SH "Detailed Description"
.PP 
Definition at line \fB542\fP of file \fBisoSpec++\&.h\fP\&.
.SH "Constructor & Destructor Documentation"
.PP 
.SS "IsoSpec::IsoStochasticGenerator::IsoStochasticGenerator (\fBIso\fP && iso, size_t no_molecules, double precision = \fC0\&.9999\fP, double beta_bias = \fC5\&.0\fP)"

.PP
Definition at line \fB923\fP of file \fBisoSpec++\&.cpp\fP\&.
.SH "Member Function Documentation"
.PP 
.SS "ISOSPEC_FORCE_INLINE bool IsoSpec::IsoStochasticGenerator::advanceToNextConfiguration ()\fC [inline]\fP, \fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP"

.PP
Advance to the next, not yet visited, most probable isotopologue\&. 
.PP
\fBReturns\fP
.RS 4
Return false if it is not possible to advance\&. 
.RE
.PP

.PP
Implements \fBIsoSpec::IsoGenerator\fP\&.
.PP
Definition at line \fB565\fP of file \fBisoSpec++\&.h\fP\&.
.SS "ISOSPEC_FORCE_INLINE size_t IsoSpec::IsoStochasticGenerator::count () const\fC [inline]\fP"

.PP
Definition at line \fB555\fP of file \fBisoSpec++\&.h\fP\&.
.SS "ISOSPEC_FORCE_INLINE void IsoSpec::IsoStochasticGenerator::get_conf_signature (int * space) const\fC [inline]\fP, \fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP"

.PP
Write the signature of configuration into target memory location\&. It must be large enough to accomodate it\&. 
.PP
Implements \fBIsoSpec::IsoGenerator\fP\&.
.PP
Definition at line \fB563\fP of file \fBisoSpec++\&.h\fP\&.
.SS "ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::lprob () const\fC [inline]\fP, \fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP"

.PP
Get the log-probability of the current isotopologue\&. 
.PP
\fBReturns\fP
.RS 4
The log-probability of the current isotopologue\&. 
.RE
.PP

.PP
Reimplemented from \fBIsoSpec::IsoGenerator\fP\&.
.PP
Definition at line \fB561\fP of file \fBisoSpec++\&.h\fP\&.
.SS "ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::mass () const\fC [inline]\fP, \fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP"

.PP
Get the mass of the current isotopologue\&. 
.PP
\fBReturns\fP
.RS 4
The mass of the current isotopologue\&. 
.RE
.PP

.PP
Reimplemented from \fBIsoSpec::IsoGenerator\fP\&.
.PP
Definition at line \fB557\fP of file \fBisoSpec++\&.h\fP\&.
.SS "ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::prob () const\fC [inline]\fP, \fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP"

.PP
Get the probability of the current isotopologue\&. 
.PP
\fBReturns\fP
.RS 4
The probability of the current isotopologue\&. 
.RE
.PP

.PP
Reimplemented from \fBIsoSpec::IsoGenerator\fP\&.
.PP
Definition at line \fB559\fP of file \fBisoSpec++\&.h\fP\&.

.SH "Author"
.PP 
Generated automatically by Doxygen for IsoSpec from the source code\&.