.TH "IsoSpec::IsoGenerator" 3 "Version 2.2.1" "IsoSpec" \" -*- nroff -*- .ad l .nh .SH NAME IsoSpec::IsoGenerator \- The generator of isotopologues\&. .SH SYNOPSIS .br .PP .PP \fC#include \fP .PP Inherits \fBIsoSpec::Iso\fP\&. .PP Inherited by \fBIsoSpec::IsoLayeredGenerator\fP, \fBIsoSpec::IsoOrderedGenerator\fP, \fBIsoSpec::IsoStochasticGenerator\fP, and \fBIsoSpec::IsoThresholdGenerator\fP\&. .SS "Public Member Functions" .in +1c .ti -1c .RI "virtual bool \fBadvanceToNextConfiguration\fP ()=0" .br .RI "Advance to the next, not yet visited, most probable isotopologue\&. " .ti -1c .RI "virtual double \fBlprob\fP () const" .br .RI "Get the log-probability of the current isotopologue\&. " .ti -1c .RI "virtual double \fBmass\fP () const" .br .RI "Get the mass of the current isotopologue\&. " .ti -1c .RI "virtual double \fBprob\fP () const" .br .RI "Get the probability of the current isotopologue\&. " .ti -1c .RI "virtual void \fBget_conf_signature\fP (int *space) const =0" .br .RI "Write the signature of configuration into target memory location\&. It must be large enough to accomodate it\&. " .ti -1c .RI "\fBIsoGenerator\fP (\fBIso\fP &&iso, bool alloc_partials=true)" .br .RI "Move constructor\&. " .ti -1c .RI "virtual \fB~IsoGenerator\fP ()" .br .RI "Destructor\&. " .in -1c Public Member Functions inherited from \fBIsoSpec::Iso\fP .in +1c .ti -1c .RI "\fBIso\fP (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *_isotopeMasses, const double *_isotopeProbabilities)" .br .RI "General constructror\&. " .ti -1c .RI "\fBIso\fP (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)" .br .ti -1c .RI "\fBIso\fP (const char *formula, bool use_nominal_masses=false)" .br .RI "Constructor from the formula object\&. " .ti -1c .RI "\fBIso\fP (const std::string &formula, bool use_nominal_masses=false)" .br .RI "Constructor from C++ std::string chemical formula\&. " .ti -1c .RI "\fBIso\fP (\fBIso\fP &&other)" .br .RI "The move constructor\&. " .ti -1c .RI "\fBIso\fP & \fBoperator=\fP (const \fBIso\fP &other)=delete" .br .ti -1c .RI "\fBIso\fP (const \fBIso\fP &other, bool fullcopy)" .br .RI "The copy constructor\&. " .ti -1c .RI "virtual \fB~Iso\fP ()" .br .RI "Destructor\&. " .ti -1c .RI "double \fBgetLightestPeakMass\fP () const" .br .RI "Get the mass of the lightest peak in the isotopic distribution\&. " .ti -1c .RI "double \fBgetHeaviestPeakMass\fP () const" .br .RI "Get the mass of the heaviest peak in the isotopic distribution\&. " .ti -1c .RI "double \fBgetMonoisotopicPeakMass\fP () const" .br .ti -1c .RI "double \fBgetModeLProb\fP () const" .br .RI "Get the log-probability of the mode-configuration (if there are many modes, they share this value)\&. " .ti -1c .RI "double \fBgetUnlikeliestPeakLProb\fP () const" .br .RI "Get the logprobability of the least probable subisotopologue\&. " .ti -1c .RI "double \fBgetModeMass\fP () const" .br .RI "Get the mass of the mode-configuration (if there are many modes, it is undefined which one will be selected)\&. " .ti -1c .RI "double \fBgetTheoreticalAverageMass\fP () const" .br .RI "Get the theoretical average mass of the molecule\&. " .ti -1c .RI "double \fBvariance\fP () const" .br .RI "Get the theoretical variance of the distribution\&. " .ti -1c .RI "double \fBstddev\fP () const" .br .RI "Get the standard deviation of the theoretical distribution\&. " .ti -1c .RI "int \fBgetDimNumber\fP () const" .br .RI "Get the number of elements in the chemical formula of the molecule\&. " .ti -1c .RI "int \fBgetAllDim\fP () const" .br .RI "Get the total number of isotopes of elements present in a chemical formula\&. " .ti -1c .RI "void \fBaddElement\fP (int atomCount, int noIsotopes, const double *isotopeMasses, const double *isotopeProbabilities)" .br .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\&. " .ti -1c .RI "void \fBsaveMarginalLogSizeEstimates\fP (double *priorities, double target_total_prob) const" .br .RI "Save estimates of logarithms of target sizes of marginals using Gaussian approximation into argument array\&. Array priorities must have length equal to dimNumber\&. " .in -1c .SS "Public Attributes" .in +1c .ti -1c .RI "const double \fBmode_lprob\fP" .br .in -1c .SS "Protected Attributes" .in +1c .ti -1c .RI "double * \fBpartialLProbs\fP" .br .ti -1c .RI "double * \fBpartialMasses\fP" .br .ti -1c .RI "double * \fBpartialProbs\fP" .br .in -1c Protected Attributes inherited from \fBIsoSpec::Iso\fP .in +1c .ti -1c .RI "int \fBdimNumber\fP" .br .ti -1c .RI "int * \fBisotopeNumbers\fP" .br .ti -1c .RI "int * \fBatomCounts\fP" .br .ti -1c .RI "unsigned int \fBconfSize\fP" .br .ti -1c .RI "int \fBallDim\fP" .br .ti -1c .RI "\fBMarginal\fP ** \fBmarginals\fP" .br .in -1c .SS "Additional Inherited Members" Static Public Member Functions inherited from \fBIsoSpec::Iso\fP .in +1c .ti -1c .RI "static \fBIso\fP \fBFromFASTA\fP (const char *fasta, bool use_nominal_masses=false, bool add_water=true)" .br .RI "Constructor (named) from aminoacid FASTA sequence as C string\&. " .ti -1c .RI "static \fBIso\fP \fBFromFASTA\fP (const std::string &fasta, bool use_nominal_masses=false, bool add_water=true)" .br .RI "Constructor (named) from aminoacid FASTA sequence as C++ std::string\&. See above for details\&. " .in -1c Protected Member Functions inherited from \fBIsoSpec::Iso\fP .in +1c .ti -1c .RI "bool \fBdoMarginalsNeedSorting\fP () const" .br .in -1c .SH "Detailed Description" .PP The generator of isotopologues\&. This class provides the common interface for all isotopic generators\&. .PP Definition at line \fB183\fP of file \fBisoSpec++\&.h\fP\&. .SH "Constructor & Destructor Documentation" .PP .SS "IsoSpec::IsoGenerator::IsoGenerator (\fBIso\fP && iso, bool alloc_partials = \fCtrue\fP)" .PP Move constructor\&. .PP Definition at line \fB442\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "IsoSpec::IsoGenerator::~IsoGenerator ()\fC [virtual]\fP" .PP Destructor\&. .PP Definition at line \fB460\fP of file \fBisoSpec++\&.cpp\fP\&. .SH "Member Function Documentation" .PP .SS "virtual bool IsoSpec::IsoGenerator::advanceToNextConfiguration ()\fC [pure 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 Implemented in \fBIsoSpec::IsoOrderedGenerator\fP, \fBIsoSpec::IsoThresholdGenerator\fP, \fBIsoSpec::IsoLayeredGenerator\fP, and \fBIsoSpec::IsoStochasticGenerator\fP\&. .SS "virtual void IsoSpec::IsoGenerator::get_conf_signature (int * space) const\fC [pure virtual]\fP" .PP Write the signature of configuration into target memory location\&. It must be large enough to accomodate it\&. .PP Implemented in \fBIsoSpec::IsoOrderedGenerator\fP, \fBIsoSpec::IsoThresholdGenerator\fP, \fBIsoSpec::IsoLayeredGenerator\fP, and \fBIsoSpec::IsoStochasticGenerator\fP\&. .SS "virtual double IsoSpec::IsoGenerator::lprob () const\fC [inline]\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 in \fBIsoSpec::IsoThresholdGenerator\fP, \fBIsoSpec::IsoLayeredGenerator\fP, and \fBIsoSpec::IsoStochasticGenerator\fP\&. .PP Definition at line \fB204\fP of file \fBisoSpec++\&.h\fP\&. .SS "virtual double IsoSpec::IsoGenerator::mass () const\fC [inline]\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 in \fBIsoSpec::IsoThresholdGenerator\fP, \fBIsoSpec::IsoLayeredGenerator\fP, and \fBIsoSpec::IsoStochasticGenerator\fP\&. .PP Definition at line \fB210\fP of file \fBisoSpec++\&.h\fP\&. .SS "virtual double IsoSpec::IsoGenerator::prob () const\fC [inline]\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 in \fBIsoSpec::IsoThresholdGenerator\fP, \fBIsoSpec::IsoLayeredGenerator\fP, and \fBIsoSpec::IsoStochasticGenerator\fP\&. .PP Definition at line \fB216\fP of file \fBisoSpec++\&.h\fP\&. .SH "Member Data Documentation" .PP .SS "const double IsoSpec::IsoGenerator::mode_lprob" .PP Definition at line \fB186\fP of file \fBisoSpec++\&.h\fP\&. .SS "double* IsoSpec::IsoGenerator::partialLProbs\fC [protected]\fP" The prefix sum of the log-probabilities of the current isotopologue\&. .PP Definition at line \fB189\fP of file \fBisoSpec++\&.h\fP\&. .SS "double* IsoSpec::IsoGenerator::partialMasses\fC [protected]\fP" The prefix sum of the masses of the current isotopologue\&. .PP Definition at line \fB190\fP of file \fBisoSpec++\&.h\fP\&. .SS "double* IsoSpec::IsoGenerator::partialProbs\fC [protected]\fP" The prefix product of the probabilities of the current isotopologue\&. .PP Definition at line \fB191\fP of file \fBisoSpec++\&.h\fP\&. .SH "Author" .PP Generated automatically by Doxygen for IsoSpec from the source code\&.