Man page - isospec_isostochasticgenerator(3)
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apt-get install libisospec++-dev
Manual
IsoSpec::IsoStochasticGenerator
NAMESYNOPSIS
Public Member Functions
Additional Inherited Members
Detailed Description
Constructor & Destructor Documentation
IsoSpec::IsoStochasticGenerator::IsoStochasticGenerator (Iso && iso, size_tno_molecules, double precision = 0.9999, double beta_bias = 5.0)
Member Function Documentation
ISOSPEC_FORCE_INLINE boolIsoSpec::IsoStochasticGenerator::advanceToNextConfiguration ()[inline], [final], [override], [virtual]
ISOSPEC_FORCE_INLINE size_t IsoSpec::IsoStochasticGenerator::count () const[inline]
ISOSPEC_FORCE_INLINE voidIsoSpec::IsoStochasticGenerator::get_conf_signature (int * space) const[inline], [final], [override], [virtual]
ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::lprob () const[inline], [final], [override], [virtual]
ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::mass () const[inline], [final], [override], [virtual]
ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::prob () const[inline], [final], [override], [virtual]
Author
NAME
IsoSpec::IsoStochasticGenerator
SYNOPSIS
Inherits IsoSpec::IsoGenerator .
Public Member Functions
IsoStochasticGenerator
(
Iso
&&iso, size_t no_molecules, double
precision=0.9999, double beta_bias=5.0)
ISOSPEC_FORCE_INLINE size_t
count
() const
ISOSPEC_FORCE_INLINE double
mass
() const override
final
Get the mass of the current isotopologue.
ISOSPEC_FORCE_INLINE double
prob
() const override
final
Get the probability of the current isotopologue.
ISOSPEC_FORCE_INLINE double
lprob
() const override
final
Get the log-probability of the current isotopologue.
ISOSPEC_FORCE_INLINE void
get_conf_signature
(int
*space) const override final
Write the signature of configuration into target memory
location. It must be large enough to accomodate it.
ISOSPEC_FORCE_INLINE bool
advanceToNextConfiguration
() override final
Advance to the next, not yet visited, most probable
isotopologue.
Public Member Functions inherited from IsoSpec::IsoGenerator
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
Definition at line 542 of file isoSpec++.h .
Constructor & Destructor Documentation
IsoSpec::IsoStochasticGenerator::IsoStochasticGenerator (Iso && iso, size_tno_molecules, double precision = 0.9999, double beta_bias = 5.0)
Definition at line 923 of file isoSpec++.cpp .
Member Function Documentation
ISOSPEC_FORCE_INLINE boolIsoSpec::IsoStochasticGenerator::advanceToNextConfiguration ()[inline], [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 565 of file isoSpec++.h .
ISOSPEC_FORCE_INLINE size_t IsoSpec::IsoStochasticGenerator::count () const[inline]
Definition at line 555 of file isoSpec++.h .
ISOSPEC_FORCE_INLINE voidIsoSpec::IsoStochasticGenerator::get_conf_signature (int * space) const[inline], [final], [override], [virtual]
Write the signature of configuration into target memory location. It must be large enough to accomodate it.
Implements IsoSpec::IsoGenerator .
Definition at line 563 of file isoSpec++.h .
ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::lprob () const[inline], [final], [override], [virtual]
Get the log-probability of the current isotopologue.
Returns
The log-probability of the current isotopologue.
Reimplemented from IsoSpec::IsoGenerator .
Definition at line 561 of file isoSpec++.h .
ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::mass () const[inline], [final], [override], [virtual]
Get the mass of the current isotopologue.
Returns
The mass of the current isotopologue.
Reimplemented from IsoSpec::IsoGenerator .
Definition at line 557 of file isoSpec++.h .
ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::prob () const[inline], [final], [override], [virtual]
Get the probability of the current isotopologue.
Returns
The probability of the current isotopologue.
Reimplemented from IsoSpec::IsoGenerator .
Definition at line 559 of file isoSpec++.h .
Author
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