Man page - isospec_isoorderedgenerator(3)
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Manual
IsoSpec::IsoOrderedGenerator
NAMESYNOPSIS
Public Member Functions
Additional Inherited Members
Detailed Description
Constructor & Destructor Documentation
IsoSpec::IsoOrderedGenerator::IsoOrderedGenerator (Iso && iso, int _tabSize= 1000, int _hashSize = 1000)
IsoSpec::IsoOrderedGenerator::˜IsoOrderedGenerator () [virtual]
Member Function Documentation
bool IsoSpec::IsoOrderedGenerator::advanceToNextConfiguration () [final],[override], [virtual]
void IsoSpec::IsoOrderedGenerator::get_conf_signature (int * space) const[inline], [final], [override], [virtual]
Author
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
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