Public Member Functions¶

IsoLayeredGeneratorTemplate (const IsoLayeredGeneratorTemplate &other)=delete
IsoLayeredGeneratorTemplate & operator= (const IsoLayeredGeneratorTemplate &other)=delete
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. double get_currentLThreshold () const
IsoLayeredGeneratorTemplate (Iso &&iso, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true, double t_prob_hint=0.99)
ISOSPEC_FORCE_INLINE bool advanceToNextConfiguration () override final
Advance to the next, not yet visited, most probable isotopologue. ISOSPEC_FORCE_INLINE bool advanceToNextConfigurationWithinLayer ()
ISOSPEC_FORCE_INLINE double lprob () const override final
Get the log-probability of the current isotopologue. 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. void terminate_search ()
Block the subsequent search of isotopologues. ISOSPEC_FORCE_INLINE void recalc (int idx)
Recalculate the current partial log-probabilities, masses, and probabilities. bool nextLayer (double offset)
void get_conf_by_indexes (int *space) const

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

template<typename MarginalType>¶

class IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >"

Definition at line 460 of file isoSpec++.h.

template<typename MarginalType > IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::IsoLayeredGeneratorTemplate (Iso && iso, int _tabSize = 1000, int _hashSize = 1000, bool reorder_marginals = true, double t_prob_hint = 0.99)¶

Definition at line 654 of file isoSpec++.cpp.

template<typename MarginalType > IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::~IsoLayeredGeneratorTemplate ()¶

Definition at line 799 of file isoSpec++.cpp.

template<typename MarginalType > ISOSPEC_FORCE_INLINE bool IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::advanceToNextConfiguration () [inline], [final], [override], [virtual]¶

Advance to the next, not yet visited, most probable isotopologue.

Returns

Implements IsoSpec::IsoGenerator.

Definition at line 510 of file isoSpec++.h.

template<typename MarginalType > ISOSPEC_FORCE_INLINE bool IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::advanceToNextConfigurationWithinLayer () [inline]¶

Definition at line 520 of file isoSpec++.h.

template<typename MarginalType > void IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::get_conf_by_indexes (int * space) const [inline]¶

Definition at line 557 of file isoSpec++.h.

template<typename MarginalType > void IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::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 482 of file isoSpec++.h.

template<typename MarginalType > double IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::get_currentLThreshold () const [inline]¶

Definition at line 504 of file isoSpec++.h.

template<typename MarginalType > ISOSPEC_FORCE_INLINE double IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::lprob () const [inline], [final], [override], [virtual]¶

Get the log-probability of the current isotopologue.

Returns

Reimplemented from IsoSpec::IsoGenerator.

Definition at line 532 of file isoSpec++.h.

template<typename MarginalType > ISOSPEC_FORCE_INLINE double IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::mass () const [inline], [final], [override], [virtual]¶

Get the mass of the current isotopologue.

Returns

Reimplemented from IsoSpec::IsoGenerator.

Definition at line 533 of file isoSpec++.h.

template<typename MarginalType > bool IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::nextLayer (double offset)¶

Definition at line 722 of file isoSpec++.cpp.

template<typename MarginalType > ISOSPEC_FORCE_INLINE double IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::prob () const [inline], [final], [override], [virtual]¶

Get the probability of the current isotopologue.

Returns

Reimplemented from IsoSpec::IsoGenerator.

Definition at line 534 of file isoSpec++.h.

template<typename MarginalType > ISOSPEC_FORCE_INLINE void IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::recalc (int idx) [inline]¶

Recalculate the current partial log-probabilities, masses, and probabilities.

Definition at line 541 of file isoSpec++.h.

template<typename MarginalType > void IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >::terminate_search ()¶

Block the subsequent search of isotopologues.

Definition at line 787 of file isoSpec++.cpp.