Classes¶

class Allocator
class ConfEqual
class ConfOrder
class ConfOrderMarginal
class ConfOrderMarginalDescending
class DirtyAllocator
class FixedEnvelope
class Iso
The Iso class for the calculation of the isotopic distribution. class IsoGenerator
The generator of isotopologues. class IsoLayeredGenerator
class IsoOrderedGenerator
The generator of isotopologues sorted by their probability of occurrence. class IsoStochasticGenerator
class IsoThresholdGenerator
The generator of isotopologues above a given threshold value. class KeyHasher
class LayeredMarginal
LayeredMarginal class. class Marginal
The marginal distribution class (a subisotopologue). class MarginalTrek
The marginal distribution class (a subisotopologue). class OrderMarginalsBySizeDecresing
class PrecalculatedMarginal
Precalculated Marginal class. struct ProbAndConfPtr
class ReverseOrder
class SSummator
class Summator
class TableOrder
class TSummator

Typedefs¶

typedef double RealType
typedef int64_t IntType
typedef int * Conf

Functions¶

template<typename T > void copyConf (const T *source, T *destination, int dim)
IntType btrd (IntType _t, RealType p, IntType m, std::mt19937 &urng=random_gen)
IntType invert (IntType t, RealType p, std::mt19937 &urng=random_gen)
IntType boost_binomial_distribution_variate (IntType t_arg, RealType p_arg, std::mt19937 &urng=random_gen)
void parse_fasta (const char *fasta, int atomCounts[6])
template<typename T > void reorder_array (T *arr, size_t *order, size_t size, bool can_destroy=false)
void release_g_lfact_table ()
double * alloc_lfact_table ()
double RationalApproximation (double t)
double NormalCDFInverse (double p)
double NormalCDFInverse (double p, double mean, double stdev)
double NormalCDF (double x, double mean, double stdev)
double NormalPDF (double x, double mean, double stdev)
double LowerIncompleteGamma2 (int a, double x)
double InverseLowerIncompleteGamma2 (int a, double x)
std::mt19937 random_gen (random_dev())
std::uniform_real_distribution< double > stdunif (0.0, 1.0)
size_t rdvariate_binom (size_t tries, double succ_prob, std::mt19937 &rgen)
double InverseChiSquareCDF2 (int k, double x)
double rdvariate_beta_1_b (double b, std::mt19937 &rgen=random_gen)
unsigned int parse_formula (const char *formula, std::vector< double > &isotope_masses, std::vector< double > &isotope_probabilities, int **isotopeNumbers, int **atomCounts, unsigned int *confSize, bool use_nominal_masses)
void writeInitialConfiguration (const int atomCnt, const int isotopeNo, const double *lprobs, int *res)
Find one of the most probable subisotopologues. double * getMLogProbs (const double *probs, int isoNo)
double get_loggamma_nominator (int x)
int verify_atom_cnt (int atomCnt)
void * quickselect (void **array, int n, int start, int end)
double combinedSum (const int *conf, const std::vector< double > **valuesContainer, int dimNumber)
double combinedSum (const int *conf, const pod_vector< double > **valuesContainer, int dimNumber)
int * getConf (void *conf)
double getLProb (void *conf)
double unnormalized_logProb (const int *conf, const double *logProbs, int dim)
double calc_mass (const int *conf, const double *masses, int dim)
template<typename T > void printArray (const T *array, int size, const char *prefix='')
template<typename T > void printVector (const std::vector< T > &vec)
template<typename T > void printOffsets (const T **array, int size, const T *offset, const char *prefix='')
template<typename T > void printNestedArray (const T **array, const int *shape, int size)
void * quickselect (const void **array, int n, int start, int end)
Quickly select the n'th positional statistic, including the weights. template<typename T > void dealloc_table (T *tbl, int dim)
template<typename T > void realloc_append (T **array, T what, size_t old_array_size)
template<typename T > size_t * get_order (T *order_array, size_t N)
template<typename T > size_t * get_inverse_order (T *order_array, size_t N)
template<typename TA , typename TB > void impose_order (size_t *O, size_t N, TA *A, TB *B)

Variables¶

const size_t isospec_number_of_isotopic_entries = ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES
const int elem_table_ID [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
const int elem_table_atomicNo [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
const double elem_table_mass [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
const double elem_table_massNo [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
const int elem_table_extraNeutrons [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
const char * elem_table_element [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
const char * elem_table_symbol [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
const bool elem_table_Radioactive [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
const double elem_table_probability [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
const double elem_table_log_probability [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
const int aa_isotope_numbers [6] = {2, 2, 2, 3, 4, 6}
const double aa_elem_masses [19]
const double aa_elem_nominal_masses [19]
const double aa_elem_probabilities [19]
const int aa_symbol_to_elem_counts [256 *6]
double * g_lfact_table = alloc_lfact_table()
const double sqrt_pi = 1.772453850905516027298167483341145182798
std::random_device random_dev
const double pi = 3.14159265358979323846264338328
const double logpi = 1.144729885849400174143427351353058711647294812915311571513623071472137769884826079783623270275489708
std::mt19937 random_gen
std::uniform_real_distribution< double > stdunif

double* IsoSpec::getMLogProbs (const double * probs, int isoNo)¶

Here we order the processor to round the numbers up rather than down. Rounding down could result in the algorithm falling in an infinite loop because of the numerical instability of summing.

Definition at line 122 of file marginalTrek++.cpp.

void IsoSpec::writeInitialConfiguration (const int atomCnt, const int isotopeNo, const double * lprobs, int * res)¶

Find one of the most probable subisotopologues. The algorithm uses the hill-climbing algorithm. It starts from a subisotopologue close to the mean of the underlying multinomial distribution. There might be more than one modes, in case of which this function will return only one of them, close to the mean.

Parameters

Here we perform hill climbing to the mode of the marginal distribution (the subisotopologue distribution). We start from the point close to the mean of the underlying multinomial distribution.

Definition at line 50 of file marginalTrek++.cpp.

const double IsoSpec::aa_elem_masses¶

Initial value:

= {


    elem_table_mass[9], elem_table_mass[10],   


    elem_table_mass[0], elem_table_mass[1],    


    elem_table_mass[11], elem_table_mass[12],  


    elem_table_mass[13], elem_table_mass[14], elem_table_mass[15],  


    elem_table_mass[29], elem_table_mass[30], elem_table_mass[31], elem_table_mass[32],  


    elem_table_mass[85], elem_table_mass[86], elem_table_mass[87], elem_table_mass[88], elem_table_mass[89], elem_table_mass[90]  
}

Definition at line 27 of file fasta.cpp.

const double IsoSpec::aa_elem_nominal_masses¶

Initial value:

= {


    elem_table_massNo[9], elem_table_massNo[10],   


    elem_table_massNo[0], elem_table_massNo[1],    


    elem_table_massNo[11], elem_table_massNo[12],  


    elem_table_massNo[13], elem_table_massNo[14], elem_table_massNo[15],  


    elem_table_massNo[29], elem_table_massNo[30], elem_table_massNo[31], elem_table_massNo[32],  


    elem_table_massNo[85], elem_table_massNo[86], elem_table_massNo[87], elem_table_massNo[88], elem_table_massNo[89], elem_table_massNo[90]  
}

Definition at line 37 of file fasta.cpp.

const double IsoSpec::aa_elem_probabilities¶

Initial value:

= {


    elem_table_probability[9], elem_table_probability[10],   


    elem_table_probability[0], elem_table_probability[1],    


    elem_table_probability[11], elem_table_probability[12],  


    elem_table_probability[13], elem_table_probability[14], elem_table_probability[15],  


    elem_table_probability[29], elem_table_probability[30], elem_table_probability[31], elem_table_probability[32],  


    elem_table_probability[85], elem_table_probability[86], elem_table_probability[87], elem_table_probability[88], elem_table_probability[89], elem_table_probability[90]  
}

Definition at line 47 of file fasta.cpp.