IsoSpec::FixedEnvelope

NAME

IsoSpec::FixedEnvelope

SYNOPSIS

Public Member Functions

FixedEnvelope (const FixedEnvelope &other)
FixedEnvelope (FixedEnvelope &&other)
FixedEnvelope (double *masses, double *probs, size_t confs_no, bool masses_sorted=false, bool probs_sorted=false, double _total_prob=NAN)
FixedEnvelope operator+ (const FixedEnvelope &other) const
FixedEnvelope operator* (const FixedEnvelope &other) const
size_t confs_no () const
int getAllDim () const
const double * masses () const
const double * probs () const
const int * confs () const
double * release_masses ()
double * release_probs ()
int * release_confs ()
void release_everything ()
double mass (size_t i) const
double prob (size_t i) const
const int * conf (size_t i) const
void sort_by_mass ()
void sort_by_prob ()
double get_total_prob ()
void scale (double factor)
void normalize ()
void shift_mass (double shift)
void resample (size_t ionic_current, double beta_bias=1.0)
double empiric_average_mass ()
double empiric_variance ()
double empiric_stddev ()
double WassersteinDistance (FixedEnvelope &other)
double OrientedWassersteinDistance (FixedEnvelope &other)
double AbyssalWassersteinDistance (FixedEnvelope &other, double abyss_depth, double other_scale=1.0)
std::tuple< double, double, double > WassersteinMatch (FixedEnvelope &other, double flow_distance, double other_scale=1.0)
FixedEnvelope bin (double bin_width=1.0, double middle=0.0)
template<bool tgetConfs> void threshold_init (Iso &&iso, double threshold, bool absolute)
template<bool tgetConfs, typename GenType = IsoLayeredGenerator> void addConfILG (const GenType &generator)
template<bool tgetConfs> void total_prob_init (Iso &&iso, double target_prob, bool trim)
template<bool tgetConfs> void stochastic_init (Iso &&iso, size_t _no_molecules, double _precision, double _beta_bias)

Static Public Member Functions

static FixedEnvelope LinearCombination (const std::vector< const FixedEnvelope * > &spectra, const std::vector< double > &intensities)
static FixedEnvelope LinearCombination (const FixedEnvelope *const *spectra, const double *intensities, size_t size)
static FixedEnvelope FromThreshold (Iso &&iso, double threshold, bool absolute, bool tgetConfs=false)
static FixedEnvelope FromThreshold (const Iso &iso, double _threshold, bool _absolute, bool tgetConfs=false)
static FixedEnvelope FromTotalProb (Iso &&iso, double target_total_prob, bool optimize, bool tgetConfs=false)
static FixedEnvelope FromTotalProb (const Iso &iso, double _target_total_prob, bool _optimize, bool tgetConfs=false)
static FixedEnvelope FromStochastic (Iso &&iso, size_t _no_molecules, double _precision=0.9999, double _beta_bias=5.0, bool tgetConfs=false)
static FixedEnvelope FromStochastic (const Iso &iso, size_t _no_molecules, double _precision=0.9999, double _beta_bias=5.0, bool tgetConfs=false)
static FixedEnvelope Binned (Iso &&iso, double target_total_prob, double bin_width, double bin_middle=0.0)
static FixedEnvelope Binned (const Iso &iso, double target_total_prob, double bin_width, double bin_middle=0.0)

Protected Member Functions

template<typename T , bool tgetConfs> ISOSPEC_FORCE_INLINE void store_conf (const T &generator)
ISOSPEC_FORCE_INLINE void store_conf (double _mass, double _prob)
template<bool tgetConfs> ISOSPEC_FORCE_INLINE void swap (size_t idx1, size_t idx2, ISOSPEC_MAYBE_UNUSED int *conf_swapspace)
template<bool tgetConfs> void reallocate_memory (size_t new_size)
void slow_reallocate_memory (size_t new_size)

Protected Attributes

double * _masses
double * _probs
int * _confs
size_t _confs_no
int allDim
bool sorted_by_mass
bool sorted_by_prob
double total_prob
size_t current_size
double * tmasses
double * tprobs
int * tconfs
int allDimSizeofInt

Friends

double AbyssalWassersteinDistanceGrad (FixedEnvelope *const *envelopes, const double *scales, double *ret_gradient, size_t N, double abyss_depth_exp, double abyss_depth_the)

Detailed Description

Definition at line 40 of file fixedEnvelopes.h.

Constructor & Destructor Documentation

ISOSPEC_FORCE_INLINE IsoSpec::FixedEnvelope::FixedEnvelope () [inline]

Definition at line 57 of file fixedEnvelopes.h.

IsoSpec::FixedEnvelope::FixedEnvelope (const FixedEnvelope & other)

Definition at line 24 of file fixedEnvelopes.cpp.

IsoSpec::FixedEnvelope::FixedEnvelope (FixedEnvelope && other)

Definition at line 35 of file fixedEnvelopes.cpp.

IsoSpec::FixedEnvelope::FixedEnvelope (double * masses, double * probs,size_t confs_no, bool masses_sorted = false, bool probs_sorted = false,double _total_prob = NAN)

Definition at line 52 of file fixedEnvelopes.cpp.

virtual IsoSpec::FixedEnvelope::˜FixedEnvelope () [inline], [virtual]

Definition at line 75 of file fixedEnvelopes.h.

Member Function Documentation

double IsoSpec::FixedEnvelope::AbyssalWassersteinDistance (FixedEnvelope &other, double abyss_depth, double other_scale = 1.0)

Definition at line 414 of file fixedEnvelopes.cpp.

template<bool tgetConfs, typename GenType = IsoLayeredGenerator> voidIsoSpec::FixedEnvelope::addConfILG (const GenType & generator) [inline]

Definition at line 172 of file fixedEnvelopes.h.

FixedEnvelope IsoSpec::FixedEnvelope::bin (double bin_width = 1.0, doublemiddle = 0.0)

Definition at line 799 of file fixedEnvelopes.cpp.

static FixedEnvelope IsoSpec::FixedEnvelope::Binned (const Iso & iso, doubletarget_total_prob, double bin_width, double bin_middle = 0.0) [inline],[static]

Definition at line 236 of file fixedEnvelopes.h.

FixedEnvelope IsoSpec::FixedEnvelope::Binned (Iso && iso, doubletarget_total_prob, double bin_width, double bin_middle = 0.0) [static]

Definition at line 1088 of file fixedEnvelopes.cpp.

const int * IsoSpec::FixedEnvelope::conf (size_t i) const [inline]

Definition at line 100 of file fixedEnvelopes.h.

const int * IsoSpec::FixedEnvelope::confs () const [inline]

Definition at line 90 of file fixedEnvelopes.h.

size_t IsoSpec::FixedEnvelope::confs_no () const [inline]

Definition at line 85 of file fixedEnvelopes.h.

double IsoSpec::FixedEnvelope::empiric_average_mass ()

Definition at line 1065 of file fixedEnvelopes.cpp.

double IsoSpec::FixedEnvelope::empiric_stddev () [inline]

Definition at line 113 of file fixedEnvelopes.h.

double IsoSpec::FixedEnvelope::empiric_variance ()

Definition at line 1075 of file fixedEnvelopes.cpp.

static FixedEnvelope IsoSpec::FixedEnvelope::FromStochastic (const Iso & iso,size_t _no_molecules, double _precision = 0.9999, double _beta_bias = 5.0,bool tgetConfs = false) [inline], [static]

Definition at line 230 of file fixedEnvelopes.h.

static FixedEnvelope IsoSpec::FixedEnvelope::FromStochastic (Iso && iso,size_t _no_molecules, double _precision = 0.9999, double _beta_bias = 5.0,bool tgetConfs = false) [inline], [static]

Definition at line 218 of file fixedEnvelopes.h.

static FixedEnvelope IsoSpec::FixedEnvelope::FromThreshold (const Iso & iso,double _threshold, bool _absolute, bool tgetConfs = false) [inline],[static]

Definition at line 194 of file fixedEnvelopes.h.

static FixedEnvelope IsoSpec::FixedEnvelope::FromThreshold (Iso && iso,double threshold, bool absolute, bool tgetConfs = false) [inline],[static]

Definition at line 183 of file fixedEnvelopes.h.

static FixedEnvelope IsoSpec::FixedEnvelope::FromTotalProb (const Iso & iso,double _target_total_prob, bool _optimize, bool tgetConfs = false)[inline], [static]

Definition at line 211 of file fixedEnvelopes.h.

static FixedEnvelope IsoSpec::FixedEnvelope::FromTotalProb (Iso && iso,double target_total_prob, bool optimize, bool tgetConfs = false) [inline],[static]

Definition at line 199 of file fixedEnvelopes.h.

double IsoSpec::FixedEnvelope::get_total_prob ()

Definition at line 192 of file fixedEnvelopes.cpp.

int IsoSpec::FixedEnvelope::getAllDim () const [inline]

Definition at line 86 of file fixedEnvelopes.h.

FixedEnvelope IsoSpec::FixedEnvelope::LinearCombination (const FixedEnvelope*const * spectra, const double * intensities, size_t size) [static]

Definition at line 271 of file fixedEnvelopes.cpp.

FixedEnvelope IsoSpec::FixedEnvelope::LinearCombination (const std::vector<const FixedEnvelope * > & spectra, const std::vector< double > &intensities) [static]

Definition at line 266 of file fixedEnvelopes.cpp.

double IsoSpec::FixedEnvelope::mass (size_t i) const [inline]

Definition at line 98 of file fixedEnvelopes.h.

const double * IsoSpec::FixedEnvelope::masses () const [inline]

Definition at line 88 of file fixedEnvelopes.h.

void IsoSpec::FixedEnvelope::normalize ()

Definition at line 210 of file fixedEnvelopes.cpp.

FixedEnvelope IsoSpec::FixedEnvelope::operator* (const FixedEnvelope & other)const

Definition at line 84 of file fixedEnvelopes.cpp.

FixedEnvelope IsoSpec::FixedEnvelope::operator+ (const FixedEnvelope & other)const

Definition at line 63 of file fixedEnvelopes.cpp.

double IsoSpec::FixedEnvelope::OrientedWassersteinDistance (FixedEnvelope &other)

Definition at line 358 of file fixedEnvelopes.cpp.

double IsoSpec::FixedEnvelope::prob (size_t i) const [inline]

Definition at line 99 of file fixedEnvelopes.h.

const double * IsoSpec::FixedEnvelope::probs () const [inline]

Definition at line 89 of file fixedEnvelopes.h.

template<bool tgetConfs> void IsoSpec::FixedEnvelope::reallocate_memory(size_t new_size) [protected]

Definition at line 851 of file fixedEnvelopes.cpp.

int * IsoSpec::FixedEnvelope::release_confs () [inline]

Definition at line 94 of file fixedEnvelopes.h.

void IsoSpec::FixedEnvelope::release_everything () [inline]

Definition at line 95 of file fixedEnvelopes.h.

double * IsoSpec::FixedEnvelope::release_masses () [inline]

Definition at line 92 of file fixedEnvelopes.h.

double * IsoSpec::FixedEnvelope::release_probs () [inline]

Definition at line 93 of file fixedEnvelopes.h.

void IsoSpec::FixedEnvelope::resample (size_t ionic_current, double beta_bias= 1.0)

Definition at line 226 of file fixedEnvelopes.cpp.

void IsoSpec::FixedEnvelope::scale (double factor)

Definition at line 203 of file fixedEnvelopes.cpp.

void IsoSpec::FixedEnvelope::shift_mass (double shift)

Definition at line 220 of file fixedEnvelopes.cpp.

void IsoSpec::FixedEnvelope::slow_reallocate_memory (size_t new_size)[protected]

Definition at line 874 of file fixedEnvelopes.cpp.

void IsoSpec::FixedEnvelope::sort_by_mass ()

Definition at line 111 of file fixedEnvelopes.cpp.

void IsoSpec::FixedEnvelope::sort_by_prob ()

Definition at line 123 of file fixedEnvelopes.cpp.

template<bool tgetConfs> template voidIsoSpec::FixedEnvelope::stochastic_init< false > (Iso && iso, size_t_no_molecules, double _precision, double _beta_bias)

Definition at line 1049 of file fixedEnvelopes.cpp.

template<typename T , bool tgetConfs> ISOSPEC_FORCE_INLINE voidIsoSpec::FixedEnvelope::store_conf (const T & generator) [inline],[protected]

Definition at line 132 of file fixedEnvelopes.h.

ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::store_conf (double _mass,double _prob) [inline], [protected]

Definition at line 139 of file fixedEnvelopes.h.

template<bool tgetConfs> ISOSPEC_FORCE_INLINE voidIsoSpec::FixedEnvelope::swap (size_t idx1, size_t idx2,ISOSPEC_MAYBE_UNUSED int * conf_swapspace) [inline], [protected]

Definition at line 152 of file fixedEnvelopes.h.

template<bool tgetConfs> template voidIsoSpec::FixedEnvelope::threshold_init< false > (Iso && iso, doublethreshold, bool absolute)

Definition at line 897 of file fixedEnvelopes.cpp.

template<bool tgetConfs> template voidIsoSpec::FixedEnvelope::total_prob_init< false > (Iso && iso, doubletarget_prob, bool trim)

Definition at line 927 of file fixedEnvelopes.cpp.

double IsoSpec::FixedEnvelope::WassersteinDistance (FixedEnvelope & other)

Definition at line 299 of file fixedEnvelopes.cpp.

std::tuple< double, double, double > IsoSpec::FixedEnvelope::WassersteinMatch(FixedEnvelope & other, double flow_distance, double other_scale = 1.0)

Definition at line 726 of file fixedEnvelopes.cpp.

Member Data Documentation

int* IsoSpec::FixedEnvelope::_confs [protected]

Definition at line 44 of file fixedEnvelopes.h.

size_t IsoSpec::FixedEnvelope::_confs_no [protected]

Definition at line 45 of file fixedEnvelopes.h.

double* IsoSpec::FixedEnvelope::_masses [protected]

Definition at line 42 of file fixedEnvelopes.h.

double* IsoSpec::FixedEnvelope::_probs [protected]

Definition at line 43 of file fixedEnvelopes.h.

int IsoSpec::FixedEnvelope::allDim [protected]

Definition at line 46 of file fixedEnvelopes.h.

int IsoSpec::FixedEnvelope::allDimSizeofInt [protected]

Definition at line 54 of file fixedEnvelopes.h.

size_t IsoSpec::FixedEnvelope::current_size [protected]

Definition at line 50 of file fixedEnvelopes.h.

bool IsoSpec::FixedEnvelope::sorted_by_mass [protected]

Definition at line 47 of file fixedEnvelopes.h.

bool IsoSpec::FixedEnvelope::sorted_by_prob [protected]

Definition at line 48 of file fixedEnvelopes.h.

int* IsoSpec::FixedEnvelope::tconfs [protected]

Definition at line 53 of file fixedEnvelopes.h.

double* IsoSpec::FixedEnvelope::tmasses [protected]

Definition at line 51 of file fixedEnvelopes.h.

double IsoSpec::FixedEnvelope::total_prob [protected]

Definition at line 49 of file fixedEnvelopes.h.

double* IsoSpec::FixedEnvelope::tprobs [protected]

Definition at line 52 of file fixedEnvelopes.h.

Author

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