plucky (3) IsoSpec_FixedEnvelope.3.gz
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> void IsoSpec::FixedEnvelope::addConfILG
(const GenType & generator) [inline]
Definition at line 172 of file fixedEnvelopes.h.
FixedEnvelope IsoSpec::FixedEnvelope::bin (double bin_width = 1.0, double middle = 0.0)
Definition at line 799 of file fixedEnvelopes.cpp.
static FixedEnvelope IsoSpec::FixedEnvelope::Binned (const Iso & iso, double target_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, double target_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 void IsoSpec::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 void IsoSpec::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 void IsoSpec::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 void IsoSpec::FixedEnvelope::threshold_init< false > (Iso && iso, double
threshold, bool absolute)
Definition at line 897 of file fixedEnvelopes.cpp.
template<bool tgetConfs> template void IsoSpec::FixedEnvelope::total_prob_init< false > (Iso && iso, double
target_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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