Man page - isospec_fixedenvelope(3)
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Manual
IsoSpec::FixedEnvelope
NAMESYNOPSIS
Public Member Functions
Static Public Member Functions
Protected Member Functions
Protected Attributes
Friends
Detailed Description
Constructor & Destructor Documentation
ISOSPEC_FORCE_INLINE IsoSpec::FixedEnvelope::FixedEnvelope () [inline]
IsoSpec::FixedEnvelope::FixedEnvelope (const FixedEnvelope & other)
IsoSpec::FixedEnvelope::FixedEnvelope (FixedEnvelope && other)
IsoSpec::FixedEnvelope::FixedEnvelope (double * masses, double * probs,size_t confs_no, bool masses_sorted = false, bool probs_sorted = false,double _total_prob = NAN)
virtual IsoSpec::FixedEnvelope::˜FixedEnvelope () [inline], [virtual]
Member Function Documentation
double IsoSpec::FixedEnvelope::AbyssalWassersteinDistance (FixedEnvelope &other, double abyss_depth, double other_scale = 1.0)
template<bool tgetConfs, typename GenType = IsoLayeredGenerator> voidIsoSpec::FixedEnvelope::addConfILG (const GenType & generator) [inline]
FixedEnvelope IsoSpec::FixedEnvelope::bin (double bin_width = 1.0, doublemiddle = 0.0)
static FixedEnvelope IsoSpec::FixedEnvelope::Binned (const Iso & iso,double target_total_prob, double bin_width, double bin_middle = 0.0)[inline], [static]
FixedEnvelope IsoSpec::FixedEnvelope::Binned (Iso && iso, doubletarget_total_prob, double bin_width, double bin_middle = 0.0) [static]
const int * IsoSpec::FixedEnvelope::conf (size_t i) const [inline]
const int * IsoSpec::FixedEnvelope::confs () const [inline]
size_t IsoSpec::FixedEnvelope::confs_no () const [inline]
double IsoSpec::FixedEnvelope::empiric_average_mass ()
double IsoSpec::FixedEnvelope::empiric_stddev () [inline]
double IsoSpec::FixedEnvelope::empiric_variance ()
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]
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]
static FixedEnvelope IsoSpec::FixedEnvelope::FromThreshold (const Iso &iso, double _threshold, bool _absolute, bool tgetConfs = false)[inline], [static]
static FixedEnvelope IsoSpec::FixedEnvelope::FromThreshold (Iso && iso,double threshold, bool absolute, bool tgetConfs = false) [inline],[static]
static FixedEnvelope IsoSpec::FixedEnvelope::FromTotalProb (const Iso &iso, double _target_total_prob, bool _optimize, bool tgetConfs = false)[inline], [static]
static FixedEnvelope IsoSpec::FixedEnvelope::FromTotalProb (Iso && iso,double target_total_prob, bool optimize, bool tgetConfs = false)[inline], [static]
double IsoSpec::FixedEnvelope::get_total_prob ()
int IsoSpec::FixedEnvelope::getAllDim () const [inline]
FixedEnvelope IsoSpec::FixedEnvelope::LinearCombination (constFixedEnvelope *const * spectra, const double * intensities, size_tsize) [static]
FixedEnvelope IsoSpec::FixedEnvelope::LinearCombination (const std::vector<const FixedEnvelope * > & spectra, const std::vector< double > &intensities) [static]
double IsoSpec::FixedEnvelope::mass (size_t i) const [inline]
const double * IsoSpec::FixedEnvelope::masses () const [inline]
void IsoSpec::FixedEnvelope::normalize ()
FixedEnvelope IsoSpec::FixedEnvelope::operator* (const FixedEnvelope &other) const
FixedEnvelope IsoSpec::FixedEnvelope::operator+ (const FixedEnvelope &other) const
double IsoSpec::FixedEnvelope::OrientedWassersteinDistance (FixedEnvelope &other)
double IsoSpec::FixedEnvelope::prob (size_t i) const [inline]
const double * IsoSpec::FixedEnvelope::probs () const [inline]
template<bool tgetConfs> void IsoSpec::FixedEnvelope::reallocate_memory(size_t new_size) [protected]
int * IsoSpec::FixedEnvelope::release_confs () [inline]
void IsoSpec::FixedEnvelope::release_everything () [inline]
double * IsoSpec::FixedEnvelope::release_masses () [inline]
double * IsoSpec::FixedEnvelope::release_probs () [inline]
void IsoSpec::FixedEnvelope::resample (size_t ionic_current, doublebeta_bias = 1.0)
void IsoSpec::FixedEnvelope::scale (double factor)
void IsoSpec::FixedEnvelope::shift_mass (double shift)
void IsoSpec::FixedEnvelope::slow_reallocate_memory (size_t new_size)[protected]
void IsoSpec::FixedEnvelope::sort_by_mass ()
void IsoSpec::FixedEnvelope::sort_by_prob ()
template<bool tgetConfs> template voidIsoSpec::FixedEnvelope::stochastic_init< false > (Iso && iso, size_t_no_molecules, double _precision, double _beta_bias)
template<typename T , bool tgetConfs> ISOSPEC_FORCE_INLINE voidIsoSpec::FixedEnvelope::store_conf (const T & generator) [inline],[protected]
ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::store_conf (double _mass,double _prob) [inline], [protected]
template<bool tgetConfs> ISOSPEC_FORCE_INLINE voidIsoSpec::FixedEnvelope::swap (size_t idx1, size_t idx2,ISOSPEC_MAYBE_UNUSED int * conf_swapspace) [inline], [protected]
template<bool tgetConfs> template voidIsoSpec::FixedEnvelope::threshold_init< false > (Iso && iso, doublethreshold, bool absolute)
template<bool tgetConfs> template voidIsoSpec::FixedEnvelope::total_prob_init< false > (Iso && iso, doubletarget_prob, bool trim)
double IsoSpec::FixedEnvelope::WassersteinDistance (FixedEnvelope & other)
std::tuple< double, double, double >IsoSpec::FixedEnvelope::WassersteinMatch (FixedEnvelope & other, doubleflow_distance, double other_scale = 1.0)
Member Data Documentation
int* IsoSpec::FixedEnvelope::_confs [protected]
size_t IsoSpec::FixedEnvelope::_confs_no [protected]
double* IsoSpec::FixedEnvelope::_masses [protected]
double* IsoSpec::FixedEnvelope::_probs [protected]
int IsoSpec::FixedEnvelope::allDim [protected]
int IsoSpec::FixedEnvelope::allDimSizeofInt [protected]
size_t IsoSpec::FixedEnvelope::current_size [protected]
bool IsoSpec::FixedEnvelope::sorted_by_mass [protected]
bool IsoSpec::FixedEnvelope::sorted_by_prob [protected]
int* IsoSpec::FixedEnvelope::tconfs [protected]
double* IsoSpec::FixedEnvelope::tmasses [protected]
double IsoSpec::FixedEnvelope::total_prob [protected]
double* IsoSpec::FixedEnvelope::tprobs [protected]
Author
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,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, 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 (constFixedEnvelope *const * spectra, const double * intensities, size_tsize) [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, doublebeta_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, doubleflow_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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