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| FixedEnvelope (const FixedEnvelope &other) |
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| FixedEnvelope (FixedEnvelope &&other) |
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| FixedEnvelope (double *masses, double *probs, size_t confs_no, bool masses_sorted=false, bool probs_sorted=false, double _total_prob=NAN) |
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FixedEnvelope | operator+ (const FixedEnvelope &other) const |
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FixedEnvelope | operator* (const FixedEnvelope &other) const |
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size_t | confs_no () const |
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int | getAllDim () const |
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const double * | masses () const |
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const double * | probs () const |
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const int * | confs () const |
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double * | release_masses () |
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double * | release_probs () |
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int * | release_confs () |
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void | release_everything () |
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double | mass (size_t i) const |
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double | prob (size_t i) const |
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const int * | conf (size_t i) const |
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void | sort_by_mass () |
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void | sort_by_prob () |
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double | get_total_prob () |
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void | scale (double factor) |
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void | normalize () |
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void | shift_mass (double shift) |
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void | resample (size_t ionic_current, double beta_bias=1.0) |
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double | empiric_average_mass () |
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double | empiric_variance () |
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double | empiric_stddev () |
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double | WassersteinDistance (FixedEnvelope &other) |
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double | OrientedWassersteinDistance (FixedEnvelope &other) |
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double | AbyssalWassersteinDistance (FixedEnvelope &other, double abyss_depth, double other_scale=1.0) |
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std::tuple< double, double, double > | WassersteinMatch (FixedEnvelope &other, double flow_distance, double other_scale=1.0) |
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FixedEnvelope | bin (double bin_width=1.0, double middle=0.0) |
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template<bool tgetConfs> |
void | threshold_init (Iso &&iso, double threshold, bool absolute) |
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template<bool tgetConfs, typename GenType = IsoLayeredGenerator> |
void | addConfILG (const GenType &generator) |
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template<bool tgetConfs> |
void | total_prob_init (Iso &&iso, double target_prob, bool trim) |
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template<bool tgetConfs> |
void | stochastic_init (Iso &&iso, size_t _no_molecules, double _precision, double _beta_bias) |
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static FixedEnvelope | LinearCombination (const std::vector< const FixedEnvelope * > &spectra, const std::vector< double > &intensities) |
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static FixedEnvelope | LinearCombination (const FixedEnvelope *const *spectra, const double *intensities, size_t size) |
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static FixedEnvelope | FromThreshold (Iso &&iso, double threshold, bool absolute, bool tgetConfs=false) |
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static FixedEnvelope | FromThreshold (const Iso &iso, double _threshold, bool _absolute, bool tgetConfs=false) |
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static FixedEnvelope | FromTotalProb (Iso &&iso, double target_total_prob, bool optimize, bool tgetConfs=false) |
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static FixedEnvelope | FromTotalProb (const Iso &iso, double _target_total_prob, bool _optimize, bool tgetConfs=false) |
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static FixedEnvelope | FromStochastic (Iso &&iso, size_t _no_molecules, double _precision=0.9999, double _beta_bias=5.0, bool tgetConfs=false) |
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static FixedEnvelope | FromStochastic (const Iso &iso, size_t _no_molecules, double _precision=0.9999, double _beta_bias=5.0, bool tgetConfs=false) |
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static FixedEnvelope | Binned (Iso &&iso, double target_total_prob, double bin_width, double bin_middle=0.0) |
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static FixedEnvelope | Binned (const Iso &iso, double target_total_prob, double bin_width, double bin_middle=0.0) |
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template<typename T , bool tgetConfs> |
ISOSPEC_FORCE_INLINE void | store_conf (const T &generator) |
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ISOSPEC_FORCE_INLINE void | store_conf (double _mass, double _prob) |
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template<bool tgetConfs> |
ISOSPEC_FORCE_INLINE void | swap (size_t idx1, size_t idx2, ISOSPEC_MAYBE_UNUSED int *conf_swapspace) |
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template<bool tgetConfs> |
void | reallocate_memory (size_t new_size) |
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void | slow_reallocate_memory (size_t new_size) |
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double | AbyssalWassersteinDistanceGrad (FixedEnvelope *const *envelopes, const double *scales, double *ret_gradient, size_t N, double abyss_depth_exp, double abyss_depth_the) |
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Definition at line 40 of file fixedEnvelopes.h.
◆ FixedEnvelope() [1/4]
ISOSPEC_FORCE_INLINE IsoSpec::FixedEnvelope::FixedEnvelope |
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inline |
◆ FixedEnvelope() [2/4]
IsoSpec::FixedEnvelope::FixedEnvelope |
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const FixedEnvelope & |
other | ) |
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◆ FixedEnvelope() [3/4]
◆ FixedEnvelope() [4/4]
IsoSpec::FixedEnvelope::FixedEnvelope |
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double * |
masses, |
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double * |
probs, |
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size_t |
confs_no, |
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bool |
masses_sorted = false , |
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bool |
probs_sorted = false , |
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double |
_total_prob = NAN |
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) |
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◆ ~FixedEnvelope()
virtual IsoSpec::FixedEnvelope::~FixedEnvelope |
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inlinevirtual |
◆ AbyssalWassersteinDistance()
double IsoSpec::FixedEnvelope::AbyssalWassersteinDistance |
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FixedEnvelope & |
other, |
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double |
abyss_depth, |
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double |
other_scale = 1.0 |
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) |
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◆ addConfILG()
template<bool tgetConfs, typename GenType = IsoLayeredGenerator>
void IsoSpec::FixedEnvelope::addConfILG |
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const GenType & |
generator | ) |
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inline |
◆ bin()
FixedEnvelope IsoSpec::FixedEnvelope::bin |
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double |
bin_width = 1.0 , |
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double |
middle = 0.0 |
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) |
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◆ Binned() [1/2]
static FixedEnvelope IsoSpec::FixedEnvelope::Binned |
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const Iso & |
iso, |
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double |
target_total_prob, |
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double |
bin_width, |
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double |
bin_middle = 0.0 |
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) |
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inlinestatic |
◆ Binned() [2/2]
FixedEnvelope IsoSpec::FixedEnvelope::Binned |
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Iso && |
iso, |
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double |
target_total_prob, |
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double |
bin_width, |
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double |
bin_middle = 0.0 |
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) |
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static |
◆ conf()
const int * IsoSpec::FixedEnvelope::conf |
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size_t |
i | ) |
const |
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inline |
◆ confs()
const int * IsoSpec::FixedEnvelope::confs |
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const |
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inline |
◆ confs_no()
size_t IsoSpec::FixedEnvelope::confs_no |
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const |
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inline |
◆ empiric_average_mass()
double IsoSpec::FixedEnvelope::empiric_average_mass |
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◆ empiric_stddev()
double IsoSpec::FixedEnvelope::empiric_stddev |
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inline |
◆ empiric_variance()
double IsoSpec::FixedEnvelope::empiric_variance |
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◆ FromStochastic() [1/2]
static FixedEnvelope IsoSpec::FixedEnvelope::FromStochastic |
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const Iso & |
iso, |
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size_t |
_no_molecules, |
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double |
_precision = 0.9999 , |
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double |
_beta_bias = 5.0 , |
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bool |
tgetConfs = false |
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) |
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inlinestatic |
◆ FromStochastic() [2/2]
static FixedEnvelope IsoSpec::FixedEnvelope::FromStochastic |
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Iso && |
iso, |
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size_t |
_no_molecules, |
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double |
_precision = 0.9999 , |
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double |
_beta_bias = 5.0 , |
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bool |
tgetConfs = false |
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) |
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inlinestatic |
◆ FromThreshold() [1/2]
static FixedEnvelope IsoSpec::FixedEnvelope::FromThreshold |
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const Iso & |
iso, |
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double |
_threshold, |
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bool |
_absolute, |
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bool |
tgetConfs = false |
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) |
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inlinestatic |
◆ FromThreshold() [2/2]
static FixedEnvelope IsoSpec::FixedEnvelope::FromThreshold |
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Iso && |
iso, |
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double |
threshold, |
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bool |
absolute, |
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bool |
tgetConfs = false |
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) |
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inlinestatic |
◆ FromTotalProb() [1/2]
static FixedEnvelope IsoSpec::FixedEnvelope::FromTotalProb |
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const Iso & |
iso, |
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double |
_target_total_prob, |
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bool |
_optimize, |
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bool |
tgetConfs = false |
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) |
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inlinestatic |
◆ FromTotalProb() [2/2]
static FixedEnvelope IsoSpec::FixedEnvelope::FromTotalProb |
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Iso && |
iso, |
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double |
target_total_prob, |
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bool |
optimize, |
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bool |
tgetConfs = false |
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) |
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inlinestatic |
◆ get_total_prob()
double IsoSpec::FixedEnvelope::get_total_prob |
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◆ getAllDim()
int IsoSpec::FixedEnvelope::getAllDim |
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const |
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inline |
◆ LinearCombination() [1/2]
FixedEnvelope IsoSpec::FixedEnvelope::LinearCombination |
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const FixedEnvelope *const * |
spectra, |
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const double * |
intensities, |
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size_t |
size |
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) |
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static |
◆ LinearCombination() [2/2]
FixedEnvelope IsoSpec::FixedEnvelope::LinearCombination |
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const std::vector< const FixedEnvelope * > & |
spectra, |
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const std::vector< double > & |
intensities |
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) |
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static |
◆ mass()
double IsoSpec::FixedEnvelope::mass |
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size_t |
i | ) |
const |
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inline |
◆ masses()
const double * IsoSpec::FixedEnvelope::masses |
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const |
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inline |
◆ normalize()
void IsoSpec::FixedEnvelope::normalize |
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◆ operator*()
◆ operator+()
◆ OrientedWassersteinDistance()
double IsoSpec::FixedEnvelope::OrientedWassersteinDistance |
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FixedEnvelope & |
other | ) |
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◆ prob()
double IsoSpec::FixedEnvelope::prob |
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size_t |
i | ) |
const |
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inline |
◆ probs()
const double * IsoSpec::FixedEnvelope::probs |
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const |
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inline |
◆ reallocate_memory()
template<bool tgetConfs>
void IsoSpec::FixedEnvelope::reallocate_memory |
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size_t |
new_size | ) |
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protected |
◆ release_confs()
int * IsoSpec::FixedEnvelope::release_confs |
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inline |
◆ release_everything()
void IsoSpec::FixedEnvelope::release_everything |
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inline |
◆ release_masses()
double * IsoSpec::FixedEnvelope::release_masses |
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inline |
◆ release_probs()
double * IsoSpec::FixedEnvelope::release_probs |
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inline |
◆ resample()
void IsoSpec::FixedEnvelope::resample |
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size_t |
ionic_current, |
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double |
beta_bias = 1.0 |
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) |
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◆ scale()
void IsoSpec::FixedEnvelope::scale |
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double |
factor | ) |
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◆ shift_mass()
void IsoSpec::FixedEnvelope::shift_mass |
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double |
shift | ) |
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◆ slow_reallocate_memory()
void IsoSpec::FixedEnvelope::slow_reallocate_memory |
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size_t |
new_size | ) |
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protected |
◆ sort_by_mass()
void IsoSpec::FixedEnvelope::sort_by_mass |
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◆ sort_by_prob()
void IsoSpec::FixedEnvelope::sort_by_prob |
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◆ stochastic_init()
template<bool tgetConfs>
template void IsoSpec::FixedEnvelope::stochastic_init< false > |
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Iso && |
iso, |
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size_t |
_no_molecules, |
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double |
_precision, |
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double |
_beta_bias |
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) |
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◆ store_conf() [1/2]
template<typename T , bool tgetConfs>
ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::store_conf |
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const T & |
generator | ) |
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inlineprotected |
◆ store_conf() [2/2]
ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::store_conf |
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double |
_mass, |
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double |
_prob |
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) |
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inlineprotected |
◆ swap()
template<bool tgetConfs>
ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::swap |
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size_t |
idx1, |
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size_t |
idx2, |
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ISOSPEC_MAYBE_UNUSED int * |
conf_swapspace |
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) |
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inlineprotected |
◆ threshold_init()
template<bool tgetConfs>
template void IsoSpec::FixedEnvelope::threshold_init< false > |
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Iso && |
iso, |
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double |
threshold, |
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bool |
absolute |
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) |
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◆ total_prob_init()
template<bool tgetConfs>
template void IsoSpec::FixedEnvelope::total_prob_init< false > |
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Iso && |
iso, |
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double |
target_prob, |
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bool |
trim |
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) |
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◆ WassersteinDistance()
double IsoSpec::FixedEnvelope::WassersteinDistance |
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FixedEnvelope & |
other | ) |
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◆ WassersteinMatch()
std::tuple< double, double, double > IsoSpec::FixedEnvelope::WassersteinMatch |
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FixedEnvelope & |
other, |
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double |
flow_distance, |
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double |
other_scale = 1.0 |
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) |
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◆ _confs
int* IsoSpec::FixedEnvelope::_confs |
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protected |
◆ _confs_no
size_t IsoSpec::FixedEnvelope::_confs_no |
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protected |
◆ _masses
double* IsoSpec::FixedEnvelope::_masses |
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protected |
◆ _probs
double* IsoSpec::FixedEnvelope::_probs |
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protected |
◆ allDim
int IsoSpec::FixedEnvelope::allDim |
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protected |
◆ allDimSizeofInt
int IsoSpec::FixedEnvelope::allDimSizeofInt |
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protected |
◆ current_size
size_t IsoSpec::FixedEnvelope::current_size |
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protected |
◆ sorted_by_mass
bool IsoSpec::FixedEnvelope::sorted_by_mass |
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protected |
◆ sorted_by_prob
bool IsoSpec::FixedEnvelope::sorted_by_prob |
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protected |
◆ tconfs
int* IsoSpec::FixedEnvelope::tconfs |
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protected |
◆ tmasses
double* IsoSpec::FixedEnvelope::tmasses |
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protected |
◆ total_prob
double IsoSpec::FixedEnvelope::total_prob |
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protected |
◆ tprobs
double* IsoSpec::FixedEnvelope::tprobs |
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protected |
The documentation for this class was generated from the following files: