.TH "IsoSpec::FixedEnvelope" 3 "Version 2.2.1" "IsoSpec" \" -*- nroff -*- .ad l .nh .SH NAME IsoSpec::FixedEnvelope .SH SYNOPSIS .br .PP .SS "Public Member Functions" .in +1c .ti -1c .RI "\fBFixedEnvelope\fP (const \fBFixedEnvelope\fP &other)" .br .ti -1c .RI "\fBFixedEnvelope\fP (\fBFixedEnvelope\fP &&other)" .br .ti -1c .RI "\fBFixedEnvelope\fP (double *masses, double *probs, size_t confs_no, bool masses_sorted=false, bool probs_sorted=false, double _total_prob=NAN)" .br .ti -1c .RI "\fBFixedEnvelope\fP \fBoperator+\fP (const \fBFixedEnvelope\fP &other) const" .br .ti -1c .RI "\fBFixedEnvelope\fP \fBoperator*\fP (const \fBFixedEnvelope\fP &other) const" .br .ti -1c .RI "size_t \fBconfs_no\fP () const" .br .ti -1c .RI "int \fBgetAllDim\fP () const" .br .ti -1c .RI "const double * \fBmasses\fP () const" .br .ti -1c .RI "const double * \fBprobs\fP () const" .br .ti -1c .RI "const int * \fBconfs\fP () const" .br .ti -1c .RI "double * \fBrelease_masses\fP ()" .br .ti -1c .RI "double * \fBrelease_probs\fP ()" .br .ti -1c .RI "int * \fBrelease_confs\fP ()" .br .ti -1c .RI "void \fBrelease_everything\fP ()" .br .ti -1c .RI "double \fBmass\fP (size_t i) const" .br .ti -1c .RI "double \fBprob\fP (size_t i) const" .br .ti -1c .RI "const int * \fBconf\fP (size_t i) const" .br .ti -1c .RI "void \fBsort_by_mass\fP ()" .br .ti -1c .RI "void \fBsort_by_prob\fP ()" .br .ti -1c .RI "double \fBget_total_prob\fP ()" .br .ti -1c .RI "void \fBscale\fP (double factor)" .br .ti -1c .RI "void \fBnormalize\fP ()" .br .ti -1c .RI "void \fBshift_mass\fP (double shift)" .br .ti -1c .RI "void \fBresample\fP (size_t ionic_current, double beta_bias=1\&.0)" .br .ti -1c .RI "double \fBempiric_average_mass\fP ()" .br .ti -1c .RI "double \fBempiric_variance\fP ()" .br .ti -1c .RI "double \fBempiric_stddev\fP ()" .br .ti -1c .RI "double \fBWassersteinDistance\fP (\fBFixedEnvelope\fP &other)" .br .ti -1c .RI "double \fBOrientedWassersteinDistance\fP (\fBFixedEnvelope\fP &other)" .br .ti -1c .RI "double \fBAbyssalWassersteinDistance\fP (\fBFixedEnvelope\fP &other, double abyss_depth, double other_scale=1\&.0)" .br .ti -1c .RI "std::tuple< double, double, double > \fBWassersteinMatch\fP (\fBFixedEnvelope\fP &other, double flow_distance, double other_scale=1\&.0)" .br .ti -1c .RI "\fBFixedEnvelope\fP \fBbin\fP (double bin_width=1\&.0, double middle=0\&.0)" .br .ti -1c .RI "template void \fBthreshold_init\fP (\fBIso\fP &&iso, double threshold, bool absolute)" .br .ti -1c .RI "template void \fBaddConfILG\fP (const GenType &generator)" .br .ti -1c .RI "template void \fBtotal_prob_init\fP (\fBIso\fP &&iso, double target_prob, bool trim)" .br .ti -1c .RI "template void \fBstochastic_init\fP (\fBIso\fP &&iso, size_t _no_molecules, double _precision, double _beta_bias)" .br .in -1c .SS "Static Public Member Functions" .in +1c .ti -1c .RI "static \fBFixedEnvelope\fP \fBLinearCombination\fP (const std::vector< const \fBFixedEnvelope\fP * > &spectra, const std::vector< double > &intensities)" .br .ti -1c .RI "static \fBFixedEnvelope\fP \fBLinearCombination\fP (const \fBFixedEnvelope\fP *const *spectra, const double *intensities, size_t size)" .br .ti -1c .RI "static \fBFixedEnvelope\fP \fBFromThreshold\fP (\fBIso\fP &&iso, double threshold, bool absolute, bool tgetConfs=false)" .br .ti -1c .RI "static \fBFixedEnvelope\fP \fBFromThreshold\fP (const \fBIso\fP &iso, double _threshold, bool _absolute, bool tgetConfs=false)" .br .ti -1c .RI "static \fBFixedEnvelope\fP \fBFromTotalProb\fP (\fBIso\fP &&iso, double target_total_prob, bool optimize, bool tgetConfs=false)" .br .ti -1c .RI "static \fBFixedEnvelope\fP \fBFromTotalProb\fP (const \fBIso\fP &iso, double _target_total_prob, bool _optimize, bool tgetConfs=false)" .br .ti -1c .RI "static \fBFixedEnvelope\fP \fBFromStochastic\fP (\fBIso\fP &&iso, size_t _no_molecules, double _precision=0\&.9999, double _beta_bias=5\&.0, bool tgetConfs=false)" .br .ti -1c .RI "static \fBFixedEnvelope\fP \fBFromStochastic\fP (const \fBIso\fP &iso, size_t _no_molecules, double _precision=0\&.9999, double _beta_bias=5\&.0, bool tgetConfs=false)" .br .ti -1c .RI "static \fBFixedEnvelope\fP \fBBinned\fP (\fBIso\fP &&iso, double target_total_prob, double bin_width, double bin_middle=0\&.0)" .br .ti -1c .RI "static \fBFixedEnvelope\fP \fBBinned\fP (const \fBIso\fP &iso, double target_total_prob, double bin_width, double bin_middle=0\&.0)" .br .in -1c .SS "Protected Member Functions" .in +1c .ti -1c .RI "template ISOSPEC_FORCE_INLINE void \fBstore_conf\fP (const T &generator)" .br .ti -1c .RI "ISOSPEC_FORCE_INLINE void \fBstore_conf\fP (double _mass, double _prob)" .br .ti -1c .RI "template ISOSPEC_FORCE_INLINE void \fBswap\fP (size_t idx1, size_t idx2, ISOSPEC_MAYBE_UNUSED int *conf_swapspace)" .br .ti -1c .RI "template void \fBreallocate_memory\fP (size_t new_size)" .br .ti -1c .RI "void \fBslow_reallocate_memory\fP (size_t new_size)" .br .in -1c .SS "Protected Attributes" .in +1c .ti -1c .RI "double * \fB_masses\fP" .br .ti -1c .RI "double * \fB_probs\fP" .br .ti -1c .RI "int * \fB_confs\fP" .br .ti -1c .RI "size_t \fB_confs_no\fP" .br .ti -1c .RI "int \fBallDim\fP" .br .ti -1c .RI "bool \fBsorted_by_mass\fP" .br .ti -1c .RI "bool \fBsorted_by_prob\fP" .br .ti -1c .RI "double \fBtotal_prob\fP" .br .ti -1c .RI "size_t \fBcurrent_size\fP" .br .ti -1c .RI "double * \fBtmasses\fP" .br .ti -1c .RI "double * \fBtprobs\fP" .br .ti -1c .RI "int * \fBtconfs\fP" .br .ti -1c .RI "int \fBallDimSizeofInt\fP" .br .in -1c .SS "Friends" .in +1c .ti -1c .RI "double \fBAbyssalWassersteinDistanceGrad\fP (\fBFixedEnvelope\fP *const *envelopes, const double *scales, double *ret_gradient, size_t N, double abyss_depth_exp, double abyss_depth_the)" .br .in -1c .SH "Detailed Description" .PP Definition at line \fB40\fP of file \fBfixedEnvelopes\&.h\fP\&. .SH "Constructor & Destructor Documentation" .PP .SS "ISOSPEC_FORCE_INLINE IsoSpec::FixedEnvelope::FixedEnvelope ()\fC [inline]\fP" .PP Definition at line \fB57\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "IsoSpec::FixedEnvelope::FixedEnvelope (const \fBFixedEnvelope\fP & other)" .PP Definition at line \fB24\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "IsoSpec::FixedEnvelope::FixedEnvelope (\fBFixedEnvelope\fP && other)" .PP Definition at line \fB35\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "IsoSpec::FixedEnvelope::FixedEnvelope (double * masses, double * probs, size_t confs_no, bool masses_sorted = \fCfalse\fP, bool probs_sorted = \fCfalse\fP, double _total_prob = \fCNAN\fP)" .PP Definition at line \fB52\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "virtual IsoSpec::FixedEnvelope::~FixedEnvelope ()\fC [inline]\fP, \fC [virtual]\fP" .PP Definition at line \fB75\fP of file \fBfixedEnvelopes\&.h\fP\&. .SH "Member Function Documentation" .PP .SS "double IsoSpec::FixedEnvelope::AbyssalWassersteinDistance (\fBFixedEnvelope\fP & other, double abyss_depth, double other_scale = \fC1\&.0\fP)" .PP Definition at line \fB414\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "template void IsoSpec::FixedEnvelope::addConfILG (const GenType & generator)\fC [inline]\fP" .PP Definition at line \fB172\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "\fBFixedEnvelope\fP IsoSpec::FixedEnvelope::bin (double bin_width = \fC1\&.0\fP, double middle = \fC0\&.0\fP)" .PP Definition at line \fB799\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "static \fBFixedEnvelope\fP IsoSpec::FixedEnvelope::Binned (const \fBIso\fP & iso, double target_total_prob, double bin_width, double bin_middle = \fC0\&.0\fP)\fC [inline]\fP, \fC [static]\fP" .PP Definition at line \fB236\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "\fBFixedEnvelope\fP IsoSpec::FixedEnvelope::Binned (\fBIso\fP && iso, double target_total_prob, double bin_width, double bin_middle = \fC0\&.0\fP)\fC [static]\fP" .PP Definition at line \fB1088\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "const int * IsoSpec::FixedEnvelope::conf (size_t i) const\fC [inline]\fP" .PP Definition at line \fB100\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "const int * IsoSpec::FixedEnvelope::confs () const\fC [inline]\fP" .PP Definition at line \fB90\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "size_t IsoSpec::FixedEnvelope::confs_no () const\fC [inline]\fP" .PP Definition at line \fB85\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "double IsoSpec::FixedEnvelope::empiric_average_mass ()" .PP Definition at line \fB1065\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "double IsoSpec::FixedEnvelope::empiric_stddev ()\fC [inline]\fP" .PP Definition at line \fB113\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "double IsoSpec::FixedEnvelope::empiric_variance ()" .PP Definition at line \fB1075\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "static \fBFixedEnvelope\fP IsoSpec::FixedEnvelope::FromStochastic (const \fBIso\fP & iso, size_t _no_molecules, double _precision = \fC0\&.9999\fP, double _beta_bias = \fC5\&.0\fP, bool tgetConfs = \fCfalse\fP)\fC [inline]\fP, \fC [static]\fP" .PP Definition at line \fB230\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "static \fBFixedEnvelope\fP IsoSpec::FixedEnvelope::FromStochastic (\fBIso\fP && iso, size_t _no_molecules, double _precision = \fC0\&.9999\fP, double _beta_bias = \fC5\&.0\fP, bool tgetConfs = \fCfalse\fP)\fC [inline]\fP, \fC [static]\fP" .PP Definition at line \fB218\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "static \fBFixedEnvelope\fP IsoSpec::FixedEnvelope::FromThreshold (const \fBIso\fP & iso, double _threshold, bool _absolute, bool tgetConfs = \fCfalse\fP)\fC [inline]\fP, \fC [static]\fP" .PP Definition at line \fB194\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "static \fBFixedEnvelope\fP IsoSpec::FixedEnvelope::FromThreshold (\fBIso\fP && iso, double threshold, bool absolute, bool tgetConfs = \fCfalse\fP)\fC [inline]\fP, \fC [static]\fP" .PP Definition at line \fB183\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "static \fBFixedEnvelope\fP IsoSpec::FixedEnvelope::FromTotalProb (const \fBIso\fP & iso, double _target_total_prob, bool _optimize, bool tgetConfs = \fCfalse\fP)\fC [inline]\fP, \fC [static]\fP" .PP Definition at line \fB211\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "static \fBFixedEnvelope\fP IsoSpec::FixedEnvelope::FromTotalProb (\fBIso\fP && iso, double target_total_prob, bool optimize, bool tgetConfs = \fCfalse\fP)\fC [inline]\fP, \fC [static]\fP" .PP Definition at line \fB199\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "double IsoSpec::FixedEnvelope::get_total_prob ()" .PP Definition at line \fB192\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "int IsoSpec::FixedEnvelope::getAllDim () const\fC [inline]\fP" .PP Definition at line \fB86\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "\fBFixedEnvelope\fP IsoSpec::FixedEnvelope::LinearCombination (const \fBFixedEnvelope\fP *const * spectra, const double * intensities, size_t size)\fC [static]\fP" .PP Definition at line \fB271\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "\fBFixedEnvelope\fP IsoSpec::FixedEnvelope::LinearCombination (const std::vector< const \fBFixedEnvelope\fP * > & spectra, const std::vector< double > & intensities)\fC [static]\fP" .PP Definition at line \fB266\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "double IsoSpec::FixedEnvelope::mass (size_t i) const\fC [inline]\fP" .PP Definition at line \fB98\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "const double * IsoSpec::FixedEnvelope::masses () const\fC [inline]\fP" .PP Definition at line \fB88\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "void IsoSpec::FixedEnvelope::normalize ()" .PP Definition at line \fB210\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "\fBFixedEnvelope\fP IsoSpec::FixedEnvelope::operator* (const \fBFixedEnvelope\fP & other) const" .PP Definition at line \fB84\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "\fBFixedEnvelope\fP IsoSpec::FixedEnvelope::operator+ (const \fBFixedEnvelope\fP & other) const" .PP Definition at line \fB63\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "double IsoSpec::FixedEnvelope::OrientedWassersteinDistance (\fBFixedEnvelope\fP & other)" .PP Definition at line \fB358\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "double IsoSpec::FixedEnvelope::prob (size_t i) const\fC [inline]\fP" .PP Definition at line \fB99\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "const double * IsoSpec::FixedEnvelope::probs () const\fC [inline]\fP" .PP Definition at line \fB89\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "template void IsoSpec::FixedEnvelope::reallocate_memory (size_t new_size)\fC [protected]\fP" .PP Definition at line \fB851\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "int * IsoSpec::FixedEnvelope::release_confs ()\fC [inline]\fP" .PP Definition at line \fB94\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "void IsoSpec::FixedEnvelope::release_everything ()\fC [inline]\fP" .PP Definition at line \fB95\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "double * IsoSpec::FixedEnvelope::release_masses ()\fC [inline]\fP" .PP Definition at line \fB92\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "double * IsoSpec::FixedEnvelope::release_probs ()\fC [inline]\fP" .PP Definition at line \fB93\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "void IsoSpec::FixedEnvelope::resample (size_t ionic_current, double beta_bias = \fC1\&.0\fP)" .PP Definition at line \fB226\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "void IsoSpec::FixedEnvelope::scale (double factor)" .PP Definition at line \fB203\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "void IsoSpec::FixedEnvelope::shift_mass (double shift)" .PP Definition at line \fB220\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "void IsoSpec::FixedEnvelope::slow_reallocate_memory (size_t new_size)\fC [protected]\fP" .PP Definition at line \fB874\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "void IsoSpec::FixedEnvelope::sort_by_mass ()" .PP Definition at line \fB111\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "void IsoSpec::FixedEnvelope::sort_by_prob ()" .PP Definition at line \fB123\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "template template void IsoSpec::FixedEnvelope::stochastic_init< false > (\fBIso\fP && iso, size_t _no_molecules, double _precision, double _beta_bias)" .PP Definition at line \fB1049\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "template ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::store_conf (const T & generator)\fC [inline]\fP, \fC [protected]\fP" .PP Definition at line \fB132\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::store_conf (double _mass, double _prob)\fC [inline]\fP, \fC [protected]\fP" .PP Definition at line \fB139\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "template ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::swap (size_t idx1, size_t idx2, ISOSPEC_MAYBE_UNUSED int * conf_swapspace)\fC [inline]\fP, \fC [protected]\fP" .PP Definition at line \fB152\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "template template void IsoSpec::FixedEnvelope::threshold_init< false > (\fBIso\fP && iso, double threshold, bool absolute)" .PP Definition at line \fB897\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "template template void IsoSpec::FixedEnvelope::total_prob_init< false > (\fBIso\fP && iso, double target_prob, bool trim)" .PP Definition at line \fB927\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "double IsoSpec::FixedEnvelope::WassersteinDistance (\fBFixedEnvelope\fP & other)" .PP Definition at line \fB299\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SS "std::tuple< double, double, double > IsoSpec::FixedEnvelope::WassersteinMatch (\fBFixedEnvelope\fP & other, double flow_distance, double other_scale = \fC1\&.0\fP)" .PP Definition at line \fB726\fP of file \fBfixedEnvelopes\&.cpp\fP\&. .SH "Member Data Documentation" .PP .SS "int* IsoSpec::FixedEnvelope::_confs\fC [protected]\fP" .PP Definition at line \fB44\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "size_t IsoSpec::FixedEnvelope::_confs_no\fC [protected]\fP" .PP Definition at line \fB45\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "double* IsoSpec::FixedEnvelope::_masses\fC [protected]\fP" .PP Definition at line \fB42\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "double* IsoSpec::FixedEnvelope::_probs\fC [protected]\fP" .PP Definition at line \fB43\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "int IsoSpec::FixedEnvelope::allDim\fC [protected]\fP" .PP Definition at line \fB46\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "int IsoSpec::FixedEnvelope::allDimSizeofInt\fC [protected]\fP" .PP Definition at line \fB54\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "size_t IsoSpec::FixedEnvelope::current_size\fC [protected]\fP" .PP Definition at line \fB50\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "bool IsoSpec::FixedEnvelope::sorted_by_mass\fC [protected]\fP" .PP Definition at line \fB47\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "bool IsoSpec::FixedEnvelope::sorted_by_prob\fC [protected]\fP" .PP Definition at line \fB48\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "int* IsoSpec::FixedEnvelope::tconfs\fC [protected]\fP" .PP Definition at line \fB53\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "double* IsoSpec::FixedEnvelope::tmasses\fC [protected]\fP" .PP Definition at line \fB51\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "double IsoSpec::FixedEnvelope::total_prob\fC [protected]\fP" .PP Definition at line \fB49\fP of file \fBfixedEnvelopes\&.h\fP\&. .SS "double* IsoSpec::FixedEnvelope::tprobs\fC [protected]\fP" .PP Definition at line \fB52\fP of file \fBfixedEnvelopes\&.h\fP\&. .SH "Author" .PP Generated automatically by Doxygen for IsoSpec from the source code\&.