IsoSpec::FixedEnvelope

       Generated automatically by Doxygen for IsoSpec from the source code.

IsoSpec                                           Version 2.2.1                        IsoSpec::FixedEnvelope(3)

ISOSPEC_FORCE_INLINEIsoSpec::FixedEnvelope::FixedEnvelope()[inline]
       Definition at line 57 of file fixedEnvelopes.h.

   IsoSpec::FixedEnvelope::FixedEnvelope(constFixedEnvelope&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_tconfs_no,boolmasses_sorted=false,boolprobs_sorted=false,double_total_prob=NAN)
       Definition at line 52 of file fixedEnvelopes.cpp.

   virtualIsoSpec::FixedEnvelope::~FixedEnvelope()[inline],[virtual]
       Definition at line 75 of file fixedEnvelopes.h.

       Definition at line 40 of file fixedEnvelopes.h.

int*IsoSpec::FixedEnvelope::_confs[protected]
       Definition at line 44 of file fixedEnvelopes.h.

   size_tIsoSpec::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.

   intIsoSpec::FixedEnvelope::allDim[protected]
       Definition at line 46 of file fixedEnvelopes.h.

   intIsoSpec::FixedEnvelope::allDimSizeofInt[protected]
       Definition at line 54 of file fixedEnvelopes.h.

   size_tIsoSpec::FixedEnvelope::current_size[protected]
       Definition at line 50 of file fixedEnvelopes.h.

   boolIsoSpec::FixedEnvelope::sorted_by_mass[protected]
       Definition at line 47 of file fixedEnvelopes.h.

   boolIsoSpec::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.

   doubleIsoSpec::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.

doubleIsoSpec::FixedEnvelope::AbyssalWassersteinDistance(FixedEnvelope&other,doubleabyss_depth,doubleother_scale=1.0)
       Definition at line 414 of file fixedEnvelopes.cpp.

   template<booltgetConfs,typenameGenType=IsoLayeredGenerator>voidIsoSpec::FixedEnvelope::addConfILG(constGenType&generator)[inline]
       Definition at line 172 of file fixedEnvelopes.h.

   FixedEnvelopeIsoSpec::FixedEnvelope::bin(doublebin_width=1.0,doublemiddle=0.0)
       Definition at line 799 of file fixedEnvelopes.cpp.

   staticFixedEnvelopeIsoSpec::FixedEnvelope::Binned(constIso&iso,doubletarget_total_prob,doublebin_width,doublebin_middle=0.0)[inline],[static]
       Definition at line 236 of file fixedEnvelopes.h.

   FixedEnvelopeIsoSpec::FixedEnvelope::Binned(Iso&&iso,doubletarget_total_prob,doublebin_width,doublebin_middle=0.0)[static]
       Definition at line 1088 of file fixedEnvelopes.cpp.

   constint*IsoSpec::FixedEnvelope::conf(size_ti)const[inline]
       Definition at line 100 of file fixedEnvelopes.h.

   constint*IsoSpec::FixedEnvelope::confs()const[inline]
       Definition at line 90 of file fixedEnvelopes.h.

   size_tIsoSpec::FixedEnvelope::confs_no()const[inline]
       Definition at line 85 of file fixedEnvelopes.h.

   doubleIsoSpec::FixedEnvelope::empiric_average_mass()
       Definition at line 1065 of file fixedEnvelopes.cpp.

   doubleIsoSpec::FixedEnvelope::empiric_stddev()[inline]
       Definition at line 113 of file fixedEnvelopes.h.

   doubleIsoSpec::FixedEnvelope::empiric_variance()
       Definition at line 1075 of file fixedEnvelopes.cpp.

   staticFixedEnvelopeIsoSpec::FixedEnvelope::FromStochastic(constIso&iso,size_t_no_molecules,double_precision=0.9999,double_beta_bias=5.0,booltgetConfs=false)[inline],[static]
       Definition at line 230 of file fixedEnvelopes.h.

   staticFixedEnvelopeIsoSpec::FixedEnvelope::FromStochastic(Iso&&iso,size_t_no_molecules,double_precision=0.9999,double_beta_bias=5.0,booltgetConfs=false)[inline],[static]
       Definition at line 218 of file fixedEnvelopes.h.

   staticFixedEnvelopeIsoSpec::FixedEnvelope::FromThreshold(constIso&iso,double_threshold,bool_absolute,booltgetConfs=false)[inline],[static]
       Definition at line 194 of file fixedEnvelopes.h.

   staticFixedEnvelopeIsoSpec::FixedEnvelope::FromThreshold(Iso&&iso,doublethreshold,boolabsolute,booltgetConfs=false)[inline],[static]
       Definition at line 183 of file fixedEnvelopes.h.

   staticFixedEnvelopeIsoSpec::FixedEnvelope::FromTotalProb(constIso&iso,double_target_total_prob,bool_optimize,booltgetConfs=false)[inline],[static]
       Definition at line 211 of file fixedEnvelopes.h.

   staticFixedEnvelopeIsoSpec::FixedEnvelope::FromTotalProb(Iso&&iso,doubletarget_total_prob,booloptimize,booltgetConfs=false)[inline],[static]
       Definition at line 199 of file fixedEnvelopes.h.

   doubleIsoSpec::FixedEnvelope::get_total_prob()
       Definition at line 192 of file fixedEnvelopes.cpp.

   intIsoSpec::FixedEnvelope::getAllDim()const[inline]
       Definition at line 86 of file fixedEnvelopes.h.

   FixedEnvelopeIsoSpec::FixedEnvelope::LinearCombination(constFixedEnvelope*const*spectra,constdouble*intensities,size_tsize)[static]
       Definition at line 271 of file fixedEnvelopes.cpp.

   FixedEnvelopeIsoSpec::FixedEnvelope::LinearCombination(conststd::vector<constFixedEnvelope*>&spectra,conststd::vector<double>&intensities)[static]
       Definition at line 266 of file fixedEnvelopes.cpp.

   doubleIsoSpec::FixedEnvelope::mass(size_ti)const[inline]
       Definition at line 98 of file fixedEnvelopes.h.

   constdouble*IsoSpec::FixedEnvelope::masses()const[inline]
       Definition at line 88 of file fixedEnvelopes.h.

   voidIsoSpec::FixedEnvelope::normalize()
       Definition at line 210 of file fixedEnvelopes.cpp.

   FixedEnvelopeIsoSpec::FixedEnvelope::operator*(constFixedEnvelope&other)const
       Definition at line 84 of file fixedEnvelopes.cpp.

   FixedEnvelopeIsoSpec::FixedEnvelope::operator+(constFixedEnvelope&other)const
       Definition at line 63 of file fixedEnvelopes.cpp.

   doubleIsoSpec::FixedEnvelope::OrientedWassersteinDistance(FixedEnvelope&other)
       Definition at line 358 of file fixedEnvelopes.cpp.

   doubleIsoSpec::FixedEnvelope::prob(size_ti)const[inline]
       Definition at line 99 of file fixedEnvelopes.h.

   constdouble*IsoSpec::FixedEnvelope::probs()const[inline]
       Definition at line 89 of file fixedEnvelopes.h.

   template<booltgetConfs>voidIsoSpec::FixedEnvelope::reallocate_memory(size_tnew_size)[protected]
       Definition at line 851 of file fixedEnvelopes.cpp.

   int*IsoSpec::FixedEnvelope::release_confs()[inline]
       Definition at line 94 of file fixedEnvelopes.h.

   voidIsoSpec::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.

   voidIsoSpec::FixedEnvelope::resample(size_tionic_current,doublebeta_bias=1.0)
       Definition at line 226 of file fixedEnvelopes.cpp.

   voidIsoSpec::FixedEnvelope::scale(doublefactor)
       Definition at line 203 of file fixedEnvelopes.cpp.

   voidIsoSpec::FixedEnvelope::shift_mass(doubleshift)
       Definition at line 220 of file fixedEnvelopes.cpp.

   voidIsoSpec::FixedEnvelope::slow_reallocate_memory(size_tnew_size)[protected]
       Definition at line 874 of file fixedEnvelopes.cpp.

   voidIsoSpec::FixedEnvelope::sort_by_mass()
       Definition at line 111 of file fixedEnvelopes.cpp.

   voidIsoSpec::FixedEnvelope::sort_by_prob()
       Definition at line 123 of file fixedEnvelopes.cpp.

   template<booltgetConfs>templatevoidIsoSpec::FixedEnvelope::stochastic_init<false>(Iso&&iso,size_t_no_molecules,double_precision,double_beta_bias)
       Definition at line 1049 of file fixedEnvelopes.cpp.

   template<typenameT,booltgetConfs>ISOSPEC_FORCE_INLINEvoidIsoSpec::FixedEnvelope::store_conf(constT&generator)[inline],[protected]
       Definition at line 132 of file fixedEnvelopes.h.

   ISOSPEC_FORCE_INLINEvoidIsoSpec::FixedEnvelope::store_conf(double_mass,double_prob)[inline],[protected]
       Definition at line 139 of file fixedEnvelopes.h.

   template<booltgetConfs>ISOSPEC_FORCE_INLINEvoidIsoSpec::FixedEnvelope::swap(size_tidx1,size_tidx2,ISOSPEC_MAYBE_UNUSEDint*conf_swapspace)[inline],[protected]
       Definition at line 152 of file fixedEnvelopes.h.

   template<booltgetConfs>templatevoidIsoSpec::FixedEnvelope::threshold_init<false>(Iso&&iso,doublethreshold,boolabsolute)
       Definition at line 897 of file fixedEnvelopes.cpp.

   template<booltgetConfs>templatevoidIsoSpec::FixedEnvelope::total_prob_init<false>(Iso&&iso,doubletarget_prob,booltrim)
       Definition at line 927 of file fixedEnvelopes.cpp.

   doubleIsoSpec::FixedEnvelope::WassersteinDistance(FixedEnvelope&other)
       Definition at line 299 of file fixedEnvelopes.cpp.

   std::tuple<double,double,double>IsoSpec::FixedEnvelope::WassersteinMatch(FixedEnvelope&other,doubleflow_distance,doubleother_scale=1.0)
       Definition at line 726 of file fixedEnvelopes.cpp.

       IsoSpec::FixedEnvelope

PublicMemberFunctionsFixedEnvelope (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)
       FixedEnvelopeoperator+ (const FixedEnvelope &other) const
       FixedEnvelopeoperator* (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)
       FixedEnvelopebin (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)

   StaticPublicMemberFunctions
       static FixedEnvelopeLinearCombination (const std::vector< const FixedEnvelope * > &spectra, const
           std::vector< double > &intensities)
       static FixedEnvelopeLinearCombination (const FixedEnvelope *const *spectra, const double *intensities,
           size_t size)
       static FixedEnvelopeFromThreshold (Iso &&iso, double threshold, bool absolute, bool tgetConfs=false)
       static FixedEnvelopeFromThreshold (const Iso &iso, double _threshold, bool _absolute, bool
           tgetConfs=false)
       static FixedEnvelopeFromTotalProb (Iso &&iso, double target_total_prob, bool optimize, bool
           tgetConfs=false)
       static FixedEnvelopeFromTotalProb (const Iso &iso, double _target_total_prob, bool _optimize, bool
           tgetConfs=false)
       static FixedEnvelopeFromStochastic (Iso &&iso, size_t _no_molecules, double _precision=0.9999, double
           _beta_bias=5.0, bool tgetConfs=false)
       static FixedEnvelopeFromStochastic (const Iso &iso, size_t _no_molecules, double _precision=0.9999,
           double _beta_bias=5.0, bool tgetConfs=false)
       static FixedEnvelopeBinned (Iso &&iso, double target_total_prob, double bin_width, double
           bin_middle=0.0)
       static FixedEnvelopeBinned (const Iso &iso, double target_total_prob, double bin_width, double
           bin_middle=0.0)

   ProtectedMemberFunctions
       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)

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