--- name: "IsoSpec_FixedEnvelope" section: "3" platform: "linux" package: "libisospec++-dev" version: "2.2.1-4.1+b3" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/IsoSpec_FixedEnvelope" --- # IsoSpec\_FixedEnvelope(3) ## 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\ void **threshold\_init** (**Iso** &&iso, double threshold, bool absolute)\ template\ void **addConfILG** (const GenType &generator)\ template\ void **total\_prob\_init** (**Iso** &&iso, double target\_prob, bool trim)\ template\ 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\ ISOSPEC\_FORCE\_INLINE void **store\_conf** (const T &generator)\ ISOSPEC\_FORCE\_INLINE void **store\_conf** (double \_mass, double \_prob)\ template\ ISOSPEC\_FORCE\_INLINE void **swap** (size\_t idx1, size\_t idx2, ISOSPEC\_MAYBE\_UNUSED int \*conf\_swapspace)\ template\ 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\ 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\ 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\ 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\ 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\ 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\ template void IsoSpec::FixedEnvelope::threshold\_init\< false \> (Iso && iso, double threshold, bool absolute) Definition at line **897** of file **fixedEnvelopes.cpp**. ### template\ 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 Generated automatically by Doxygen for IsoSpec from the source code.