IsoSpec::FixedEnvelope(3)

💖 IsoSpec::FixedEnvelope 💖

okay bestie, this is the IsoSpec::FixedEnvelope(3) page from the Library Functions Manual. part 1 is here and it's long, so we're keeping every single signature, attribute, and definition line. no skipping, no summarizing. periodt. 💅

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✨ NAME ✨

IsoSpec::FixedEnvelope

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🌸 SYNOPSIS 🌸

👑 Public Member Functions

here's the whole public lineup, bestie — every overload, every const, every default, exactly as written:

       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)

slay. that's the public API and it's a lot in the best way. 🫶

🌟 Static Public Member Functions

these are the static ones — here they are exactly:

       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)

okay so many From... and Binned and LinearCombination — all here, all exact. 🔥

🛡️ Protected Member Functions

backstage pass only, bestie. these are protected:

       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

the internal state, the way it's just sitting there holding the data:

• 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

one friend function, because sometimes you need a bestie with access:

       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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📖 Detailed Description 📖

Definition at line 40 of file fixedEnvelopes.h.

that's it. short and sweet. the header file is fixedEnvelopes.h and it's giving canonical. 💖

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🍼 Constructor & Destructor Documentation 💀

now the birth and death of a FixedEnvelope, bestie. every constructor and the destructor, with definitions exactly where they live.

🌱 constructor 1

ISOSPEC_FORCE_INLINE IsoSpec::FixedEnvelope::FixedEnvelope () [inline]

Definition at line 57 of file fixedEnvelopes.h.

🌱 constructor 2

IsoSpec::FixedEnvelope::FixedEnvelope (const FixedEnvelope & other)

Definition at line 25 of file fixedEnvelopes.cpp.

🌱 constructor 3

IsoSpec::FixedEnvelope::FixedEnvelope (FixedEnvelope && other)

Definition at line 36 of file fixedEnvelopes.cpp.

🌱 constructor 4

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 53 of file fixedEnvelopes.cpp.

💀 destructor

virtual IsoSpec::FixedEnvelope::~FixedEnvelope () [inline],  [virtual]

Definition at line 75 of file fixedEnvelopes.h.

💖 Member Function Documentation 💖

Okay bestie, this is the part where we meet every single method on IsoSpec::FixedEnvelope. I'm not skipping a single signature, default value, tag, or Definition at line … receipt. It's giving complete, it's giving thorough, and it's giving no cap. 🌈

• double IsoSpec::FixedEnvelope::AbyssalWassersteinDistance (FixedEnvelope & other, double abyss_depth, double other_scale = 1.0) — receipt: Definition at line 415 of file fixedEnvelopes.cpp. 🌊
• template<bool tgetConfs, typename GenType = IsoLayeredGenerator> void IsoSpec::FixedEnvelope::addConfILG (const GenType & generator) [inline] — receipt: Definition at line 172 of file fixedEnvelopes.h. ✨
• FixedEnvelope IsoSpec::FixedEnvelope::bin (double bin_width = 1.0, double middle = 0.0) — receipt: Definition at line 803 of file fixedEnvelopes.cpp. 🎀
• FixedEnvelope IsoSpec::FixedEnvelope::Binned (const Iso & iso, double target_total_prob, double bin_width, double bin_middle = 0.0) [inline], [static] — receipt: 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] — receipt: Definition at line 1092 of file fixedEnvelopes.cpp. 💫
• const int * IsoSpec::FixedEnvelope::conf (size_t i) const [inline] — receipt: Definition at line 100 of file fixedEnvelopes.h. 🧚
• const int * IsoSpec::FixedEnvelope::confs () const [inline] — receipt: Definition at line 90 of file fixedEnvelopes.h. 🌸
• size_t IsoSpec::FixedEnvelope::confs_no () const [inline] — receipt: Definition at line 85 of file fixedEnvelopes.h. 🦋
• double IsoSpec::FixedEnvelope::empiric_average_mass () — receipt: Definition at line 1069 of file fixedEnvelopes.cpp. ⭐
• double IsoSpec::FixedEnvelope::empiric_stddev () [inline] — receipt: Definition at line 113 of file fixedEnvelopes.h. 💜
• double IsoSpec::FixedEnvelope::empiric_variance () — receipt: Definition at line 1079 of file fixedEnvelopes.cpp. 🔥
• 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] — receipt: Definition at line 230 of file fixedEnvelopes.h. 🌈
• FixedEnvelope IsoSpec::FixedEnvelope::FromStochastic (Iso && iso, size_t _no_molecules, double _precision = 0.9999, double _beta_bias = 5.0, bool tgetConfs = false) [inline], [static] — receipt: Definition at line 218 of file fixedEnvelopes.h. 🍓
• FixedEnvelope IsoSpec::FixedEnvelope::FromThreshold (const Iso & iso, double _threshold, bool _absolute, bool tgetConfs = false) [inline], [static] — receipt: Definition at line 194 of file fixedEnvelopes.h. 👑
• FixedEnvelope IsoSpec::FixedEnvelope::FromThreshold (Iso && iso, double threshold, bool absolute, bool tgetConfs = false) [inline], [static] — receipt: Definition at line 183 of file fixedEnvelopes.h. 💅
• FixedEnvelope IsoSpec::FixedEnvelope::FromTotalProb (const Iso & iso, double _target_total_prob, bool _optimize, bool tgetConfs = false) [inline], [static] — receipt: Definition at line 211 of file fixedEnvelopes.h. 🫶
• FixedEnvelope IsoSpec::FixedEnvelope::FromTotalProb (Iso && iso, double target_total_prob, bool optimize, bool tgetConfs = false) [inline], [static] — receipt: Definition at line 199 of file fixedEnvelopes.h. 💀
• double IsoSpec::FixedEnvelope::get_total_prob () — receipt: Definition at line 193 of file fixedEnvelopes.cpp. 😭
• int IsoSpec::FixedEnvelope::getAllDim () const [inline] — receipt: Definition at line 86 of file fixedEnvelopes.h. 🙈
• FixedEnvelope IsoSpec::FixedEnvelope::LinearCombination (const FixedEnvelope *const * spectra, const double * intensities, size_t size) [static] — receipt: Definition at line 272 of file fixedEnvelopes.cpp. 🎀
• FixedEnvelope IsoSpec::FixedEnvelope::LinearCombination (const std::vector< const FixedEnvelope * > & spectra, const std::vector< double > & intensities) [static] — receipt: Definition at line 267 of file fixedEnvelopes.cpp. 💖
• double IsoSpec::FixedEnvelope::mass (size_t i) const [inline] — receipt: Definition at line 98 of file fixedEnvelopes.h. 🌸
• const double * IsoSpec::FixedEnvelope::masses () const [inline] — receipt: Definition at line 88 of file fixedEnvelopes.h. 🦋
• void IsoSpec::FixedEnvelope::normalize () — receipt: Definition at line 211 of file fixedEnvelopes.cpp. ✨
• FixedEnvelope IsoSpec::FixedEnvelope::operator* (const FixedEnvelope & other) const — receipt: Definition at line 85 of file fixedEnvelopes.cpp. 🔥
• FixedEnvelope IsoSpec::FixedEnvelope::operator+ (const FixedEnvelope & other) const — receipt: Definition at line 64 of file fixedEnvelopes.cpp. 💜
• double IsoSpec::FixedEnvelope::OrientedWassersteinDistance (FixedEnvelope & other) — receipt: Definition at line 359 of file fixedEnvelopes.cpp. 🌈
• double IsoSpec::FixedEnvelope::prob (size_t i) const [inline] — receipt: Definition at line 99 of file fixedEnvelopes.h. 🍓
• const double * IsoSpec::FixedEnvelope::probs () const [inline] — receipt: Definition at line 89 of file fixedEnvelopes.h. 👑
• template<bool tgetConfs> void IsoSpec::FixedEnvelope::reallocate_memory (size_t new_size) [protected] — receipt: Definition at line 855 of file fixedEnvelopes.cpp. 💅
• int * IsoSpec::FixedEnvelope::release_confs () [inline] — receipt: Definition at line 94 of file fixedEnvelopes.h. 🫶
• void IsoSpec::FixedEnvelope::release_everything () [inline] — receipt: Definition at line 95 of file fixedEnvelopes.h. 💀
• double * IsoSpec::FixedEnvelope::release_masses () [inline] — receipt: Definition at line 92 of file fixedEnvelopes.h. 😭
• double * IsoSpec::FixedEnvelope::release_probs () [inline] — receipt: Definition at line 93 of file fixedEnvelopes.h. 🙈
• void IsoSpec::FixedEnvelope::resample (size_t ionic_current, double beta_bias = 1.0) — receipt: Definition at line 227 of file fixedEnvelopes.cpp. 🎀
• void IsoSpec::FixedEnvelope::scale (double factor) — receipt: Definition at line 204 of file fixedEnvelopes.cpp. 💖
• void IsoSpec::FixedEnvelope::shift_mass (double shift) — receipt: Definition at line 221 of file fixedEnvelopes.cpp. 🌸
• void IsoSpec::FixedEnvelope::slow_reallocate_memory (size_t new_size) [protected] — receipt: Definition at line 878 of file fixedEnvelopes.cpp. 🦋
• void IsoSpec::FixedEnvelope::sort_by_mass () — receipt: Definition at line 112 of file fixedEnvelopes.cpp. ✨
• void IsoSpec::FixedEnvelope::sort_by_prob () — receipt: Definition at line 124 of file fixedEnvelopes.cpp. 🔥
• template<bool tgetConfs> template void IsoSpec::FixedEnvelope::stochastic_init< false > (Iso && iso, size_t _no_molecules, double _precision, double _beta_bias) — receipt: Definition at line 1053 of file fixedEnvelopes.cpp. 💜
• template<typename T, bool tgetConfs> ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::store_conf (const T & generator) [inline], [protected] — receipt: Definition at line 132 of file fixedEnvelopes.h. 🌈
• ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::store_conf (double _mass, double _prob) [inline], [protected] — receipt: Definition at line 139 of file fixedEnvelopes.h. 🍓
• template<bool tgetConfs> ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::swap (size_t idx1, size_t idx2, ISOSPEC_MAYBE_UNUSED int * conf_swapspace) [inline], [protected] — receipt: Definition at line 152 of file fixedEnvelopes.h. 👑
• template<bool tgetConfs> template void IsoSpec::FixedEnvelope::threshold_init< false > (Iso && iso, double threshold, bool absolute) — receipt: Definition at line 901 of file fixedEnvelopes.cpp. 💅
• template<bool tgetConfs> template void IsoSpec::FixedEnvelope::total_prob_init< false > (Iso && iso, double target_prob, bool trim) — receipt: Definition at line 931 of file fixedEnvelopes.cpp. 🫶
• double IsoSpec::FixedEnvelope::WassersteinDistance (FixedEnvelope & other) — receipt: Definition at line 300 of file fixedEnvelopes.cpp. 💀
• std::tuple< double, double, double > IsoSpec::FixedEnvelope::WassersteinMatch (FixedEnvelope & other, double flow_distance, double other_scale = 1.0) — receipt: Definition at line 730 of file fixedEnvelopes.cpp. 😭

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🎀 Member Data Documentation 🎀

These are the protected data members, bestie. They're the backstage pass. Every single one, with its receipt. 💖

• int* IsoSpec::FixedEnvelope::_confs [protected] — receipt: Definition at line 44 of file fixedEnvelopes.h. 🙈
• size_t IsoSpec::FixedEnvelope::_confs_no [protected] — receipt: Definition at line 45 of file fixedEnvelopes.h. 🎀
• double* IsoSpec::FixedEnvelope::_masses [protected] — receipt: Definition at line 42 of file fixedEnvelopes.h. 💖
• double* IsoSpec::FixedEnvelope::_probs [protected] — receipt: Definition at line 43 of file fixedEnvelopes.h. 🌸
• int IsoSpec::FixedEnvelope::allDim [protected] — receipt: Definition at line 46 of file fixedEnvelopes.h. 🦋
• int IsoSpec::FixedEnvelope::allDimSizeofInt [protected] — receipt: Definition at line 54 of file fixedEnvelopes.h. ✨
• size_t IsoSpec::FixedEnvelope::current_size [protected] — receipt: Definition at line 50 of file fixedEnvelopes.h. 🔥
• bool IsoSpec::FixedEnvelope::sorted_by_mass [protected] — receipt: Definition at line 47 of file fixedEnvelopes.h. 💜
• bool IsoSpec::FixedEnvelope::sorted_by_prob [protected] — receipt: Definition at line 48 of file fixedEnvelopes.h. 🌈
• int* IsoSpec::FixedEnvelope::tconfs [protected] — receipt: Definition at line 53 of file fixedEnvelopes.h. 🍓
• double* IsoSpec::FixedEnvelope::tmasses [protected] — receipt: Definition at line 51 of file fixedEnvelopes.h. 👑
• double IsoSpec::FixedEnvelope::total_prob [protected] — receipt: Definition at line 49 of file fixedEnvelopes.h. 💅
• double* IsoSpec::FixedEnvelope::tprobs [protected] — receipt: Definition at line 52 of file fixedEnvelopes.h. 🫶

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💖 Author 💖

Generated automatically by Doxygen for IsoSpec from the source code. That's the whole author note, and honestly, Doxygen ate and left no crumbs. 🤖✨

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Okay bestie, that's the whole page. The footer's got IsoSpec as the source/version and IsoSpec::FixedEnvelope(3) as the manpage section — no date in this footer, but the vibe is timeless. Stay slay, and may your envelopes always be fixed. 💅💖