a_ion_losses_cd_ | PILISModel | protected |
a_ion_losses_cr_ | PILISModel | protected |
addPeaks_(DoubleReal mz, int charge, DoubleReal mz_offset, DoubleReal intensity, RichPeakSpectrum &spectrum, const IsotopeDistribution &id, const String &name) | PILISModel | protected |
b2_ion_losses_cd_ | PILISModel | protected |
b2_ion_losses_cr_ | PILISModel | protected |
b_ion_losses_cd_ | PILISModel | protected |
b_ion_losses_cr_ | PILISModel | protected |
check_defaults_ | DefaultParamHandler | protected |
DefaultParamHandler(const String &name) | DefaultParamHandler | |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
defaults_ | DefaultParamHandler | protected |
defaultsToParam_() | DefaultParamHandler | protected |
error_name_ | DefaultParamHandler | protected |
evaluate() | PILISModel | |
getAvailableBackboneCharge_(const AASequence &ion, Residue::ResidueType res_type, int charge) | PILISModel | protected |
getDefaults() const | DefaultParamHandler | |
getInitialTransitionProbabilities_(std::vector< DoubleReal > &bb_init, std::vector< DoubleReal > &cr_init, std::vector< DoubleReal > &sc_init, DoubleReal &precursor_init, const std::vector< DoubleReal > &bb_charges, const std::vector< DoubleReal > &sc_charges, const AASequence &peptide) | PILISModel | protected |
getName() const | DefaultParamHandler | |
getParameters() const | DefaultParamHandler | |
getSpectrum(RichPeakSpectrum &spec, const AASequence &peptide, UInt charge) | PILISModel | |
getSubsections() const | DefaultParamHandler | |
hmm_ | PILISModel | protected |
init(bool generate_models=true) | PILISModel | |
operator=(const PILISModel &mode) | PILISModel | |
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
param_ | DefaultParamHandler | protected |
parseHMMModel_(const TextFile::ConstIterator &begin, const TextFile::ConstIterator &end, HiddenMarkovModel &hmm, Param ¶m) | PILISModel | protected |
peaks_ | PILISModel | protected |
PILISModel() | PILISModel | |
PILISModel(const PILISModel &model) | PILISModel | |
precursor_model_cd_ | PILISModel | protected |
precursor_model_cr_ | PILISModel | protected |
prot_dist_ | PILISModel | protected |
readFromFile(const String &filename) | PILISModel | |
setName(const String &name) | DefaultParamHandler | |
setParameters(const Param ¶m) | DefaultParamHandler | |
spectra_aligner_ | PILISModel | protected |
subsections_ | DefaultParamHandler | protected |
train(const RichPeakSpectrum &, const AASequence &peptide, UInt charge) | PILISModel | |
tsg_ | PILISModel | protected |
updateMembers_() | PILISModel | protectedvirtual |
valid_ | PILISModel | protected |
warn_empty_defaults_ | DefaultParamHandler | protected |
writeGraphMLFile(const String &filename) | PILISModel | |
writeParameters_(std::ostream &os, const Param ¶m) | PILISModel | protected |
writeToFile(const String &filename) | PILISModel | |
y_ion_losses_cd_ | PILISModel | protected |
y_ion_losses_cr_ | PILISModel | protected |
~DefaultParamHandler() | DefaultParamHandler | virtual |
~PILISModel() | PILISModel | virtual |