| OpenMS 2.5.0

CompNovoIdentificationBase Member List

This is the complete list of members for CompNovoIdentificationBase, including all inherited members.

aa_to_weight_ | CompNovoIdentificationBase | protected
check_defaults_ | DefaultParamHandler | protected
compareSpectra_(const PeakSpectrum &s1, const PeakSpectrum &s2) | CompNovoIdentificationBase | protected
CompNovoIdentificationBase() | CompNovoIdentificationBase |
CompNovoIdentificationBase(const CompNovoIdentificationBase &source) | CompNovoIdentificationBase |
countMissedCleavagesTryptic_(const String &peptide) const | CompNovoIdentificationBase | protected
decomp_cache_ | CompNovoIdentificationBase | protected
decomp_weights_precision_ | CompNovoIdentificationBase | protected
DefaultParamHandler(const String &name) | DefaultParamHandler |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |
defaults_ | DefaultParamHandler | protected
defaultsToParam_() | DefaultParamHandler | protected
error_name_ | DefaultParamHandler | protected
filterDecomps_(std::vector< MassDecomposition > &decomps) | CompNovoIdentificationBase | protected
filterPermuts_(std::set< String > &permut) | CompNovoIdentificationBase | protected
fragment_mass_tolerance_ | CompNovoIdentificationBase | protected
getCIDSpectrum_(PeakSpectrum &spec, const String &sequence, Size charge, double prefix=0.0, double suffix=0.0) | CompNovoIdentificationBase | protected
getCIDSpectrumLight_(PeakSpectrum &spec, const String &sequence, double prefix, double suffix) | CompNovoIdentificationBase | protected
getDecompositions_(std::vector< MassDecomposition > &decomps, double mass, bool no_caching=false) | CompNovoIdentificationBase | protected
getDefaults() const | DefaultParamHandler |
getETDSpectrum_(PeakSpectrum &spec, const String &sequence, Size, double prefix=0.0, double suffix=0.0) | CompNovoIdentificationBase | protected
getIdentifications(std::vector< PeptideIdentification > &ids, const PeakMap &exp)=0 | CompNovoIdentificationBase | pure virtual
getModifiedAASequence_(const String &sequence) | CompNovoIdentificationBase | protected
getModifiedStringFromAASequence_(const AASequence &sequence) | CompNovoIdentificationBase | protected
getName() const | DefaultParamHandler |
getParameters() const | DefaultParamHandler |
getSubsections() const | DefaultParamHandler |
initIsotopeDistributions_() | CompNovoIdentificationBase | protected
IonScore typedef | CompNovoIdentificationBase |
isotope_distributions_ | CompNovoIdentificationBase | private
mass_decomp_algorithm_ | CompNovoIdentificationBase | protected
max_decomp_weight_ | CompNovoIdentificationBase | protected
max_isotope_ | CompNovoIdentificationBase | protected
max_mz_ | CompNovoIdentificationBase | protected
max_number_aa_per_decomp_ | CompNovoIdentificationBase | protected
max_number_pivot_ | CompNovoIdentificationBase | protected
max_subscore_number_ | CompNovoIdentificationBase | protected
min_aa_weight_ | CompNovoIdentificationBase | protected
min_mz_ | CompNovoIdentificationBase | protected
name_to_residue_ | CompNovoIdentificationBase | protected
operator=(const CompNovoIdentificationBase &source) | CompNovoIdentificationBase |
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual
operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual
param_ | DefaultParamHandler | protected
permute_(const String &prefix, String s, std::set< String > &permutations) | CompNovoIdentificationBase | protected static
permute_cache_ | CompNovoIdentificationBase | protected
residue_to_name_ | CompNovoIdentificationBase | protected
selectPivotIons_(std::vector< Size > &pivots, Size left, Size right, Map< double, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec, double precursor_weight, bool full_range=false) | CompNovoIdentificationBase | protected
setName(const String &name) | DefaultParamHandler |
setParameters(const Param &param) | DefaultParamHandler |
subsections_ | DefaultParamHandler | protected
subspec_to_sequences_ | CompNovoIdentificationBase | protected
tryptic_only_ | CompNovoIdentificationBase | protected
updateMembers_() override | CompNovoIdentificationBase | protected virtual
warn_empty_defaults_ | DefaultParamHandler | protected
windowMower_(PeakSpectrum &spec, double windowsize, Size no_peaks) | CompNovoIdentificationBase | protected
zhang_ | CompNovoIdentificationBase | protected
~CompNovoIdentificationBase() override | CompNovoIdentificationBase |
~DefaultParamHandler() | DefaultParamHandler | virtual