OpenMS
CompNovoIdentificationBase Member List

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

aa_to_weight_CompNovoIdentificationBaseprotected
check_defaults_DefaultParamHandlerprotected
compareSpectra_(const PeakSpectrum &s1, const PeakSpectrum &s2) constCompNovoIdentificationBaseprotected
CompNovoIdentificationBase()CompNovoIdentificationBase
CompNovoIdentificationBase(const CompNovoIdentificationBase &source)CompNovoIdentificationBase
countMissedCleavagesTryptic_(const String &peptide) constCompNovoIdentificationBaseprotected
decomp_cache_CompNovoIdentificationBaseprotected
decomp_weights_precision_CompNovoIdentificationBaseprotected
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
error_name_DefaultParamHandlerprotected
filterDecomps_(std::vector< MassDecomposition > &decomps)CompNovoIdentificationBaseprotected
filterPermuts_(std::set< String > &permut) constCompNovoIdentificationBaseprotected
fragment_mass_tolerance_CompNovoIdentificationBaseprotected
getCIDSpectrum_(PeakSpectrum &spec, const String &sequence, Size charge, double prefix=0.0, double suffix=0.0)CompNovoIdentificationBaseprotected
getCIDSpectrumLight_(PeakSpectrum &spec, const String &sequence, double prefix, double suffix)CompNovoIdentificationBaseprotected
getDecompositions_(std::vector< MassDecomposition > &decomps, double mass, bool no_caching=false)CompNovoIdentificationBaseprotected
getDefaults() constDefaultParamHandler
getETDSpectrum_(PeakSpectrum &spec, const String &sequence, Size, double prefix=0.0, double suffix=0.0)CompNovoIdentificationBaseprotected
getIdentifications(std::vector< PeptideIdentification > &ids, const PeakMap &exp)=0CompNovoIdentificationBasepure virtual
getModifiedAASequence_(const String &sequence)CompNovoIdentificationBaseprotected
getModifiedStringFromAASequence_(const AASequence &sequence)CompNovoIdentificationBaseprotected
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
initIsotopeDistributions_()CompNovoIdentificationBaseprotected
IonScore typedefCompNovoIdentificationBase
isotope_distributions_CompNovoIdentificationBaseprivate
mass_decomp_algorithm_CompNovoIdentificationBaseprotected
max_decomp_weight_CompNovoIdentificationBaseprotected
max_isotope_CompNovoIdentificationBaseprotected
max_mz_CompNovoIdentificationBaseprotected
max_number_aa_per_decomp_CompNovoIdentificationBaseprotected
max_number_pivot_CompNovoIdentificationBaseprotected
max_subscore_number_CompNovoIdentificationBaseprotected
min_aa_weight_CompNovoIdentificationBaseprotected
min_mz_CompNovoIdentificationBaseprotected
name_to_residue_CompNovoIdentificationBaseprotected
operator=(const CompNovoIdentificationBase &source)CompNovoIdentificationBase
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs)DefaultParamHandler
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
permute_(const String &prefix, String s, std::set< String > &permutations)CompNovoIdentificationBaseprotectedstatic
permute_cache_CompNovoIdentificationBaseprotected
residue_to_name_CompNovoIdentificationBaseprotected
selectPivotIons_(std::vector< Size > &pivots, Size left, Size right, std::map< double, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec, double precursor_weight, bool full_range=false)CompNovoIdentificationBaseprotected
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
subsections_DefaultParamHandlerprotected
subspec_to_sequences_CompNovoIdentificationBaseprotected
tryptic_only_CompNovoIdentificationBaseprotected
updateMembers_() overrideCompNovoIdentificationBaseprotectedvirtual
warn_empty_defaults_DefaultParamHandlerprotected
windowMower_(PeakSpectrum &spec, double windowsize, Size no_peaks)CompNovoIdentificationBaseprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
zhang_CompNovoIdentificationBaseprotected
~CompNovoIdentificationBase() overrideCompNovoIdentificationBase
~DefaultParamHandler()DefaultParamHandlervirtual