FragmentIndex Member List

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

add_a_ions_	FragmentIndex	private
add_b_ions_	FragmentIndex	private
add_c_ions_	FragmentIndex	private
add_x_ions_	FragmentIndex	private
add_y_ions_	FragmentIndex	private
add_z_ions_	FragmentIndex	private
bucket_min_mz_	FragmentIndex	protected
bucketsize_	FragmentIndex	protected
build(const std::vector< FASTAFile::FASTAEntry > &fasta_entries)	FragmentIndex
check_defaults_	DefaultParamHandler	protected
clear()	FragmentIndex
DefaultParamHandler(const String &name)	DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)	DefaultParamHandler
DefaultParamHandler()	DefaultParamHandler	private
defaults_	DefaultParamHandler	protected
defaultsToParam_()	DefaultParamHandler	protected
digestion_enzyme_	FragmentIndex	private
error_name_	DefaultParamHandler	protected
fi_fragments_	FragmentIndex	protected
fi_peptides_	FragmentIndex	protected
fragment_max_mz_	FragmentIndex	protected
fragment_min_mz_	FragmentIndex	protected
fragment_mz_tolerance_	FragmentIndex	protected
fragment_mz_tolerance_unit_ppm_	FragmentIndex	protected
FragmentIndex()	FragmentIndex
generatePeptides(const std::vector< FASTAFile::FASTAEntry > &fasta_entries)	FragmentIndex	protected
getDefaults() const	DefaultParamHandler
getName() const	DefaultParamHandler
getParameters() const	DefaultParamHandler
getPeptides() const	FragmentIndex
getPeptidesInPrecursorRange(float precursor_mass, const std::pair< float, float > &window)	FragmentIndex
getSubsections() const	DefaultParamHandler
is_build_	FragmentIndex	protected
isBuild() const	FragmentIndex
isOpenSearchMode_() const	FragmentIndex	inlineprivate
max_fragment_charge_	FragmentIndex	private
max_isotope_error_	FragmentIndex	private
max_precursor_charge_	FragmentIndex	private
max_processed_hits_	FragmentIndex	private
max_variable_mods_per_peptide_	FragmentIndex	private
min_isotope_error_	FragmentIndex	private
min_matched_peaks_	FragmentIndex	private
min_precursor_charge_	FragmentIndex	private
missed_cleavages_	FragmentIndex	private
modifications_fixed_	FragmentIndex	private
modifications_variable_	FragmentIndex	private
open_precursor_window_lower_	FragmentIndex	private
open_precursor_window_upper_	FragmentIndex	private
operator=(const DefaultParamHandler &rhs)	DefaultParamHandler
operator==(const DefaultParamHandler &rhs) const	DefaultParamHandler	virtual
param_	DefaultParamHandler	protected
peptide_max_length_	FragmentIndex	private
peptide_max_mass_	FragmentIndex	private
peptide_min_length_	FragmentIndex	private
peptide_min_mass_	FragmentIndex	private
precursor_mz_tolerance_	FragmentIndex	protected
precursor_mz_tolerance_unit_ppm_	FragmentIndex	protected
query(const Peak1D &peak, const std::pair< size_t, size_t > &peptide_idx_range, uint16_t peak_charge)	FragmentIndex
queryPeaks(SpectrumMatchesTopN &candidates, const MSSpectrum &spectrum, const std::pair< size_t, size_t > &candidates_range, const int16_t isotope_error, const uint16_t precursor_charge)	FragmentIndex	private
querySpectrum(const MSSpectrum &spectrum, SpectrumMatchesTopN &sms)	FragmentIndex
searchDifferentPrecursorRanges(const MSSpectrum &spectrum, float precursor_mass, SpectrumMatchesTopN &sms, uint16_t charge)	FragmentIndex	private
setName(const String &name)	DefaultParamHandler
setParameters(const Param &param)	DefaultParamHandler
subsections_	DefaultParamHandler	protected
trimHits(SpectrumMatchesTopN &init_hits) const	FragmentIndex	private
updateMembers_() override	FragmentIndex	protectedvirtual
warn_empty_defaults_	DefaultParamHandler	protected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")	DefaultParamHandler	static
~DefaultParamHandler()	DefaultParamHandler	virtual
~FragmentIndex() override=default	FragmentIndex