RNPxlSearch Member List

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

addDataProcessing_(ConsensusMap &map, const DataProcessing &dp) const	TOPPBase	protected
addDataProcessing_(FeatureMap &map, const DataProcessing &dp) const	TOPPBase	protected
addDataProcessing_(PeakMap &map, const DataProcessing &dp) const	TOPPBase	inlineprotected
addEmptyLine_()	TOPPBase	protected
ANNOTATIONS_MARKER_ION_PREFIX	RNPxlSearch	protectedstatic
can_xl_	RNPxlSearch	private
CANNOT_WRITE_OUTPUT_FILE enum value	TOPPBase
checkIfIniParametersAreApplicable_(const Param &ini_params)	TOPPBase	protected
checkParam_(const Param &param, const String &filename, const String &location) const	TOPPBase	protected
citations_	TOPPBase	protected
cite_openms_	TOPPBase	protectedstatic
debug_level_	TOPPBase	protected
EXECUTION_OK enum value	TOPPBase
ExitCodes enum name	TOPPBase
EXTERNAL_PROGRAM_ERROR enum value	TOPPBase
fast_scoring_	RNPxlSearch	private
findEntry_(const String &name) const	TOPPBase	protected
getDoubleList_(const String &name) const	TOPPBase	protected
getDoubleOption_(const String &name) const	TOPPBase	protected
getFlag_(const String &name) const	TOPPBase	protected
getIniLocation_() const	TOPPBase	inlineprotected
getIntList_(const String &name) const	TOPPBase	protected
getIntOption_(const String &name) const	TOPPBase	protected
getParam_() const	TOPPBase	protected
getParamArgument_(const Param::ParamEntry &entry) const	TOPPBase	protected
getProcessingInfo_(DataProcessing::ProcessingAction action) const	TOPPBase	protected
getProcessingInfo_(const std::set< DataProcessing::ProcessingAction > &actions) const	TOPPBase	protected
getStringList_(const String &name) const	TOPPBase	protected
getStringOption_(const String &name) const	TOPPBase	protected
ILLEGAL_PARAMETERS enum value	TOPPBase
INCOMPATIBLE_INPUT_DATA enum value	TOPPBase
initializeSpectrumGenerators(TheoreticalSpectrumGenerator &total_loss_spectrum_generator, TheoreticalSpectrumGenerator &partial_loss_spectrum_generator, TheoreticalSpectrumGenerator &a_ion_sub_score_spectrum_generator, TheoreticalSpectrumGenerator &immonium_ion_sub_score_spectrum_generator, TheoreticalSpectrumGenerator &precursor_ion_sub_score_spectrum_generator) const	RNPxlSearch	inlineprotected
INPUT_FILE_CORRUPT enum value	TOPPBase
INPUT_FILE_EMPTY enum value	TOPPBase
INPUT_FILE_NOT_FOUND enum value	TOPPBase
INPUT_FILE_NOT_READABLE enum value	TOPPBase
inputFileReadable_(const String &filename, const String &param_name) const	TOPPBase	protected
INTERNAL_ERROR enum value	TOPPBase
localization_	RNPxlSearch	private
log_type_	TOPPBase	protected
main(int argc, const char **argv)	TOPPBase
main_(int, const char **) override	RNPxlSearch	inlineprotectedvirtual
makeAutoRemoveTempDirectory_(Int keep_debug=2)	TOPPBase	protected
makeTempDirectory_() const	TOPPBase	protected
mapPrecursorMassesToScans(const Int min_precursor_charge, const Int max_precursor_charge, const IntList &precursor_isotopes, const double small_peptide_mass_filter_threshold, const Size peptide_min_size, const PeakMap &spectra, multimap< double, pair< Size, int >> &multimap_mass_2_scan_index) const	RNPxlSearch	inlineprotected
MISSING_PARAMETERS enum value	TOPPBase
NucleotideToFeasibleFragmentAdducts typedef	RNPxlSearch	protected
official_	TOPPBase	protected
outputFileWritable_(const String &filename, const String &param_name) const	TOPPBase	protected
paramEntryToParameterInformation_(const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const	TOPPBase	protected
paramToParameterInformation_(const Param &param) const	TOPPBase	protected
PARSE_ERROR enum value	TOPPBase
parseRange_(const String &text, double &low, double &high) const	TOPPBase	protected
parseRange_(const String &text, Int &low, Int &high) const	TOPPBase	protected
postProcessHits_(const PeakMap &exp, vector< vector< AnnotatedHit > > &annotated_hits, vector< ProteinIdentification > &protein_ids, vector< PeptideIdentification > &peptide_ids, Size top_hits, const RNPxlModificationMassesResult &mm, const vector< ResidueModification > &fixed_modifications, const vector< ResidueModification > &variable_modifications, Size max_variable_mods_per_peptide)	RNPxlSearch	inlineprotected
postScoreHits_(const PeakMap &exp, vector< vector< AnnotatedHit > > &annotated_hits, Size top_hits, const RNPxlModificationMassesResult &mm, const vector< ResidueModification > &fixed_modifications, const vector< ResidueModification > &variable_modifications, Size max_variable_mods_per_peptide, const TheoreticalSpectrumGenerator &partial_loss_spectrum_generator, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const RNPxlParameterParsing::PrecursorsToMS2Adducts &all_feasible_adducts)	RNPxlSearch	inlineprotected
preprocessSpectra_(PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool single_charge_spectra, bool annotate_charge=false)	RNPxlSearch	inlineprotected
printUsage_()	TOPPBase	protected
registerDoubleList_(const String &name, const String &argument, DoubleList default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerDoubleOption_(const String &name, const String &argument, double default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerFlag_(const String &name, const String &description, bool advanced=false)	TOPPBase	protected
registerFullParam_(const Param &param)	TOPPBase	protected
registerInputFile_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())	TOPPBase	protected
registerInputFileList_(const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())	TOPPBase	protected
registerIntList_(const String &name, const String &argument, IntList default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerIntOption_(const String &name, const String &argument, Int default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerOptionsAndFlags_() override	RNPxlSearch	inlineprotectedvirtual
registerOutputFile_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerOutputFileList_(const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerParamSubsectionsAsTOPPSubsections_(const Param &param)	TOPPBase	protected
registerStringList_(const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerStringOption_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerSubsection_(const String &name, const String &description)	TOPPBase	protected
registerTOPPSubsection_(const String &name, const String &description)	TOPPBase	protected
removeTempDirectory_(const String &dirname, Int keep_debug=2) const	TOPPBase	protected
RNPxlSearch()	RNPxlSearch	inline
runExternalProcess_(const QString &executable, const QStringList &arguments, const QString &workdir="") const	TOPPBase	protected
scorePartialLossFragments_(const PeakSpectrum &exp_spectrum, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &partial_loss_spectrum_z1, const PeakSpectrum &partial_loss_spectrum_z2, const PeakSpectrum &marker_ions_sub_score_spectrum_z1, float &partial_loss_sub_score, float &marker_ions_sub_score, float &plss_MIC, float &plss_err, float &plss_Morph) const	RNPxlSearch	inlineprotected
scoreTotalLossFragments_(const PeakSpectrum &exp_spectrum, const PeakSpectrum &total_loss_spectrum, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &a_ion_sub_score_spectrum, const PeakSpectrum &precursor_sub_score_spectrum, const PeakSpectrum &immonium_sub_score_spectrum, float &total_loss_score, float &tlss_MIC, float &tlss_err, float &tlss_Morph, float &immonium_sub_score, float &precursor_sub_score, float &a_ion_sub_score) const	RNPxlSearch	inlineprotected
setMaxFloat_(const String &name, double max)	TOPPBase	protected
setMaxInt_(const String &name, Int max)	TOPPBase	protected
setMaxNumberOfThreads(int num_threads)	TOPPBase	static
setMinFloat_(const String &name, double min)	TOPPBase	protected
setMinInt_(const String &name, Int min)	TOPPBase	protected
setValidFormats_(const String &name, const std::vector< String > &formats, const bool force_OpenMS_format=true)	TOPPBase	protected
setValidStrings_(const String &name, const std::vector< String > &strings)	TOPPBase	protected
setValidStrings_(const String &name, const std::string vstrings[], int count)	TOPPBase	protected
test_mode_	TOPPBase	protected
toolName_() const	TOPPBase	protected
topp_ini_file_	TOPPBase	protectedstatic
TOPPBase(const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={})	TOPPBase
UNEXPECTED_RESULT enum value	TOPPBase
UNKNOWN_ERROR enum value	TOPPBase
verboseVersion_	TOPPBase	protected
version_	TOPPBase	protected
writeCTD_()	TOPPBase	protected
writeDebug_(const String &text, UInt min_level) const	TOPPBase	protected
writeDebug_(const String &text, const Param &param, UInt min_level) const	TOPPBase	protected
writeLog_(const String &text) const	TOPPBase	protected
writeWSDL_(const String &filename)	TOPPBase	protected
~TOPPBase()	TOPPBase	virtual