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SimpleSearchEngine Member List

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

addDataProcessing_(ConsensusMap &map, const DataProcessing &dp) const TOPPBaseprotected
addDataProcessing_(FeatureMap &map, const DataProcessing &dp) const TOPPBaseprotected
addDataProcessing_(MSExperiment< PeakType, CT > &map, const DataProcessing &dp) const TOPPBaseinlineprotected
addEmptyLine_()TOPPBaseprotected
CANNOT_WRITE_OUTPUT_FILE enum valueTOPPBase
checkIfIniParametersAreApplicable_(const Param &ini_params)TOPPBaseprotected
checkParam_(const Param &param, const String &filename, const String &location) const TOPPBaseprotected
computeHyperScore(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const MSSpectrum< Peak1D > &exp_spectrum, const MSSpectrum< RichPeak1D > &theo_spectrum)SimpleSearchEngineinlineprotected
debug_level_TOPPBaseprotected
deisotopeAndSingleChargeMSSpectrum(SpectrumType &in, Int min_charge, Int max_charge, double fragment_tolerance, bool fragment_unit_ppm, bool keep_only_deisotoped=false, Size min_isopeaks=3, Size max_isopeaks=10, bool make_single_charged=true)SimpleSearchEngineinlineprotectedstatic
EXECUTION_OK enum valueTOPPBase
ExitCodes enum nameTOPPBase
EXTERNAL_PROGRAM_ERROR enum valueTOPPBase
findEntry_(const String &name) const TOPPBaseprotected
getDocumentIDTagger_() const TOPPBaseprotected
getDoubleList_(const String &name) const TOPPBaseprotected
getDoubleOption_(const String &name) const TOPPBaseprotected
getFlag_(const String &name) const TOPPBaseprotected
getIniLocation_() const TOPPBaseinlineprotected
getIntList_(const String &name) const TOPPBaseprotected
getIntOption_(const String &name) const TOPPBaseprotected
getModifications_(StringList modNames)SimpleSearchEngineinlineprotected
getParam_() const TOPPBaseprotected
getParamArgument_(const Param::ParamEntry &entry) const TOPPBaseprotected
getProcessingInfo_(DataProcessing::ProcessingAction action) const TOPPBaseprotected
getProcessingInfo_(const std::set< DataProcessing::ProcessingAction > &actions) const TOPPBaseprotected
getStringList_(const String &name) const TOPPBaseprotected
getStringOption_(const String &name) const TOPPBaseprotected
ILLEGAL_PARAMETERS enum valueTOPPBase
INCOMPATIBLE_INPUT_DATA enum valueTOPPBase
INPUT_FILE_CORRUPT enum valueTOPPBase
INPUT_FILE_EMPTY enum valueTOPPBase
INPUT_FILE_NOT_FOUND enum valueTOPPBase
INPUT_FILE_NOT_READABLE enum valueTOPPBase
inputFileReadable_(const String &filename, const String &param_name) const TOPPBaseprotected
INTERNAL_ERROR enum valueTOPPBase
log_type_TOPPBaseprotected
logfactorial(UInt x)SimpleSearchEngineinlineprotected
main(int argc, const char **argv)TOPPBase
main_(int, const char **)SimpleSearchEngineinlineprotectedvirtual
MISSING_PARAMETERS enum valueTOPPBase
official_TOPPBaseprotected
outputFileWritable_(const String &filename, const String &param_name) const TOPPBaseprotected
paramEntryToParameterInformation_(const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const TOPPBaseprotected
paramToParameterInformation_(const Param &param) const TOPPBaseprotected
PARSE_ERROR enum valueTOPPBase
parseRange_(const String &text, double &low, double &high) const TOPPBaseprotected
parseRange_(const String &text, Int &low, Int &high) const TOPPBaseprotected
postProcessHits_(const PeakMap &exp, const vector< vector< PeptideHit > > &peptide_hits, vector< ProteinIdentification > &protein_ids, vector< PeptideIdentification > &peptide_ids, Size top_hits)SimpleSearchEngineinlineprotected
preprocessSpectra_(PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm)SimpleSearchEngineinlineprotected
printUsage_()TOPPBaseprotected
registerDoubleList_(const String &name, const String &argument, DoubleList default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerDoubleOption_(const String &name, const String &argument, double default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerFlag_(const String &name, const String &description, bool advanced=false)TOPPBaseprotected
registerFullParam_(const Param &param)TOPPBaseprotected
registerInputFile_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())TOPPBaseprotected
registerInputFileList_(const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerIntList_(const String &name, const String &argument, IntList default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerIntOption_(const String &name, const String &argument, Int default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerOptionsAndFlags_()SimpleSearchEngineinlineprotectedvirtual
registerOutputFile_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerOutputFileList_(const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerParamSubsectionsAsTOPPSubsections_(const Param &param)TOPPBaseprotected
registerStringList_(const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerStringOption_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerSubsection_(const String &name, const String &description)TOPPBaseprotected
registerTOPPSubsection_(const String &name, const String &description)TOPPBaseprotected
setMaxFloat_(const String &name, double max)TOPPBaseprotected
setMaxInt_(const String &name, Int max)TOPPBaseprotected
setMaxNumberOfThreads(int num_threads)TOPPBasestatic
setMinFloat_(const String &name, double min)TOPPBaseprotected
setMinInt_(const String &name, Int min)TOPPBaseprotected
setValidFormats_(const String &name, const std::vector< String > &formats, const bool force_OpenMS_format=true)TOPPBaseprotected
setValidStrings_(const String &name, const std::vector< String > &strings)TOPPBaseprotected
SimpleSearchEngine()SimpleSearchEngineinline
test_mode_TOPPBaseprotected
toolName_() const TOPPBaseprotected
topp_ini_file_TOPPBaseprotectedstatic
TOPPBase(const String &name, const String &description, bool official=true, bool id_tag_support=false, bool require_args=true, const String &version="")TOPPBase
UNEXPECTED_RESULT enum valueTOPPBase
UNKNOWN_ERROR enum valueTOPPBase
verboseVersion_TOPPBaseprotected
version_TOPPBaseprotected
writeCTD_()TOPPBaseprotected
writeDebug_(const String &text, UInt min_level) const TOPPBaseprotected
writeDebug_(const String &text, const Param &param, UInt min_level) const TOPPBaseprotected
writeLog_(const String &text) const TOPPBaseprotected
writeWSDL_(const String &filename)TOPPBaseprotected
~TOPPBase()TOPPBasevirtual

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11