Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
TOPPMetaProSIP Member List

This is the complete list of members for TOPPMetaProSIP, 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
ADDITIONAL_ISOTOPESTOPPMetaProSIPprotected
calculateCorrelation(Size n_element, const vector< double > &isotopic_intensities, IsotopePatterns patterns, MapRateToScoreType &map_rate_to_correlation_score, bool use_N15, double mass, double min_correlation_distance_to_averagine)TOPPMetaProSIPinlineprotected
calculateGlobalLR(const vector< double > &isotopic_intensities)TOPPMetaProSIPinlineprotected
CANNOT_WRITE_OUTPUT_FILE enum valueTOPPBase
checkIfIniParametersAreApplicable_(const Param &ini_params)TOPPBaseprotected
checkParam_(const Param &param, const String &filename, const String &location) const TOPPBaseprotected
debug_level_TOPPBaseprotected
EXECUTION_OK enum valueTOPPBase
ExitCodes enum nameTOPPBase
EXTERNAL_PROGRAM_ERROR enum valueTOPPBase
extractIncorporationsAtCorrelationMaxima(SIPPeptide &sip_peptide, const IsotopePatterns &patterns, double weight_merge_window=5.0, double min_corr_threshold=0.5, double min_decomposition_weight=10.0)TOPPMetaProSIPinlineprotected
extractIncorporationsAtHeighestDecompositionWeights(SIPPeptide &sip_peptide, const IsotopePatterns &patterns, double weight_merge_window=5.0, double min_corr_threshold=0.5, double min_low_RIA_threshold=-1, double min_decomposition_weight=10.0)TOPPMetaProSIPinlineprotected
extractIsotopicIntensities(Size element_count, double mass_diff, double mz_tolerance_ppm, double seed_rt, double seed_mz, double seed_charge, const MSExperiment< Peak1D > &peak_map)TOPPMetaProSIPinlineprotected
extractPeakSpectrum(Size element_count, double mass_diff, double rt, double feature_hit_theoretical_mz, Int feature_hit_charge, const MSExperiment<> &peak_map)TOPPMetaProSIPinlineprotected
FEATURE_STRINGTOPPMetaProSIPprotected
filterIsotopicIntensities(vector< double >::const_iterator &pattern_begin, vector< double >::const_iterator &pattern_end, vector< double >::const_iterator &intensities_begin, vector< double >::const_iterator &intensities_end, double TIC_threshold=0.99)TOPPMetaProSIPinlineprotected
findApexRT(const FeatureMap::iterator feature_it, double hit_rt, const MSExperiment< Peak1D > &peak_map, Size n_scans)TOPPMetaProSIPinlineprotected
findEntry_(const String &name) const TOPPBaseprotected
getBestRateScorePair(const MapRateToScoreType &map_rate_to_score, double &best_rate, double &best_score)TOPPMetaProSIPinlineprotected
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
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
isotopicIntensitiesToSpectrum(double mz_start, double mass_diff, Int charge, vector< double > isotopic_intensities)TOPPMetaProSIPinlineprotected
log_type_TOPPBaseprotected
main(int argc, const char **argv)TOPPBase
main_(int, const char **)TOPPMetaProSIPinlineprotectedvirtual
mergeSpectra(const MSExperiment<> &to_merge)TOPPMetaProSIPinlineprotected
MISSING_PARAMETERS enum valueTOPPBase
normalizeToMax(const MapRateToScoreType &map_rate_to_decomposition_weight)TOPPMetaProSIPinlineprotected
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
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_()TOPPMetaProSIPinlineprotectedvirtual
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
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
TOPPMetaProSIP()TOPPMetaProSIPinline
UNASSIGNED_ID_STRINGTOPPMetaProSIPprotected
UNEXPECTED_RESULT enum valueTOPPBase
UNIDENTIFIED_STRINGTOPPMetaProSIPprotected
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
writePeakIntensities_(SVOutStream &out_stream, vector< double > isotopic_intensities, bool write_13Cpeaks)TOPPMetaProSIPinlineprotected
writeWSDL_(const String &filename)TOPPBaseprotected
~TOPPBase()TOPPBasevirtual

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:57 using doxygen 1.8.9.1