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TOPPMetaProSIP Member List

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

addDataProcessing_(ConsensusMap &map, const DataProcessing &dp) constTOPPBaseprotected
addDataProcessing_(FeatureMap &map, const DataProcessing &dp) constTOPPBaseprotected
addDataProcessing_(PeakMap &map, const DataProcessing &dp) constTOPPBaseinlineprotected
addEmptyLine_()TOPPBaseprotected
ADDITIONAL_ISOTOPESTOPPMetaProSIPprotected
calculateCorrelation(Size n_element, const vector< double > &isotopic_intensities, IsotopePatterns patterns, MapRateToScoreType &map_rate_to_correlation_score, String labeling_element, 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) constTOPPBaseprotected
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 PeakMap &peak_map)TOPPMetaProSIPinlineprotected
extractPeakSpectrum(Size element_count, double mass_diff, double rt, double feature_hit_theoretical_mz, Int feature_hit_charge, const PeakMap &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 PeakMap &peak_map, Size n_scans)TOPPMetaProSIPinlineprotected
findEntry_(const String &name) constTOPPBaseprotected
getBestRateScorePair(const MapRateToScoreType &map_rate_to_score, double &best_rate, double &best_score)TOPPMetaProSIPinlineprotected
getDocumentIDTagger_() constTOPPBaseprotected
getDoubleList_(const String &name) constTOPPBaseprotected
getDoubleOption_(const String &name) constTOPPBaseprotected
getFlag_(const String &name) constTOPPBaseprotected
getIniLocation_() constTOPPBaseinlineprotected
getIntList_(const String &name) constTOPPBaseprotected
getIntOption_(const String &name) constTOPPBaseprotected
getParam_() constTOPPBaseprotected
getParamArgument_(const Param::ParamEntry &entry) constTOPPBaseprotected
getProcessingInfo_(DataProcessing::ProcessingAction action) constTOPPBaseprotected
getProcessingInfo_(const std::set< DataProcessing::ProcessingAction > &actions) constTOPPBaseprotected
getStringList_(const String &name) constTOPPBaseprotected
getStringOption_(const String &name) constTOPPBaseprotected
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) constTOPPBaseprotected
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
makeTempDirectory_() constTOPPBaseprotected
mergeSpectra(const PeakMap &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) constTOPPBaseprotected
paramEntryToParameterInformation_(const Param::ParamEntry &entry, const String &argument="", const String &full_name="") constTOPPBaseprotected
paramToParameterInformation_(const Param &param) constTOPPBaseprotected
PARSE_ERROR enum valueTOPPBase
parseRange_(const String &text, double &low, double &high) constTOPPBaseprotected
parseRange_(const String &text, Int &low, Int &high) constTOPPBaseprotected
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, const StringList &tags=StringList())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
removeTempDirectory_(const String &dirname, Int keep_debug=2) constTOPPBaseprotected
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
setValidStrings_(const String &name, const std::string vstrings[], int count)TOPPBaseprotected
test_mode_TOPPBaseprotected
toolName_() constTOPPBaseprotected
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) constTOPPBaseprotected
writeDebug_(const String &text, const Param &param, UInt min_level) constTOPPBaseprotected
writeLog_(const String &text) constTOPPBaseprotected
writePeakIntensities_(SVOutStream &out_stream, vector< double > isotopic_intensities, bool write_13Cpeaks)TOPPMetaProSIPinlineprotected
writeWSDL_(const String &filename)TOPPBaseprotected
~TOPPBase()TOPPBasevirtual

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:06 using doxygen 1.8.13