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void | registerOptionsAndFlags_ () |
| Sets the valid command line options (with argument) and flags (without argument). More...
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void | 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) |
| > filter intensity to remove noise or additional incorporation peaks that otherwise might interfere with correlation calculation More...
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void | 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) |
| Returns highest scoring rate and score pair in the map. More...
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void | getBestRateScorePair (const MapRateToScoreType &map_rate_to_score, double &best_rate, double &best_score) |
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PeakSpectrum | extractPeakSpectrum (Size element_count, double mass_diff, double rt, double feature_hit_theoretical_mz, Int feature_hit_charge, const PeakMap &peak_map) |
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vector< double > | extractIsotopicIntensities (Size element_count, double mass_diff, double mz_tolerance_ppm, double seed_rt, double seed_mz, double seed_charge, const PeakMap &peak_map) |
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void | writePeakIntensities_ (SVOutStream &out_stream, vector< double > isotopic_intensities, bool write_13Cpeaks) |
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MapRateToScoreType | normalizeToMax (const MapRateToScoreType &map_rate_to_decomposition_weight) |
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vector< double > | findApexRT (const FeatureMap::iterator feature_it, double hit_rt, const PeakMap &peak_map, Size n_scans) |
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PeakSpectrum | mergeSpectra (const PeakMap &to_merge) |
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PeakSpectrum | isotopicIntensitiesToSpectrum (double mz_start, double mass_diff, Int charge, vector< double > isotopic_intensities) |
| > converts a vector of isotopic intensities to a peak spectrum starting at mz=mz_start with mass_diff/charge step size More...
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void | 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) |
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void | 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) |
| > Collect decomposition coefficients. Starting at the largest decomposition weights merge smaller weights in the merge window. More...
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double | calculateGlobalLR (const vector< double > &isotopic_intensities) |
| > calculate the global labeling ration based on all but the first 4 peaks More...
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ExitCodes | main_ (int, const char **) |
| The actual "main" method. main_() is invoked by main(). More...
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const String & | getIniLocation_ () const |
| Returns the location of the ini file where parameters are taken from. E.g. if the command line was TOPPTool -instance 17 , then this will be "TOPPTool:17:" . Note the ':' at the end. More...
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const String & | toolName_ () const |
| Returns the tool name. More...
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void | printUsage_ () |
| Prints the tool-specific command line options and appends the common options. More...
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bool | parseRange_ (const String &text, double &low, double &high) const |
| Parses a range string ([a]:[b]) into two variables (doubles) More...
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bool | parseRange_ (const String &text, Int &low, Int &high) const |
| Parses a range string ([a]:[b]) into two variables (integers) More...
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const DocumentIDTagger & | getDocumentIDTagger_ () const |
| get DocumentIDTagger to assign DocumentIDs to maps More...
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bool | writeCTD_ () |
| Write common tool description (CTD) file. More...
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ExitCodes | writeWSDL_ (const String &filename) |
| Write WSDL file and validate it. Returns EXECUTION_OK or INTERNAL_ERROR (if validation failed) More...
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String | getParamArgument_ (const Param::ParamEntry &entry) const |
| Utility function that determines a suitable argument value for the given Param::ParamEntry. More...
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std::vector< ParameterInformation > | paramToParameterInformation_ (const Param ¶m) const |
| Translates the given parameter object into a vector of ParameterInformation, that can be utilized for cl parsing. More...
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ParameterInformation | paramEntryToParameterInformation_ (const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const |
| Transforms a ParamEntry object to command line parameter (ParameterInformation). More...
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void | registerParamSubsectionsAsTOPPSubsections_ (const Param ¶m) |
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void | registerFullParam_ (const Param ¶m) |
| Register command line parameters for all entries in a Param object. More...
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void | registerStringOption_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false) |
| Registers a string option. More...
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void | setValidStrings_ (const String &name, const std::vector< String > &strings) |
| Sets the valid strings for a string option or a whole string list. More...
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void | setValidStrings_ (const String &name, const std::string vstrings[], int count) |
| Sets the valid strings for a string option or a whole string list. More...
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void | registerInputFile_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList()) |
| Registers an input file option. More...
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void | registerOutputFile_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false) |
| Registers an output file option. More...
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void | setValidFormats_ (const String &name, const std::vector< String > &formats, const bool force_OpenMS_format=true) |
| Sets the formats for a input/output file option or for all members of an input/output file lists. More...
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void | registerDoubleOption_ (const String &name, const String &argument, double default_value, const String &description, bool required=true, bool advanced=false) |
| Registers a double option. More...
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void | setMinInt_ (const String &name, Int min) |
| Sets the minimum value for the integer parameter(can be a list of integers,too) name . More...
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void | setMaxInt_ (const String &name, Int max) |
| Sets the maximum value for the integer parameter(can be a list of integers,too) name . More...
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void | setMinFloat_ (const String &name, double min) |
| Sets the minimum value for the floating point parameter(can be a list of floating points,too) name . More...
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void | setMaxFloat_ (const String &name, double max) |
| Sets the maximum value for the floating point parameter(can be a list of floating points,too) name . More...
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void | registerIntOption_ (const String &name, const String &argument, Int default_value, const String &description, bool required=true, bool advanced=false) |
| Registers an integer option. More...
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void | registerIntList_ (const String &name, const String &argument, IntList default_value, const String &description, bool required=true, bool advanced=false) |
| Registers a list of integers option. More...
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void | registerDoubleList_ (const String &name, const String &argument, DoubleList default_value, const String &description, bool required=true, bool advanced=false) |
| Registers a list of doubles option. More...
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void | registerStringList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false) |
| Registers a list of strings option. More...
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void | registerInputFileList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList()) |
| Registers a list of input files option. More...
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void | registerOutputFileList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false) |
| Registers a list of output files option. More...
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void | registerFlag_ (const String &name, const String &description, bool advanced=false) |
| Registers a flag. More...
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void | registerSubsection_ (const String &name, const String &description) |
| Registers an allowed subsection in the INI file (usually from OpenMS algorithms). More...
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void | registerTOPPSubsection_ (const String &name, const String &description) |
| Registers an allowed subsection in the INI file originating from the TOPP tool itself. More...
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void | addEmptyLine_ () |
| Adds an empty line between registered variables in the documentation. More...
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String | getStringOption_ (const String &name) const |
| Returns the value of a previously registered string option. More...
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double | getDoubleOption_ (const String &name) const |
| Returns the value of a previously registered double option. More...
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Int | getIntOption_ (const String &name) const |
| Returns the value of a previously registered integer option. More...
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StringList | getStringList_ (const String &name) const |
| Returns the value of a previously registered StringList. More...
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IntList | getIntList_ (const String &name) const |
| Returns the value of a previously registered IntList. More...
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DoubleList | getDoubleList_ (const String &name) const |
| Returns the value of a previously registered DoubleList. More...
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bool | getFlag_ (const String &name) const |
| Returns the value of a previously registered flag. More...
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const ParameterInformation & | findEntry_ (const String &name) const |
| Finds the entry in the parameters_ array that has the name name . More...
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Param const & | getParam_ () const |
| Return all parameters relevant to this TOPP tool. More...
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void | checkParam_ (const Param ¶m, const String &filename, const String &location) const |
| Checks top-level entries of param according to the information during registration. More...
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void | checkIfIniParametersAreApplicable_ (const Param &ini_params) |
| Checks if the parameters of the provided ini file are applicable to this tool. More...
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void | writeLog_ (const String &text) const |
| Writes a string to the log file and to std::cout. More...
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void | writeDebug_ (const String &text, UInt min_level) const |
| Writes a text to the log file and to std::cout if the debug level is at least min_level . More...
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void | writeDebug_ (const String &text, const Param ¶m, UInt min_level) const |
| Writes a String followed by a Param to the log file and to std::cout if the debug level is at least min_level . More...
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String | makeTempDirectory_ () const |
| Creates a unique temporary directory and returns its name. More...
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void | removeTempDirectory_ (const String &dirname, Int keep_debug=2) const |
| Removes a (temporary) directory. More...
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void | inputFileReadable_ (const String &filename, const String ¶m_name) const |
| Checks if an input file exists, is readable and is not empty. More...
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void | outputFileWritable_ (const String &filename, const String ¶m_name) const |
| Checks if an output file is writable. More...
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void | addDataProcessing_ (ConsensusMap &map, const DataProcessing &dp) const |
| Data processing setter for consensus maps. More...
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void | addDataProcessing_ (FeatureMap &map, const DataProcessing &dp) const |
| Data processing setter for feature maps. More...
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void | addDataProcessing_ (PeakMap &map, const DataProcessing &dp) const |
| Data processing setter for peak maps. More...
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DataProcessing | getProcessingInfo_ (DataProcessing::ProcessingAction action) const |
| Returns the data processing information. More...
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DataProcessing | getProcessingInfo_ (const std::set< DataProcessing::ProcessingAction > &actions) const |
| Returns the data processing information. More...
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