Public Member Functions | |
| TOPPOpenPepXL () | |
 Public Member Functions inherited from TOPPBase | |
| TOPPBase (const String &name, const String &description, bool official=true, bool id_tag_support=false, bool require_args=true, const String &version="") | |
| Constructor. More... | |
| virtual | ~TOPPBase () |
| Destructor. More... | |
| ExitCodes | main (int argc, const char **argv) |
| Main routine of all TOPP applications. More... | |
Protected Member Functions | |
| void | registerOptionsAndFlags_ () |
| Sets the valid command line options (with argument) and flags (without argument). More... | |
| OPXLDataStructs::PreprocessedPairSpectra | preprocessPairs_ (const PeakMap &spectra, const vector< pair< Size, Size > > &spectrum_pairs, const double cross_link_mass_iso_shift, double fragment_mass_tolerance, double fragment_mass_tolerance_xlinks, bool fragment_mass_tolerance_unit_ppm) |
| ExitCodes | main_ (int, const char **) |
| The actual "main" method. main_() is invoked by main(). More... | |
| Protected Member Functions inherited from TOPPBase | |
| 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... | |
| const String & | toolName_ () const |
| Returns the tool name. More... | |
| void | printUsage_ () |
| Prints the tool-specific command line options and appends the common options. More... | |
| bool | parseRange_ (const String &text, double &low, double &high) const |
| Parses a range string ([a]:[b]) into two variables (doubles) More... | |
| bool | parseRange_ (const String &text, Int &low, Int &high) const |
| Parses a range string ([a]:[b]) into two variables (integers) More... | |
| const DocumentIDTagger & | getDocumentIDTagger_ () const |
| get DocumentIDTagger to assign DocumentIDs to maps More... | |
| bool | writeCTD_ () |
| Write common tool description (CTD) file. More... | |
| ExitCodes | writeWSDL_ (const String &filename) |
| Write WSDL file and validate it. Returns EXECUTION_OK or INTERNAL_ERROR (if validation failed) More... | |
| String | getParamArgument_ (const Param::ParamEntry &entry) const |
| Utility function that determines a suitable argument value for the given Param::ParamEntry. More... | |
| 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... | |
| ParameterInformation | paramEntryToParameterInformation_ (const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const |
| Transforms a ParamEntry object to command line parameter (ParameterInformation). More... | |
| void | registerParamSubsectionsAsTOPPSubsections_ (const Param ¶m) |
| void | registerFullParam_ (const Param ¶m) |
| Register command line parameters for all entries in a Param object. More... | |
| 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... | |
| void | setValidStrings_ (const String &name, const std::vector< String > &strings) |
| Sets the valid strings for a string option or a whole string list. More... | |
| 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... | |
| 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... | |
| 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... | |
| 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... | |
| 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... | |
| void | setMinInt_ (const String &name, Int min) |
Sets the minimum value for the integer parameter(can be a list of integers,too) name. More... | |
| void | setMaxInt_ (const String &name, Int max) |
Sets the maximum value for the integer parameter(can be a list of integers,too) name. More... | |
| 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... | |
| 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... | |
| 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... | |
| 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... | |
| 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... | |
| 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... | |
| 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... | |
| 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... | |
| void | registerFlag_ (const String &name, const String &description, bool advanced=false) |
| Registers a flag. More... | |
| void | registerSubsection_ (const String &name, const String &description) |
| Registers an allowed subsection in the INI file (usually from OpenMS algorithms). More... | |
| void | registerTOPPSubsection_ (const String &name, const String &description) |
| Registers an allowed subsection in the INI file originating from the TOPP tool itself. More... | |
| void | addEmptyLine_ () |
| Adds an empty line between registered variables in the documentation. More... | |
| String | getStringOption_ (const String &name) const |
| Returns the value of a previously registered string option. More... | |
| double | getDoubleOption_ (const String &name) const |
| Returns the value of a previously registered double option. More... | |
| Int | getIntOption_ (const String &name) const |
| Returns the value of a previously registered integer option. More... | |
| StringList | getStringList_ (const String &name) const |
| Returns the value of a previously registered StringList. More... | |
| IntList | getIntList_ (const String &name) const |
| Returns the value of a previously registered IntList. More... | |
| DoubleList | getDoubleList_ (const String &name) const |
| Returns the value of a previously registered DoubleList. More... | |
| bool | getFlag_ (const String &name) const |
| Returns the value of a previously registered flag. More... | |
| const ParameterInformation & | findEntry_ (const String &name) const |
Finds the entry in the parameters_ array that has the name name. More... | |
| Param const & | getParam_ () const |
| Return all parameters relevant to this TOPP tool. More... | |
| 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... | |
| void | checkIfIniParametersAreApplicable_ (const Param &ini_params) |
| Checks if the parameters of the provided ini file are applicable to this tool. More... | |
| void | writeLog_ (const String &text) const |
| Writes a string to the log file and to std::cout. More... | |
| 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... | |
| 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... | |
| String | makeTempDirectory_ () const |
| Creates a unique temporary directory and returns its name. More... | |
| void | removeTempDirectory_ (const String &dirname, Int keep_debug=2) const |
| Removes a (temporary) directory. More... | |
| void | inputFileReadable_ (const String &filename, const String ¶m_name) const |
| Checks if an input file exists, is readable and is not empty. More... | |
| void | outputFileWritable_ (const String &filename, const String ¶m_name) const |
| Checks if an output file is writable. More... | |
| void | addDataProcessing_ (ConsensusMap &map, const DataProcessing &dp) const |
| Data processing setter for consensus maps. More... | |
| void | addDataProcessing_ (FeatureMap &map, const DataProcessing &dp) const |
| Data processing setter for feature maps. More... | |
| void | addDataProcessing_ (PeakMap &map, const DataProcessing &dp) const |
| Data processing setter for peak maps. More... | |
| DataProcessing | getProcessingInfo_ (DataProcessing::ProcessingAction action) const |
| Returns the data processing information. More... | |
| DataProcessing | getProcessingInfo_ (const std::set< DataProcessing::ProcessingAction > &actions) const |
| Returns the data processing information. More... | |
Additional Inherited Members | |
| Public Types inherited from TOPPBase | |
| enum | ExitCodes { EXECUTION_OK, INPUT_FILE_NOT_FOUND, INPUT_FILE_NOT_READABLE, INPUT_FILE_CORRUPT, INPUT_FILE_EMPTY, CANNOT_WRITE_OUTPUT_FILE, ILLEGAL_PARAMETERS, MISSING_PARAMETERS, UNKNOWN_ERROR, EXTERNAL_PROGRAM_ERROR, PARSE_ERROR, INCOMPATIBLE_INPUT_DATA, INTERNAL_ERROR, UNEXPECTED_RESULT } |
| Exit codes. More... | |
| Static Public Member Functions inherited from TOPPBase | |
| static void | setMaxNumberOfThreads (int num_threads) |
| Sets the maximal number of usable threads. More... | |
| Protected Attributes inherited from TOPPBase | |
| String | version_ |
| Version string (if empty, the OpenMS/TOPP version is printed) More... | |
| String | verboseVersion_ |
| Version string including additional revision/date time information. Note: This differs from version_ only if not provided by the user. More... | |
| bool | official_ |
| Flag indicating if this an official TOPP tool. More... | |
| ProgressLogger::LogType | log_type_ |
| Type of progress logging. More... | |
| bool | test_mode_ |
| Test mode. More... | |
| Int | debug_level_ |
| Debug level set by -debug. More... | |
| Static Protected Attributes inherited from TOPPBase | |
| static String | topp_ini_file_ |
| .TOPP.ini file for storing system default parameters More... | |
Constructor & Destructor Documentation
◆ TOPPOpenPepXL()
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inline |
Member Function Documentation
◆ main_()
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inlineprotectedvirtual |
The actual "main" method. main_() is invoked by main().
Implements TOPPBase.
References PeakFileOptions::addMSLevel(), OPXLDataStructs::ProteinProteinCrossLink::alpha, IDMapper::annotate(), OPXLDataStructs::ProteinProteinCrossLink::beta, ProteinIdentification::SearchParameters::charges, PeakFileOptions::clearMSLevels(), OPXLDataStructs::CrossLinkSpectrumMatch::cross_link, OPXLDataStructs::ProteinProteinCrossLink::cross_link_position, OPXLDataStructs::ProteinProteinCrossLink::cross_linker_mass, ProteinIdentification::SearchParameters::db, ProteinIdentification::SearchParameters::digestion_enzyme, ProgressLogger::endProgress(), ProteinIdentification::SearchParameters::fixed_modifications, OPXLDataStructs::CrossLinkSpectrumMatch::frag_annotations, ProteinIdentification::SearchParameters::fragment_mass_tolerance, ProteinIdentification::SearchParameters::fragment_mass_tolerance_ppm, TheoreticalSpectrumGeneratorXLMS::getCommonIonSpectrum(), PeptideIdentification::getMetaValue(), AASequence::getMonoWeight(), MzMLFile::getOptions(), DefaultParamHandler::getParameters(), SpectrumSettings::getPrecursors(), MSExperiment::getPrimaryMSRunPath(), OPXLDataStructs::ProteinProteinCrossLink::getType(), TheoreticalSpectrumGeneratorXLMS::getXLinkIonSpectrum(), OPXLDataStructs::CrossLinkSpectrumMatch::HyperAlpha, OPXLDataStructs::CrossLinkSpectrumMatch::HyperBeta, OPXLDataStructs::CrossLinkSpectrumMatch::HyperBoth, OPXLDataStructs::CrossLinkSpectrumMatch::HyperCommon, OPXLDataStructs::CrossLinkSpectrumMatch::HyperXlink, OPXLDataStructs::CrossLinkSpectrumMatch::int_sum, OpenMS::Constants::k, ConsensusXMLFile::load(), MzMLFile::load(), FASTAFile::load(), LOG_DEBUG, ProteinIdentification::SearchParameters::mass_type, OPXLDataStructs::CrossLinkSpectrumMatch::match_odds, OPXLDataStructs::CrossLinkSpectrumMatch::matched_common_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::matched_common_beta, OPXLDataStructs::CrossLinkSpectrumMatch::matched_xlink_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::matched_xlink_beta, ProteinIdentification::SearchParameters::missed_cleavages, OPXLDataStructs::CrossLinkSpectrumMatch::percTIC, OPXLDataStructs::CrossLinkSpectrumMatch::pre_score, ProteinIdentification::SearchParameters::precursor_mass_tolerance, ProteinIdentification::SearchParameters::precursor_mass_tolerance_ppm, OpenMS::Constants::PROTON_MASS_U, OPXLDataStructs::CrossLinkSpectrumMatch::PScoreAlpha, OPXLDataStructs::CrossLinkSpectrumMatch::PScoreBeta, OPXLDataStructs::CrossLinkSpectrumMatch::PScoreBoth, OPXLDataStructs::CrossLinkSpectrumMatch::PScoreCommon, OPXLDataStructs::CrossLinkSpectrumMatch::PScoreXlink, PeptideIndexing::run(), OPXLDataStructs::CrossLinkSpectrumMatch::scan_index_heavy, OPXLDataStructs::CrossLinkSpectrumMatch::scan_index_light, OPXLDataStructs::CrossLinkSpectrumMatch::score, EnzymaticDigestion::setEnzyme(), ProgressLogger::setLogType(), MetaInfoInterface::setMetaValue(), EnzymaticDigestion::setMissedCleavages(), DefaultParamHandler::setParameters(), Param::setValue(), AASequence::size(), OPXLDataStructs::PreprocessedPairSpectra::spectra_all_peaks, OPXLDataStructs::PreprocessedPairSpectra::spectra_common_peaks, OPXLDataStructs::PreprocessedPairSpectra::spectra_xlink_peaks, ProgressLogger::startProgress(), MzIdentMLFile::store(), IdXMLFile::store(), AASequence::toString(), ProteinIdentification::SearchParameters::variable_modifications, OPXLDataStructs::CrossLinkSpectrumMatch::wTIC, OPXLDataStructs::CrossLinkSpectrumMatch::xcorrc_max, and OPXLDataStructs::CrossLinkSpectrumMatch::xcorrx_max.
◆ preprocessPairs_()
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inlineprotected |
◆ registerOptionsAndFlags_()
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inlineprotectedvirtual |
Sets the valid command line options (with argument) and flags (without argument).
The options '-ini' '-log' '-instance' '-debug' and the flag '–help' are automatically registered.
Implements TOPPBase.