TOPPOpenPepXL Class Reference

Inheritance diagram for TOPPOpenPepXL:

Public Member Functions
	TOPPOpenPepXL ()
Public Member Functions inherited from TOPPBase
	TOPPBase (const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={})
	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_ () override
	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, bool deisotope)
ExitCodes	main_ (int, const char **) override
	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...
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 &param) 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 &param)
void	registerFullParam_ (const Param &param)
	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 &param, 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 &param, 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 (you have to clean it up yourself) More...
String	makeAutoRemoveTempDirectory_ (Int keep_debug=2)
	Creates a unique temporary directory and returns its name (will be cleaned up automatically if debug level is high enough) More...
void	removeTempDirectory_ (const String &dirname, Int keep_debug=2) const
	Removes a (temporary) directory. More...
ExitCodes	runExternalProcess_ (const QString &executable, const QStringList &arguments, const QString &workdir="") const
	Runs an external process via QProcess and reports its status in the logs. More...
void	inputFileReadable_ (const String &filename, const String &param_name) const
	Checks if an input file exists, is readable and is not empty. More...
void	outputFileWritable_ (const String &filename, const String &param_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...
std::vector< Citation >	citations_
	Papers, specific for this tool (will be shown in '–help') 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...
static const Citation	cite_openms_
	The OpenMS citation. More...

Constructor & Destructor Documentation

TOPPOpenPepXL()

TOPPOpenPepXL ( )

inline

Member Function Documentation

main_()

ExitCodes main_ ( int  argc, const char **  argv  )

inlineoverrideprotectedvirtual

The actual "main" method. main_() is invoked by main().

Implements TOPPBase.

References PeakFileOptions::addMSLevel(), OPXLDataStructs::ProteinProteinCrossLink::alpha, IDMapper::annotate(), OPXLDataStructs::ProteinProteinCrossLink::beta, OpenMS::Constants::C13C12_MASSDIFF_U, 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, OpenMS::getDataArrayByName(), MSSpectrum::getIntegerDataArrays(), TheoreticalSpectrumGeneratorXLMS::getLinearIonSpectrum(), MetaInfoInterface::getMetaValue(), AASequence::getMonoWeight(), MzMLFile::getOptions(), DefaultParamHandler::getParameters(), SpectrumSettings::getPrecursors(), MSExperiment::getPrimaryMSRunPath(), OPXLDataStructs::ProteinProteinCrossLink::getType(), TheoreticalSpectrumGeneratorXLMS::getXLinkIonSpectrum(), OPXLDataStructs::CrossLinkSpectrumMatch::int_sum, OPXLDataStructs::CrossLinkSpectrumMatch::intsum_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::intsum_beta, OpenMS::Constants::k, ConsensusXMLFile::load(), MzMLFile::load(), FASTAFile::load(), LOG_DEBUG, OPXLDataStructs::CrossLinkSpectrumMatch::log_occupancy, OPXLDataStructs::CrossLinkSpectrumMatch::log_occupancy_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::log_occupancy_beta, ProteinIdentification::SearchParameters::mass_type, OPXLDataStructs::CrossLinkSpectrumMatch::match_odds, OPXLDataStructs::CrossLinkSpectrumMatch::match_odds_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::match_odds_beta, OPXLDataStructs::CrossLinkSpectrumMatch::matched_linear_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::matched_linear_beta, OPXLDataStructs::CrossLinkSpectrumMatch::matched_xlink_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::matched_xlink_beta, OpenMS::Math::mean(), ProteinIdentification::SearchParameters::missed_cleavages, OPXLDataStructs::CrossLinkSpectrumMatch::num_iso_peaks_mean, OPXLDataStructs::CrossLinkSpectrumMatch::num_iso_peaks_mean_linear_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::num_iso_peaks_mean_linear_beta, OPXLDataStructs::CrossLinkSpectrumMatch::num_iso_peaks_mean_xlinks_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::num_iso_peaks_mean_xlinks_beta, OPXLDataStructs::CrossLinkSpectrumMatch::percTIC, OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum, OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_beta, OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_linear, OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_linear_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_linear_beta, OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_xlinks, OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_xlinks_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_xlinks_beta, OPXLDataStructs::CrossLinkSpectrumMatch::pre_score, OPXLDataStructs::ProteinProteinCrossLink::precursor_correction, OPXLDataStructs::CrossLinkSpectrumMatch::precursor_correction, OPXLDataStructs::CrossLinkSpectrumMatch::precursor_error_ppm, ProteinIdentification::SearchParameters::precursor_mass_tolerance, ProteinIdentification::SearchParameters::precursor_mass_tolerance_ppm, OpenMS::Constants::PROTON_MASS_U, PeptideIndexing::run(), OPXLDataStructs::CrossLinkSpectrumMatch::scan_index_heavy, OPXLDataStructs::CrossLinkSpectrumMatch::scan_index_light, OPXLDataStructs::CrossLinkSpectrumMatch::score, ProteaseDigestion::setEnzyme(), ProgressLogger::setLogType(), MetaInfoInterface::setMetaValue(), EnzymaticDigestion::setMissedCleavages(), DefaultParamHandler::setParameters(), Param::setValue(), AASequence::size(), OPXLDataStructs::PreprocessedPairSpectra::spectra_all_peaks, OPXLDataStructs::PreprocessedPairSpectra::spectra_linear_peaks, OPXLDataStructs::PreprocessedPairSpectra::spectra_xlink_peaks, ProgressLogger::startProgress(), XQuestResultXMLFile::store(), MzIdentMLFile::store(), IdXMLFile::store(), AASequence::toString(), OPXLDataStructs::CrossLinkSpectrumMatch::total_current, ProteinIdentification::SearchParameters::variable_modifications, OPXLDataStructs::CrossLinkSpectrumMatch::wTIC, OPXLDataStructs::CrossLinkSpectrumMatch::wTICold, OPXLDataStructs::CrossLinkSpectrumMatch::xcorrc_max, OPXLDataStructs::CrossLinkSpectrumMatch::xcorrx_max, and OPXLDataStructs::CrossLinkSpectrumMatch::xquest_score.

preprocessPairs_()

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, bool  deisotope  )

inlineprotected

References NLargest::filterSpectrum(), seqan::find(), OpenMS::getDataArrayByName(), MSSpectrum::getIntegerDataArrays(), Peak1D::getMZ(), SpectrumSettings::getPrecursors(), LOG_DEBUG, Peak1D::setMZ(), MetaInfoDescription::setName(), SpectrumSettings::setPrecursors(), and MSSpectrum::sortByPosition().

registerOptionsAndFlags_()

void registerOptionsAndFlags_ ( )

inlineoverrideprotectedvirtual

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.