Inheritance diagram for TOPPGNPSExport:

Collaboration diagram for TOPPGNPSExport:

Public Member Functions
	TOPPGNPSExport ()

Public Member Functions inherited from TOPPBase
	TOPPBase ()=delete
	No default constructor. More...

	TOPPBase (const TOPPBase &)=delete
	No default copy constructor. More...

	TOPPBase (const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={}, bool toolhandler_test=true)
	Constructor. More...

virtual	~TOPPBase ()
	Destructor. More...

ExitCodes	main (int argc, const char **argv)
	Main routine of all TOPP applications. More...

String	getToolPrefix () const
	Returns the prefix used to identify the tool. More...

Protected Member Functions
void	registerOptionsAndFlags_ () override
	Sets the valid command line options (with argument) and flags (without argument). More...

ExitCodes	main_ (int, const char **) override
	The actual "main" method. main_() is invoked by main(). More...

Protected Member Functions inherited from TOPPBase
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	fileParamValidityCheck_ (const StringList &param_value, const String &param_name, const ParameterInformation &p) const
	checks if files of an input file list exist More...

void	fileParamValidityCheck_ (String &param_value, const String &param_name, const ParameterInformation &p) const
	checks if an input file exists (respecting the flags) More...

void	checkIfIniParametersAreApplicable_ (const Param &ini_params)
	Checks if the parameters of the provided ini file are applicable to this tool. More...

void	printUsage_ ()
	Prints the tool-specific command line options and appends the common options. 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...

ExitCodes	runExternalProcess_ (const QString &executable, const QStringList &arguments, const QString &workdir="") const
	Runs an external process via ExternalProcess and prints its stderr output on failure or if debug_level > 4. More...

ExitCodes	runExternalProcess_ (const QString &executable, const QStringList &arguments, String &proc_stdout, String &proc_stderr, const QString &workdir="") const

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	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...

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...

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...

bool	writeCTD_ ()
	Write common tool description (CTD) file. More...

Private Member Functions
void	binPeaks_ (const vector< Peak1D > &peaks, const double bin_width, vector< Peak1D > &binned_peaks)
	Bin peaks by similar m/z position and averaged intensities. More...

void	flattenAndBinSpectra_ (MSExperiment &exp, const double bin_width, vector< Peak1D > &merged_peaks)
	Flatten spectra from MSExperiment into a single vector of Peak1D peaks. More...

void	writeMSMSBlockHeader_ (ofstream &output_file, const String &output_type, const int &scan_index, const String &feature_id, const int &feature_charge, const String &feature_mz, const String &spec_index, const String &feature_rt)
	Private function that outputs MS/MS Block Header. More...

void	writeMSMSBlock_ (ofstream &output_file, const vector< Peak1D > &peaks)
	Private function to write peak mass and intensity to output file. More...

void	sortElementMapsByIntensity_ (const ConsensusFeature &feature, vector< pair< int, double >> &element_maps)
	Private method used to sort PeptideIdentification map indices in order of annotation's intensity. More...

void	getElementPeptideIdentificationsByElementIntensity_ (const ConsensusFeature &feature, vector< pair< int, double >> &sorted_element_maps, vector< pair< int, int >> &pepts)
	Retrieve list of PeptideIdentification parameters from ConsensusFeature metadata, sorted by map intensity. More...

Static Private Attributes
static constexpr double	DEF_COSINE_SIMILARITY = 0.9

static constexpr double	DEF_MERGE_BIN_SIZE = static_cast<double>(BinnedSpectrum::DEFAULT_BIN_WIDTH_HIRES)

static constexpr double	DEF_PREC_MASS_TOL = 0.5

static constexpr bool	DEF_PREC_MASS_TOL_ISPPM = false

static constexpr double	DEF_PEPT_CUTOFF = 5

static constexpr double	DEF_MSMAP_CACHE = 50

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...

bool	toolhandler_test_
	Enable the ToolHandler tests. 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

◆ TOPPGNPSExport()

TOPPGNPSExport ( )

inline

Member Function Documentation

◆ binPeaks_()

void binPeaks_	(	const vector< Peak1D > &	peaks,
		const double	bin_width,
		vector< Peak1D > &	binned_peaks
	)

inlineprivate

Bin peaks by similar m/z position and averaged intensities.

Parameters

peaks	Vector of Peak1D peaks sorted by m/z position
bin_width	Size of bin
binned_peaks	Result vector with binned peaks passed in by reference

◆ flattenAndBinSpectra_()

void flattenAndBinSpectra_	(	MSExperiment &	exp,
		const double	bin_width,
		vector< Peak1D > &	merged_peaks
	)

inlineprivate

Flatten spectra from MSExperiment into a single vector of Peak1D peaks.

Parameters

exp	MSExperiment containing at least 1 spectrum
bin_width	Size of binned scan (m/z)
merged_peaks	Result vector of peaks passed in by reference

References MSExperiment::getSpectra(), and MSExperiment::getSpectrum().

◆ getElementPeptideIdentificationsByElementIntensity_()

void getElementPeptideIdentificationsByElementIntensity_	(	const ConsensusFeature &	feature,
		vector< pair< int, double >> &	sorted_element_maps,
		vector< pair< int, int >> &	pepts
	)

inlineprivate

Retrieve list of PeptideIdentification parameters from ConsensusFeature metadata, sorted by map intensity.

Parameters

feature	ConsensusFeature feature containing PeptideIdentification annotations
sorted_element_maps	Sorted list of element_maps
pepts	Result vector of <map_index,spectrum_index> of PeptideIdentification annotations sorted by map intensity in feature

References BaseFeature::getPeptideIdentifications().

◆ main_()

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

inlineoverrideprotectedvirtual

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

Implements TOPPBase.

References MSExperiment::addSpectrum(), ConsensusFeature::begin(), BinnedSpectrum::DEFAULT_BIN_OFFSET_HIRES, ConsensusFeature::end(), BaseFeature::getCharge(), Peak2D::getMZ(), UniqueIdInterface::getUniqueId(), ConsensusXMLFile::load(), MzMLFile::load(), ProgressLogger::setLogType(), ProgressLogger::setProgress(), and ProgressLogger::startProgress().

◆ 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.

◆ sortElementMapsByIntensity_()

void sortElementMapsByIntensity_	(	const ConsensusFeature &	feature,
		vector< pair< int, double >> &	element_maps
	)

inlineprivate

Private method used to sort PeptideIdentification map indices in order of annotation's intensity.

Parameters

feature	ConsensusFeature annotated with PeptideIdentifications
featureMaps_sortedByInt	Result vector of map indices in order of PeptideIdentification intensity

References ConsensusFeature::begin(), and ConsensusFeature::end().

◆ writeMSMSBlock_()

void writeMSMSBlock_	(	ofstream &	output_file,
		const vector< Peak1D > &	peaks
	)

inlineprivate

Private function to write peak mass and intensity to output file.

Parameters

output_file	Stream that will write to file
peaks	Vector of peaks that will be outputted

◆ writeMSMSBlockHeader_()

void writeMSMSBlockHeader_	(	ofstream &	output_file,
		const String &	output_type,
		const int &	scan_index,
		const String &	feature_id,
		const int &	feature_charge,
		const String &	feature_mz,
		const String &	spec_index,
		const String &	feature_rt
	)

inlineprivate

Private function that outputs MS/MS Block Header.

Parameters

output_file	Stream that will write to file
scan_index	Current scan index in GNPSExport formatted output
feature_id	ConsensusFeature Id found in input mzXML file
feature_charge	ConsensusFeature's highest charge as mentioned in the input mzXML file
feature_mz	m/z position of PeptideIdentification with highest intensity
spec_index	Spectrum index of PeptideIdentification with highest intensity
feature_rt	ConsensusFeature's retention time specified in input mzXML file

Member Data Documentation

◆ DEF_COSINE_SIMILARITY

constexpr double DEF_COSINE_SIMILARITY = 0.9

staticconstexprprivate

◆ DEF_MERGE_BIN_SIZE

constexpr double DEF_MERGE_BIN_SIZE = static_cast<double>(BinnedSpectrum::DEFAULT_BIN_WIDTH_HIRES)

staticconstexprprivate

◆ DEF_MSMAP_CACHE

constexpr double DEF_MSMAP_CACHE = 50

staticconstexprprivate

◆ DEF_PEPT_CUTOFF

constexpr double DEF_PEPT_CUTOFF = 5

staticconstexprprivate

◆ DEF_PREC_MASS_TOL

constexpr double DEF_PREC_MASS_TOL = 0.5

staticconstexprprivate

◆ DEF_PREC_MASS_TOL_ISPPM

constexpr bool DEF_PREC_MASS_TOL_ISPPM = false

staticconstexprprivate

Public Member Functions

Protected Member Functions

Private Member Functions

Static Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ TOPPGNPSExport()

Member Function Documentation

◆ binPeaks_()

◆ flattenAndBinSpectra_()

◆ getElementPeptideIdentificationsByElementIntensity_()

◆ main_()

◆ registerOptionsAndFlags_()

◆ sortElementMapsByIntensity_()

◆ writeMSMSBlock_()

◆ writeMSMSBlockHeader_()

Member Data Documentation

◆ DEF_COSINE_SIMILARITY

◆ DEF_MERGE_BIN_SIZE

◆ DEF_MSMAP_CACHE

◆ DEF_PEPT_CUTOFF

◆ DEF_PREC_MASS_TOL

◆ DEF_PREC_MASS_TOL_ISPPM