TOPPFLASHDeconv Class Reference

Inheritance diagram for TOPPFLASHDeconv:

Collaboration diagram for TOPPFLASHDeconv:

Public Member Functions
	TOPPFLASHDeconv ()
Public Member Functions inherited from TOPPBase
	TOPPBase ()=delete
	No default constructor.
	TOPPBase (const TOPPBase &)=delete
	No default copy constructor.
	TOPPBase (const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={}, bool toolhandler_test=true)
	Constructor.
virtual	~TOPPBase ()
	Destructor.
ExitCodes	main (int argc, const char **argv)
	Main routine of all TOPP applications.
String	getToolPrefix () const
	Returns the prefix used to identify the tool.
String	getDocumentationURL () const
	Returns a link to the documentation of the tool (accessible on our servers and only after inclusion in the nightly branch or a release).

Protected Member Functions
void	registerOptionsAndFlags_ () override
	Sets the valid command line options (with argument) and flags (without argument).
Param	getSubsectionDefaults_ (const String &prefix) const override
ExitCodes	main_ (int, const char **) override
	The actual "main" method. main_() is invoked by main().
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.
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.
ParameterInformation	paramEntryToParameterInformation_ (const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const
	Transforms a ParamEntry object to command line parameter (ParameterInformation).
void	registerParamSubsectionsAsTOPPSubsections_ (const Param &param)
void	registerFullParam_ (const Param &param)
	Register command line parameters for all entries in a Param object.
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.
void	setValidStrings_ (const String &name, const std::vector< String > &strings)
	Sets the valid strings for a string option or a whole string list.
void	setValidStrings_ (const String &name, const std::string vstrings[], int count)
	Sets the valid strings for a string option or a whole string list.
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.
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.
void	registerOutputPrefix_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
	Registers an output file prefix used for tools with multiple file output.
void	registerOutputDir_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
	Registers an output directory used for tools with multiple output files which are not an output file list, i.e. do not correspond to the number of input files.
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.
void	registerDoubleOption_ (const String &name, const String &argument, double default_value, const String &description, bool required=true, bool advanced=false)
	Registers a double option.
void	setMinInt_ (const String &name, Int min)
	Sets the minimum value for the integer parameter(can be a list of integers,too) name.
void	setMaxInt_ (const String &name, Int max)
	Sets the maximum value for the integer parameter(can be a list of integers,too) name.
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.
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.
void	registerIntOption_ (const String &name, const String &argument, Int default_value, const String &description, bool required=true, bool advanced=false)
	Registers an integer option.
void	registerIntList_ (const String &name, const String &argument, const IntList &default_value, const String &description, bool required=true, bool advanced=false)
	Registers a list of integers option.
void	registerDoubleList_ (const String &name, const String &argument, const DoubleList &default_value, const String &description, bool required=true, bool advanced=false)
	Registers a list of doubles option.
void	registerStringList_ (const String &name, const String &argument, const StringList &default_value, const String &description, bool required=true, bool advanced=false)
	Registers a list of strings option.
void	registerInputFileList_ (const String &name, const String &argument, const StringList &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())
	Registers a list of input files option.
void	registerOutputFileList_ (const String &name, const String &argument, const StringList &default_value, const String &description, bool required=true, bool advanced=false)
	Registers a list of output files option.
void	registerFlag_ (const String &name, const String &description, bool advanced=false)
	Registers a flag.
void	registerSubsection_ (const String &name, const String &description)
	Registers an allowed subsection in the INI file (usually from OpenMS algorithms).
void	registerTOPPSubsection_ (const String &name, const String &description)
	Registers an allowed subsection in the INI file originating from the TOPP tool itself.
void	addEmptyLine_ ()
	Adds an empty line between registered variables in the documentation.
String	getStringOption_ (const String &name) const
	Returns the value of a previously registered string option (use getOutputDirOption() for output directories)
String	getOutputDirOption (const String &name) const
	Returns the value of a previously registered output_dir option.
double	getDoubleOption_ (const String &name) const
	Returns the value of a previously registered double option.
Int	getIntOption_ (const String &name) const
	Returns the value of a previously registered integer option.
StringList	getStringList_ (const String &name) const
	Returns the value of a previously registered StringList.
IntList	getIntList_ (const String &name) const
	Returns the value of a previously registered IntList.
DoubleList	getDoubleList_ (const String &name) const
	Returns the value of a previously registered DoubleList.
bool	getFlag_ (const String &name) const
	Returns the value of a previously registered flag.
const ParameterInformation &	findEntry_ (const String &name) const
	Finds the entry in the parameters_ array that has the name name.
Param const &	getParam_ () const
	Return all parameters relevant to this TOPP tool.
void	checkParam_ (const Param &param, const String &filename, const String &location) const
	Checks top-level entries of param according to the information during registration.
void	fileParamValidityCheck_ (const StringList &param_value, const String &param_name, const ParameterInformation &p) const
	checks if files of an input file list exist
void	fileParamValidityCheck_ (String &param_value, const String &param_name, const ParameterInformation &p) const
	checks if an input file exists (respecting the flags)
void	checkIfIniParametersAreApplicable_ (const Param &ini_params)
	Checks if the parameters of the provided ini file are applicable to this tool.
void	printUsage_ ()
	Prints the tool-specific command line options and appends the common options.
void	writeLogInfo_ (const String &text) const
	Writes a string to the log file and to OPENMS_LOG_INFO.
void	writeLogWarn_ (const String &text) const
	Writes a string to the log file and to OPENMS_LOG_WARN.
void	writeLogError_ (const String &text) const
	Writes a string to the log file and to OPENMS_LOG_ERROR.
void	writeDebug_ (const String &text, UInt min_level) const
	Writes a string to the log file and to OPENMS_LOG_DEBUG if the debug level is at least min_level.
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 OPENMS_LOG_DEBUG if the debug level is at least min_level.
ExitCodes	runExternalProcess_ (const QString &executable, const QStringList &arguments, const QString &workdir="", const std::map< QString, QString > &env=std::map< QString, QString >()) const
	Runs an external process via ExternalProcess and prints its stderr output on failure or if debug_level > 4.
ExitCodes	runExternalProcess_ (const QString &executable, const QStringList &arguments, String &proc_stdout, String &proc_stderr, const QString &workdir="", const std::map< QString, QString > &env=std::map< QString, QString >()) 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.
const String &	toolName_ () const
	Returns the tool name.
void	inputFileReadable_ (const String &filename, const String &param_name) const
	Checks if an input file exists, is readable and is not empty.
void	outputFileWritable_ (const String &filename, const String &param_name) const
	Checks if an output file is writable.
bool	parseRange_ (const String &text, double &low, double &high) const
	Parses a range string ([a]:[b]) into two variables (doubles)
bool	parseRange_ (const String &text, Int &low, Int &high) const
	Parses a range string ([a]:[b]) into two variables (integers)
void	addDataProcessing_ (ConsensusMap &map, const DataProcessing &dp) const
	Data processing setter for consensus maps.
void	addDataProcessing_ (FeatureMap &map, const DataProcessing &dp) const
	Data processing setter for feature maps.
void	addDataProcessing_ (PeakMap &map, const DataProcessing &dp) const
	Data processing setter for peak maps.
DataProcessing	getProcessingInfo_ (DataProcessing::ProcessingAction action) const
	Returns the data processing information.
DataProcessing	getProcessingInfo_ (const std::set< DataProcessing::ProcessingAction > &actions) const
	Returns the data processing information.
template<typename Writer >
void	writeToolDescription_ (Writer &writer, std::string write_type, std::string fileExtension)
	Helper function avoiding repeated code between CTD, JSON and CWL.

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 , EXTERNAL_PROGRAM_NOTFOUND }
	Exit codes. More...
Static Public Member Functions inherited from TOPPBase
static void	setMaxNumberOfThreads (int num_threads)
	Sets the maximal number of usable threads.
Static Public Attributes inherited from TOPPBase
static const char *	TAG_OUTPUT_FILE = "output file"
static const char *	TAG_INPUT_FILE = "input file"
static const char *	TAG_OUTPUT_DIR = "output dir"
static const char *	TAG_OUTPUT_PREFIX = "output prefix"
static const char *	TAG_ADVANCED = "advanced"
static const char *	TAG_REQUIRED = "required"
static const Citation	cite_openms
	The latest and greatest OpenMS citation.
Protected Attributes inherited from TOPPBase
String	version_
	Version string (if empty, the OpenMS/TOPP version is printed)
String	verboseVersion_
	Version string including additional revision/date time information. Note: This differs from version_ only if not provided by the user.
bool	official_
	Flag indicating if this an official TOPP tool.
std::vector< Citation >	citations_
	Papers, specific for this tool (will be shown in '–help')
bool	toolhandler_test_
	Enable the ToolHandler tests.
ProgressLogger::LogType	log_type_
	Type of progress logging.
bool	test_mode_
	Test mode.
Int	debug_level_
	Debug level set by -debug.
Static Protected Attributes inherited from TOPPBase
static String	topp_ini_file_
	.TOPP.ini file for storing system default parameters

Constructor & Destructor Documentation

TOPPFLASHDeconv()

TOPPFLASHDeconv ( )

inline

Member Function Documentation

getSubsectionDefaults_()

Param getSubsectionDefaults_ ( const String &  prefix ) const

inlineoverrideprotectedvirtual

Returns default parameters for each subsection. FLASHDeconvAlgorithm stores all parameters in a single Param object with prefixes (SD:, ft:, iq:). This function splits them into separate subsections for a cleaner CLI interface: -FD:* -> top-level algorithm parameters (after removing SD:, ft:, iq: prefixed params) -SD:* -> spectral deconvolution parameters -ft:* -> feature tracing parameters -iq:* -> isobaric quantification parameters

Reimplemented from TOPPBase.

References DefaultParamHandler::getDefaults(), and Param::removeAll().

main_()

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

inlineoverrideprotectedvirtual

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

Implements TOPPBase.

References TOPPBase::CANNOT_WRITE_OUTPUT_FILE, Param::copy(), TOPPBase::EXECUTION_OK, files(), FLASHDeconvAlgorithm::getAveragine(), FLASHDeconvAlgorithm::getDecoyAveragine(), TOPPBase::getDoubleOption_(), TOPPBase::getFlag_(), TOPPBase::getIntOption_(), FLASHDeconvAlgorithm::getNoiseDecoyWeight(), MzMLFile::getOptions(), TOPPBase::getParam_(), TOPPBase::getStringOption_(), FLASHDeconvAlgorithm::getTolerances(), Param::getValue(), Param::insert(), MzMLFile::load(), TOPPBase::log_type_, OPENMS_LOG_FATAL_ERROR, OPENMS_LOG_INFO, FLASHDeconvAlgorithm::run(), ProgressLogger::setLogType(), PeakFileOptions::setMSLevels(), PeakFileOptions::setMZRange(), MzMLFile::setOptions(), DefaultParamHandler::setParameters(), PeakFileOptions::setRTRange(), FLASHDeconvSpectrumFile::writeDeconvolvedMasses(), FLASHDeconvSpectrumFile::writeDeconvolvedMassesHeader(), FLASHDeconvFeatureFile::writeFeatures(), FLASHDeconvFeatureFile::writeHeader(), FLASHDeconvSpectrumFile::writeIsobaricQuantification(), FLASHDeconvSpectrumFile::writeMzML(), FLASHDeconvSpectrumFile::writeTopFD(), FLASHDeconvFeatureFile::writeTopFDFeatureHeader(), FLASHDeconvFeatureFile::writeTopFDFeatures(), and FLASHDeconvSpectrumFile::writeTopFDHeader().

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.

References TOPPBase::registerDoubleOption_(), TOPPBase::registerFlag_(), TOPPBase::registerInputFile_(), TOPPBase::registerIntOption_(), TOPPBase::registerOutputFile_(), TOPPBase::registerSubsection_(), TOPPBase::setMaxInt_(), TOPPBase::setMinInt_(), and TOPPBase::setValidFormats_().