Base class for Search Engine Adapters. More...

#include <OpenMS/APPLICATIONS/SearchEngineBase.h>

Inheritance diagram for SearchEngineBase:

Collaboration diagram for SearchEngineBase:

Public Member Functions
	SearchEngineBase ()=delete
	No default constructor. More...

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

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

	~SearchEngineBase () override
	Destructor. More...

String	getRawfileName (int ms_level=2) const
	Reads the '-in' argument from internal parameters (usually an mzML file) and checks if MS2 spectra are present and are centroided. More...

String	getDBFilename (const String &db="") const
	Reads the '-database' argument from internal parameters (or from `db`) and tries to find the db in search directories (if it cannot be found immediately). If not found, an exception is thrown. More...

virtual void	registerPeptideIndexingParameter_ (Param peptide_indexing_parameter)
	Adds option to reassociate peptides with proteins (and annotate target/decoy information) More...

virtual SearchEngineBase::ExitCodes	reindex_ (std::vector< ProteinIdentification > &protein_identifications, std::vector< PeptideIdentification > &peptide_identifications) const
	Reindex peptide to protein association. More...

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...

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). 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...

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. More...

Protected Member Functions inherited from TOPPBase
virtual void	registerOptionsAndFlags_ ()=0
	Sets the valid command line options (with argument) and flags (without argument). 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	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. More...

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. 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, const 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, const 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, const 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, const 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, const 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 (use `getOutputDirOption()` for output directories) More...

String	getOutputDirOption (const String &name) const
	Returns the value of a previously registered output_dir 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...

virtual ExitCodes	main_ (int argc, const char **argv)=0
	The actual "main" method. main_() is invoked by main(). More...

void	writeLogInfo_ (const String &text) const
	Writes a string to the log file and to OPENMS_LOG_INFO. More...

void	writeLogWarn_ (const String &text) const
	Writes a string to the log file and to OPENMS_LOG_WARN. More...

void	writeLogError_ (const String &text) const
	Writes a string to the log file and to OPENMS_LOG_ERROR. More...

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`. 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 OPENMS_LOG_DEBUG 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...

template<typename Writer >
void	writeToolDescription_ (Writer &writer, std::string write_type, std::string fileExtension)
	Helper function avoiding repeated code between CTD, JSON and CWL. 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...

Detailed Description

Base class for Search Engine Adapters.

It is build on top of TOPPBase and provides convenience functions for regular tasks in SearchEngines.

This base class enforces a common parameter scheme upon each adapter. E.g. '-database' and '-in'. This might be extended/changed in the future.

Constructor & Destructor Documentation

◆ SearchEngineBase() [1/3]

SearchEngineBase ( )

delete

No default constructor.

◆ SearchEngineBase() [2/3]

SearchEngineBase ( const SearchEngineBase & )

delete

No default copy constructor.

◆ SearchEngineBase() [3/3]

SearchEngineBase	(	const String &	name,
		const String &	description,
		bool	official = `true`,
		const std::vector< Citation > &	citations = `{}`,
		bool	toolhandler_test = `true`
	)

Constructor.

Must match TOPPBase' Ctor!

Parameters

name	Tool name.
description	Short description of the tool (one line).
official	If this is an official TOPP tool contained in the OpenMS/TOPP release. If true the tool name is checked against the list of TOPP tools and a warning printed if missing.
citations	Add one or more citations if they are associated specifically to this TOPP tool; they will be printed during `--help`
toolhandler_test	Check if this tool is registered with the ToolHandler (disable for unit tests only)

◆ ~SearchEngineBase()

~SearchEngineBase ( )

override

Destructor.

Member Function Documentation

◆ getDBFilename()

String getDBFilename ( const String & db = "" ) const

Reads the '-database' argument from internal parameters (or from db) and tries to find the db in search directories (if it cannot be found immediately). If not found, an exception is thrown.

Parameters

db	[Optional] Instead of reading the '-database', you can provide a custom name here (might be required for special db formats, see OMSSA)

Returns: filename for DB (might be a relative or absolute path)

Exceptions

OpenMS::Exception::FileNotFound if database name could not be resolved

◆ getRawfileName()

String getRawfileName ( int ms_level = 2 ) const

Reads the '-in' argument from internal parameters (usually an mzML file) and checks if MS2 spectra are present and are centroided.

If the file is an mzML file, the spectra annotation can be checked. If no MS2 or profile MS2 data is found, an exception is thrown. If the file is any other format, the overhead of reading in the file is too large and we just issue a general warning that centroided data should be used.

Parameters

ms_level The MS level to check for their type (centroided/profile)

Returns: A filename (might be a relative or absolute path)

Exceptions

OpenMS::Exception::FileEmpty	if no spectra are found (mzML only)
OpenMS::Exception::IllegalArgument	if spectra are not centroided (mzML only)

◆ registerPeptideIndexingParameter_()

virtual void registerPeptideIndexingParameter_ ( Param peptide_indexing_parameter )

virtual

Adds option to reassociate peptides with proteins (and annotate target/decoy information)

Parameters

peptide_indexing_parameter peptide indexer settings. May be modified to enable search engine specific defaults (e.g., not-tryptic etc.).

◆ reindex_()

virtual SearchEngineBase::ExitCodes reindex_	(	std::vector< ProteinIdentification > &	protein_identifications,
		std::vector< PeptideIdentification > &	peptide_identifications
	)		const

virtual

Reindex peptide to protein association.

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SearchEngineBase() [1/3]

◆ SearchEngineBase() [2/3]

◆ SearchEngineBase() [3/3]

◆ ~SearchEngineBase()

Member Function Documentation

◆ getDBFilename()

◆ getRawfileName()

◆ registerPeptideIndexingParameter_()

◆ reindex_()