#include <OpenMS/ANALYSIS/ID/SiriusAdapterAlgorithm.h>

Inheritance diagram for SiriusAdapterAlgorithm:

Collaboration diagram for SiriusAdapterAlgorithm:

Classes
class	Fingerid

class	ParameterModifier

class	ParameterSection

class	Passatutto

class	Preprocessing

class	Project

class	Sirius

class	SiriusTemporaryFileSystemObjects
	Struct for temporary folder structure. More...

Public Member Functions
	SiriusAdapterAlgorithm ()
	default constructor More...

bool	isFeatureOnly () const

UInt	getFilterByNumMassTraces () const

double	getPrecursorMzTolerance () const

double	getPrecursorRtTolerance () const

bool	precursorMzToleranceUnitIsPPM () const

bool	isNoMasstraceInfoIsotopePattern () const

int	getIsotopePatternIterations () const

int	getNumberOfSiriusCandidates () const
	Accessors for Sirius Parameters. More...

void	updateExistingParameter (const Param &param)
	Updates all parameters that already exist in this DefaultParamHandler with the values provided by the input param object. More...

bool	hasFullNameParameter (const String &name) const
	Checks whether this DefaultParamHandler has a ParamEntry with the provided name. More...

void	preprocessingSirius (const String &featureinfo, const MSExperiment &spectra, FeatureMapping::FeatureMappingInfo &fm_info, FeatureMapping::FeatureToMs2Indices &feature_mapping) const
	Preprocessing needed for SIRIUS. More...

void	logFeatureSpectraNumber (const String &featureinfo, const FeatureMapping::FeatureToMs2Indices &feature_mapping, const MSExperiment &spectra) const
	logs number of features and spectra used More...

void	logInSiriusAccount (String &executable, const String &email, const String &password) const
	Log in to Sirius with personal user account (required in Sirius >= 5). More...

const vector< String >	callSiriusQProcess (const String &tmp_ms_file, const String &tmp_out_dir, String &executable, const String &out_csifingerid, const bool decoy_generation) const
	Call SIRIUS with QProcess. More...

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Static Public Member Functions
static String	determineSiriusExecutable (String &executable)
	Checks if the provided String points to a valid SIRIUS executable, otherwise tries to select the executable from the environment. More...

static void	sortSiriusWorkspacePathsByScanIndex (std::vector< String > &subdirs)
	Sort function using the extracted scan_index from the sirius workspace file path. More...

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Private Types
using	SiriusSubtool = ParameterSection

Private Attributes
Preprocessing	preprocessing

Project	project

Sirius	sirius

Fingerid	fingerid

Passatutto	passatutto

Additional Inherited Members
Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Member Typedef Documentation

◆ SiriusSubtool

using SiriusSubtool = ParameterSection

private

Constructor & Destructor Documentation

◆ SiriusAdapterAlgorithm()

SiriusAdapterAlgorithm ( )

default constructor

Member Function Documentation

◆ callSiriusQProcess()

const vector< String > callSiriusQProcess	(	const String &	tmp_ms_file,
		const String &	tmp_out_dir,
		String &	executable,
		const String &	out_csifingerid,
		const bool	decoy_generation
	)		const

Call SIRIUS with QProcess.

Parameters

tmp_ms_file	path to temporary .ms file
tmp_out_dir	path to temporary output folder
executable	path to executable
out_csifingerid	path to CSI:FingerID output (can be empty).

Returns: Vector with paths to a compound

◆ determineSiriusExecutable()

static String determineSiriusExecutable ( String & executable )

static

Checks if the provided String points to a valid SIRIUS executable, otherwise tries to select the executable from the environment.

Returns: Path to SIRIUS executable

Parameters

executable Path to the potential executable

◆ getFilterByNumMassTraces()

UInt getFilterByNumMassTraces ( ) const

inline

◆ getIsotopePatternIterations()

int getIsotopePatternIterations ( ) const

inline

◆ getNumberOfSiriusCandidates()

int getNumberOfSiriusCandidates ( ) const

inline

Accessors for Sirius Parameters.

◆ getPrecursorMzTolerance()

double getPrecursorMzTolerance ( ) const

inline

◆ getPrecursorRtTolerance()

double getPrecursorRtTolerance ( ) const

inline

◆ hasFullNameParameter()

bool hasFullNameParameter ( const String & name ) const

Checks whether this DefaultParamHandler has a ParamEntry with the provided name.

Parameters

name	The name of the ParamEntry that should be checked for its existence in this DefaultParamHandler

Returns: Whether this DefaultParamHandler has an ParamEntry for the provided name.

◆ isFeatureOnly()

bool isFeatureOnly ( ) const

inline

◆ isNoMasstraceInfoIsotopePattern()

bool isNoMasstraceInfoIsotopePattern ( ) const

inline

◆ logFeatureSpectraNumber()

void logFeatureSpectraNumber	(	const String &	featureinfo,
		const FeatureMapping::FeatureToMs2Indices &	feature_mapping,
		const MSExperiment &	spectra
	)		const

logs number of features and spectra used

Prints the number of features and spectra used (OPENMS_LOG_INFO)

Parameters

featureinfo	Path to featureXML
feature_mapping	FeatureToMs2Indices with feature mapping
spectra	Input of MSExperiment with spectra information

◆ logInSiriusAccount()

void logInSiriusAccount	(	String &	executable,
		const String &	email,
		const String &	password
	)		const

Log in to Sirius with personal user account (required in Sirius >= 5).

Parameters

email	User account E-Mail.
password	User account password.

◆ precursorMzToleranceUnitIsPPM()

bool precursorMzToleranceUnitIsPPM ( ) const

inline

◆ preprocessingSirius()

void preprocessingSirius	(	const String &	featureinfo,
		const MSExperiment &	spectra,
		FeatureMapping::FeatureMappingInfo &	fm_info,
		FeatureMapping::FeatureToMs2Indices &	feature_mapping
	)		const

Preprocessing needed for SIRIUS.

Returns: FeatureToMS2Indices

Filter number of masstraces and perform feature mapping.

Parameters

featureinfo	Path to featureXML
spectra	Input of MSExperiment with spectra information
fm_info	Emtpy - stores FeatureMaps and KDTreeMaps internally
feature_mapping	Empty FeatureToMs2Indices

◆ sortSiriusWorkspacePathsByScanIndex()

static void sortSiriusWorkspacePathsByScanIndex ( std::vector< String > & subdirs )

static

Sort function using the extracted scan_index from the sirius workspace file path.

Returns: Vector of sorted sirius workspace paths based on the scan_index

◆ updateExistingParameter()

void updateExistingParameter ( const Param & param )

Updates all parameters that already exist in this DefaultParamHandler with the values provided by the input param object.

Parameters

param The Param object supplying updated parameter values. Keys that exist in the param parameter, but not in this DefaultParamHander, are ignored.

Member Data Documentation

◆ fingerid

Fingerid fingerid

private

◆ passatutto

Passatutto passatutto

private

◆ preprocessing

Preprocessing preprocessing

private

◆ project

Project project

private

◆ sirius

Sirius sirius

private

Classes

Public Member Functions

Static Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ SiriusSubtool

Constructor & Destructor Documentation

◆ SiriusAdapterAlgorithm()

Member Function Documentation

◆ callSiriusQProcess()

◆ determineSiriusExecutable()

◆ getFilterByNumMassTraces()

◆ getIsotopePatternIterations()

◆ getNumberOfSiriusCandidates()

◆ getPrecursorMzTolerance()

◆ getPrecursorRtTolerance()

◆ hasFullNameParameter()

◆ isFeatureOnly()

◆ isNoMasstraceInfoIsotopePattern()

◆ logFeatureSpectraNumber()

◆ logInSiriusAccount()

◆ precursorMzToleranceUnitIsPPM()

◆ preprocessingSirius()

◆ sortSiriusWorkspacePathsByScanIndex()

◆ updateExistingParameter()

Member Data Documentation

◆ fingerid

◆ passatutto

◆ preprocessing

◆ project

◆ sirius