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

Inheritance diagram for SiriusAdapterAlgorithm:

Classes
struct	SiriusTmpStruct
	Struct for temporary folder structure. More...

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

String	getFeatureOnly ()

String	getNoMasstraceInfoIsotopePattern ()

String	getConverterMode ()

int	getIsotopePatternIterations ()

int	getCandidates ()

int	getTopNHits ()

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...

virtual 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 SiriusAdapterAlgorithm::SiriusTmpStruct	constructSiriusTmpStruct ()
	Construct temporary folder structure for SIRIUS (SiriusTmpStruct) More...

static std::pair< String, String >	checkSiriusExecutablePath (String &executable)
	Checks if executable was povided. More...

static void	preprocessingSirius (const String &featureinfo, const MSExperiment &spectra, std::vector< FeatureMap > &v_fp, KDTreeFeatureMaps &fp_map_kd, const SiriusAdapterAlgorithm &sirius_algo, FeatureMapping::FeatureToMs2Indices &feature_mapping)
	Preprocessing needed for SIRIUS. More...

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

static const std::vector< String >	callSiriusQProcess (const String &tmp_ms_file, const String &tmp_out_dir, String &executable, const String &out_csifingerid, const SiriusAdapterAlgorithm &sirius_algo)
	Call SIRIUS with QProcess. More...

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
unsigned int	filter_by_num_masstraces_

double	precursor_mz_tolerance_

String	precursor_mz_tolerance_unit_

double	precursor_rt_tolerance_

int	isotope_pattern_iterations_

String	feature_only_

String	no_masstrace_info_isotope_pattern_

String	converter_mode_

String	profile_

int	candidates_

String	database_

int	noise_

int	ppm_max_

String	isotope_

String	elements_

int	compound_timeout_

int	tree_timeout_

int	top_n_hits_

int	cores_

String	auto_charge_

String	ion_tree_

String	no_recalibration_

String	most_intense_ms2_

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...

Class Documentation

◆ OpenMS::SiriusAdapterAlgorithm::SiriusTmpStruct

struct OpenMS::SiriusAdapterAlgorithm::SiriusTmpStruct

Struct for temporary folder structure.

Class Members
String	tmp_dir
String	tmp_ms_file
String	tmp_out_dir

Constructor & Destructor Documentation

◆ SiriusAdapterAlgorithm()

SiriusAdapterAlgorithm ( )

default constructor

Member Function Documentation

◆ callSiriusQProcess()

static const std::vector<String> callSiriusQProcess	(	const String &	tmp_ms_file,
		const String &	tmp_out_dir,
		String &	executable,
		const String &	out_csifingerid,
		const SiriusAdapterAlgorithm &	sirius_algo
	)

static

Call SIRIUS with QProcess.

Returns: Vector with paths to a compound

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).
sirius_algo	Parameters needed for SIRIUS

◆ checkFeatureSpectraNumber()

static void checkFeatureSpectraNumber	(	const String &	featureinfo,
		const FeatureMapping::FeatureToMs2Indices &	feature_mapping,
		const MSExperiment &	spectra,
		const SiriusAdapterAlgorithm &	sirius_algo
	)

static

logs number of features and spectra used

Prints the number of features and spectra used (LOG_INFO)

Parameters

featureinfo	Path to featureXML
feature_mapping	FeatureToMs2Indices with feature mapping
spectra	Input of MSExperiment with spectra information
sirius_algo	Parameters needed for preprocessing

◆ checkSiriusExecutablePath()

static std::pair<String, String> checkSiriusExecutablePath ( String & executable )

static

Checks if executable was povided.

Returns: Pair "path to executable" and "path to the working directory"

Parameters

executable Path to the executable

◆ constructSiriusTmpStruct()

static SiriusAdapterAlgorithm::SiriusTmpStruct constructSiriusTmpStruct ( )

static

Construct temporary folder structure for SIRIUS (SiriusTmpStruct)

Returns: SiriusTmpStruct

◆ getCandidates()

int getCandidates ( )

◆ getConverterMode()

String getConverterMode ( )

◆ getFeatureOnly()

String getFeatureOnly ( )

◆ getIsotopePatternIterations()

int getIsotopePatternIterations ( )

◆ getNoMasstraceInfoIsotopePattern()

String getNoMasstraceInfoIsotopePattern ( )

◆ getTopNHits()

int getTopNHits ( )

◆ preprocessingSirius()

static void preprocessingSirius	(	const String &	featureinfo,
		const MSExperiment &	spectra,
		std::vector< FeatureMap > &	v_fp,
		KDTreeFeatureMaps &	fp_map_kd,
		const SiriusAdapterAlgorithm &	sirius_algo,
		FeatureMapping::FeatureToMs2Indices &	feature_mapping
	)

static

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
fp_map_kd	KDTree used for query and match spectra with features
sirius_algo	Parameters needed for preprocessing
feature_mapping	Empty FeatureToMs2Indices

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ auto_charge_

String auto_charge_

protected

◆ candidates_

int candidates_

protected

◆ compound_timeout_

int compound_timeout_

protected

◆ converter_mode_

String converter_mode_

protected

◆ cores_

int cores_

protected

◆ database_

String database_

protected

◆ elements_

String elements_

protected

◆ feature_only_

String feature_only_

protected

◆ filter_by_num_masstraces_

unsigned int filter_by_num_masstraces_

protected

◆ ion_tree_

String ion_tree_

protected

◆ isotope_

String isotope_

protected

◆ isotope_pattern_iterations_

int isotope_pattern_iterations_

protected

◆ most_intense_ms2_

String most_intense_ms2_

protected

◆ no_masstrace_info_isotope_pattern_

String no_masstrace_info_isotope_pattern_

protected

◆ no_recalibration_

String no_recalibration_

protected

◆ noise_

int noise_

protected

◆ ppm_max_

int ppm_max_

protected

◆ precursor_mz_tolerance_

double precursor_mz_tolerance_

protected

◆ precursor_mz_tolerance_unit_

String precursor_mz_tolerance_unit_

protected

◆ precursor_rt_tolerance_

double precursor_rt_tolerance_

protected

◆ profile_

String profile_

protected

◆ top_n_hits_

int top_n_hits_

protected

◆ tree_timeout_

int tree_timeout_

protected

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Class Documentation

◆ OpenMS::SiriusAdapterAlgorithm::SiriusTmpStruct

Constructor & Destructor Documentation

◆ SiriusAdapterAlgorithm()

Member Function Documentation

◆ callSiriusQProcess()

◆ checkFeatureSpectraNumber()

◆ checkSiriusExecutablePath()

◆ constructSiriusTmpStruct()

◆ getCandidates()

◆ getConverterMode()

◆ getFeatureOnly()

◆ getIsotopePatternIterations()

◆ getNoMasstraceInfoIsotopePattern()

◆ getTopNHits()

◆ preprocessingSirius()

◆ updateMembers_()

Member Data Documentation

◆ auto_charge_

◆ candidates_

◆ compound_timeout_

◆ converter_mode_

◆ cores_

◆ database_

◆ elements_

◆ feature_only_

◆ filter_by_num_masstraces_

◆ ion_tree_

◆ isotope_

◆ isotope_pattern_iterations_

◆ most_intense_ms2_

◆ no_masstrace_info_isotope_pattern_

◆ no_recalibration_

◆ noise_

◆ ppm_max_

◆ precursor_mz_tolerance_

◆ precursor_mz_tolerance_unit_

◆ precursor_rt_tolerance_

◆ profile_

◆ top_n_hits_

◆ tree_timeout_