The MRMFeatureFilter either flags components and/or transitions that do not pass the QC criteria or filters out components and/or transitions that do not pass the QC criteria. More...

#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFilter.h>

Inheritance diagram for MRMFeatureFilter:

Public Member Functions
void	updateMembers_ () override
	Synchronize members with param class. More...

void	FilterFeatureMap (FeatureMap &features, const MRMFeatureQC &filter_criteria, const TargetedExperiment &transitions)
	Flags or filters features and subordinates in a FeatureMap. More...

void	FeatureMapToAttachment (FeatureMap &features, QcMLFile::Attachment &attachment)
	Converts a FeatureMap to a qcMLFile::Attachment. More...

double	calculateIonRatio (const Feature &component_1, const Feature &component_2, const String &feature_name)
	Calculates the ion ratio between two transitions. More...

double	calculateRTDifference (Feature &component_1, Feature &component_2)
	Calculates the retention time difference between two features. More...

double	calculateResolution (Feature &component_1, Feature &component_2)
	Calculates the resolution between two features. More...

bool	checkMetaValue (const Feature &component, const String &meta_value_key, const double &meta_value_l, const double &meta_value_u, bool &key_exists) const
	Checks if the metaValue is within the user specified range. More...

std::map< String, int >	countLabelsAndTransitionTypes (const Feature &component_group, const TargetedExperiment &transitions)
	Count the number of heavy/light labels and quantifying/detecting/identifying transitions. More...

String	uniqueJoin (std::vector< String > &str_vec, String &delim)
	Sorts, removes duplicates, and concatenates a list of Strings. More...


	MRMFeatureFilter ()
	Constructor. More...

	~MRMFeatureFilter () override
	Destructor. 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...

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...

Private Member Functions
template<typename T >
bool	checkRange (const T &value, const T &value_l, const T &value_u) const

Private Attributes
String	flag_or_filter_
	flag or filter (i.e., remove) features that do not pass the QC More...

bool	report_xic_
	include the data points for the extracted ion chromatogram (XIC) in the attachment More...

bool	report_tic_
	include the data points for the total ion chromatogram (TIC) in the attachment More...

QcMLFile::Attachment	attachment_
	qcMLFile Attachment More...

FeatureMap	features_
	FeatureMap. More...

std::map< String, std::vector< QcMLFile::QualityParameter > >	component_group_qc_report_
	component group/peptide/compound QCs More...

std::map< String, std::vector< QcMLFile::QualityParameter > >	component_qc_report_
	component/transition QCs More...

std::map< std::vector< String >, std::vector< QcMLFile::QualityParameter > >	multi_component_group_qc_report_
	multi transition QCs More...

Additional Inherited Members
Protected Member Functions inherited from DefaultParamHandler
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...

Detailed Description

The MRMFeatureFilter either flags components and/or transitions that do not pass the QC criteria or filters out components and/or transitions that do not pass the QC criteria.

Constructor & Destructor Documentation

◆ MRMFeatureFilter()

MRMFeatureFilter ( )

Constructor.

◆ ~MRMFeatureFilter()

~MRMFeatureFilter ( )

override

Destructor.

Member Function Documentation

◆ calculateIonRatio()

double calculateIonRatio	(	const Feature &	component_1,
		const Feature &	component_2,
		const String &	feature_name
	)

Calculates the ion ratio between two transitions.

Parameters

component_1	component of the numerator
component_2	component of the denominator
feature_name	name of the feature to calculate the ratio on e.g., peak_apex, peak_area

Returns: The ratio.

◆ calculateResolution()

double calculateResolution	(	Feature &	component_1,
		Feature &	component_2
	)

Calculates the resolution between two features.

Parameters

component_1	component 1
component_2	component 2

Returns: The difference.

◆ calculateRTDifference()

double calculateRTDifference	(	Feature &	component_1,
		Feature &	component_2
	)

Calculates the retention time difference between two features.

Parameters

component_1	First eluting component
component_2	Second eluting component

Returns: The difference.

◆ checkMetaValue()

bool checkMetaValue	(	const Feature &	component,
		const String &	meta_value_key,
		const double &	meta_value_l,
		const double &	meta_value_u,
		bool &	key_exists
	)		const

Checks if the metaValue is within the user specified range.

Parameters

[in]	component	component of the numerator
[in]	meta_value_key	Name of the metaValue
[in]	meta_value_l	Lower bound (inclusive) for the metaValue range
[in]	meta_value_u	Upper bound (inclusive) for the metaValue range
[out]	key_exists	true if the given key is found, false otherwise

Returns: True if the metaValue is within the bounds, and False otherwise.

◆ checkRange()

bool checkRange	(	const T &	value,
		const T &	value_l,
		const T &	value_u
	)		const

private

◆ countLabelsAndTransitionTypes()

std::map<String,int> countLabelsAndTransitionTypes	(	const Feature &	component_group,
		const TargetedExperiment &	transitions
	)

Count the number of heavy/light labels and quantifying/detecting/identifying transitions.

Parameters

component	component_group with subordinates
transitions	transitions from a TargetedExperiment

Returns: Map of labels/transition types and their corresponding number.

◆ FeatureMapToAttachment()

void FeatureMapToAttachment	(	FeatureMap &	features,
		QcMLFile::Attachment &	attachment
	)

Converts a FeatureMap to a qcMLFile::Attachment.

Parameters

features	FeatureMap to flag or filter
attachment	qcML Attachment

◆ FilterFeatureMap()

void FilterFeatureMap	(	FeatureMap &	features,
		const MRMFeatureQC &	filter_criteria,
		const TargetedExperiment &	transitions
	)

Flags or filters features and subordinates in a FeatureMap.

Parameters

features	FeatureMap to flag or filter
filter_criteria	MRMFeatureQC class defining QC parameters
transitions	transitions from a TargetedExperiment

◆ uniqueJoin()

String uniqueJoin	(	std::vector< String > &	str_vec,
		String &	delim
	)

Sorts, removes duplicates, and concatenates a list of Strings.

Parameters

str_vec	vector of Strings
delim	token to separate Strings in the list

Returns: A concatenated string.

◆ updateMembers_()

void updateMembers_ ( )

overridevirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ attachment_

QcMLFile::Attachment attachment_

private

qcMLFile Attachment

◆ component_group_qc_report_

std::map<String,std::vector<QcMLFile::QualityParameter> > component_group_qc_report_

private

component group/peptide/compound QCs

◆ component_qc_report_

std::map<String,std::vector<QcMLFile::QualityParameter> > component_qc_report_

private

component/transition QCs

◆ features_

FeatureMap features_

private

FeatureMap.

◆ flag_or_filter_

String flag_or_filter_

private

flag or filter (i.e., remove) features that do not pass the QC

◆ multi_component_group_qc_report_

std::map<std::vector<String>,std::vector<QcMLFile::QualityParameter> > multi_component_group_qc_report_

private

multi transition QCs

◆ report_tic_

bool report_tic_

private

include the data points for the total ion chromatogram (TIC) in the attachment

◆ report_xic_

bool report_xic_

private

include the data points for the extracted ion chromatogram (XIC) in the attachment

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MRMFeatureFilter()

◆ ~MRMFeatureFilter()

Member Function Documentation

◆ calculateIonRatio()

◆ calculateResolution()

◆ calculateRTDifference()

◆ checkMetaValue()

◆ checkRange()

◆ countLabelsAndTransitionTypes()

◆ FeatureMapToAttachment()

◆ FilterFeatureMap()

◆ uniqueJoin()

◆ updateMembers_()

Member Data Documentation

◆ attachment_

◆ component_group_qc_report_

◆ component_qc_report_

◆ features_

◆ flag_or_filter_

◆ multi_component_group_qc_report_

◆ report_tic_

◆ report_xic_