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

Inheritance diagram for IDScoreSwitcherAlgorithm:

Collaboration diagram for IDScoreSwitcherAlgorithm:

Public Types
enum class	ScoreType { RAW , RAW_EVAL , PP , PEP , FDR , QVAL }

Public Member Functions
	IDScoreSwitcherAlgorithm ()

bool	isScoreType (const String &score_name, const ScoreType &type)
	Checks if the given `score_name` is of ScoreType `type`. More...

template<typename IDType >
void	switchScores (IDType &id, Size &counter)

void	switchToGeneralScoreType (std::vector< PeptideIdentification > &id, ScoreType type, Size &counter)

void	switchToGeneralScoreType (ConsensusMap &cmap, ScoreType type, Size &counter, bool unassigned_peptides_too=true)

template<typename IDType >
String	findScoreType (IDType &id, IDScoreSwitcherAlgorithm::ScoreType type)
	finds a certain score type in an ID and its metavalues if present, otherwise returns empty string 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...

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

Private Attributes
const double	tolerance_ = 1e-6
	relative tolerance for score comparisons: More...

String	new_score_
	will be set according to the algorithm parameters More...

String	new_score_type_

String	old_score_

bool	higher_better_
	will be set according to the algorithm parameters More...

std::map< ScoreType, std::set< String > >	type_to_str_
	a map from ScoreType to their names as used around OpenMS More...

std::map< ScoreType, bool >	type_to_better_
	a map from ScoreType to their ordering More...

Additional Inherited Members
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...

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...

Member Enumeration Documentation

◆ ScoreType

enum ScoreType

strong

This is a rough hierarchy of possible score types in MS In an ideal case this should be reimplemented to follow ontology hierarchies as soon as e.g. MS-OBO is complete and we switched the Metavalues to CV terms.

Enumerator
RAW
RAW_EVAL
PP
PEP
FDR
QVAL

Constructor & Destructor Documentation

◆ IDScoreSwitcherAlgorithm()

IDScoreSwitcherAlgorithm ( )

Member Function Documentation

◆ findScoreType()

String findScoreType	(	IDType &	id,
		IDScoreSwitcherAlgorithm::ScoreType	type
	)

inline

finds a certain score type in an ID and its metavalues if present, otherwise returns empty string

References OPENMS_LOG_INFO, and OPENMS_LOG_WARN.

◆ isScoreType()

bool isScoreType	(	const String &	score_name,
		const ScoreType &	type
	)

inline

Checks if the given score_name is of ScoreType type.

◆ switchScores()

void switchScores	(	IDType &	id,
		Size &	counter
	)

inline

Switches all main scores in all hits in id according to the settings in the param object of the switcher class if the old score type and new score type have the same name (e.g., "q-value") we greate a meta value entry with appended "~" to the old score type (to not overwrite the meta value of the new one).

References DataValue::isEmpty().

◆ switchToGeneralScoreType() [1/2]

void switchToGeneralScoreType	(	ConsensusMap &	cmap,
		ScoreType	type,
		Size &	counter,
		bool	unassigned_peptides_too = `true`
	)

inline

Looks at the first Hit of the given id and according to the given type , deduces a fitting score and score direction to be switched to. Then tries to switch all hits.

References MapUtilities< MapType >::applyFunctionOnPeptideIDs(), String::chop(), String::hasSuffix(), and OPENMS_LOG_WARN.

◆ switchToGeneralScoreType() [2/2]

void switchToGeneralScoreType	(	std::vector< PeptideIdentification > &	id,
		ScoreType	type,
		Size &	counter
	)

inline

Looks at the first Hit of the given id and according to the given type , deduces a fitting score and score direction to be switched to. Then tries to switch all hits.

References String::chop(), String::hasSuffix(), and OPENMS_LOG_WARN.

◆ updateMembers_()

void updateMembers_ ( )

overrideprivatevirtual

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

◆ higher_better_

bool higher_better_

private

will be set according to the algorithm parameters

◆ new_score_

String new_score_

private

will be set according to the algorithm parameters

◆ new_score_type_

String new_score_type_

private

◆ old_score_

String old_score_

private

◆ tolerance_

const double tolerance_ = 1e-6

private

relative tolerance for score comparisons:

◆ type_to_better_

std::map<ScoreType, bool> type_to_better_

private

Initial value:

=
        {
            {ScoreType::RAW, true}, 
            {ScoreType::RAW_EVAL, false},
            {ScoreType::PP, true},
            {ScoreType::PEP, false},
            {ScoreType::FDR, false},
            {ScoreType::QVAL, false}
        }

a map from ScoreType to their ordering

◆ type_to_str_

std::map<ScoreType, std::set<String> > type_to_str_

private

Initial value:

=
        {
            {ScoreType::RAW, {"XTandem", "OMSSA", "SEQUEST:xcorr", "Mascot", "mvh", "Sage"}},
            
            
            
            
            
            {ScoreType::RAW_EVAL, {"expect", "SpecEValue", "E-Value", "evalue", "MS:1002053", "MS:1002257"}},
            {ScoreType::PP, {"Posterior Probability"}},
            {ScoreType::PEP, {"Posterior Error Probability", "pep", "MS:1001493"}}, 
            {ScoreType::FDR, {"FDR", "fdr", "false discovery rate"}},
            {ScoreType::QVAL, {"q-value", "qvalue", "MS:1001491", "q-Value", "qval"}}
        }

a map from ScoreType to their names as used around OpenMS

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Enumeration Documentation

◆ ScoreType

Constructor & Destructor Documentation

◆ IDScoreSwitcherAlgorithm()

Member Function Documentation

◆ findScoreType()

◆ isScoreType()

◆ switchScores()

◆ switchToGeneralScoreType() [1/2]

◆ switchToGeneralScoreType() [2/2]

◆ updateMembers_()

Member Data Documentation

◆ higher_better_

◆ new_score_

◆ new_score_type_

◆ old_score_

◆ tolerance_

◆ type_to_better_

◆ type_to_str_