OpenSwathPercolatorScoring Class Reference

In-process Percolator scoring for OpenSWATH OSW and OSWPQ results. More...

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

Inheritance diagram for OpenSwathPercolatorScoring:

Collaboration diagram for OpenSwathPercolatorScoring:

Classes
struct	ScoreSummary
	Small execution summary returned by score() More...

Public Types
enum class	Level {   MS1 , MS2 , MS1MS2 , TRANSITION ,   SIZE_OF_LEVEL }
	Supported OpenSWATH scoring levels. More...

Public Member Functions
	OpenSwathPercolatorScoring ()
	~OpenSwathPercolatorScoring () override
ScoreSummary	score (const std::string &input_path, Level level, const std::string &output_path="")
	Score an OpenSWATH OSW / OSWPQ file in place or into a copy.
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.
virtual	~DefaultParamHandler ()
	Destructor.
DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.
void	setParameters (const Param &param)
	Sets the parameters.
const Param &	getParameters () const
	Non-mutable access to the parameters.
const Param &	getDefaults () const
	Non-mutable access to the default parameters.
const std::string &	getName () const
	Non-mutable access to the name.
void	setName (const std::string &name)
	Mutable access to the name.
const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.

Static Public Attributes
static const std::array< std::string, static_cast< Size >(Level::SIZE_OF_LEVEL)>	names_of_level
	String names of the supported scoring levels.

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method.
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.

Private Attributes
std::unique_ptr< Impl >	impl_

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!
std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!
std::string	error_name_
	Name that is displayed in error messages during the parameter checking.
bool	check_defaults_
	If this member is set to false no checking if parameters in done;.
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

Detailed Description

In-process Percolator scoring for OpenSWATH OSW and OSWPQ results.

The scorer reads OpenSWATH feature tables, converts them into a domain-agnostic Percolator::RescoreInput, performs target/decoy rescoring, and writes the resulting score, q-value, PEP, and peak-group rank back to the source format. Rows with missing active OpenSWATH features are skipped instead of being imputed to zero, matching PyProphet's cleanup step.

Peak-group-level q-values / PEPs follow the OpenSWATH / PyProphet convention: Percolator provides the discriminant, top-ranked target/decoy peak groups define the error model, and the resulting statistics are then projected back onto all scored candidates.

Supported levels:

• MS1: writes SCORE_MS1 (SQLite) or score_ms1_* columns (.oswpq)
• MS2: writes SCORE_MS2 (SQLite) or score_ms2_* columns (.oswpq)
• MS1MS2: uses combined MS2 + MS1 features and writes SCORE_MS2 / score_ms2_* (matching the historical PyProphet convention)
• Transition: requires prior MS2/MS1MS2 scoring and writes SCORE_TRANSITION / score_transition_*

Transition-level scoring reuses the historical OpenMS / PyProphet-style candidate filters: only transitions from non-decoy precursors whose peak-group rank and PEP pass the configured thresholds and whose transition-level isotope-overlap / log-SN filters pass are rescored.

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Class Documentation

OpenMS::OpenSwathPercolatorScoring::ScoreSummary

struct OpenMS::OpenSwathPercolatorScoring::ScoreSummary

Small execution summary returned by score()

Collaboration diagram for OpenSwathPercolatorScoring::ScoreSummary:

Class Members
Size	decoy_rows = 0
Size	feature_count = 0
Size	target_rows = 0
Size	total_rows = 0

Member Enumeration Documentation

Level

enum class Level

strong

Supported OpenSWATH scoring levels.

Enumerator
MS1
MS2
MS1MS2
TRANSITION
SIZE_OF_LEVEL

Constructor & Destructor Documentation

OpenSwathPercolatorScoring()

OpenSwathPercolatorScoring

(

)

~OpenSwathPercolatorScoring()

~OpenSwathPercolatorScoring ( )

override

Member Function Documentation

score()

ScoreSummary score	(	const std::string &	input_path,
		Level	level,
		const std::string &	output_path = ""
	)

Score an OpenSWATH OSW / OSWPQ file in place or into a copy.

Parameters

[in]	input_path	Input .osw SQLite file or .oswpq directory/archive
[in]	level	OpenSWATH scoring level to rescore
[in]	output_path	Optional output path. If empty, score in place. Non-empty outputs preserve the input container kind (SQLite -> SQLite, directory -> directory, archive -> archive).

Returns

Small execution summary for the rescored rows.

Exceptions

Exception::FileNotFound	if the input file does not exist
Exception::Precondition	if required prerequisite scores are missing
Exception::InvalidValue	if no usable feature columns are available

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

impl_

std::unique_ptr<Impl> impl_

private

names_of_level

const std::array<std::string, static_cast<Size>(Level::SIZE_OF_LEVEL)> names_of_level

static

String names of the supported scoring levels.