Read and update OpenSWATH results in an OSWPQ directory or archive. More...

#include <OpenMS/FORMAT/OSWParquetFile.h>

Inheritance diagram for OSWParquetFile:

Classes
struct	InferenceResults
	Results for one inference level/context, including an explicitly empty result. More...

Public Member Functions
	OSWParquetFile (const std::string &filename, const OpenSwath::LightTargetedExperiment &library, bool load_transition_metadata=true)
	Open a workflow and build its prepared-library lookup.

	~OSWParquetFile () override
	Release the workspace without implicitly committing archive changes.

	OSWParquetFile (const OSWParquetFile &)=delete

OSWParquetFile &	operator= (const OSWParquetFile &)=delete

	OSWParquetFile (OSWParquetFile &&)
	Transfer ownership of the workspace.

OSWParquetFile &	operator= (OSWParquetFile &&)
	Transfer ownership, releasing the old workspace without committing it.

std::vector< LevelContextInputRow >	readLevelContextData (InferenceLevel level, InferenceContext context) const
	Read compact peptide-, protein-, or gene-level rows for context inference.

void	writeLevelContextResults (std::vector< InferenceResults > results)
	Write inference tables and synchronize the corresponding feature score columns.

std::vector< OpenSwathExportRow >	readOpenSwathExportRows (const OpenSwathExportFilterConfig &config) const
	Read filtered rows for result and matrix exporters.

OpenSwathFeatureScoreTable	readOpenSwathFeatureScoreTable (const OpenSwathParquetExportConfig &config) const
	Read feature score rows for the Parquet exporter.

OpenSwathTransitionScoreTable	readOpenSwathTransitionScoreTable (const OpenSwathParquetExportConfig &config) const
	Read transition score rows for the Parquet exporter.

std::map< Int64, std::string >	readRunBasenames () const
	Read run IDs and user-facing filename stems.

void	commit ()
	Persist pending archive changes and refresh the sidecar index; a no-op if unchanged.

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.

virtual	~ProgressLogger ()
	Destructor.

	ProgressLogger (const ProgressLogger &other)
	Copy constructor.

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!

LogType	getLogType () const
	Returns the type of progress log being used.

void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.

void	startProgress (SignedSize begin, SignedSize end, const std::string &label) const
	Initializes the progress display.

void	setProgress (SignedSize value) const
	Sets the current progress.

void	endProgress (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end)

Private Attributes
std::unique_ptr< Impl >	impl_

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static std::atomic< int >	recursion_depth_

Detailed Description

Read and update OpenSWATH results in an OSWPQ directory or archive.

Provides the result-storage operations used by OpenDIA without exposing Arrow types. The prepared library must use the same canonical numeric IDs as the library used to write the workflow. Its lookup data is owned by this object; the supplied experiment need not outlive the constructor.

An archive is unpacked once into an owned temporary directory. Updates to that workspace are visible to subsequent reads, but only commit() repacks the archive. Destruction releases temporary files without committing. For directory inputs, writes take effect immediately and cannot be rolled back. Feature tables are processed one run at a time; only the run table is cached.

Class Documentation

◆ OpenMS::OSWParquetFile::InferenceResults

struct OpenMS::OSWParquetFile::InferenceResults

Results for one inference level/context, including an explicitly empty result.

Class Members
InferenceContext	context = InferenceContext::Global
InferenceLevel	level = InferenceLevel::Peptide
vector< LevelContextResultRow >	rows

Constructor & Destructor Documentation

◆ OSWParquetFile() [1/3]

OSWParquetFile	(	const std::string &	filename,
		const OpenSwath::LightTargetedExperiment &	library,
		bool	load_transition_metadata = `true`
	)

Open a workflow and build its prepared-library lookup.

Parameters

[in]	filename	OSWPQ directory or ZIP archive
[in]	library	Prepared library with canonical numeric IDs
[in]	load_transition_metadata	Retain transition metadata for feature/transition exports and transition quantification; may be false for inference-only use

◆ ~OSWParquetFile()

~OSWParquetFile ( )

override

Release the workspace without implicitly committing archive changes.

◆ OSWParquetFile() [2/3]

OSWParquetFile ( const OSWParquetFile & )

delete

◆ OSWParquetFile() [3/3]

OSWParquetFile ( OSWParquetFile && )

Transfer ownership of the workspace.

Member Function Documentation

◆ commit()

void commit ( )

Persist pending archive changes and refresh the sidecar index; a no-op if unchanged.

◆ operator=() [1/2]

OSWParquetFile & operator= ( const OSWParquetFile & )

delete

◆ operator=() [2/2]

OSWParquetFile & operator= ( OSWParquetFile && )

Transfer ownership, releasing the old workspace without committing it.

◆ readLevelContextData()

std::vector< LevelContextInputRow > readLevelContextData	(	InferenceLevel	level,
		InferenceContext	context
	)		const

Read compact peptide-, protein-, or gene-level rows for context inference.

◆ readOpenSwathExportRows()

std::vector< OpenSwathExportRow > readOpenSwathExportRows ( const OpenSwathExportFilterConfig & config ) const

Read filtered rows for result and matrix exporters.

◆ readOpenSwathFeatureScoreTable()

OpenSwathFeatureScoreTable readOpenSwathFeatureScoreTable ( const OpenSwathParquetExportConfig & config ) const

Read feature score rows for the Parquet exporter.

◆ readOpenSwathTransitionScoreTable()

OpenSwathTransitionScoreTable readOpenSwathTransitionScoreTable ( const OpenSwathParquetExportConfig & config ) const

Read transition score rows for the Parquet exporter.

◆ readRunBasenames()

std::map< Int64, std::string > readRunBasenames ( ) const

Read run IDs and user-facing filename stems.

◆ writeLevelContextResults()

void writeLevelContextResults ( std::vector< InferenceResults > results )

Write inference tables and synchronize the corresponding feature score columns.