This class serves for reading in and writing OpenSWATH OSW files. More...

#include <OpenMS/FORMAT/OSWFile.h>

Collaboration diagram for OSWFile:

Classes
struct	PercolatorFeature

Public Types
enum class	OSWLevel { MS1 , MS2 , TRANSITION , SIZE_OF_OSWLEVEL }
	for Percolator data read/write operations More...

Public Member Functions
	OSWFile (const String &filename)

	OSWFile (const OSWFile &rhs)=default

OSWFile &	operator= (const OSWFile &rhs)=default

void	read (OSWData &swath_result)

void	readMinimal (OSWData &swath_result)

void	readProtein (OSWData &swath_result, const Size index)
	populates a protein at index `index` within `swath_results` with Peptides, unless the protein already has peptides More...

UInt64	getRunID () const

Static Public Member Functions
static void	readToPIN (const std::string &filename, const OSWFile::OSWLevel osw_level, std::ostream &pin_output, const double ipf_max_peakgroup_pep, const double ipf_max_transition_isotope_overlap, const double ipf_min_transition_sn)
	Reads an OSW SQLite file and returns the data on MS1-, MS2- or transition-level as ostream (e.g. stringstream or ofstream). More...

static void	writeFromPercolator (const std::string &osw_filename, const OSWFile::OSWLevel osw_level, const std::map< std::string, PercolatorFeature > &features)
	Updates an OpenSWATH OSW SQLite file with the MS1-, MS2- or transition-level results of Percolator. More...

Static Public Attributes
static constexpr Size	ALL_PROTEINS = -1
	query all proteins, not just one with a particular ID More...

static const std::array< std::string,(Size) OSWLevel::SIZE_OF_OSWLEVEL >	names_of_oswlevel

Protected Member Functions
void	readTransitions_ (OSWData &swath_result)

void	getFullProteins_ (OSWData &swath_result, Size prot_index=ALL_PROTEINS)
	fill one (`prot_id`) or all proteins into `swath_result` More...

void	readMeta_ (OSWData &data)
	set source file and sqMass run-ID More...

Private Attributes
String	filename_
	sql file to open/write to More...

SqliteConnector	conn_
	SQL connection. Stays open as long as this object lives. More...

bool	has_SCOREMS2_
	database contains pyProphet's score_MS2 table with qvalues More...

Detailed Description

This class serves for reading in and writing OpenSWATH OSW files.

See OpenSwathOSWWriter for more functionality.

The reader and writer returns data in a format suitable for PercolatorAdapter. OSW files have a flexible data structure. They contain all peptide query parameters of TraML/PQP files with the detected and quantified features of OpenSwathWorkflow (feature, feature_ms1, feature_ms2 & feature_transition).

The OSWFile reader extracts the feature information from the OSW file for each level (MS1, MS2 & transition) separately and generates Percolator input files. For each of the three Percolator reports, OSWFile writer adds a table (score_ms1, score_ms2, score_transition) with the respective confidence metrics. These tables can be mapped to the corresponding feature tables, are very similar to PyProphet results and can thus be used interchangeably.

Member Enumeration Documentation

◆ OSWLevel

enum OSWLevel

strong

for Percolator data read/write operations

Enumerator
MS1
MS2
TRANSITION
SIZE_OF_OSWLEVEL

Constructor & Destructor Documentation

◆ OSWFile() [1/2]

OSWFile ( const String & filename )

opens an OSW file for reading.

Exceptions

Exception::FileNotReadable if filename does not exist

◆ OSWFile() [2/2]

OSWFile ( const OSWFile & rhs )

default

Member Function Documentation

◆ getFullProteins_()

void getFullProteins_	(	OSWData &	swath_result,
		Size	prot_index = `ALL_PROTEINS`
	)

protected

fill one (prot_id) or all proteins into swath_result

Parameters

[out]	swath_result	Output data. Proteins are cleared before if ALL_PROTEINS is used.
	prot_index	Using ALL_PROTEINS queries all proteins (could take some time)

◆ getRunID()

UInt64 getRunID ( ) const

extract the RUN::ID from the sqMass file

Exceptions

Exception::SqlOperationFailed more than on run exists

◆ operator=()

OSWFile& operator= ( const OSWFile & rhs )

default

◆ read()

void read ( OSWData & swath_result )

read data from an SQLLite OSW file into swath_result Depending on the number of proteins, this could take a while.

Note: If you just want the proteins and transitions without peptides and features, use readMinimal().

◆ readMeta_()

void readMeta_ ( OSWData & data )

protected

set source file and sqMass run-ID

◆ readMinimal()

void readMinimal ( OSWData & swath_result )

Reads in transitions and a list of protein names/IDs but no peptide/feature/transition mapping data (which could be very expensive). Use in conjunction with on-demand readProtein() to fully populate proteins with peptide/feature data as needed.

Note: If you read in all proteins afterwards in one go anyway, using the read() method will be faster (by about 30%)

◆ readProtein()

void readProtein	(	OSWData &	swath_result,
		const Size	index
	)

populates a protein at index index within swath_results with Peptides, unless the protein already has peptides

Internally uses the proteins ID to search for cross referencing peptides and transitions in the OSW file.

Parameters

swath_result	OSWData obtained from the readMinimal() method
index	Index into swath_result.getProteins()[index]. Make sure the index is within the vector's size.

Exceptions

Exception::InvalidValue if the protein at index does not have any peptides present in the OSW file

◆ readToPIN()

static void readToPIN	(	const std::string &	filename,
		const OSWFile::OSWLevel	osw_level,
		std::ostream &	pin_output,
		const double	ipf_max_peakgroup_pep,
		const double	ipf_max_transition_isotope_overlap,
		const double	ipf_min_transition_sn
	)

static

Reads an OSW SQLite file and returns the data on MS1-, MS2- or transition-level as ostream (e.g. stringstream or ofstream).

◆ readTransitions_()

void readTransitions_ ( OSWData & swath_result )

protected

populate transitions of swath_result

Clears swath_result entirely (incl. proteins) before adding transitions.

◆ writeFromPercolator()

static void writeFromPercolator	(	const std::string &	osw_filename,
		const OSWFile::OSWLevel	osw_level,
		const std::map< std::string, PercolatorFeature > &	features
	)

static

Updates an OpenSWATH OSW SQLite file with the MS1-, MS2- or transition-level results of Percolator.

Member Data Documentation

◆ ALL_PROTEINS

constexpr Size ALL_PROTEINS = -1

staticconstexpr

query all proteins, not just one with a particular ID

◆ conn_

SqliteConnector conn_

private

SQL connection. Stays open as long as this object lives.

◆ filename_

String filename_

private

sql file to open/write to

◆ has_SCOREMS2_

bool has_SCOREMS2_

private

database contains pyProphet's score_MS2 table with qvalues

◆ names_of_oswlevel

const std::array<std::string, (Size)OSWLevel::SIZE_OF_OSWLEVEL> names_of_oswlevel

static

Classes

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Attributes

Detailed Description

Member Enumeration Documentation

◆ OSWLevel

Constructor & Destructor Documentation

◆ OSWFile() [1/2]

◆ OSWFile() [2/2]

Member Function Documentation

◆ getFullProteins_()

◆ getRunID()

◆ operator=()

◆ read()

◆ readMeta_()

◆ readMinimal()

◆ readProtein()

◆ readToPIN()

◆ readTransitions_()

◆ writeFromPercolator()

Member Data Documentation

◆ ALL_PROTEINS

◆ conn_

◆ filename_

◆ has_SCOREMS2_

◆ names_of_oswlevel