OpenSwathOSWWriter Class Reference

Class to write out an OpenSwath OSW SQLite output (PyProphet input). More...

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

Collaboration diagram for OpenSwathOSWWriter:

Classes
struct	OSWData
	Buffered OSW table rows ready for insertion through prepared statements. More...
struct	OSWValue
	Typed OSW cell value used for direct SQLite binding. More...

Public Types
using	FeatureRow = std::array< OSWValue, FEATURE_COLUMN_COUNT >
using	FeatureMS1Row = std::array< OSWValue, FEATURE_MS1_COLUMN_COUNT >
using	FeatureMS2Row = std::array< OSWValue, FEATURE_MS2_COLUMN_COUNT >
using	FeaturePrecursorRow = std::array< OSWValue, FEATURE_PRECURSOR_COLUMN_COUNT >
using	FeatureTransitionRow = std::array< OSWValue, FEATURE_TRANSITION_COLUMN_COUNT >

Public Member Functions
	OpenSwathOSWWriter (const std::string &output_filename, bool uis_scores=false)
bool	isActive () const
void	writeHeader ()
	Initializes file by generating SQLite tables.
void	addRun (const UInt64 run_id, const std::string &input_filename)
	Add a RUN entry to the OSW file. Can be called multiple times to register multiple runs.
void	setRunId (const UInt64 run_id)
	Set the current run id used when prepareLine generates FEATURE entries.
std::string	getScore (const Feature &feature, const std::string &score_name) const
	Prepare scores for SQLite insertion.
std::vector< std::string >	getSeparateScore (const Feature &feature, const std::string &score_name) const
	Prepare concatenated scores for SQLite insertion.
OSWData	prepareRows (const OpenSwath::LightCompound &pep, const OpenSwath::LightTransition *transition, const FeatureMap &output, const std::string &id) const
	Prepare feature rows for SQLite insertion.
void	prepareRowsInto (OSWData &rows, const OpenSwath::LightCompound &pep, const OpenSwath::LightTransition *transition, const FeatureMap &output, const std::string &id) const
	Append feature rows for SQLite insertion into an existing buffer.
std::string	prepareLine (const OpenSwath::LightCompound &pep, const OpenSwath::LightTransition *transition, const FeatureMap &output, const std::string &id) const
	Prepare a single line (feature) for output.
void	writeRows (const OSWData &osw_output)
	Write buffered OSW rows to disk.
void	writeLines (const std::vector< std::string > &to_osw_output)
	Write data to disk.

Static Public Attributes
static constexpr Size	FEATURE_COLUMN_COUNT = 11
static constexpr Size	FEATURE_MS1_COLUMN_COUNT = 18
static constexpr Size	FEATURE_MS2_COLUMN_COUNT = 38
static constexpr Size	FEATURE_PRECURSOR_COLUMN_COUNT = 4
static constexpr Size	FEATURE_TRANSITION_COLUMN_COUNT = 43

Private Attributes
std::string	output_filename_
OpenMS::UInt64	run_id_ = 0
bool	doWrite_
bool	enable_uis_scoring_
std::unique_ptr< SqliteConnector >	conn_
std::mutex	conn_mutex_

Detailed Description

Class to write out an OpenSwath OSW SQLite output (PyProphet input).

The class can take a FeatureMap and create buffered rows from it suitable for output to OSW using the prepareRows function. The SQL data is directly linked to the PQP file format described in the TransitionPQPFile class. See also OpenSwathTSVWriter for another output format.

The file format has the following tables:

RUN
ID	INT	Primary Key (run id)
FILENAME	TEXT	Original filename associated with the run

FEATURE
ID	INT	Primary Key (feature id)
RUN_ID	INT	Foreign Key (RUN.ID)
PRECURSOR_ID	INT	Foreign Key (TransitionPQPFile PRECURSOR.ID)
EXP_RT	REAL	Experimental RT (retention time) of the feature
NORM_RT	REAL	Normalized RT (retention time) of the feature. The position of the peak group in the normalized retention time space (e.g. fx(RT) where fx describes the transformation fx)
DELTA_RT	REAL	The difference in retention between expected retention time of the assay and the measured feature retention time (EXP_RT)
LEFT_WIDTH	REAL	Retention time start of the peak (left width) in seconds
RIGHT_WIDTH	REAL	Retention time end of the peak (right width) in seconds

FEATURE_MS1
FEATURE_ID	INT	Foreign Key (FEATURE.ID)
AREA_INTENSITY	REAL	Precursor intensity (area)
APEX_INTENSITY	REAL	Precursor intensity (apex)
VAR_...	REAL	Precursor score used in pyProphet

FEATURE_MS2
FEATURE_ID	INT	Foreign Key (FEATURE.ID)
AREA_INTENSITY	REAL	Summed fragment ion intensity (area)
TOTAL_AREA_INTENSITY	REAL	Summed total XIC of the whole chromatogram
APEX_INTENSITY	REAL	Summed fragment ion intensity (apex)
TOTAL_MI	REAL	Total mutual information (MI)
VAR_...	REAL	Fragment ion score used in pyProphet

FEATURE_PRECURSOR
FEATURE_ID	INT	Foreign Key (FEATURE.ID)
ISOTOPE	INT	Isotope identifier
AREA_INTENSITY	REAL	Precursor isotope ion intensity (area)
APEX_INTENSITY	REAL	Precursor isotope ion intensity (apex)

FEATURE_TRANSITION
FEATURE_ID	INT	Foreign Key (FEATURE.ID)
TRANSITION_ID	INT	Foreign Key (transition identifier)
AREA_INTENSITY	REAL	Fragment ion intensity (area)
TOTAL_AREA_INTENSITY	REAL	Total XIC of the whole chromatogram
APEX_INTENSITY	REAL	Fragment ion intensity (apex)
TOTAL_MI	REAL	Total mutual information (MI)
VAR_...	REAL	Fragment ion score used in pyProphet

Member Typedef Documentation

FeatureMS1Row

using FeatureMS1Row = std::array<OSWValue, FEATURE_MS1_COLUMN_COUNT>

FeatureMS2Row

using FeatureMS2Row = std::array<OSWValue, FEATURE_MS2_COLUMN_COUNT>

FeaturePrecursorRow

using FeaturePrecursorRow = std::array<OSWValue, FEATURE_PRECURSOR_COLUMN_COUNT>

FeatureRow

using FeatureRow = std::array<OSWValue, FEATURE_COLUMN_COUNT>

FeatureTransitionRow

using FeatureTransitionRow = std::array<OSWValue, FEATURE_TRANSITION_COLUMN_COUNT>

Constructor & Destructor Documentation

OpenSwathOSWWriter()

OpenSwathOSWWriter	(	const std::string &	output_filename,
		bool	uis_scores = false
	)

Member Function Documentation

addRun()

void addRun	(	const UInt64	run_id,
		const std::string &	input_filename
	)

Add a RUN entry to the OSW file. Can be called multiple times to register multiple runs.

getScore()

std::string getScore	(	const Feature &	feature,
		const std::string &	score_name
	)		const

Prepare scores for SQLite insertion.

Some scores might not be defined, those are reported as NULL

Parameters

[in]	feature	The feature being evaluated
[in]	score_name	The name of the queried score

Returns

A string with the queried score

getSeparateScore()

std::vector< std::string > getSeparateScore	(	const Feature &	feature,
		const std::string &	score_name
	)		const

Prepare concatenated scores for SQLite insertion.

Some scores might not be defined, those are reported as NULL

Parameters

[in]	feature	The feature being evaluated
[in]	score_name	The name of the queried score

Returns

A vector of strings with the queried scores

isActive()

bool isActive

(

)

const

prepareLine()

std::string prepareLine	(	const OpenSwath::LightCompound &	pep,
		const OpenSwath::LightTransition *	transition,
		const FeatureMap &	output,
		const std::string &	id
	)		const

Prepare a single line (feature) for output.

The result can be flushed to disk using writeLines (either line by line or after collecting several lines).

Parameters

[in]	pep	The compound (peptide/metabolite) used for extraction
[in]	transition	The transition used for extraction
[in]	output	The feature map containing all features (each feature will generate one entry in the output)
[in]	id	The transition group identifier (peptide/metabolite id)

Returns

A string to be written using writeLines

prepareRows()

OSWData prepareRows	(	const OpenSwath::LightCompound &	pep,
		const OpenSwath::LightTransition *	transition,
		const FeatureMap &	output,
		const std::string &	id
	)		const

Prepare feature rows for SQLite insertion.

This is the preferred high-throughput path. It avoids constructing full SQL statements for every feature and lets writeRows bind values into reusable prepared statements.

Parameters

[in]	pep	The compound (peptide/metabolite) used for extraction
[in]	transition	The transition used for extraction
[in]	output	The feature map containing all features
[in]	id	The transition group identifier (peptide/metabolite id)

Returns

Buffered OSW table rows

prepareRowsInto()

void prepareRowsInto	(	OSWData &	rows,
		const OpenSwath::LightCompound &	pep,
		const OpenSwath::LightTransition *	transition,
		const FeatureMap &	output,
		const std::string &	id
	)		const

Append feature rows for SQLite insertion into an existing buffer.

This avoids constructing small per-assay OSWData buffers in high-throughput schedulers.

Parameters

[in,out]	rows	The row buffer to append to
[in]	pep	The compound (peptide/metabolite) used for extraction
[in]	transition	The transition used for extraction
[in]	output	The feature map containing all features
[in]	id	The transition group identifier (peptide/metabolite id)

setRunId()

void setRunId

(

const UInt64

run_id

)

Set the current run id used when prepareLine generates FEATURE entries.

writeHeader()

void writeHeader

(

)

Initializes file by generating SQLite tables.

writeLines()

void writeLines

(

const std::vector< std::string > &

to_osw_output

)

Write data to disk.

Takes a set of pre-prepared data statements from prepareLine and flushes them to disk

Parameters

[in]

to_osw_output

Statements generated by prepareLine

Note

Try to call this function as little as possible (it opens a new database connection each time)

Only call inside an OpenMP critical section

writeRows()

void writeRows

(

const OSWData &

osw_output

)

Write buffered OSW rows to disk.

Uses one SQLite transaction and reusable prepared statements for each OSW table. This is the preferred writer path for newly generated output.

Parameters

[in]

osw_output

Rows generated by prepareRows

Note

Try to call this function as little as possible (it opens a new database connection each time)

Only call inside an OpenMP critical section

Member Data Documentation

conn_

std::unique_ptr<SqliteConnector> conn_

mutableprivate

conn_mutex_

std::mutex conn_mutex_

mutableprivate

doWrite_

bool doWrite_

private

enable_uis_scoring_

bool enable_uis_scoring_

private

FEATURE_COLUMN_COUNT

constexpr Size FEATURE_COLUMN_COUNT = 11

staticconstexpr

FEATURE_MS1_COLUMN_COUNT

constexpr Size FEATURE_MS1_COLUMN_COUNT = 18

staticconstexpr

FEATURE_MS2_COLUMN_COUNT

constexpr Size FEATURE_MS2_COLUMN_COUNT = 38

staticconstexpr

FEATURE_PRECURSOR_COLUMN_COUNT

constexpr Size FEATURE_PRECURSOR_COLUMN_COUNT = 4

staticconstexpr

FEATURE_TRANSITION_COLUMN_COUNT

constexpr Size FEATURE_TRANSITION_COLUMN_COUNT = 43

staticconstexpr

output_filename_

std::string output_filename_

private

run_id_

OpenMS::UInt64 run_id_ = 0

private