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:

Public Member Functions
	OpenSwathOSWWriter (const String &output_filename, const UInt64 run_id, const String &input_filename="inputfile", bool ms1_scores=false, bool sonar=false, bool uis_scores=false)
bool	isActive () const
void	writeHeader ()
	Initializes file by generating SQLite tables. More...
String	getScore (const Feature &feature, std::string score_name) const
	Prepare scores for SQLite insertion. More...
std::vector< String >	getSeparateScore (const Feature &feature, std::string score_name) const
	Prepare concatenated scores for SQLite insertion. More...
String	prepareLine (const OpenSwath::LightCompound &, const OpenSwath::LightTransition *, const FeatureMap &output, const String &id) const
	Prepare a single line (feature) for output. More...
void	writeLines (const std::vector< String > &to_osw_output)
	Write data to disk. More...

Private Attributes
String	output_filename_
String	input_filename_
OpenMS::UInt64	run_id_
bool	doWrite_
bool	use_ms1_traces_
bool	sonar_
bool	enable_uis_scoring_

Detailed Description

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

The class can take a FeatureMap and create a set of string from it suitable for output to OSW using the prepareLine 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

Constructor & Destructor Documentation

OpenSwathOSWWriter()

OpenSwathOSWWriter	(	const String &	output_filename,
		const UInt64	run_id,
		const String &	input_filename = "inputfile",
		bool	ms1_scores = false,
		bool	sonar = false,
		bool	uis_scores = false
	)

Member Function Documentation

getScore()

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

Prepare scores for SQLite insertion.

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

Parameters

feature	The feature being evaluated
score_name	The name of the queried score

Returns

A string with the queried score

getSeparateScore()

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

Prepare concatenated scores for SQLite insertion.

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

Parameters

feature	The feature being evaluated
score_name	The name of the queried score

Returns

A vector of strings with the queried scores

isActive()

bool isActive

(

)

const

prepareLine()

String prepareLine	(	const OpenSwath::LightCompound &	,
		const OpenSwath::LightTransition *	,
		const FeatureMap &	output,
		const 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

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

Returns

A string to be written using writeLines

writeHeader()

void writeHeader

(

)

Initializes file by generating SQLite tables.

writeLines()

void writeLines

(

const std::vector< String > &

to_osw_output

)

Write data to disk.

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

Parameters

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

Member Data Documentation

doWrite_

bool doWrite_

private

enable_uis_scoring_

bool enable_uis_scoring_

private

input_filename_

String input_filename_

private

output_filename_

String output_filename_

private

run_id_

OpenMS::UInt64 run_id_

private

sonar_

bool sonar_

private

use_ms1_traces_

bool use_ms1_traces_

private