OpenSwathOSWWriter Class Reference

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

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

Public Member Functions
	OpenSwathOSWWriter (const String &output_filename, 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	prepareLine (const OpenSwath::LightCompound &, const OpenSwath::LightTransition *, FeatureMap &output, 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...

Static Public Member Functions
static int	callback (void *, int argc, char **argv, char **azColName)

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.

Constructor & Destructor Documentation

OpenSwathOSWWriter()

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

inline

Member Function Documentation

callback()

static int callback ( void *  , int  argc, char **  argv, char **  azColName  )

inlinestatic

isActive()

bool isActive ( ) const

inline

prepareLine()

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

inline

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

References String::toInt().

writeHeader()

void writeHeader ( )

inline

Initializes file by generating SQLite tables.

writeLines()

void writeLines ( const std::vector< String > &  to_osw_output )

inline

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