OpenSwathTSVWriter Class Reference

Class to write out an OpenSwath TSV output (mProphet input) More...

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

Public Member Functions
	OpenSwathTSVWriter (String output_filename, String input_filename="inputfile", bool ms1_scores=false, bool sonar=false, bool uis_scores=false)
bool	isActive ()
void	writeHeader ()
	Initializes file by writing TSV header. More...
String	prepareLine (const OpenSwath::LightCompound &pep, const OpenSwath::LightTransition *transition, const FeatureMap &output, const String id)
	Prepare a single line (feature) for output. More...
void	writeLines (std::vector< String > to_output)
	Write data to disk. More...

Private Attributes
std::ofstream	ofs
String	input_filename_
bool	doWrite_
bool	use_ms1_traces_
bool	sonar_
bool	enable_uis_scoring_

Detailed Description

Class to write out an OpenSwath TSV output (mProphet input)

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

These lines can also be directly written to a file using writeLines

Constructor & Destructor Documentation

OpenSwathTSVWriter()

OpenSwathTSVWriter ( String  output_filename, String  input_filename = "inputfile", bool  ms1_scores = false, bool  sonar = false, bool  uis_scores = false  )

inline

Member Function Documentation

isActive()

bool isActive ( )

inline

prepareLine()

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

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 LightCompound::charge, LightTransition::decoy, LightCompound::modifications, LightCompound::peptide_group_label, LightTransition::precursor_mz, LightCompound::protein_refs, LightCompound::sequence, and String::substr().

writeHeader()

void writeHeader ( )

inline

Initializes file by writing TSV header.

writeLines()

void writeLines ( std::vector< String >  to_output )

inline

Write data to disk.

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

Parameters

to_output

Statements generated by prepareLine to be written to a file

Note

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

ofs

std::ofstream ofs

private

sonar_

bool sonar_

private

use_ms1_traces_

bool use_ms1_traces_

private