MQEvidence Class Reference

Builds a MaxQuant Evidence.txt. More...

#include <OpenMS/QC/MQEvidenceExporter.h>

Collaboration diagram for MQEvidence:

Public Member Functions
	MQEvidence (const OpenMS::String &path)
	Creates MQEvidence object and evidence.txt in given path. More...
	~MQEvidence ()
	Closes f_stream. More...
void	exportFeatureMap (const OpenMS::FeatureMap &feature_map, const OpenMS::ConsensusMap &cmap, const OpenMS::MSExperiment &exp={}, const std::map< OpenMS::String, OpenMS::String > &prot_map={})
	Exports a FeatureMap to the evidence.txt. More...

Private Member Functions
void	exportHeader_ ()
	Writes the header of evidence.txt (Names of columns) More...
void	exportRowFromFeature_ (const OpenMS::Feature &f, const OpenMS::ConsensusMap &cmap, const OpenMS::Size c_feature_number, const OpenMS::String &raw_file, const std::multimap< OpenMS::String, std::pair< OpenMS::Size, OpenMS::Size >> &UIDs, const OpenMS::ProteinIdentification::Mapping &mp_f, const OpenMS::MSExperiment &exp={}, const std::map< OpenMS::String, OpenMS::String > &prot_map={})
	Export one Feature as a row in MQEvidence.txt. More...

Private Attributes
std::fstream	file_
	Stream where the data is added to create evidence.txt. More...
OpenMS::Size	id_ = 0
	number of rows in evidence.txt to give each row a specific id More...
OpenMS::String	filename_
	path and name of the evidence.txt More...

Detailed Description

Builds a MaxQuant Evidence.txt.

This class is closely related to QualityControl, it creates an evidence.txt similar to a MaxQuant evidence.txt. But not all columns of a MaxQuant file get exported. By the construction of an object, the column names of the evidence values are added to the evidence.txt. For the construction a valid path is needed (check out constructor) where the evidence.txt can be stored. To fill the output evidence.txt with data from the MS/MS run use the exportFeatureMap function, it needs a FeatureMap and the matching ConsensusMap as an input. To check if the created evidence.txt is writable use the function isValid.

Constructor & Destructor Documentation

MQEvidence()

MQEvidence ( const OpenMS::String &  path )

explicit

Creates MQEvidence object and evidence.txt in given path.

  If the path for the constructor is empty (path not valid), no evidence.txt is created.
  If the creation of the fstream object is successful a constant header is added to the evidence.txt
  If the path does not exist, it will be created

Exceptions

Exception::FileNotWritable

if evidence.txt could not be created

Parameters

path	that is the path where evidence.txt has to be stored

~MQEvidence()

~MQEvidence

(

)

Closes f_stream.

Member Function Documentation

exportFeatureMap()

void exportFeatureMap	(	const OpenMS::FeatureMap &	feature_map,
		const OpenMS::ConsensusMap &	cmap,
		const OpenMS::MSExperiment &	exp = {},
		const std::map< OpenMS::String, OpenMS::String > &	prot_map = {}
	)

Exports a FeatureMap to the evidence.txt.

Exports one row per feature from the FeatureMap to the evidence.txt file.

Exceptions

Exception::FileNotWritable	if evidence.txt is not writable
Exception::MissingInformation	if Feature_map has no corresponding ConsensusFeature

Parameters

feature_map	which contains Features to extract evidence data
cmap	ConsensusMap to extract evidence data if Feature has no valid PeptideIdentifications
exp	MS Experiment holds evidence data to extract
prot_map	Mapping a protein_accession to its description(proteinname, genename...)

exportHeader_()

void exportHeader_ ( )

private

Writes the header of evidence.txt (Names of columns)

exportRowFromFeature_()

void exportRowFromFeature_ ( const OpenMS::Feature &  f, const OpenMS::ConsensusMap &  cmap, const OpenMS::Size  c_feature_number, const OpenMS::String &  raw_file, const std::multimap< OpenMS::String, std::pair< OpenMS::Size, OpenMS::Size >> &  UIDs, const OpenMS::ProteinIdentification::Mapping &  mp_f, const OpenMS::MSExperiment &  exp = {}, const std::map< OpenMS::String, OpenMS::String > &  prot_map = {}  )

private

Export one Feature as a row in MQEvidence.txt.

If the feature has no PepID's or the corresponding CF has no PepIDs, no row will be exported

Parameters

f	Feature to extract evidence data
cmap	ConsensusMap to extract evidence data if Feature has no valid PeptideIdentifications
c_feature_number	Index of corresponding ConsensusFeature in ConsensusMap
raw_file	is specifying the raw_file the feature belongs to
UIDs	UIDs of all PeptideIdentifications of the ConsensusMap
mp_f	Mapping between the FeatureMap and ProteinIdentifications for the UID from PeptideIdenfitication::buildUIDfromAllPepIds
exp	MS Experiment holds evidence data to extract
prot_map	Mapping a protein_accession to its description(proteinname, genename...)

Member Data Documentation

file_

std::fstream file_

private

Stream where the data is added to create evidence.txt.

filename_

OpenMS::String filename_

private

path and name of the evidence.txt

id_

OpenMS::Size id_ = 0

private

number of rows in evidence.txt to give each row a specific id