Builds a MaxQuant Evidence.txt. More...

#include <QualityControl/include/MQEvidenceExporter.h>

Public Member Functions
	MQEvidence (const std::string &path)
	Creates MQEvidence object and evidence.txt in given path.

	~MQEvidence ()
	Closes f_stream.

void	exportFeatureMap (const OpenMS::FeatureMap &feature_map, const OpenMS::ConsensusMap &cmap, const OpenMS::MSExperiment &exp={}, const std::map< std::string, std::string > &prot_map={})
	Exports a FeatureMap to the evidence.txt.

Private Member Functions
void	exportHeader_ ()
	Writes the header of evidence.txt (Names of columns)

void	exportRowFromFeature_ (const OpenMS::Feature &f, const OpenMS::ConsensusMap &cmap, const OpenMS::Size c_feature_number, const std::string &raw_file, const std::multimap< std::string, std::pair< OpenMS::Size, OpenMS::Size > > &UIDs, const OpenMS::ProteinIdentification::Mapping &mp_f, const OpenMS::MSExperiment &exp={}, const std::map< std::string, std::string > &prot_map={})
	Export one Feature as a row in MQEvidence.txt.

Private Attributes
std::fstream	file_
	Stream where the data is added to create evidence.txt.

OpenMS::Size	id_ = 0
	number of rows in evidence.txt to give each row a specific id

std::string	filename_
	path and name of the evidence.txt

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 std::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

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

References exportHeader_(), file_, filename_, OPENMS_LOG_FATAL_ERROR, and OpenMS::to_path().

◆ ~MQEvidence()

~MQEvidence ( )

Closes f_stream.

References file_.

Member Function Documentation

◆ exportFeatureMap()

void exportFeatureMap	(	const OpenMS::FeatureMap &	feature_map,
		const OpenMS::ConsensusMap &	cmap,
		const OpenMS::MSExperiment &	exp = `{}`,
		const std::map< std::string, std::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

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

References File::basename(), PeptideIdentification::buildUIDsFromAllPepIDs(), IdentifierMSRunMapper::create(), exportRowFromFeature_(), file_, filename_, DocumentIdentifier::getLoadedFilePath(), FeatureMap::getPrimaryMSRunPath(), FeatureMap::getProteinIdentifications(), MQExporterHelper::isValid(), MQExporterHelper::makeFeatureUIDtoConsensusMapIndex_(), and OPENMS_LOG_ERROR.

◆ exportHeader_()

void exportHeader_ ( )

private

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

References file_.

Referenced by MQEvidence().

◆ exportRowFromFeature_()

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

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