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...

bool	isValid ()
	Checks if evidence.txt is writable (i.e. the path in the ctor was not empty and could be created) More...

void	exportFeatureMap (const OpenMS::FeatureMap &feature_map, const OpenMS::ConsensusMap &cmap)
	Exports a FeatureMap to the evidence.txt. More...

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

OpenMS::Size	proteinGroupID_ (const OpenMS::String &protein_accession)
	returns the MaxQuant unique evidence number of a protein accession More...

std::map< OpenMS::Size, OpenMS::Size >	makeFeatureUIDtoConsensusMapIndex_ (const OpenMS::ConsensusMap &cmap)
	Creates map that has the information which FeatureUID is mapped to which ConsensusFeature in ConsensusMap. More...

bool	hasValidPepID_ (const OpenMS::Feature &f, const OpenMS::Size c_feature_number, const std::multimap< OpenMS::String, std::pair< OpenMS::Size, OpenMS::Size >> &UIDs, const OpenMS::ProteinIdentification::Mapping &mp_f)
	Checks if Feature has valid PeptideIdentifications. More...

bool	hasPeptideIdentifications_ (const OpenMS::ConsensusFeature &cf)
	Checks if ConsensusFeature has valid PeptideIdentifications. 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)
	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...

std::map< OpenMS::String, OpenMS::Size >	protein_id_
	map that maps each accession to its distinct number in this evidence.txt 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
	)

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

◆ 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
	)

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

◆ hasPeptideIdentifications_()

bool hasPeptideIdentifications_ ( const OpenMS::ConsensusFeature & cf )

private

Checks if ConsensusFeature has valid PeptideIdentifications.

If there are no PeptideIdentifications, the functions returns false to show that something went wrong.

Parameters

cf	is used to extract PeptideIdentifications

Returns: Returns true if the ConsensusFeature has any PepIDs; otherwise false

◆ hasValidPepID_()

bool hasValidPepID_	(	const OpenMS::Feature &	f,
		const OpenMS::Size	c_feature_number,
		const std::multimap< OpenMS::String, std::pair< OpenMS::Size, OpenMS::Size >> &	UIDs,
		const OpenMS::ProteinIdentification::Mapping &	mp_f
	)

private

Checks if Feature has valid PeptideIdentifications.

If there are no PeptideIdentifications or the best hit of the Feature cannot be found in corresponding ConsensusFeature, the functions returns false to show that something went wrong.

Parameters

f	Feature to extract PeptideIdentifications
c_feature_number	Index of corresponding ConsensusFeature in ConsensusMap
UIDs	UIDs of all PeptideIdentifications of the ConsensusMap
mp_f	Mapping between the FeatureMap and ProteinIdentifications for the UID

Returns: Returns true if the PeptideIdentifications exist and are valid

◆ isValid()

bool isValid ( )

Checks if evidence.txt is writable (i.e. the path in the ctor was not empty and could be created)

Returns: Returns true if evidence.txt is writable

◆ makeFeatureUIDtoConsensusMapIndex_()

std::map<OpenMS::Size, OpenMS::Size> makeFeatureUIDtoConsensusMapIndex_ ( const OpenMS::ConsensusMap & cmap )

private

Creates map that has the information which FeatureUID is mapped to which ConsensusFeature in ConsensusMap.

Exceptions

Exception::Precondition if FeatureHandle exists twice in ConsensusMap

Parameters

cmap	ConsensusMap that includes ConsensusFeatures

Returns: Returns map, the index is a FeatureID, the value is the index of the ConsensusFeature in the vector of ConsensusMap

◆ proteinGroupID_()

OpenMS::Size proteinGroupID_ ( const OpenMS::String & protein_accession )

private

returns the MaxQuant unique evidence number of a protein accession

Obtains a unique, consecutive number for each distinct protein, which can be used as a protein ID in the evidence.txt (in lack of a proper proteingroup ID which maps to proteinGroups.txt)

Parameters

protein_accession The accession of the protein

Returns: Returns distinct number for every Protein

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

◆ protein_id_

std::map<OpenMS::String, OpenMS::Size> protein_id_

private

map that maps each accession to its distinct number in this evidence.txt

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MQEvidence()

◆ ~MQEvidence()

Member Function Documentation

◆ exportFeatureMap()

◆ exportHeader_()

◆ exportRowFromFeature_()

◆ hasPeptideIdentifications_()

◆ hasValidPepID_()

◆ isValid()

◆ makeFeatureUIDtoConsensusMapIndex_()

◆ proteinGroupID_()

Member Data Documentation

◆ file_

◆ filename_

◆ id_

◆ protein_id_