MQMsms Class Reference

Builds a MaxQuant msms.txt. More...

#include <OpenMS/QC/MQMsmsExporter.h>

Collaboration diagram for MQMsms:

Public Member Functions
	MQMsms (const OpenMS::String &path)
	Creates MQMsms object and msms.txt in given path. More...
	~MQMsms ()
	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={})

Private Member Functions
void	exportHeader_ ()
	Writes the header of msms.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 msms.txt. More...

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

Detailed Description

Builds a MaxQuant msms.txt.

This class is closely related to QualityControl, it creates an msms.txt similar to a MaxQuant msms.txt. But not all columns of a MaxQuant file get exported. By the construction of an object, the column names of the msms values are added to the msms.txt. For the construction a valid path is needed (check out constructor) where the msms.txt can be stored. To fill the output msms.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 msms.txt is writable use the function isValid.

Constructor & Destructor Documentation

MQMsms()

MQMsms ( const OpenMS::String &  path )

explicit

Creates MQMsms object and msms.txt in given path.

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

Exceptions

Exception::FileNotWritable

if msms.txt could not be created

Parameters

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

~MQMsms()

~MQMsms

(

)

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 = {}
	)

exportHeader_()

void exportHeader_ ( )

private

Writes the header of msms.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 msms.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 msms 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 msms.txt.

filename_

OpenMS::String filename_

private

path and name of the msms.txt

id_

OpenMS::Size id_ = 0

private

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