This class can convert TraML and TSV files into each other. More...

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

Inheritance diagram for TransitionTSVReader:

Classes
struct	TSVTransition
	Internal structure to represent a transition. More...

Public Member Functions
void	convertTargetedExperimentToTSV (const char *filename, OpenMS::TargetedExperiment &targeted_exp)
	Write out a targeted experiment (TraML structure) into a tsv file. More...

void	convertTSVToTargetedExperiment (const char *filename, FileTypes::Type filetype, OpenMS::TargetedExperiment &targeted_exp)
	Read in a tsv/mrm file and construct a targeted experiment (TraML structure) More...

void	convertTSVToTargetedExperiment (const char *filename, FileTypes::Type filetype, OpenSwath::LightTargetedExperiment &targeted_exp)
	Read in a tsv file and construct a targeted experiment (Light transition structure) More...

void	validateTargetedExperiment (OpenMS::TargetedExperiment &targeted_exp)
	Validate a TargetedExperiment (check that all ids are unique) More...


	TransitionTSVReader ()
	Constructor. More...

	~TransitionTSVReader ()
	Destructor. More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress () const
	Ends the progress display. More...

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Protected Member Functions
void	TSVToTargetedExperiment_ (std::vector< TSVTransition > &transition_list, OpenMS::TargetedExperiment &exp)
	Convert a list of TSVTransition to a TargetedExperiment. More...

void	TSVToTargetedExperiment_ (std::vector< TSVTransition > &transition_list, OpenSwath::LightTargetedExperiment &exp)
	Convert a list of TSVTransition to a LightTargetedExperiment. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Private Member Functions
void	writeTSVOutput_ (const char *filename, OpenMS::TargetedExperiment &targeted_exp)
	Write a TargetedExperiment to a file. More...

Conversion functions from TSVTransition objects to TraML datastructures
These functions convert the relevant data from a TSVTransition to the datastructures used by the TraML handler, namely ReactionMonitoringTransition, TargetedExperiment::Protein and TargetedExperiment::Peptide.
typedef std::vector< OpenMS::TargetedExperiment::Protein >	ProteinVectorType
	Typedefs. More...

typedef std::vector< OpenMS::TargetedExperiment::Peptide >	PeptideVectorType

typedef std::vector< OpenMS::ReactionMonitoringTransition >	TransitionVectorType

String	retentionTimeInterpretation_
	Members. More...

bool	override_group_label_check_

bool	force_invalid_mods_

static const char *	strarray_ []

static const std::vector< std::string >	header_names_

TransitionTSVReader::TSVTransition	convertTransition_ (const ReactionMonitoringTransition *it, OpenMS::TargetedExperiment &targeted_exp)

void	updateMembers_ ()
	Synchronize members with param class. More...

void	getTSVHeader_ (const std::string &line, char &delimiter, std::vector< std::string > header, std::map< std::string, int > &header_dict)
	Determine separator in a CSV file and check for correct headers. More...

void	readUnstructuredTSVInput_ (const char *filename, FileTypes::Type filetype, std::vector< TSVTransition > &transition_list)
	Read tab or comma separated input with columns defined by their column headers only. More...

void	cleanupTransitions_ (TSVTransition &mytransition)
	Cleanup of the read fields (removing quotes etc.) More...

void	resolveMixedSequenceGroups_ (std::vector< TSVTransition > &transition_list)

void	createTransition_ (std::vector< TSVTransition >::iterator &tr_it, OpenMS::ReactionMonitoringTransition &rm_trans)
	Populate a new ReactionMonitoringTransition object from a row in the csv. More...

void	createProtein_ (std::vector< TSVTransition >::iterator &tr_it, OpenMS::TargetedExperiment::Protein &protein)
	Populate a new TargetedExperiment::Protein object from a row in the csv. More...

void	interpretRetentionTime_ (std::vector< TargetedExperiment::RetentionTime > &retention_times, const OpenMS::DataValue rt_value)
	Helper function to assign retention times to compounds and peptides. More...

void	createPeptide_ (std::vector< TSVTransition >::iterator &tr_it, OpenMS::TargetedExperiment::Peptide &peptide)
	Populate a new TargetedExperiment::Peptide object from a row in the csv. More...

void	createCompound_ (std::vector< TSVTransition >::iterator &tr_it, OpenMS::TargetedExperiment::Compound &compound)
	Populate a new TargetedExperiment::Compound object (a metabolite) from a row in the csv. More...

void	addModification_ (std::vector< TargetedExperiment::Peptide::Modification > &mods, int location, const ResidueModification &rmod)

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. More...

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

This class can convert TraML and TSV files into each other.

The TSV are tab-separated and need to have the following columns:

PrecursorMz (float) ProductMz (float) Tr_calibrated (float) transition_name (free text, needs to be unique for each transition [in this file]) CE (float) LibraryIntensity (float) transition_group_id (free text, designates the transition group [e.g. peptide] to which this transition belongs) decoy (1==decoy, 0== no decoy; determines whether the transition is a decoy transition or not) PeptideSequence (free text, sequence only (no modifications) ) ProteinName (free text) Annotation (free text, e.g. y7) FullUniModPeptideName (free text, should contain modifications*) MissedCleavages Replicates NrModifications PrecursorCharge (integer) PeptideGroupLabel (free text, designates to which peptide label group (as defined in MS:1000893) the peptide belongs to) LabelType (free text, optional description of which label was used, e.g. heavy or light) detecting_transition (bool, should this transition be used for peak-picking (detection) of the peak group?) identifying_transition (bool, should this transition be used for UIS identification together with the detecting transitions?) quantifying_transition (bool, should this transition be used for quantification?)

Member Typedef Documentation

◆ PeptideVectorType

typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType

private

◆ ProteinVectorType

typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType

private

Typedefs.

◆ TransitionVectorType

typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType

private

Constructor & Destructor Documentation

◆ TransitionTSVReader()

TransitionTSVReader ( )

Constructor.

◆ ~TransitionTSVReader()

~TransitionTSVReader ( )

Destructor.

Member Function Documentation

◆ addModification_()

void addModification_	(	std::vector< TargetedExperiment::Peptide::Modification > &	mods,
		int	location,
		const ResidueModification &	rmod
	)

private

◆ cleanupTransitions_()

void cleanupTransitions_ ( TSVTransition & mytransition )

private

Cleanup of the read fields (removing quotes etc.)

◆ convertTargetedExperimentToTSV()

void convertTargetedExperimentToTSV	(	const char *	filename,
		OpenMS::TargetedExperiment &	targeted_exp
	)

Write out a targeted experiment (TraML structure) into a tsv file.

Parameters

filename	The output file
targeted_exp	The targeted experiment

◆ convertTransition_()

TransitionTSVReader::TSVTransition convertTransition_	(	const ReactionMonitoringTransition *	it,
		OpenMS::TargetedExperiment &	targeted_exp
	)

protected

◆ convertTSVToTargetedExperiment() [1/2]

void convertTSVToTargetedExperiment	(	const char *	filename,
		FileTypes::Type	filetype,
		OpenMS::TargetedExperiment &	targeted_exp
	)

Read in a tsv/mrm file and construct a targeted experiment (TraML structure)

Parameters

filename	The input file
filetype	The type of file ("mrm" or "tsv")
targeted_exp	The output targeted experiment

Referenced by SortPairDoubleByFirst().

◆ convertTSVToTargetedExperiment() [2/2]

void convertTSVToTargetedExperiment	(	const char *	filename,
		FileTypes::Type	filetype,
		OpenSwath::LightTargetedExperiment &	targeted_exp
	)

Read in a tsv file and construct a targeted experiment (Light transition structure)

Parameters

filename	The input file
filetype	The type of file ("mrm" or "tsv")
targeted_exp	The output targeted experiment

◆ createCompound_()

void createCompound_	(	std::vector< TSVTransition >::iterator &	tr_it,
		OpenMS::TargetedExperiment::Compound &	compound
	)

private

Populate a new TargetedExperiment::Compound object (a metabolite) from a row in the csv.

◆ createPeptide_()

void createPeptide_	(	std::vector< TSVTransition >::iterator &	tr_it,
		OpenMS::TargetedExperiment::Peptide &	peptide
	)

private

Populate a new TargetedExperiment::Peptide object from a row in the csv.

◆ createProtein_()

void createProtein_	(	std::vector< TSVTransition >::iterator &	tr_it,
		OpenMS::TargetedExperiment::Protein &	protein
	)

private

Populate a new TargetedExperiment::Protein object from a row in the csv.

◆ createTransition_()

void createTransition_	(	std::vector< TSVTransition >::iterator &	tr_it,
		OpenMS::ReactionMonitoringTransition &	rm_trans
	)

private

Populate a new ReactionMonitoringTransition object from a row in the csv.

◆ getTSVHeader_()

void getTSVHeader_	(	const std::string &	line,
		char &	delimiter,
		std::vector< std::string >	header,
		std::map< std::string, int > &	header_dict
	)

private

Determine separator in a CSV file and check for correct headers.

Parameters

line	The header to be parsed
delimiter	The delimiter which will be determined from the input
header	The fields of the header
header_dict	The map which maps the fields in the header to their position

◆ interpretRetentionTime_()

void interpretRetentionTime_	(	std::vector< TargetedExperiment::RetentionTime > &	retention_times,
		const OpenMS::DataValue	rt_value
	)

private

Helper function to assign retention times to compounds and peptides.

◆ readUnstructuredTSVInput_()

void readUnstructuredTSVInput_	(	const char *	filename,
		FileTypes::Type	filetype,
		std::vector< TSVTransition > &	transition_list
	)

private

Read tab or comma separated input with columns defined by their column headers only.

Parameters

filename	The input file
filetype	The type of file ("mrm" or "tsv")
transition_list	The output list of transitions

◆ resolveMixedSequenceGroups_()

void resolveMixedSequenceGroups_ ( std::vector< TSVTransition > & transition_list )

private

Resolve cases where the same peptide label group has different sequences.

Since members in a peptide label group (MS:1000893) should only be isotopically modified forms of the same peptide, having different peptide sequences (different AA order) within the same group most likely constitutes an error. This function will fix the error by erasing the provided "peptide group label" for a peptide and replace it with the peptide id (transition group id).

Parameters

transition_list The list of read transitions to be fixed.

◆ TSVToTargetedExperiment_() [1/2]

void TSVToTargetedExperiment_	(	std::vector< TSVTransition > &	transition_list,
		OpenMS::TargetedExperiment &	exp
	)

protected

Convert a list of TSVTransition to a TargetedExperiment.

Converts the list (read from csv/mrm) file into a object model using the TargetedExperiment with proper hierarchical structure from Transition to Peptide to Protein.

◆ TSVToTargetedExperiment_() [2/2]

void TSVToTargetedExperiment_	(	std::vector< TSVTransition > &	transition_list,
		OpenSwath::LightTargetedExperiment &	exp
	)

protected

Convert a list of TSVTransition to a LightTargetedExperiment.

Converts the list (read from csv/mrm) file into a object model using the LightTargetedExperiment with proper hierarchical structure from Transition to Peptide to Protein.

◆ updateMembers_()

void updateMembers_ ( )

protectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

◆ validateTargetedExperiment()

void validateTargetedExperiment ( OpenMS::TargetedExperiment & targeted_exp )

Validate a TargetedExperiment (check that all ids are unique)

◆ writeTSVOutput_()

void writeTSVOutput_	(	const char *	filename,
		OpenMS::TargetedExperiment &	targeted_exp
	)

private

Write a TargetedExperiment to a file.

Parameters

filename	Name of the output file
targeted_exp	The data structure to be written to the file

Member Data Documentation

◆ force_invalid_mods_

bool force_invalid_mods_

private

◆ header_names_

const std::vector<std::string> header_names_

staticprivate

◆ override_group_label_check_

bool override_group_label_check_

private

◆ retentionTimeInterpretation_

String retentionTimeInterpretation_

private

Members.

◆ strarray_

const char* strarray_[]

staticprivate

Classes

Public Member Functions

Protected Member Functions

Private Member Functions

Conversion functions from TSVTransition objects to TraML datastructures

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ PeptideVectorType

◆ ProteinVectorType

◆ TransitionVectorType

Constructor & Destructor Documentation

◆ TransitionTSVReader()

◆ ~TransitionTSVReader()

Member Function Documentation

◆ addModification_()

◆ cleanupTransitions_()

◆ convertTargetedExperimentToTSV()

◆ convertTransition_()

◆ convertTSVToTargetedExperiment() [1/2]

◆ convertTSVToTargetedExperiment() [2/2]

◆ createCompound_()

◆ createPeptide_()

◆ createProtein_()

◆ createTransition_()

◆ getTSVHeader_()

◆ interpretRetentionTime_()

◆ readUnstructuredTSVInput_()

◆ resolveMixedSequenceGroups_()

◆ TSVToTargetedExperiment_() [1/2]

◆ TSVToTargetedExperiment_() [2/2]

◆ updateMembers_()

◆ validateTargetedExperiment()

◆ writeTSVOutput_()

Member Data Documentation

◆ force_invalid_mods_

◆ header_names_

◆ override_group_label_check_

◆ retentionTimeInterpretation_

◆ strarray_