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

Inheritance diagram for TransitionTSVFile:

Collaboration diagram for TransitionTSVFile:

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

Private Member Functions
Reader helper functions
void	getTSVHeader_ (const std::string &line, char &delimiter, std::map< std::string, int > &header_dict) const
	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	spectrastRTExtract (const String &str_inp, double &value, bool &spectrast_legacy)
	Extract retention time from a SpectraST comment string. More...

bool	spectrastAnnotationExtract (const String &str_inp, TSVTransition &mytransition)
	Extract annotation from a SpectraST comment string. More...

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

Conversion functions from TSVTransition objects to OpenMS datastructures
These functions convert the relevant data from a TSVTransition to the datastructures used by the TraML handler or by the internal LightTargetedExperiment.
typedef std::vector< OpenMS::TargetedExperiment::Protein >	ProteinVectorType

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

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

String	retentionTimeInterpretation_

bool	override_group_label_check_

bool	force_invalid_mods_

static const char *	strarray_ []

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

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...

TransitionTSVFile::TSVTransition	convertTransition_ (const ReactionMonitoringTransition *it, OpenMS::TargetedExperiment &targeted_exp)
	Convert an OpenMS transition to a TSVTransition for output writing. More...

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

Conversion helper functions
void	resolveMixedSequenceGroups_ (std::vector< TSVTransition > &transition_list) const
	Resolve cases where the same peptide label group has different sequences. More...

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_ (String protein_name, const String &uniprot_id, 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 >::const_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 >::const_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)
	Add a modification at the specified location. More...

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

	TransitionTSVFile ()
	Constructor. More...

	~TransitionTSVFile () override
	Destructor. More...

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

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

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

virtual	~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	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) 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...

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...

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

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

  @brief This class supports reading and writing of OpenSWATH transition
  lists.

  The transition lists can be either comma- or tab-separated plain
  text files (CSV or TSV format).  Modifications should be provided in
  UniMod format<sup>1</sup>, but can also be provided in TPP format. 
  For another file format that stores transitions, see also TransitionPQPFile.

  The following columns are required:

  <table>
    <tr> <td BGCOLOR="#EBEBEB">PrecursorMz*</td> <td>float</td> <td>This describes the precursor ion \a m/z</td> </tr>
    <tr> <td BGCOLOR="#EBEBEB">ProductMz*</td> <td>float; synonyms: FragmentMz</td> <td>This specifies the product ion \a m/z</td> </tr>
    <tr> <td BGCOLOR="#EBEBEB">LibraryIntensity*</td> <td>float; synonyms: RelativeFragmentIntensity</td> <td>This specifies the relative intensity of the fragment ion</td></tr>
    <tr> <td BGCOLOR="#EBEBEB">NormalizedRetentionTime*</td> <td>float; synonyms: RetentionTime, Tr_recalibrated, iRT, RetentionTimeCalculatorScore</td> <td>This specifies the expected retention time (normalized retention time) </td></tr>
  </table>

For targeted proteomics files, the following additional columns should be provided:

GeneName**	free text;	Gene name (unique gene identifier)
ProteinId**	free text; synonyms: ProteinName	Protein identifier
PeptideSequence**	free text	sequence only (no modifications); synonyms: Sequence, StrippedSequence
ModifiedPeptideSequence**	free text	should contain modifications¹; synonyms: FullUniModPeptideName, FullPeptideName, ModifiedSequence
PrecursorCharge**	integer; synonyms: Charge	contains the charge of the precursor ion
ProductCharge**	integer; synonyms: FragmentCharge	contains the fragment charge
FragmentType	free text	contains the type of the fragment, e.g. "b" or "y"
FragmentSeriesNumber	integer; synonyms: FragmentNumber	e.g. for y7 use "7" here

OpenSWATH uses grouped transitions to detect candidate analyte signals. These groups are by default generated based on the input, but can also be manually specified:

  <table>
    <tr> <td BGCOLOR="#EBEBEB">TransitionGroupId**</td> <td>free text; synomys: TransitionGroupName, transition_group_id</td><td> designates the transition group [e.g. peptide] to which this transition belongs</td> </tr>
    <tr> <td BGCOLOR="#EBEBEB">TransitionId**</td> <td>free text; synonyms: TransitionName, transition_name </td> <td> needs to be unique for each transition [in this file]</td> </tr>
    <tr> <td BGCOLOR="#EBEBEB">Decoy</td> <td>1: decoy, 0: target; synomys: decoy, IsDecoy </td> <td> determines whether the transition is a decoy transition or not</td> </tr>
    <tr> <td BGCOLOR="#EBEBEB">PeptideGroupLabel</td> <td>free text </td> <td> designates to which peptide label group (as defined in MS:1000893) the peptide belongs to<sup>2</sup></td> </tr>
    <tr> <td BGCOLOR="#EBEBEB">DetectingTransition</td> <td> 0 or 1; synonyms: detecting_transition</td> <td>1: use transition to detect peak group, 0: don't use transition for detection</td> </tr>
    <tr> <td BGCOLOR="#EBEBEB">IdentifyingTransition</td> <td> 0 or 1; synonyms: identifying_transition</td> <td>1: use transition for peptidoform inference in the <a href="http://openswath.org/en/latest/docs/ipf.html">IPF Workflow</a>, 0: don't use transition for identification</td> </tr>
    <tr> <td BGCOLOR="#EBEBEB">QuantifyingTransition</td> <td> 0 or 1; synonyms: quantifying_transition</td> <td>1: use transition to quantify peak group, 0: don't use transition for quantification</td> </tr>
  </table>

Optionally, the following columns can be specified but they are not actively used by OpenSWATH:

CollisionEnergy	float; synonyms: CE	Collision energy
Annotation	free text	Transition-level annotation, e.g. y7
UniprotId	free text; synonyms: UniprotID	A Uniprot identifier
LabelType	free text	optional description of which label was used, e.g. heavy or light

For targeted metabolomics files, the following fields are also supported:

  <table>
    <tr> <td BGCOLOR="#EBEBEB">CompoundName**</td> <td>free text; synonyms: CompoundId</td><td>Should be unique for the analyte, if present the file will be interpreted as a metabolomics file </td></tr>
    <tr> <td BGCOLOR="#EBEBEB">SMILES</td><td>free text</td><td>SMILES identifier of the compound</td></tr>
    <tr> <td BGCOLOR="#EBEBEB">SumFormula</td><td>free text</td><td>molecular formula of the compound (e.g. H2O)</td></tr>
  </table>

Fields indicated with * are strictly required to create a TraML file. Fields indicated with ** are recommended, but only required for a specific application (such as using the transition list for an analysis tool such as OpenSwathWorkflow) or in a specific context (proteomics or metabolomics).

Remarks:

1. modifications should be supplied inside the sequence using UniMod identifiers or freetext identifiers that are understood by OpenMS. See also OpenMS::AASequence for more information. For example:
  - PEPT(Phosphorylation)IDE(UniMod:27)A )
1. peptide label groups designate groups of peptides that are isotopically modified forms of the same peptide species. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label. For example:
  - PEPTIDEAK -> gets label "PEPTIDEAK_gr1"
  - PEPTIDEAK[+8] -> gets label "PEPTIDEAK_gr1"
  - PEPT(Phosphorylation)IDEAK -> gets label "PEPTIDEAK_gr2"
  - PEPT(Phosphorylation)IDEAK[+8] -> gets label "PEPTIDEAK_gr2"

Parameters of this class are:

Name	Type	Default	Restrictions	Description
retentionTimeInterpretation	string	iRT	iRT, seconds, minutes	How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)
override_group_label_check	string	false	true, false	Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group). Only turn this off if you know what you are doing.
force_invalid_mods	string	false	true, false	Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Member Typedef Documentation

◆ PeptideVectorType

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

private

◆ ProteinVectorType

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

private

◆ TransitionVectorType

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

private

Constructor & Destructor Documentation

◆ TransitionTSVFile()

TransitionTSVFile ( )

Constructor.

◆ ~TransitionTSVFile()

~TransitionTSVFile ( )

override

Destructor.

Member Function Documentation

◆ addModification_()

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

private

Add a modification at the specified location.

◆ 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_()

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

protected

Convert an OpenMS transition to a TSVTransition for output writing.

◆ 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 TOPPOpenSwathBase::loadTransitionList().

◆ 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 >::const_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 >::const_iterator	tr_it,
		OpenMS::TargetedExperiment::Peptide &	peptide
	)

private

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

◆ createProtein_()

void createProtein_	(	String	protein_name,
		const String &	uniprot_id,
		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::map< std::string, int > &	header_dict
	)		const

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_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 ) const

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 sequences) 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 identifier (transition group id).

Parameters

transition_list The list of transitions to be fixed.

◆ spectrastAnnotationExtract()

bool spectrastAnnotationExtract	(	const String &	str_inp,
		TSVTransition &	mytransition
	)

private

Extract annotation from a SpectraST comment string.

◆ spectrastRTExtract()

void spectrastRTExtract	(	const String &	str_inp,
		double &	value,
		bool &	spectrast_legacy
	)

private

Extract retention time from a SpectraST comment string.

◆ 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_ ( )

overrideprotectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

◆ validateTargetedExperiment()

void validateTargetedExperiment ( const 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

◆ strarray_

const char* strarray_[]

staticprivate

Classes

Private Member Functions

Conversion functions from TSVTransition objects to OpenMS datastructures

Conversion helper functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ PeptideVectorType

◆ ProteinVectorType

◆ TransitionVectorType

Constructor & Destructor Documentation

◆ TransitionTSVFile()

◆ ~TransitionTSVFile()

Member Function Documentation

◆ addModification_()

◆ cleanupTransitions_()

◆ convertTargetedExperimentToTSV()

◆ convertTransition_()

◆ convertTSVToTargetedExperiment() [1/2]

◆ convertTSVToTargetedExperiment() [2/2]

◆ createCompound_()

◆ createPeptide_()

◆ createProtein_()

◆ createTransition_()

◆ getTSVHeader_()

◆ interpretRetentionTime_()

◆ readUnstructuredTSVInput_()

◆ resolveMixedSequenceGroups_()

◆ spectrastAnnotationExtract()

◆ spectrastRTExtract()

◆ TSVToTargetedExperiment_() [1/2]

◆ TSVToTargetedExperiment_() [2/2]

◆ updateMembers_()

◆ validateTargetedExperiment()

◆ writeTSVOutput_()

Member Data Documentation

◆ force_invalid_mods_

◆ header_names_

◆ override_group_label_check_

◆ retentionTimeInterpretation_

◆ strarray_