TargetedExperiment Class Reference

A description of a targeted experiment containing precursor and production ions. More...

#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>

Collaboration diagram for TargetedExperiment:

Classes
struct	SummaryStatistics

Public Types
typedef TargetedExperimentHelper::CV	CV
typedef TargetedExperimentHelper::Protein	Protein
typedef TargetedExperimentHelper::RetentionTime	RetentionTime
typedef TargetedExperimentHelper::Compound	Compound
typedef TargetedExperimentHelper::Peptide	Peptide
typedef TargetedExperimentHelper::Contact	Contact
typedef TargetedExperimentHelper::Publication	Publication
typedef TargetedExperimentHelper::Instrument	Instrument
typedef TargetedExperimentHelper::Prediction	Prediction
typedef TargetedExperimentHelper::Interpretation	Interpretation
typedef ReactionMonitoringTransition	Transition
typedef Residue	IonType
typedef std::map< String, const Protein * >	ProteinReferenceMapType
typedef std::map< String, const Peptide * >	PeptideReferenceMapType
typedef std::map< String, const Compound * >	CompoundReferenceMapType

Public Member Functions
Constructors and destructors
	TargetedExperiment ()
	default constructor More...
	TargetedExperiment (const TargetedExperiment &rhs)
	copy constructor More...
virtual	~TargetedExperiment ()
	destructor More...
TargetedExperiment &	operator= (const TargetedExperiment &rhs)
	assignment operator More...
Predicates
bool	operator== (const TargetedExperiment &rhs) const
bool	operator!= (const TargetedExperiment &rhs) const
TargetedExperiment	operator+ (const TargetedExperiment &rhs) const
	Joins two targeted experiments. More...
TargetedExperiment &	operator+= (const TargetedExperiment &rhs)
	Add one targeted experiment to another. More...
void	clear (bool clear_meta_data)
	Clears all data and meta data. More...
SummaryStatistics	getSummary () const
	return summary stats about this TE. More...
Accessors
void	setCVs (const std::vector< CV > &cvs)
const std::vector< CV > &	getCVs () const
void	addCV (const CV &cv)
void	setContacts (const std::vector< Contact > &contacts)
const std::vector< Contact > &	getContacts () const
void	addContact (const Contact &contact)
void	setPublications (const std::vector< Publication > &publications)
const std::vector< Publication > &	getPublications () const
void	addPublication (const Publication &publication)
void	setTargetCVTerms (const CVTermList &cv_terms)
const CVTermList &	getTargetCVTerms () const
void	addTargetCVTerm (const CVTerm &cv_term)
void	setTargetMetaValue (const String &name, const DataValue &value)
void	setInstruments (const std::vector< Instrument > &instruments)
const std::vector< Instrument > &	getInstruments () const
void	addInstrument (const Instrument &instrument)
void	setSoftware (const std::vector< Software > &software)
const std::vector< Software > &	getSoftware () const
void	addSoftware (const Software &software)
void	setProteins (const std::vector< Protein > &proteins)
const std::vector< Protein > &	getProteins () const
const Protein &	getProteinByRef (const String &ref) const
bool	hasProtein (const String &ref) const
void	addProtein (const Protein &protein)
void	setCompounds (const std::vector< Compound > &rhs)
const std::vector< Compound > &	getCompounds () const
void	addCompound (const Compound &rhs)
void	setPeptides (const std::vector< Peptide > &rhs)
const std::vector< Peptide > &	getPeptides () const
bool	hasPeptide (const String &ref) const
const Peptide &	getPeptideByRef (const String &ref) const
bool	hasCompound (const String &ref) const
const Compound &	getCompoundByRef (const String &ref) const
void	addPeptide (const Peptide &rhs)
void	setTransitions (const std::vector< ReactionMonitoringTransition > &transitions)
	set transition list More...
const std::vector< ReactionMonitoringTransition > &	getTransitions () const
	returns the transition list More...
void	addTransition (const ReactionMonitoringTransition &transition)
	adds a transition to the list More...
void	setIncludeTargets (const std::vector< IncludeExcludeTarget > &targets)
const std::vector< IncludeExcludeTarget > &	getIncludeTargets () const
void	addIncludeTarget (const IncludeExcludeTarget &target)
void	setExcludeTargets (const std::vector< IncludeExcludeTarget > &targets)
const std::vector< IncludeExcludeTarget > &	getExcludeTargets () const
void	addExcludeTarget (const IncludeExcludeTarget &target)
void	setSourceFiles (const std::vector< SourceFile > &source_files)
	sets the source files More...
const std::vector< SourceFile > &	getSourceFiles () const
	returns the source file list More...
void	addSourceFile (const SourceFile &source_file)
	adds a source file to the list More...

Sorting peaks
std::vector< CV >	cvs_
std::vector< Contact >	contacts_
std::vector< Publication >	publications_
std::vector< Instrument >	instruments_
CVTermList	targets_
std::vector< Software >	software_
std::vector< Protein >	proteins_
std::vector< Compound >	compounds_
std::vector< Peptide >	peptides_
std::vector< ReactionMonitoringTransition >	transitions_
std::vector< IncludeExcludeTarget >	include_targets_
std::vector< IncludeExcludeTarget >	exclude_targets_
std::vector< SourceFile >	source_files_
ProteinReferenceMapType	protein_reference_map_
bool	protein_reference_map_dirty_
PeptideReferenceMapType	peptide_reference_map_
bool	peptide_reference_map_dirty_
CompoundReferenceMapType	compound_reference_map_
bool	compound_reference_map_dirty_
void	sortTransitionsByProductMZ ()
	Lexicographically sorts the transitions by their product m/z. More...
void	sortTransitionsByName ()
	Lexicographically sorts the transitions by their name. More...
bool	containsInvalidReferences () const
	Checks whether the data structure (and the underlying TraML file) contains invalid references. More...
void	createProteinReferenceMap_ () const
void	createPeptideReferenceMap_ () const
void	createCompoundReferenceMap_ () const

Detailed Description

A description of a targeted experiment containing precursor and production ions.

A targeted experiment contains transitions used in SRM/MRM as well as SWATH-MS/DIA analysis using a targeted approach. This container holds descriptions of the precursors and product ions analyzed in such a targeted experiment. Generally, the precursor ions can be peptides or small molecules (for metabolomics) and each precursor has a set of product ions associated with it.

The TargetedExperiment can be stored to disk either in .traml format using the TraMLFile or in .tsv format using the TransitionTSVFile.

---

Class Documentation

OpenMS::TargetedExperiment::SummaryStatistics

struct OpenMS::TargetedExperiment::SummaryStatistics

Collaboration diagram for TargetedExperiment::SummaryStatistics:

Class Members
Size	compound_count
bool	contains_invalid_references
map< DecoyTransitionType, size_t >	decoy_counts	# target/decoy transitions
Size	peptide_count
Size	protein_count
Size	transition_count

Member Typedef Documentation

Compound

typedef TargetedExperimentHelper::Compound Compound

CompoundReferenceMapType

typedef std::map<String, const Compound *> CompoundReferenceMapType

Contact

typedef TargetedExperimentHelper::Contact Contact

CV

typedef TargetedExperimentHelper::CV CV

Instrument

typedef TargetedExperimentHelper::Instrument Instrument

Interpretation

typedef TargetedExperimentHelper::Interpretation Interpretation

IonType

typedef Residue IonType

Peptide

typedef TargetedExperimentHelper::Peptide Peptide

PeptideReferenceMapType

typedef std::map<String, const Peptide *> PeptideReferenceMapType

Prediction

typedef TargetedExperimentHelper::Prediction Prediction

Protein

typedef TargetedExperimentHelper::Protein Protein

ProteinReferenceMapType

typedef std::map<String, const Protein *> ProteinReferenceMapType

Publication

typedef TargetedExperimentHelper::Publication Publication

RetentionTime

typedef TargetedExperimentHelper::RetentionTime RetentionTime

Transition

typedef ReactionMonitoringTransition Transition

Constructor & Destructor Documentation

TargetedExperiment() [1/2]

TargetedExperiment

(

)

default constructor

TargetedExperiment() [2/2]

TargetedExperiment

(

const TargetedExperiment &

rhs

)

copy constructor

~TargetedExperiment()

virtual ~TargetedExperiment ( )

virtual

destructor

Member Function Documentation

addCompound()

void addCompound

(

const Compound &

rhs

)

addContact()

void addContact

(

const Contact &

contact

)

addCV()

void addCV

(

const CV &

cv

)

addExcludeTarget()

void addExcludeTarget

(

const IncludeExcludeTarget &

target

)

addIncludeTarget()

void addIncludeTarget

(

const IncludeExcludeTarget &

target

)

addInstrument()

void addInstrument

(

const Instrument &

instrument

)

addPeptide()

void addPeptide

(

const Peptide &

rhs

)

addProtein()

void addProtein

(

const Protein &

protein

)

addPublication()

void addPublication

(

const Publication &

publication

)

addSoftware()

void addSoftware

(

const Software &

software

)

addSourceFile()

void addSourceFile

(

const SourceFile &

source_file

)

adds a source file to the list

addTargetCVTerm()

void addTargetCVTerm

(

const CVTerm &

cv_term

)

addTransition()

void addTransition

(

const ReactionMonitoringTransition &

transition

)

adds a transition to the list

clear()

void clear

(

bool

clear_meta_data

)

Clears all data and meta data.

Parameters

clear_meta_data

If true, all meta data is cleared in addition to the data.

containsInvalidReferences()

bool containsInvalidReferences

(

)

const

Checks whether the data structure (and the underlying TraML file) contains invalid references.

First checks whether all of the references are unique (protein, peptide, compound). Secondly, checks that each reference is valid and points either to a protein, peptide or compound.

Returns false if the file is valid.

createCompoundReferenceMap_()

void createCompoundReferenceMap_ ( ) const

protected

createPeptideReferenceMap_()

void createPeptideReferenceMap_ ( ) const

protected

createProteinReferenceMap_()

void createProteinReferenceMap_ ( ) const

protected

getCompoundByRef()

const Compound& getCompoundByRef

(

const String &

ref

)

const

Referenced by OpenMS::ChromatogramExtractor::extract_id_< OpenMS::TargetedExperiment >().

getCompounds()

const std::vector<Compound>& getCompounds

(

)

const

Referenced by ChromatogramExtractor::prepareSpectra_().

getContacts()

const std::vector<Contact>& getContacts

(

)

const

getCVs()

const std::vector<CV>& getCVs

(

)

const

getExcludeTargets()

const std::vector<IncludeExcludeTarget>& getExcludeTargets

(

)

const

getIncludeTargets()

const std::vector<IncludeExcludeTarget>& getIncludeTargets

(

)

const

getInstruments()

const std::vector<Instrument>& getInstruments

(

)

const

getPeptideByRef()

const Peptide& getPeptideByRef

(

const String &

ref

)

const

Referenced by OpenMS::ChromatogramExtractor::extract_id_< OpenMS::TargetedExperiment >().

getPeptides()

const std::vector<Peptide>& getPeptides

(

)

const

Referenced by ChromatogramExtractor::prepareSpectra_(), and ConfidenceScoring::scoreMap().

getProteinByRef()

const Protein& getProteinByRef

(

const String &

ref

)

const

getProteins()

const std::vector<Protein>& getProteins

(

)

const

getPublications()

const std::vector<Publication>& getPublications

(

)

const

getSoftware()

const std::vector<Software>& getSoftware

(

)

const

getSourceFiles()

const std::vector<SourceFile>& getSourceFiles

(

)

const

returns the source file list

getSummary()

SummaryStatistics getSummary

(

)

const

return summary stats about this TE.

getTargetCVTerms()

const CVTermList& getTargetCVTerms

(

)

const

getTransitions()

const std::vector<ReactionMonitoringTransition>& getTransitions

(

)

const

returns the transition list

Referenced by ChromatogramExtractor::extractChromatograms(), ChromatogramExtractor::prepareSpectra_(), and ConfidenceScoring::scoreMap().

hasCompound()

bool hasCompound

(

const String &

ref

)

const

Referenced by OpenMS::ChromatogramExtractor::extract_id_< OpenMS::TargetedExperiment >().

hasPeptide()

bool hasPeptide

(

const String &

ref

)

const

Referenced by OpenMS::ChromatogramExtractor::extract_id_< OpenMS::TargetedExperiment >().

hasProtein()

bool hasProtein

(

const String &

ref

)

const

operator!=()

bool operator!=

(

const TargetedExperiment &

rhs

)

const

operator+()

TargetedExperiment operator+

(

const TargetedExperiment &

rhs

)

const

Joins two targeted experiments.

Proteins, peptides and transitions are merged (see operator+= for details).

operator+=()

TargetedExperiment& operator+=

(

const TargetedExperiment &

rhs

)

Add one targeted experiment to another.

Parameters

rhs	The targeted experiment to add to this one.

operator=()

TargetedExperiment& operator=

(

const TargetedExperiment &

rhs

)

assignment operator

operator==()

bool operator==

(

const TargetedExperiment &

rhs

)

const

setCompounds()

void setCompounds

(

const std::vector< Compound > &

rhs

)

setContacts()

void setContacts

(

const std::vector< Contact > &

contacts

)

setCVs()

void setCVs

(

const std::vector< CV > &

cvs

)

setExcludeTargets()

void setExcludeTargets

(

const std::vector< IncludeExcludeTarget > &

targets

)

setIncludeTargets()

void setIncludeTargets

(

const std::vector< IncludeExcludeTarget > &

targets

)

setInstruments()

void setInstruments

(

const std::vector< Instrument > &

instruments

)

setPeptides()

void setPeptides

(

const std::vector< Peptide > &

rhs

)

setProteins()

void setProteins

(

const std::vector< Protein > &

proteins

)

setPublications()

void setPublications

(

const std::vector< Publication > &

publications

)

setSoftware()

void setSoftware

(

const std::vector< Software > &

software

)

setSourceFiles()

void setSourceFiles

(

const std::vector< SourceFile > &

source_files

)

sets the source files

setTargetCVTerms()

void setTargetCVTerms

(

const CVTermList &

cv_terms

)

setTargetMetaValue()

void setTargetMetaValue	(	const String &	name,
		const DataValue &	value
	)

setTransitions()

void setTransitions

(

const std::vector< ReactionMonitoringTransition > &

transitions

)

set transition list

sortTransitionsByName()

void sortTransitionsByName

(

)

Lexicographically sorts the transitions by their name.

sortTransitionsByProductMZ()

void sortTransitionsByProductMZ

(

)

Lexicographically sorts the transitions by their product m/z.

Referenced by ChromatogramExtractor::extractChromatograms().

Member Data Documentation

compound_reference_map_

CompoundReferenceMapType compound_reference_map_

mutableprotected

compound_reference_map_dirty_

bool compound_reference_map_dirty_

mutableprotected

compounds_

std::vector<Compound> compounds_

protected

contacts_

std::vector<Contact> contacts_

protected

cvs_

std::vector<CV> cvs_

protected

exclude_targets_

std::vector<IncludeExcludeTarget> exclude_targets_

protected

include_targets_

std::vector<IncludeExcludeTarget> include_targets_

protected

instruments_

std::vector<Instrument> instruments_

protected

peptide_reference_map_

PeptideReferenceMapType peptide_reference_map_

mutableprotected

peptide_reference_map_dirty_

bool peptide_reference_map_dirty_

mutableprotected

peptides_

std::vector<Peptide> peptides_

protected

protein_reference_map_

ProteinReferenceMapType protein_reference_map_

mutableprotected

protein_reference_map_dirty_

bool protein_reference_map_dirty_

mutableprotected

proteins_

std::vector<Protein> proteins_

protected

publications_

std::vector<Publication> publications_

protected

software_

std::vector<Software> software_

protected

source_files_

std::vector<SourceFile> source_files_

protected

targets_

CVTermList targets_

protected

transitions_

std::vector<ReactionMonitoringTransition> transitions_

protected