This class stores an prediction of an SRM/MRM transition. More...

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

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 std::map< String, const Protein * >	ProteinReferenceMapType
typedef std::map< String, const Peptide * >	PeptideReferenceMapType
Public Member Functions
TargetedExperiment &	operator= (const TargetedExperiment &rhs)
	assignment operator
TargetedExperiment	operator+ (const TargetedExperiment &rhs) const
	Joins two targeted experiments.
TargetedExperiment &	operator+= (const TargetedExperiment &rhs)
	Add one targeted experiment to another.
void	clear (bool clear_meta_data)
	Clears all data and meta data.
Constructors and destructors

	TargetedExperiment ()
	default constructor
	TargetedExperiment (const TargetedExperiment &rhs)
	copy constructor
virtual	~TargetedExperiment ()
	destructor
Predicates

bool	operator== (const TargetedExperiment &rhs) const
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)
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
const Peptide &	getPeptideByRef (const String &ref)
void	addPeptide (const Peptide &rhs)
void	setTransitions (const std::vector< ReactionMonitoringTransition > &transitions)
	set transition list
const std::vector < ReactionMonitoringTransition > &	getTransitions () const
	returns the transition list
void	addTransition (const ReactionMonitoringTransition &transition)
	adds a transition to the list
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
const std::vector< SourceFile > &	getSourceFiles () const
	returns the source file list
void	addSourceFile (const SourceFile &source_file)
	adds a source file to the list
Sorting peaks

void	sortTransitionsByProductMZ ()
	Lexicographically sorts the transitions by their product m/z.
Protected Member Functions
void	createProteinReferenceMap_ ()
void	createPeptideReferenceMap_ ()
Protected Attributes
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_

Detailed Description

This class stores an prediction of an SRM/MRM transition.

Member Typedef Documentation

typedef TargetedExperimentHelper::Compound Compound

typedef TargetedExperimentHelper::Contact Contact

typedef TargetedExperimentHelper::CV CV

typedef TargetedExperimentHelper::Instrument Instrument

typedef TargetedExperimentHelper::Peptide Peptide

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

typedef TargetedExperimentHelper::Prediction Prediction

typedef TargetedExperimentHelper::Protein Protein

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

typedef TargetedExperimentHelper::Publication Publication

typedef TargetedExperimentHelper::RetentionTime RetentionTime

Constructor & Destructor Documentation

TargetedExperiment ( )

default constructor

TargetedExperiment ( const TargetedExperiment & rhs )

copy constructor

virtual ~TargetedExperiment ( ) [virtual]

destructor

Member Function Documentation

void addCompound ( const Compound & rhs )

void addContact ( const Contact & contact )

void addCV ( const CV & cv )

void addExcludeTarget ( const IncludeExcludeTarget & target )

void addIncludeTarget ( const IncludeExcludeTarget & target )

void addInstrument ( const Instrument & instrument )

void addPeptide ( const Peptide & rhs )

void addProtein ( const Protein & protein )

void addPublication ( const Publication & publication )

void addSoftware ( const Software & software )

void addSourceFile ( const SourceFile & source_file )

adds a source file to the list

void addTargetCVTerm ( const CVTerm & cv_term )

void addTransition ( const ReactionMonitoringTransition & transition )

adds a transition to the list

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.

void createPeptideReferenceMap_ ( ) [protected]

void createProteinReferenceMap_ ( ) [protected]

const std::vector<Compound>& getCompounds ( ) const

const std::vector<Contact>& getContacts ( ) const

const std::vector<CV>& getCVs ( ) const

const std::vector<IncludeExcludeTarget>& getExcludeTargets ( ) const

const std::vector<IncludeExcludeTarget>& getIncludeTargets ( ) const

const std::vector<Instrument>& getInstruments ( ) const

const Peptide& getPeptideByRef ( const String & ref )

const std::vector<Peptide>& getPeptides ( ) const

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

const Protein& getProteinByRef ( const String & ref )

const std::vector<Protein>& getProteins ( ) const

const std::vector<Publication>& getPublications ( ) const

const std::vector<Software>& getSoftware ( ) const

const std::vector<SourceFile>& getSourceFiles ( ) const

returns the source file list

const CVTermList& getTargetCVTerms ( ) const

const std::vector<ReactionMonitoringTransition>& getTransitions ( ) const

returns the transition list

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

TargetedExperiment operator+ ( const TargetedExperiment & rhs ) const

Joins two targeted experiments.

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

TargetedExperiment& operator+= ( const TargetedExperiment & rhs )

Add one targeted experiment to another.

Parameters:

rhs

The targeted experiment to add to this one.

TargetedExperiment& operator= ( const TargetedExperiment & rhs )

assignment operator

bool operator== ( const TargetedExperiment & rhs ) const

void setCompounds ( const std::vector< Compound > & rhs )

void setContacts ( const std::vector< Contact > & contacts )

void setCVs ( const std::vector< CV > & cvs )

void setExcludeTargets ( const std::vector< IncludeExcludeTarget > & targets )

void setIncludeTargets ( const std::vector< IncludeExcludeTarget > & targets )

void setInstruments ( const std::vector< Instrument > & instruments )

void setPeptides ( const std::vector< Peptide > & rhs )

void setProteins ( const std::vector< Protein > & proteins )

void setPublications ( const std::vector< Publication > & publications )

void setSoftware ( const std::vector< Software > & software )

void setSourceFiles ( const std::vector< SourceFile > & source_files )

sets the source files

void setTargetCVTerms ( const CVTermList & cv_terms )

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

void setTransitions ( const std::vector< ReactionMonitoringTransition > & transitions )

set transition list

void sortTransitionsByProductMZ ( )

Lexicographically sorts the transitions by their product m/z.

Referenced by ChromatogramExtractor::extractChromatograms().

Member Data Documentation

std::vector<Compound> compounds_ [protected]

std::vector<Contact> contacts_ [protected]

std::vector<CV> cvs_ [protected]

std::vector<IncludeExcludeTarget> exclude_targets_ [protected]

std::vector<IncludeExcludeTarget> include_targets_ [protected]

std::vector<Instrument> instruments_ [protected]

PeptideReferenceMapType peptide_reference_map_ [protected]

bool peptide_reference_map_dirty_ [protected]

std::vector<Peptide> peptides_ [protected]

ProteinReferenceMapType protein_reference_map_ [protected]

bool protein_reference_map_dirty_ [protected]

std::vector<Protein> proteins_ [protected]

std::vector<Publication> publications_ [protected]

std::vector<Software> software_ [protected]

std::vector<SourceFile> source_files_ [protected]

CVTermList targets_ [protected]

std::vector<ReactionMonitoringTransition> transitions_ [protected]

TargetedExperiment Class Reference

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation