OpenMS  2.6.0
Classes | Public Types | List of all members
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:


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...
TargetedExperimentoperator= (const TargetedExperiment &rhs)
 assignment operator More...
bool operator== (const TargetedExperiment &rhs) const
bool operator!= (const TargetedExperiment &rhs) const
TargetedExperiment operator+ (const TargetedExperiment &rhs) const
 Joins two targeted experiments. More...
TargetedExperimentoperator+= (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...
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 CVTermListgetTargetCVTerms () 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 ProteingetProteinByRef (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 PeptidegetPeptideByRef (const String &ref) const
bool hasCompound (const String &ref) const
const CompoundgetCompoundByRef (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< CVcvs_
std::vector< Contactcontacts_
std::vector< Publicationpublications_
std::vector< Instrumentinstruments_
CVTermList targets_
std::vector< Softwaresoftware_
std::vector< Proteinproteins_
std::vector< Compoundcompounds_
std::vector< Peptidepeptides_
std::vector< ReactionMonitoringTransitiontransitions_
std::vector< IncludeExcludeTargetinclude_targets_
std::vector< IncludeExcludeTargetexclude_targets_
std::vector< SourceFilesource_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...
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

◆ CompoundReferenceMapType

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

◆ Contact

◆ CV

◆ Instrument

◆ Interpretation

◆ IonType

typedef Residue IonType

◆ Peptide

◆ PeptideReferenceMapType

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

◆ Prediction

◆ Protein

◆ ProteinReferenceMapType

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

◆ Publication

◆ RetentionTime

◆ Transition

Constructor & Destructor Documentation

◆ TargetedExperiment() [1/2]

default constructor

◆ TargetedExperiment() [2/2]

copy constructor

◆ ~TargetedExperiment()

virtual ~TargetedExperiment ( )


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.

clear_meta_dataIf 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

◆ createPeptideReferenceMap_()

void createPeptideReferenceMap_ ( ) const

◆ createProteinReferenceMap_()

void createProteinReferenceMap_ ( ) const

◆ getCompoundByRef()

const Compound& getCompoundByRef ( const String ref) const

◆ getCompounds()

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

◆ 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

◆ getPeptides()

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

◆ 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

◆ hasCompound()

bool hasCompound ( const String ref) const

◆ hasPeptide()

bool hasPeptide ( const String ref) const

◆ 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.

rhsThe 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

◆ 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_

◆ compound_reference_map_dirty_

bool compound_reference_map_dirty_

◆ compounds_

std::vector<Compound> compounds_

◆ contacts_

std::vector<Contact> contacts_

◆ cvs_

std::vector<CV> cvs_

◆ exclude_targets_

std::vector<IncludeExcludeTarget> exclude_targets_

◆ include_targets_

std::vector<IncludeExcludeTarget> include_targets_

◆ instruments_

std::vector<Instrument> instruments_

◆ peptide_reference_map_

PeptideReferenceMapType peptide_reference_map_

◆ peptide_reference_map_dirty_

bool peptide_reference_map_dirty_

◆ peptides_

std::vector<Peptide> peptides_

◆ protein_reference_map_

ProteinReferenceMapType protein_reference_map_

◆ protein_reference_map_dirty_

bool protein_reference_map_dirty_

◆ proteins_

std::vector<Protein> proteins_

◆ publications_

std::vector<Publication> publications_

◆ software_

std::vector<Software> software_

◆ source_files_

std::vector<SourceFile> source_files_

◆ targets_

CVTermList targets_

◆ transitions_

std::vector<ReactionMonitoringTransition> transitions_