| OpenMS 2.5.0

Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | 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>`

## 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

TargetedExperiment & | operator= (const TargetedExperiment &rhs)
| assignment operator More...
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...
bool | containsInvalidReferences () const
| Checks whether the data structure (and the underlying TraML file) contains invalid references. More...
Constructors and destructors
| TargetedExperiment ()
| default constructor More...
| TargetedExperiment (const TargetedExperiment &rhs)
| copy constructor More...
virtual | ~TargetedExperiment ()
| destructor More...
Predicates
bool | operator== (const TargetedExperiment &rhs) const
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) 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
void | sortTransitionsByProductMZ ()
| Lexicographically sorts the transitions by their product m/z. More...

## Protected Member Functions

void | createProteinReferenceMap_ () const
void | createPeptideReferenceMap_ () const
void | createCompoundReferenceMap_ () const

## 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_
CompoundReferenceMapType | compound_reference_map_
bool | compound_reference_map_dirty_

## 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.

## 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

## ◆ 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

## ◆ 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

## ◆ 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

## ◆ 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.

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

## ◆ 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_

mutable protected

## ◆ compound_reference_map_dirty_

bool compound_reference_map_dirty_

mutable protected

## ◆ 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_

mutable protected

## ◆ peptide_reference_map_dirty_

bool peptide_reference_map_dirty_

mutable protected

## ◆ peptides_

std::vector<Peptide> peptides_

protected

## ◆ protein_reference_map_

ProteinReferenceMapType protein_reference_map_

mutable protected

## ◆ protein_reference_map_dirty_

bool protein_reference_map_dirty_

mutable protected

## ◆ 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