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TargetedExperiment Class Reference

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
ReactionMonitoringTransition 
Transition
 
typedef std::map< String,
const Protein * > 
ProteinReferenceMapType
 
typedef std::map< String,
const Peptide * > 
PeptideReferenceMapType
 

Public Member Functions

TargetedExperimentoperator= (const TargetedExperiment &rhs)
 assignment operator More...
 
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...
 
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 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)
 
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 PeptidegetPeptideByRef (const String &ref)
 
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_ ()
 
void createPeptideReferenceMap_ ()
 

Protected Attributes

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
< ReactionMonitoringTransition
transitions_
 
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_
 

Detailed Description

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

Member Typedef Documentation

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

Constructor & Destructor Documentation

default constructor

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_dataIf 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
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
bool operator!= ( const TargetedExperiment rhs) const
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
rhsThe 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

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:44 using doxygen 1.8.5