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 | |
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... | |
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) |
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 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< 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_ |
This class stores an prediction of an SRM/MRM transition.
typedef TargetedExperimentHelper::CV CV |
typedef std::map<String, const Peptide *> PeptideReferenceMapType |
typedef std::map<String, const Protein *> ProteinReferenceMapType |
default constructor
TargetedExperiment | ( | const TargetedExperiment & | rhs | ) |
copy constructor
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destructor
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.
clear_meta_data | If true, all meta data is cleared in addition to the data. |
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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 std::vector<Peptide>& getPeptides | ( | ) | const |
Referenced by ChromatogramExtractor::prepareSpectra_().
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(), ChromatogramExtractor::prepareSpectra_(), and OpenSwathWorkflow::simpleExtractChromatograms().
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.
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 setTransitions | ( | const std::vector< ReactionMonitoringTransition > & | transitions | ) |
set transition list
void sortTransitionsByProductMZ | ( | ) |
Lexicographically sorts the transitions by their product m/z.
Referenced by ChromatogramExtractor::extractChromatograms().
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OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 16:18:44 using doxygen 1.8.5 |