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 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 |
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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virtual |
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 |
| 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.
| 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 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |