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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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 |