125 void clear(
bool clear_meta_data);
131 void setCVs(
const std::vector<CV> & cvs);
133 const std::vector<CV> & getCVs()
const;
135 void addCV(
const CV & cv);
138 void setContacts(
const std::vector<Contact> & contacts);
140 const std::vector<Contact> & getContacts()
const;
142 void addContact(
const Contact & contact);
145 void setPublications(
const std::vector<Publication> & publications);
147 const std::vector<Publication> & getPublications()
const;
149 void addPublication(
const Publication & publication);
152 void setTargetCVTerms(
const CVTermList & cv_terms);
156 void addTargetCVTerm(
const CVTerm & cv_term);
161 void setInstruments(
const std::vector<Instrument> & instruments);
163 const std::vector<Instrument> & getInstruments()
const;
165 void addInstrument(
const Instrument & instrument);
168 void setSoftware(
const std::vector<Software> & software);
170 const std::vector<Software> & getSoftware()
const;
172 void addSoftware(
const Software & software);
175 void setProteins(
const std::vector<Protein> & proteins);
177 const std::vector<Protein> & getProteins()
const;
179 const Protein & getProteinByRef(
const String & ref)
const;
181 bool hasProtein(
const String & ref)
const;
183 void addProtein(
const Protein & protein);
186 void setCompounds(
const std::vector<Compound> & rhs);
188 const std::vector<Compound> & getCompounds()
const;
190 void addCompound(
const Compound & rhs);
192 void setPeptides(
const std::vector<Peptide> & rhs);
194 const std::vector<Peptide> & getPeptides()
const;
196 bool hasPeptide(
const String & ref)
const;
198 const Peptide & getPeptideByRef(
const String & ref)
const;
200 bool hasCompound(
const String & ref)
const;
202 const Compound & getCompoundByRef(
const String & ref)
const;
204 void addPeptide(
const Peptide & rhs);
207 void setTransitions(
const std::vector<ReactionMonitoringTransition> & transitions);
210 const std::vector<ReactionMonitoringTransition> & getTransitions()
const;
215 void setIncludeTargets(
const std::vector<IncludeExcludeTarget> & targets);
217 const std::vector<IncludeExcludeTarget> & getIncludeTargets()
const;
221 void setExcludeTargets(
const std::vector<IncludeExcludeTarget> & targets);
223 const std::vector<IncludeExcludeTarget> & getExcludeTargets()
const;
228 void setSourceFiles(
const std::vector<SourceFile> & source_files);
231 const std::vector<SourceFile> & getSourceFiles()
const;
234 void addSourceFile(
const SourceFile & source_file);
242 void sortTransitionsByProductMZ();
254 bool containsInvalidReferences()
const;
258 void createProteinReferenceMap_()
const;
260 void createPeptideReferenceMap_()
const;
262 void createCompoundReferenceMap_()
const;
304 namespace TargetedExperimentHelper
CVTermList targets_
Definition: TargetedExperiment.h:272
A more convenient string class.
Definition: String.h:57
std::vector< IncludeExcludeTarget > include_targets_
Definition: TargetedExperiment.h:284
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
Definition: TargetedExperimentHelper.h:572
TargetedExperimentHelper::Peptide Peptide
Definition: TargetedExperiment.h:69
ProteinReferenceMapType protein_reference_map_
Definition: TargetedExperiment.h:290
std::vector< Protein > proteins_
Definition: TargetedExperiment.h:276
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:46
Product ion interpretation.
Definition: TargetedExperimentHelper.h:665
std::vector< Peptide > peptides_
Definition: TargetedExperiment.h:280
Description of the software used for processing.
Definition: Software.h:48
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Representation of a residue.
Definition: Residue.h:61
Residue IonType
Definition: TargetedExperiment.h:76
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
bool peptide_reference_map_dirty_
Definition: TargetedExperiment.h:296
std::vector< SourceFile > source_files_
Definition: TargetedExperiment.h:288
std::vector< Compound > compounds_
Definition: TargetedExperiment.h:278
std::map< String, const Peptide * > PeptideReferenceMapType
Definition: TargetedExperiment.h:79
std::vector< Contact > contacts_
Definition: TargetedExperiment.h:266
std::vector< Instrument > instruments_
Definition: TargetedExperiment.h:270
TargetedExperimentHelper::Prediction Prediction
Definition: TargetedExperiment.h:73
TargetedExperimentHelper::Protein Protein
Definition: TargetedExperiment.h:66
Representation of controlled vocabulary term.
Definition: CVTerm.h:50
std::vector< CV > cvs_
Definition: TargetedExperiment.h:264
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:399
TargetedExperimentHelper::Interpretation Interpretation
Definition: TargetedExperiment.h:74
std::map< String, const Protein * > ProteinReferenceMapType
Definition: TargetedExperiment.h:78
std::map< String, const Compound * > CompoundReferenceMapType
Definition: TargetedExperiment.h:80
bool protein_reference_map_dirty_
Definition: TargetedExperiment.h:292
Definition: TargetedExperimentHelper.h:85
This class stores a SRM/MRM transition.
Definition: IncludeExcludeTarget.h:52
std::vector< ReactionMonitoringTransition > transitions_
Definition: TargetedExperiment.h:282
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
PeptideReferenceMapType peptide_reference_map_
Definition: TargetedExperiment.h:294
std::vector< IncludeExcludeTarget > exclude_targets_
Definition: TargetedExperiment.h:286
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:61
Definition: TargetedExperimentHelper.h:600
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:152
TargetedExperimentHelper::Instrument Instrument
Definition: TargetedExperiment.h:72
Definition: TargetedExperimentHelper.h:628
std::vector< Software > software_
Definition: TargetedExperiment.h:274
TargetedExperimentHelper::Publication Publication
Definition: TargetedExperiment.h:71
Definition: TargetedExperimentHelper.h:111
ReactionMonitoringTransition Transition
Definition: TargetedExperiment.h:75
CompoundReferenceMapType compound_reference_map_
Definition: TargetedExperiment.h:298
bool compound_reference_map_dirty_
Definition: TargetedExperiment.h:300
TargetedExperimentHelper::Contact Contact
Definition: TargetedExperiment.h:70
TargetedExperimentHelper::Compound Compound
Definition: TargetedExperiment.h:68
std::vector< Publication > publications_
Definition: TargetedExperiment.h:268
TargetedExperimentHelper::CV CV
Definition: TargetedExperiment.h:65
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:451
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
TargetedExperimentHelper::RetentionTime RetentionTime
Definition: TargetedExperiment.h:67