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OpenMS
2.5.0
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Go to the documentation of this file.
128 void clear(
bool clear_meta_data);
134 void setCVs(
const std::vector<CV> & cvs);
136 const std::vector<CV> & getCVs()
const;
138 void addCV(
const CV & cv);
141 void setContacts(
const std::vector<Contact> & contacts);
143 const std::vector<Contact> & getContacts()
const;
145 void addContact(
const Contact & contact);
148 void setPublications(
const std::vector<Publication> & publications);
150 const std::vector<Publication> & getPublications()
const;
152 void addPublication(
const Publication & publication);
155 void setTargetCVTerms(
const CVTermList & cv_terms);
159 void addTargetCVTerm(
const CVTerm & cv_term);
164 void setInstruments(
const std::vector<Instrument> & instruments);
166 const std::vector<Instrument> & getInstruments()
const;
168 void addInstrument(
const Instrument & instrument);
171 void setSoftware(
const std::vector<Software> & software);
173 const std::vector<Software> & getSoftware()
const;
175 void addSoftware(
const Software & software);
178 void setProteins(
const std::vector<Protein> & proteins);
180 const std::vector<Protein> & getProteins()
const;
184 bool hasProtein(
const String & ref)
const;
186 void addProtein(
const Protein & protein);
189 void setCompounds(
const std::vector<Compound> & rhs);
191 const std::vector<Compound> & getCompounds()
const;
193 void addCompound(
const Compound & rhs);
195 void setPeptides(
const std::vector<Peptide> & rhs);
197 const std::vector<Peptide> & getPeptides()
const;
199 bool hasPeptide(
const String & ref)
const;
203 bool hasCompound(
const String & ref)
const;
207 void addPeptide(
const Peptide & rhs);
210 void setTransitions(
const std::vector<ReactionMonitoringTransition> & transitions);
213 const std::vector<ReactionMonitoringTransition> & getTransitions()
const;
218 void setIncludeTargets(
const std::vector<IncludeExcludeTarget> & targets);
220 const std::vector<IncludeExcludeTarget> & getIncludeTargets()
const;
224 void setExcludeTargets(
const std::vector<IncludeExcludeTarget> & targets);
226 const std::vector<IncludeExcludeTarget> & getExcludeTargets()
const;
231 void setSourceFiles(
const std::vector<SourceFile> & source_files);
234 const std::vector<SourceFile> & getSourceFiles()
const;
237 void addSourceFile(
const SourceFile & source_file);
245 void sortTransitionsByProductMZ();
257 bool containsInvalidReferences()
const;
261 void createProteinReferenceMap_()
const;
263 void createPeptideReferenceMap_()
const;
265 void createCompoundReferenceMap_()
const;
307 namespace TargetedExperimentHelper
Description of the software used for processing.
Definition: Software.h:48
CompoundReferenceMapType compound_reference_map_
Definition: TargetedExperiment.h:301
ProteinReferenceMapType protein_reference_map_
Definition: TargetedExperiment.h:293
Definition: TargetedExperimentHelper.h:478
TargetedExperimentHelper::Interpretation Interpretation
Definition: TargetedExperiment.h:77
std::vector< IncludeExcludeTarget > include_targets_
Definition: TargetedExperiment.h:287
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370
TargetedExperimentHelper::Protein Protein
Definition: TargetedExperiment.h:69
bool protein_reference_map_dirty_
Definition: TargetedExperiment.h:295
TargetedExperimentHelper::Compound Compound
Definition: TargetedExperiment.h:71
std::vector< Protein > proteins_
Definition: TargetedExperiment.h:279
A more convenient string class.
Definition: String.h:58
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
This class stores a SRM/MRM transition.
Definition: IncludeExcludeTarget.h:52
bool peptide_reference_map_dirty_
Definition: TargetedExperiment.h:299
Residue IonType
Definition: TargetedExperiment.h:79
TargetedExperimentHelper::RetentionTime RetentionTime
Definition: TargetedExperiment.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::vector< Contact > contacts_
Definition: TargetedExperiment.h:269
TargetedExperimentHelper::CV CV
Definition: TargetedExperiment.h:68
std::vector< IncludeExcludeTarget > exclude_targets_
Definition: TargetedExperiment.h:289
Representation of a residue.
Definition: Residue.h:61
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
bool compound_reference_map_dirty_
Definition: TargetedExperiment.h:303
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
Definition: TargetedExperimentHelper.h:98
std::vector< Instrument > instruments_
Definition: TargetedExperiment.h:273
Definition: TargetedExperimentHelper.h:495
TargetedExperimentHelper::Publication Publication
Definition: TargetedExperiment.h:74
TargetedExperimentHelper::Prediction Prediction
Definition: TargetedExperiment.h:76
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:333
std::map< String, const Peptide * > PeptideReferenceMapType
Definition: TargetedExperiment.h:82
TargetedExperimentHelper::Contact Contact
Definition: TargetedExperiment.h:73
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
TargetedExperimentHelper::Instrument Instrument
Definition: TargetedExperiment.h:75
Definition: TargetedExperimentHelper.h:72
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
Representation of controlled vocabulary term.
Definition: CVTerm.h:52
std::vector< Peptide > peptides_
Definition: TargetedExperiment.h:283
std::vector< ReactionMonitoringTransition > transitions_
Definition: TargetedExperiment.h:285
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:127
PeptideReferenceMapType peptide_reference_map_
Definition: TargetedExperiment.h:297
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:46
std::vector< Publication > publications_
Definition: TargetedExperiment.h:271
Definition: TargetedExperimentHelper.h:461
std::map< String, const Protein * > ProteinReferenceMapType
Definition: TargetedExperiment.h:81
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
std::vector< SourceFile > source_files_
Definition: TargetedExperiment.h:291
std::vector< Software > software_
Definition: TargetedExperiment.h:277
std::map< String, const Compound * > CompoundReferenceMapType
Definition: TargetedExperiment.h:83
std::vector< CV > cvs_
Definition: TargetedExperiment.h:267
ReactionMonitoringTransition Transition
Definition: TargetedExperiment.h:78
TargetedExperimentHelper::Peptide Peptide
Definition: TargetedExperiment.h:72
CVTermList targets_
Definition: TargetedExperiment.h:275
Product ion interpretation.
Definition: TargetedExperimentHelper.h:520
std::vector< Compound > compounds_
Definition: TargetedExperiment.h:281