35 #ifndef OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H 36 #define OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H 126 void clear(
bool clear_meta_data);
132 void setCVs(
const std::vector<CV> & cvs);
134 const std::vector<CV> & getCVs()
const;
136 void addCV(
const CV & cv);
139 void setContacts(
const std::vector<Contact> & contacts);
141 const std::vector<Contact> & getContacts()
const;
143 void addContact(
const Contact & contact);
146 void setPublications(
const std::vector<Publication> & publications);
148 const std::vector<Publication> & getPublications()
const;
150 void addPublication(
const Publication & publication);
153 void setTargetCVTerms(
const CVTermList & cv_terms);
157 void addTargetCVTerm(
const CVTerm & cv_term);
162 void setInstruments(
const std::vector<Instrument> & instruments);
164 const std::vector<Instrument> & getInstruments()
const;
166 void addInstrument(
const Instrument & instrument);
169 void setSoftware(
const std::vector<Software> & software);
171 const std::vector<Software> & getSoftware()
const;
173 void addSoftware(
const Software & software);
176 void setProteins(
const std::vector<Protein> & proteins);
178 const std::vector<Protein> & getProteins()
const;
180 const Protein & getProteinByRef(
const String & ref)
const;
182 bool hasProtein(
const String & ref)
const;
184 void addProtein(
const Protein & protein);
187 void setCompounds(
const std::vector<Compound> & rhs);
189 const std::vector<Compound> & getCompounds()
const;
191 void addCompound(
const Compound & rhs);
193 void setPeptides(
const std::vector<Peptide> & rhs);
195 const std::vector<Peptide> & getPeptides()
const;
197 bool hasPeptide(
const String & ref)
const;
199 const Peptide & getPeptideByRef(
const String & ref)
const;
201 bool hasCompound(
const String & ref)
const;
203 const Compound & getCompoundByRef(
const String & ref)
const;
205 void addPeptide(
const Peptide & rhs);
208 void setTransitions(
const std::vector<ReactionMonitoringTransition> & transitions);
211 const std::vector<ReactionMonitoringTransition> & getTransitions()
const;
216 void setIncludeTargets(
const std::vector<IncludeExcludeTarget> & targets);
218 const std::vector<IncludeExcludeTarget> & getIncludeTargets()
const;
222 void setExcludeTargets(
const std::vector<IncludeExcludeTarget> & targets);
224 const std::vector<IncludeExcludeTarget> & getExcludeTargets()
const;
229 void setSourceFiles(
const std::vector<SourceFile> & source_files);
232 const std::vector<SourceFile> & getSourceFiles()
const;
235 void addSourceFile(
const SourceFile & source_file);
243 void sortTransitionsByProductMZ();
255 bool containsInvalidReferences();
259 void createProteinReferenceMap_()
const;
261 void createPeptideReferenceMap_()
const;
263 void createCompoundReferenceMap_()
const;
305 namespace TargetedExperimentHelper
312 #endif // OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H
CVTermList targets_
Definition: TargetedExperiment.h:273
A more convenient string class.
Definition: String.h:57
std::vector< IncludeExcludeTarget > include_targets_
Definition: TargetedExperiment.h:285
Representation of controlled vocabulary term list.
Definition: CVTermList.h:53
Definition: TargetedExperimentHelper.h:437
TargetedExperimentHelper::Peptide Peptide
Definition: TargetedExperiment.h:70
ProteinReferenceMapType protein_reference_map_
Definition: TargetedExperiment.h:291
std::vector< Protein > proteins_
Definition: TargetedExperiment.h:277
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:47
Definition: TargetedExperimentHelper.h:524
std::vector< Peptide > peptides_
Definition: TargetedExperiment.h:281
Description of the software used for processing.
Definition: Software.h:49
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Representation of a residue.
Definition: Residue.h:62
Residue IonType
Definition: TargetedExperiment.h:77
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:57
bool peptide_reference_map_dirty_
Definition: TargetedExperiment.h:297
std::vector< SourceFile > source_files_
Definition: TargetedExperiment.h:289
std::vector< Compound > compounds_
Definition: TargetedExperiment.h:279
std::map< String, const Peptide * > PeptideReferenceMapType
Definition: TargetedExperiment.h:80
std::vector< Contact > contacts_
Definition: TargetedExperiment.h:267
std::vector< Instrument > instruments_
Definition: TargetedExperiment.h:271
TargetedExperimentHelper::Prediction Prediction
Definition: TargetedExperiment.h:74
TargetedExperimentHelper::Protein Protein
Definition: TargetedExperiment.h:67
Representation of controlled vocabulary term.
Definition: CVTerm.h:51
std::vector< CV > cvs_
Definition: TargetedExperiment.h:265
Definition: TargetedExperimentHelper.h:181
TargetedExperimentHelper::Interpretation Interpretation
Definition: TargetedExperiment.h:75
std::map< String, const Protein * > ProteinReferenceMapType
Definition: TargetedExperiment.h:79
std::map< String, const Compound * > CompoundReferenceMapType
Definition: TargetedExperiment.h:81
bool protein_reference_map_dirty_
Definition: TargetedExperiment.h:293
Definition: TargetedExperimentHelper.h:85
This class stores a SRM/MRM transition.
Definition: IncludeExcludeTarget.h:53
std::vector< ReactionMonitoringTransition > transitions_
Definition: TargetedExperiment.h:283
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
PeptideReferenceMapType peptide_reference_map_
Definition: TargetedExperiment.h:295
std::vector< IncludeExcludeTarget > exclude_targets_
Definition: TargetedExperiment.h:287
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:62
Definition: TargetedExperimentHelper.h:465
Definition: TargetedExperimentHelper.h:142
TargetedExperimentHelper::Instrument Instrument
Definition: TargetedExperiment.h:73
Definition: TargetedExperimentHelper.h:493
std::vector< Software > software_
Definition: TargetedExperiment.h:275
TargetedExperimentHelper::Publication Publication
Definition: TargetedExperiment.h:72
Definition: TargetedExperimentHelper.h:111
ReactionMonitoringTransition Transition
Definition: TargetedExperiment.h:76
CompoundReferenceMapType compound_reference_map_
Definition: TargetedExperiment.h:299
bool compound_reference_map_dirty_
Definition: TargetedExperiment.h:301
TargetedExperimentHelper::Contact Contact
Definition: TargetedExperiment.h:71
TargetedExperimentHelper::Compound Compound
Definition: TargetedExperiment.h:69
std::vector< Publication > publications_
Definition: TargetedExperiment.h:269
TargetedExperimentHelper::CV CV
Definition: TargetedExperiment.h:66
Definition: TargetedExperimentHelper.h:266
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
TargetedExperimentHelper::RetentionTime RetentionTime
Definition: TargetedExperiment.h:68