35 #ifndef OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H
36 #define OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H
114 void clear(
bool clear_meta_data);
120 void setCVs(
const std::vector<CV> & cvs);
122 const std::vector<CV> & getCVs()
const;
124 void addCV(
const CV & cv);
127 void setContacts(
const std::vector<Contact> & contacts);
129 const std::vector<Contact> & getContacts()
const;
131 void addContact(
const Contact & contact);
134 void setPublications(
const std::vector<Publication> & publications);
136 const std::vector<Publication> & getPublications()
const;
138 void addPublication(
const Publication & publication);
141 void setTargetCVTerms(
const CVTermList & cv_terms);
145 void addTargetCVTerm(
const CVTerm & cv_term);
150 void setInstruments(
const std::vector<Instrument> & instruments);
152 const std::vector<Instrument> & getInstruments()
const;
154 void addInstrument(
const Instrument & instrument);
157 void setSoftware(
const std::vector<Software> & software);
159 const std::vector<Software> & getSoftware()
const;
161 void addSoftware(
const Software & software);
164 void setProteins(
const std::vector<Protein> & proteins);
166 const std::vector<Protein> & getProteins()
const;
168 const Protein & getProteinByRef(
const String & ref);
170 void addProtein(
const Protein & protein);
173 void setCompounds(
const std::vector<Compound> & rhs);
175 const std::vector<Compound> & getCompounds()
const;
177 void addCompound(
const Compound & rhs);
179 void setPeptides(
const std::vector<Peptide> & rhs);
181 const std::vector<Peptide> & getPeptides()
const;
183 const Peptide & getPeptideByRef(
const String & ref);
185 void addPeptide(
const Peptide & rhs);
188 void setTransitions(
const std::vector<ReactionMonitoringTransition> & transitions);
191 const std::vector<ReactionMonitoringTransition> & getTransitions()
const;
196 void setIncludeTargets(
const std::vector<IncludeExcludeTarget> & targets);
198 const std::vector<IncludeExcludeTarget> & getIncludeTargets()
const;
202 void setExcludeTargets(
const std::vector<IncludeExcludeTarget> & targets);
204 const std::vector<IncludeExcludeTarget> & getExcludeTargets()
const;
209 void setSourceFiles(
const std::vector<SourceFile> & source_files);
212 const std::vector<SourceFile> & getSourceFiles()
const;
215 void addSourceFile(
const SourceFile & source_file);
223 void sortTransitionsByProductMZ();
228 void createProteinReferenceMap_();
230 void createPeptideReferenceMap_();
269 namespace TargetedExperimentHelper
276 #endif // OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H
CVTermList targets_
Definition: TargetedExperiment.h:240
A more convenient string class.
Definition: String.h:57
std::vector< IncludeExcludeTarget > include_targets_
Definition: TargetedExperiment.h:252
Representation of controlled vocabulary term list.
Definition: CVTermList.h:54
Definition: TargetedExperimentHelper.h:360
TargetedExperimentHelper::Peptide Peptide
Definition: TargetedExperiment.h:61
ProteinReferenceMapType protein_reference_map_
Definition: TargetedExperiment.h:258
std::vector< Protein > proteins_
Definition: TargetedExperiment.h:244
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:47
std::vector< Peptide > peptides_
Definition: TargetedExperiment.h:248
Description of the software used for processing.
Definition: Software.h:49
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
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:264
std::vector< SourceFile > source_files_
Definition: TargetedExperiment.h:256
std::vector< Compound > compounds_
Definition: TargetedExperiment.h:246
std::map< String, const Peptide * > PeptideReferenceMapType
Definition: TargetedExperiment.h:69
std::vector< Contact > contacts_
Definition: TargetedExperiment.h:234
std::vector< Instrument > instruments_
Definition: TargetedExperiment.h:238
TargetedExperimentHelper::Prediction Prediction
Definition: TargetedExperiment.h:65
TargetedExperimentHelper::Protein Protein
Definition: TargetedExperiment.h:58
Representation of controlled vocabulary term.
Definition: CVTerm.h:51
std::vector< CV > cvs_
Definition: TargetedExperiment.h:232
Definition: TargetedExperimentHelper.h:172
std::map< String, const Protein * > ProteinReferenceMapType
Definition: TargetedExperiment.h:68
bool protein_reference_map_dirty_
Definition: TargetedExperiment.h:260
Definition: TargetedExperimentHelper.h:76
This class stores a SRM/MRM transition.
Definition: IncludeExcludeTarget.h:53
std::vector< ReactionMonitoringTransition > transitions_
Definition: TargetedExperiment.h:250
PeptideReferenceMapType peptide_reference_map_
Definition: TargetedExperiment.h:262
std::vector< IncludeExcludeTarget > exclude_targets_
Definition: TargetedExperiment.h:254
This class stores an prediction of an SRM/MRM transition.
Definition: TargetedExperiment.h:53
Definition: TargetedExperimentHelper.h:388
Definition: TargetedExperimentHelper.h:133
TargetedExperimentHelper::Instrument Instrument
Definition: TargetedExperiment.h:64
Definition: TargetedExperimentHelper.h:416
std::vector< Software > software_
Definition: TargetedExperiment.h:242
TargetedExperimentHelper::Publication Publication
Definition: TargetedExperiment.h:63
Definition: TargetedExperimentHelper.h:102
ReactionMonitoringTransition Transition
Definition: TargetedExperiment.h:66
TargetedExperimentHelper::Contact Contact
Definition: TargetedExperiment.h:62
TargetedExperimentHelper::Compound Compound
Definition: TargetedExperiment.h:60
std::vector< Publication > publications_
Definition: TargetedExperiment.h:236
TargetedExperimentHelper::CV CV
Definition: TargetedExperiment.h:57
Definition: TargetedExperimentHelper.h:211
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:55
TargetedExperimentHelper::RetentionTime RetentionTime
Definition: TargetedExperiment.h:59