35 #ifndef OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H
36 #define OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H
111 void clear(
bool clear_meta_data);
117 void setCVs(
const std::vector<CV> & cvs);
119 const std::vector<CV> & getCVs()
const;
121 void addCV(
const CV & cv);
124 void setContacts(
const std::vector<Contact> & contacts);
126 const std::vector<Contact> & getContacts()
const;
128 void addContact(
const Contact & contact);
131 void setPublications(
const std::vector<Publication> & publications);
133 const std::vector<Publication> & getPublications()
const;
135 void addPublication(
const Publication & publication);
138 void setTargetCVTerms(
const CVTermList & cv_terms);
142 void addTargetCVTerm(
const CVTerm & cv_term);
147 void setInstruments(
const std::vector<Instrument> & instruments);
149 const std::vector<Instrument> & getInstruments()
const;
151 void addInstrument(
const Instrument & instrument);
154 void setSoftware(
const std::vector<Software> & software);
156 const std::vector<Software> & getSoftware()
const;
158 void addSoftware(
const Software & software);
161 void setProteins(
const std::vector<Protein> & proteins);
163 const std::vector<Protein> & getProteins()
const;
167 void addProtein(
const Protein & protein);
170 void setCompounds(
const std::vector<Compound> & rhs);
172 const std::vector<Compound> & getCompounds()
const;
174 void addCompound(
const Compound & rhs);
176 void setPeptides(
const std::vector<Peptide> & rhs);
178 const std::vector<Peptide> & getPeptides()
const;
182 void addPeptide(
const Peptide & rhs);
185 void setTransitions(
const std::vector<ReactionMonitoringTransition> & transitions);
188 const std::vector<ReactionMonitoringTransition> & getTransitions()
const;
193 void setIncludeTargets(
const std::vector<IncludeExcludeTarget> & targets);
195 const std::vector<IncludeExcludeTarget> & getIncludeTargets()
const;
199 void setExcludeTargets(
const std::vector<IncludeExcludeTarget> & targets);
201 const std::vector<IncludeExcludeTarget> & getExcludeTargets()
const;
206 void setSourceFiles(
const std::vector<SourceFile> & source_files);
209 const std::vector<SourceFile> & getSourceFiles()
const;
212 void addSourceFile(
const SourceFile & source_file);
220 void sortTransitionsByProductMZ();
225 void createProteinReferenceMap_();
227 void createPeptideReferenceMap_();
266 namespace TargetedExperimentHelper
273 #endif // OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H
CVTermList targets_
Definition: TargetedExperiment.h:237
A more convenient string class.
Definition: String.h:56
std::vector< IncludeExcludeTarget > include_targets_
Definition: TargetedExperiment.h:249
Representation of controlled vocabulary term list.
Definition: CVTermList.h:54
Definition: TargetedExperimentHelper.h:374
TargetedExperimentHelper::Peptide Peptide
Definition: TargetedExperiment.h:61
ProteinReferenceMapType protein_reference_map_
Definition: TargetedExperiment.h:255
std::vector< Protein > proteins_
Definition: TargetedExperiment.h:241
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:47
std::vector< Peptide > peptides_
Definition: TargetedExperiment.h:245
Description of the software used for processing.
Definition: Software.h:49
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:261
std::vector< SourceFile > source_files_
Definition: TargetedExperiment.h:253
std::vector< Compound > compounds_
Definition: TargetedExperiment.h:243
std::map< String, const Peptide * > PeptideReferenceMapType
Definition: TargetedExperiment.h:68
std::vector< Contact > contacts_
Definition: TargetedExperiment.h:231
std::vector< Instrument > instruments_
Definition: TargetedExperiment.h:235
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:229
Definition: TargetedExperimentHelper.h:172
std::map< String, const Protein * > ProteinReferenceMapType
Definition: TargetedExperiment.h:67
bool protein_reference_map_dirty_
Definition: TargetedExperiment.h:257
Definition: TargetedExperimentHelper.h:76
This class stores a SRM/MRM transition.
Definition: IncludeExcludeTarget.h:53
std::vector< ReactionMonitoringTransition > transitions_
Definition: TargetedExperiment.h:247
PeptideReferenceMapType peptide_reference_map_
Definition: TargetedExperiment.h:259
std::vector< IncludeExcludeTarget > exclude_targets_
Definition: TargetedExperiment.h:251
This class stores an prediction of an SRM/MRM transition.
Definition: TargetedExperiment.h:53
Definition: TargetedExperimentHelper.h:402
Definition: TargetedExperimentHelper.h:133
TargetedExperimentHelper::Instrument Instrument
Definition: TargetedExperiment.h:64
Definition: TargetedExperimentHelper.h:430
std::vector< Software > software_
Definition: TargetedExperiment.h:239
TargetedExperimentHelper::Publication Publication
Definition: TargetedExperiment.h:63
Definition: TargetedExperimentHelper.h:102
TargetedExperimentHelper::Contact Contact
Definition: TargetedExperiment.h:62
TargetedExperimentHelper::Compound Compound
Definition: TargetedExperiment.h:60
std::vector< Publication > publications_
Definition: TargetedExperiment.h:233
TargetedExperimentHelper::CV CV
Definition: TargetedExperiment.h:57
Definition: TargetedExperimentHelper.h:211
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:53
TargetedExperimentHelper::RetentionTime RetentionTime
Definition: TargetedExperiment.h:59