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TargetedExperiment.h
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34 
35 #ifndef OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H
36 #define OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H
37 
41 #include <OpenMS/METADATA/CVTerm.h>
45 
46 #include <vector>
47 
48 namespace OpenMS
49 {
53  class OPENMS_DLLAPI TargetedExperiment
54  {
55 public:
56 
67 
68  typedef std::map<String, const Protein *> ProteinReferenceMapType;
69  typedef std::map<String, const Peptide *> PeptideReferenceMapType;
70 
76 
79 
81  virtual ~TargetedExperiment();
83 
85  TargetedExperiment & operator=(const TargetedExperiment & rhs);
86 
90  bool operator==(const TargetedExperiment & rhs) const;
91 
92  bool operator!=(const TargetedExperiment & rhs) const;
94 
100  TargetedExperiment operator+(const TargetedExperiment & rhs) const;
101 
107  TargetedExperiment & operator+=(const TargetedExperiment & rhs);
108 
114  void clear(bool clear_meta_data);
115 
119  // cv list
120  void setCVs(const std::vector<CV> & cvs);
121 
122  const std::vector<CV> & getCVs() const;
123 
124  void addCV(const CV & cv);
125 
126  // contact list
127  void setContacts(const std::vector<Contact> & contacts);
128 
129  const std::vector<Contact> & getContacts() const;
130 
131  void addContact(const Contact & contact);
132 
133  // publication list
134  void setPublications(const std::vector<Publication> & publications);
135 
136  const std::vector<Publication> & getPublications() const;
137 
138  void addPublication(const Publication & publication);
139 
140  // target list
141  void setTargetCVTerms(const CVTermList & cv_terms);
142 
143  const CVTermList & getTargetCVTerms() const;
144 
145  void addTargetCVTerm(const CVTerm & cv_term);
146 
147  void setTargetMetaValue(const String & name, const DataValue & value);
148 
149  // instrument list
150  void setInstruments(const std::vector<Instrument> & instruments);
151 
152  const std::vector<Instrument> & getInstruments() const;
153 
154  void addInstrument(const Instrument & instrument);
155 
156  // software list
157  void setSoftware(const std::vector<Software> & software);
158 
159  const std::vector<Software> & getSoftware() const;
160 
161  void addSoftware(const Software & software);
162 
163  // protein list
164  void setProteins(const std::vector<Protein> & proteins);
165 
166  const std::vector<Protein> & getProteins() const;
167 
168  const Protein & getProteinByRef(const String & ref);
169 
170  void addProtein(const Protein & protein);
171 
172  // compound list
173  void setCompounds(const std::vector<Compound> & rhs);
174 
175  const std::vector<Compound> & getCompounds() const;
176 
177  void addCompound(const Compound & rhs);
178 
179  void setPeptides(const std::vector<Peptide> & rhs);
180 
181  const std::vector<Peptide> & getPeptides() const;
182 
183  const Peptide & getPeptideByRef(const String & ref);
184 
185  void addPeptide(const Peptide & rhs);
186 
188  void setTransitions(const std::vector<ReactionMonitoringTransition> & transitions);
189 
191  const std::vector<ReactionMonitoringTransition> & getTransitions() const;
192 
194  void addTransition(const ReactionMonitoringTransition & transition);
195 
196  void setIncludeTargets(const std::vector<IncludeExcludeTarget> & targets);
197 
198  const std::vector<IncludeExcludeTarget> & getIncludeTargets() const;
199 
200  void addIncludeTarget(const IncludeExcludeTarget & target);
201 
202  void setExcludeTargets(const std::vector<IncludeExcludeTarget> & targets);
203 
204  const std::vector<IncludeExcludeTarget> & getExcludeTargets() const;
205 
206  void addExcludeTarget(const IncludeExcludeTarget & target);
207 
209  void setSourceFiles(const std::vector<SourceFile> & source_files);
210 
212  const std::vector<SourceFile> & getSourceFiles() const;
213 
215  void addSourceFile(const SourceFile & source_file);
217 
219 
220 
223  void sortTransitionsByProductMZ();
225 
226 protected:
227 
228  void createProteinReferenceMap_();
229 
230  void createPeptideReferenceMap_();
231 
232  std::vector<CV> cvs_;
233 
234  std::vector<Contact> contacts_;
235 
236  std::vector<Publication> publications_;
237 
238  std::vector<Instrument> instruments_;
239 
241 
242  std::vector<Software> software_;
243 
244  std::vector<Protein> proteins_;
245 
246  std::vector<Compound> compounds_;
247 
248  std::vector<Peptide> peptides_;
249 
250  std::vector<ReactionMonitoringTransition> transitions_;
251 
252  std::vector<IncludeExcludeTarget> include_targets_;
253 
254  std::vector<IncludeExcludeTarget> exclude_targets_;
255 
256  std::vector<SourceFile> source_files_;
257 
258  ProteinReferenceMapType protein_reference_map_;
259 
261 
262  PeptideReferenceMapType peptide_reference_map_;
263 
265 
266  };
267 
268 
269  namespace TargetedExperimentHelper
270  {
271  } // namespace TargetedExperimentHelper
272 
273 
274 } // namespace OpenMS
275 
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
Definition: TargetedExperimentHelper.h:332
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

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:35 using doxygen 1.8.9.1