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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 
66 
67  typedef std::map<String, const Protein *> ProteinReferenceMapType;
68  typedef std::map<String, const Peptide *> PeptideReferenceMapType;
69 
75 
78 
80  virtual ~TargetedExperiment();
82 
84  TargetedExperiment & operator=(const TargetedExperiment & rhs);
85 
89  bool operator==(const TargetedExperiment & rhs) const;
91 
97  TargetedExperiment operator+(const TargetedExperiment & rhs) const;
98 
104  TargetedExperiment & operator+=(const TargetedExperiment & rhs);
105 
111  void clear(bool clear_meta_data);
112 
116  // cv list
117  void setCVs(const std::vector<CV> & cvs);
118 
119  const std::vector<CV> & getCVs() const;
120 
121  void addCV(const CV & cv);
122 
123  // contact list
124  void setContacts(const std::vector<Contact> & contacts);
125 
126  const std::vector<Contact> & getContacts() const;
127 
128  void addContact(const Contact & contact);
129 
130  // publication list
131  void setPublications(const std::vector<Publication> & publications);
132 
133  const std::vector<Publication> & getPublications() const;
134 
135  void addPublication(const Publication & publication);
136 
137  // target list
138  void setTargetCVTerms(const CVTermList & cv_terms);
139 
140  const CVTermList & getTargetCVTerms() const;
141 
142  void addTargetCVTerm(const CVTerm & cv_term);
143 
144  void setTargetMetaValue(const String & name, const DataValue & value);
145 
146  // instrument list
147  void setInstruments(const std::vector<Instrument> & instruments);
148 
149  const std::vector<Instrument> & getInstruments() const;
150 
151  void addInstrument(const Instrument & instrument);
152 
153  // software list
154  void setSoftware(const std::vector<Software> & software);
155 
156  const std::vector<Software> & getSoftware() const;
157 
158  void addSoftware(const Software & software);
159 
160  // protein list
161  void setProteins(const std::vector<Protein> & proteins);
162 
163  const std::vector<Protein> & getProteins() const;
164 
165  const Protein & getProteinByRef(const String & ref);
166 
167  void addProtein(const Protein & protein);
168 
169  // compound list
170  void setCompounds(const std::vector<Compound> & rhs);
171 
172  const std::vector<Compound> & getCompounds() const;
173 
174  void addCompound(const Compound & rhs);
175 
176  void setPeptides(const std::vector<Peptide> & rhs);
177 
178  const std::vector<Peptide> & getPeptides() const;
179 
180  const Peptide & getPeptideByRef(const String & ref);
181 
182  void addPeptide(const Peptide & rhs);
183 
185  void setTransitions(const std::vector<ReactionMonitoringTransition> & transitions);
186 
188  const std::vector<ReactionMonitoringTransition> & getTransitions() const;
189 
191  void addTransition(const ReactionMonitoringTransition & transition);
192 
193  void setIncludeTargets(const std::vector<IncludeExcludeTarget> & targets);
194 
195  const std::vector<IncludeExcludeTarget> & getIncludeTargets() const;
196 
197  void addIncludeTarget(const IncludeExcludeTarget & target);
198 
199  void setExcludeTargets(const std::vector<IncludeExcludeTarget> & targets);
200 
201  const std::vector<IncludeExcludeTarget> & getExcludeTargets() const;
202 
203  void addExcludeTarget(const IncludeExcludeTarget & target);
204 
206  void setSourceFiles(const std::vector<SourceFile> & source_files);
207 
209  const std::vector<SourceFile> & getSourceFiles() const;
210 
212  void addSourceFile(const SourceFile & source_file);
214 
216 
217 
220  void sortTransitionsByProductMZ();
222 
223 protected:
224 
225  void createProteinReferenceMap_();
226 
227  void createPeptideReferenceMap_();
228 
229  std::vector<CV> cvs_;
230 
231  std::vector<Contact> contacts_;
232 
233  std::vector<Publication> publications_;
234 
235  std::vector<Instrument> instruments_;
236 
238 
239  std::vector<Software> software_;
240 
241  std::vector<Protein> proteins_;
242 
243  std::vector<Compound> compounds_;
244 
245  std::vector<Peptide> peptides_;
246 
247  std::vector<ReactionMonitoringTransition> transitions_;
248 
249  std::vector<IncludeExcludeTarget> include_targets_;
250 
251  std::vector<IncludeExcludeTarget> exclude_targets_;
252 
253  std::vector<SourceFile> source_files_;
254 
256 
258 
260 
262 
263  };
264 
265 
266  namespace TargetedExperimentHelper
267  {
268  } // namespace TargetedExperimentHelper
269 
270 
271 } // namespace OpenMS
272 
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
Definition: TargetedExperimentHelper.h:346
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

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:21 using doxygen 1.8.5