| OpenMS 2.5.0

TargetedExperiment.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h>
39 #include <OpenMS/ANALYSIS/TARGETED/IncludeExcludeTarget.h>
40 #include <OpenMS/METADATA/CVTerm.h>
41 #include <OpenMS/METADATA/CVTermList.h>
42 #include <OpenMS/METADATA/Software.h>
43 #include <OpenMS/METADATA/SourceFile.h>
44 #include <OpenMS/ANALYSIS/TARGETED/TargetedExperimentHelper.h>
45
46 #include <vector>
47
48 namespace OpenMS
49 {
64 class OPENMS_DLLAPI TargetedExperiment
65 {
66 public:
67
68 typedef TargetedExperimentHelper::CV CV;
69 typedef TargetedExperimentHelper::Protein Protein;
70 typedef TargetedExperimentHelper::RetentionTime RetentionTime;
71 typedef TargetedExperimentHelper::Compound Compound;
72 typedef TargetedExperimentHelper::Peptide Peptide;
73 typedef TargetedExperimentHelper::Contact Contact;
74 typedef TargetedExperimentHelper::Publication Publication;
75 typedef TargetedExperimentHelper::Instrument Instrument;
76 typedef TargetedExperimentHelper::Prediction Prediction;
77 typedef TargetedExperimentHelper::Interpretation Interpretation;
78 typedef ReactionMonitoringTransition Transition;
79 typedef Residue IonType; // IonType enum of Interpretation class
80
81 typedef std::map<String, const Protein *> ProteinReferenceMapType;
82 typedef std::map<String, const Peptide *> PeptideReferenceMapType;
83 typedef std::map<String, const Compound *> CompoundReferenceMapType;
84
88 TargetedExperiment();
90
92 TargetedExperiment(const TargetedExperiment & rhs);
93
95 virtual ~TargetedExperiment();
97
99 TargetedExperiment & operator=(const TargetedExperiment & rhs);
100
104 bool operator==(const TargetedExperiment & rhs) const;
105
106 bool operator!=(const TargetedExperiment & rhs) const;
108
114 TargetedExperiment operator+(const TargetedExperiment & rhs) const;
115
121 TargetedExperiment & operator+=(const TargetedExperiment & rhs);
122
128 void clear(bool clear_meta_data);
129
133 // cv list
134 void setCVs(const std::vector<CV> & cvs);
135
136 const std::vector<CV> & getCVs() const;
137
138 void addCV(const CV & cv);
139
140 // contact list
141 void setContacts(const std::vector<Contact> & contacts);
142
143 const std::vector<Contact> & getContacts() const;
144
145 void addContact(const Contact & contact);
146
147 // publication list
148 void setPublications(const std::vector<Publication> & publications);
149
150 const std::vector<Publication> & getPublications() const;
151
152 void addPublication(const Publication & publication);
153
154 // target list
155 void setTargetCVTerms(const CVTermList & cv_terms);
156
157 const CVTermList & getTargetCVTerms() const;
158
159 void addTargetCVTerm(const CVTerm & cv_term);
160
161 void setTargetMetaValue(const String & name, const DataValue & value);
162
163 // instrument list
164 void setInstruments(const std::vector<Instrument> & instruments);
165
166 const std::vector<Instrument> & getInstruments() const;
167
168 void addInstrument(const Instrument & instrument);
169
170 // software list
171 void setSoftware(const std::vector<Software> & software);
172
173 const std::vector<Software> & getSoftware() const;
174
175 void addSoftware(const Software & software);
176
177 // protein list
178 void setProteins(const std::vector<Protein> & proteins);
179
180 const std::vector<Protein> & getProteins() const;
181
182 const Protein & getProteinByRef(const String & ref) const;
183
184 bool hasProtein(const String & ref) const;
185
186 void addProtein(const Protein & protein);
187
188 // compound list
189 void setCompounds(const std::vector<Compound> & rhs);
190
191 const std::vector<Compound> & getCompounds() const;
192
193 void addCompound(const Compound & rhs);
194
195 void setPeptides(const std::vector<Peptide> & rhs);
196
197 const std::vector<Peptide> & getPeptides() const;
198
199 bool hasPeptide(const String & ref) const;
200
201 const Peptide & getPeptideByRef(const String & ref) const;
202
203 bool hasCompound(const String & ref) const;
204
205 const Compound & getCompoundByRef(const String & ref) const;
206
207 void addPeptide(const Peptide & rhs);
208
210 void setTransitions(const std::vector<ReactionMonitoringTransition> & transitions);
211
213 const std::vector<ReactionMonitoringTransition> & getTransitions() const;
214
216 void addTransition(const ReactionMonitoringTransition & transition);
217
218 void setIncludeTargets(const std::vector<IncludeExcludeTarget> & targets);
219
220 const std::vector<IncludeExcludeTarget> & getIncludeTargets() const;
221
222 void addIncludeTarget(const IncludeExcludeTarget & target);
223
224 void setExcludeTargets(const std::vector<IncludeExcludeTarget> & targets);
225
226 const std::vector<IncludeExcludeTarget> & getExcludeTargets() const;
227
228 void addExcludeTarget(const IncludeExcludeTarget & target);
229
231 void setSourceFiles(const std::vector<SourceFile> & source_files);
232
234 const std::vector<SourceFile> & getSourceFiles() const;
235
237 void addSourceFile(const SourceFile & source_file);
239
241
242
245 void sortTransitionsByProductMZ();
247
257 bool containsInvalidReferences() const;
258
259 protected:
260
261 void createProteinReferenceMap_() const;
262
263 void createPeptideReferenceMap_() const;
264
265 void createCompoundReferenceMap_() const;
266
267 std::vector<CV> cvs_;
268
269 std::vector<Contact> contacts_;
270
271 std::vector<Publication> publications_;
272
273 std::vector<Instrument> instruments_;
274
275 CVTermList targets_;
276
277 std::vector<Software> software_;
278
279 std::vector<Protein> proteins_;
280
281 std::vector<Compound> compounds_;
282
283 std::vector<Peptide> peptides_;
284
285 std::vector<ReactionMonitoringTransition> transitions_;
286
287 std::vector<IncludeExcludeTarget> include_targets_;
288
289 std::vector<IncludeExcludeTarget> exclude_targets_;
290
291 std::vector<SourceFile> source_files_;
292
293 mutable ProteinReferenceMapType protein_reference_map_;
294
295 mutable bool protein_reference_map_dirty_;
296
297 mutable PeptideReferenceMapType peptide_reference_map_;
298
299 mutable bool peptide_reference_map_dirty_;
300
301 mutable CompoundReferenceMapType compound_reference_map_;
302
303 mutable bool compound_reference_map_dirty_;
304
305 };
306
307 namespace TargetedExperimentHelper
308 {
309 } // namespace TargetedExperimentHelper
310
311
312 } // namespace OpenMS
313
OpenMS::CVTermList
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
OpenMS::SourceFile
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:46
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::DataValue
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
OpenMS::TargetedExperiment::proteins_
std::vector< Protein > proteins_
Definition: TargetedExperiment.h:279
OpenMS::TargetedExperiment::contacts_
std::vector< Contact > contacts_
Definition: TargetedExperiment.h:269
OpenMS::Residue
Representation of a residue.
Definition: Residue.h:61
OpenMS::TargetedExperiment::protein_reference_map_dirty_
bool protein_reference_map_dirty_
Definition: TargetedExperiment.h:295
OpenMS::TargetedExperimentHelper::RetentionTime
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:127
OpenMS::TargetedExperiment::instruments_
std::vector< Instrument > instruments_
Definition: TargetedExperiment.h:273
OpenMS::TargetedExperiment::IonType
Residue IonType
Definition: TargetedExperiment.h:79
OpenMS::TargetedExperiment::Contact
TargetedExperimentHelper::Contact Contact
Definition: TargetedExperiment.h:73
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
IncludeExcludeTarget.h
StandardTypes.h
OpenMS::TargetedExperiment::Instrument
TargetedExperimentHelper::Instrument Instrument
Definition: TargetedExperiment.h:75
OpenMS::TargetedExperiment::ProteinReferenceMapType
std::map< String, const Protein * > ProteinReferenceMapType
Definition: TargetedExperiment.h:81
OpenMS::TargetedExperimentHelper::Contact
Definition: TargetedExperimentHelper.h:444
ReactionMonitoringTransition.h
OpenMS::Software
Description of the software used for processing.
Definition: Software.h:48
CVTerm.h
OpenMS::TargetedExperiment::Protein
TargetedExperimentHelper::Protein Protein
Definition: TargetedExperiment.h:69
OpenMS::TargetedExperiment::include_targets_
std::vector< IncludeExcludeTarget > include_targets_
Definition: TargetedExperiment.h:287
OpenMS::TargetedExperiment::Interpretation
TargetedExperimentHelper::Interpretation Interpretation
Definition: TargetedExperiment.h:77
OpenMS::TargetedExperiment::peptide_reference_map_dirty_
bool peptide_reference_map_dirty_
Definition: TargetedExperiment.h:299
OpenMS::CVTerm
Representation of controlled vocabulary term.
Definition: CVTerm.h:52
OpenMS::TargetedExperiment::targets_
CVTermList targets_
Definition: TargetedExperiment.h:275
OpenMS::TargetedExperiment::Peptide
TargetedExperimentHelper::Peptide Peptide
Definition: TargetedExperiment.h:72
OpenMS::TargetedExperimentHelper::Compound
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:333
OpenMS::TargetedExperiment::PeptideReferenceMapType
std::map< String, const Peptide * > PeptideReferenceMapType
Definition: TargetedExperiment.h:82
OpenMS::TargetedExperimentHelper::Protein
Definition: TargetedExperimentHelper.h:98
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::TargetedExperiment::CV
TargetedExperimentHelper::CV CV
Definition: TargetedExperiment.h:68
OpenMS::TargetedExperiment::software_
std::vector< Software > software_
Definition: TargetedExperiment.h:277
OpenMS::TargetedExperiment::compounds_
std::vector< Compound > compounds_
Definition: TargetedExperiment.h:281
OpenMS::TargetedExperiment::compound_reference_map_
CompoundReferenceMapType compound_reference_map_
Definition: TargetedExperiment.h:301
Software.h
OpenMS::TargetedExperimentHelper::Instrument
Definition: TargetedExperimentHelper.h:478
OpenMS::ReactionMonitoringTransition
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
OpenMS::TargetedExperiment::compound_reference_map_dirty_
bool compound_reference_map_dirty_
Definition: TargetedExperiment.h:303
CVTermList.h
OpenMS::TargetedExperiment::exclude_targets_
std::vector< IncludeExcludeTarget > exclude_targets_
Definition: TargetedExperiment.h:289
OpenMS::TargetedExperimentHelper::CV
Definition: TargetedExperimentHelper.h:72
SourceFile.h
OpenMS::TargetedExperiment::peptides_
std::vector< Peptide > peptides_
Definition: TargetedExperiment.h:283
OpenMS::TargetedExperiment::Publication
TargetedExperimentHelper::Publication Publication
Definition: TargetedExperiment.h:74
OpenMS::TargetedExperimentHelper::Interpretation
Product ion interpretation.
Definition: TargetedExperimentHelper.h:520
OpenMS::TargetedExperiment::CompoundReferenceMapType
std::map< String, const Compound * > CompoundReferenceMapType
Definition: TargetedExperiment.h:83
OpenMS::TargetedExperimentHelper::Publication
Definition: TargetedExperimentHelper.h:461
OpenMS::TargetedExperiment::source_files_
std::vector< SourceFile > source_files_
Definition: TargetedExperiment.h:291
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370
OpenMS::IncludeExcludeTarget
This class stores a SRM/MRM transition.
Definition: IncludeExcludeTarget.h:52
OpenMS::TargetedExperiment::Compound
TargetedExperimentHelper::Compound Compound
Definition: TargetedExperiment.h:71
OpenMS::TargetedExperiment::transitions_
std::vector< ReactionMonitoringTransition > transitions_
Definition: TargetedExperiment.h:285
OpenMS::TargetedExperiment::cvs_
std::vector< CV > cvs_
Definition: TargetedExperiment.h:267
OpenMS::TargetedExperimentHelper::Prediction
Definition: TargetedExperimentHelper.h:495
OpenMS::TargetedExperiment::Transition
ReactionMonitoringTransition Transition
Definition: TargetedExperiment.h:78
OpenMS::TargetedExperiment::Prediction
TargetedExperimentHelper::Prediction Prediction
Definition: TargetedExperiment.h:76
OpenMS::TargetedExperiment::protein_reference_map_
ProteinReferenceMapType protein_reference_map_
Definition: TargetedExperiment.h:293
OpenMS::TargetedExperiment::RetentionTime
TargetedExperimentHelper::RetentionTime RetentionTime
Definition: TargetedExperiment.h:70
TargetedExperimentHelper.h
OpenMS::TargetedExperiment::peptide_reference_map_
PeptideReferenceMapType peptide_reference_map_
Definition: TargetedExperiment.h:297
OpenMS::TargetedExperiment::publications_
std::vector< Publication > publications_
Definition: TargetedExperiment.h:271
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806