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MSQuantifications.h
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31 // $Maintainer: Mathias Walzer$
32 // $Authors: Mathias Walzer$
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34 
35 #ifndef OPENMS_METADATA_MSQUANTIFICATIONS_H
36 #define OPENMS_METADATA_MSQUANTIFICATIONS_H
37 
42 //~ #include <OpenMS/KERNEL/ConsensusFeature.h>
46 
47 #include <vector>
48 #include <map>
49 
50 namespace OpenMS
51 {
52  class OPENMS_DLLAPI MSQuantifications :
54  {
55 public:
57 
58  typedef CVTermList ParamGroupList; // userparams are exclusively inside the CVTermList's MetaInfoInterface
60 
61  enum QUANT_TYPES {MS1LABEL = 0, MS2LABEL, LABELFREE, SIZE_OF_QUANT_TYPES}; // derived from processing applied
62  static const std::string NamesOfQuantTypes[SIZE_OF_QUANT_TYPES];
63 
65  //~ InputFiles: //~ searchdb abbildung version,releasedate,#entries,dbname ber paramgrouplist
66  //~ struct ParamGroupList
67  //~ {
68  //~ ParamGroupList()
69  //~ {
70  //~ }
71 
72  //~ ParamGroupList(const ParamGroupList& rhs)
73  //~ : cv_params(rhs.cv_params)
74  //~ {
75  //~ }
76 
77  //~ ~ParamGroupList()
78  //~ {
79  //~ }
80 
81  //~ ParamGroupList& operator = (const ParamGroupList& rhs)
82  //~ {
83  //~ if (&rhs != this)
84  //~ {
85  //~ cv_params = rhs.cv_params;
86  //~ user_params = rhs.user_params;
87  //~ }
88  //~ return *this;
89  //~ }
90 
91  //~ MetaInfoInterface user_params;
92  //~ CVTermList cv_params;
93  //~ };
94 
96  {
98  {
99  }
100 
102  cv_params_(rhs.cv_params_)
103  {
104  user_params_ = rhs.user_params_;
105  quant_type_ = rhs.quant_type_;
106  }
107 
109  {
110  }
111 
113  {
114  if (&rhs != this)
115  {
116  cv_params_ = rhs.cv_params_;
117  user_params_ = rhs.user_params_;
118  quant_type_ = rhs.quant_type_;
119  }
120  return *this;
121  }
122 
126  };
127 
128  struct Assay
129  {
130  //TODO feature_maps_ also in Assay?! srsly?!
132  {
133  }
134 
135  Assay(const Assay & rhs)
136  {
137  uid_ = rhs.uid_;
138  mods_ = rhs.mods_;
139  raw_files_ = rhs.raw_files_;
140  feature_maps_ = rhs.feature_maps_;
141  }
142 
143  virtual ~Assay()
144  {
145  }
146 
147  Assay & operator=(const Assay & rhs)
148  {
149  if (&rhs != this)
150  {
151  uid_ = rhs.uid_;
152  mods_ = rhs.mods_;
153  raw_files_ = rhs.raw_files_;
154  feature_maps_ = rhs.feature_maps_;
155  }
156  return *this;
157  }
158 
160  std::vector<std::pair<String, double> > mods_;
161  std::vector<ExperimentalSettings> raw_files_;
162  std::map<size_t, FeatureMap > feature_maps_; // iTRAQ needs no FeatureMaps so ExperimentalSettings are not directly mapped to FeatureMaps
163  };
164 
165  // TODO handle referencing from consensusmaps to featuremaps/rawfiles
166  // TODO add ContactPerson or something to (Consensus)FeatureMap or DataProcessing (see below)
167  // TODO rewrite OpenMS::DataProcessing - data not yet linked in openms core formats - below should go in analysissummary of MSQuantifications - input/output not possible to be carried along
168  //~ if(DataProcessing::NamesOfProcessingAction[*it] == String("Quantitation"))
169  //~ {
170  //~ if (processing.getSoftware().getName()==String("SILACAnalyzer"))
171  //~ {
172  //~ experiment_type = MS1LABEL;
173  //~ }
174  //~ else if (processing.getSoftware().getName()==String("ITRAQAnalyzer"))
175  //~ {
176  //~ experiment_type = MS2LABEL;
177  //~ }
178  //~ else
179  //~ {
180  //~ experiment_type = LABELFREE;
181  //~ }
182  //~ }
183  //~ QUANT_TYPES experiment_type = MS1LABEL;
184 
187 
189  MSQuantifications(FeatureMap fm, ExperimentalSettings& es, std::vector<DataProcessing>& dps, std::vector<std::vector<std::pair<String, double> > > labels = (std::vector<std::vector<std::pair<String, double> > >()));
190 
193 
195  MSQuantifications(const MSQuantifications & source);
196 
198  MSQuantifications & operator=(const MSQuantifications & source);
199 
201  bool operator==(const MSQuantifications & rhs) const;
202 
204  bool operator!=(const MSQuantifications & rhs) const;
205 
219  // void load(const String & filename, bool trim_lines = false, Int first_n = -1);
220 
221  const std::vector<DataProcessing> getDataProcessingList() const;
222  const std::vector<Assay> & getAssays() const;
223  std::vector<Assay> & getAssays();
224  // std::map<String, ConsensusFeature::Ratio> & getRatios(); // TODO : implement
225  const std::vector<ConsensusMap> & getConsensusMaps() const;
226  std::vector<ConsensusMap> & getConsensusMaps();
227  void setConsensusMaps(const std::vector<ConsensusMap> & );
228  const std::vector<FeatureMap > & getFeatureMaps() const;
229  const AnalysisSummary & getAnalysisSummary() const;
230  AnalysisSummary & getAnalysisSummary();
231  void setDataProcessingList(std::vector<DataProcessing> & dpl);
232  void setAnalysisSummaryQuantType(QUANT_TYPES r);
233  void addConsensusMap(ConsensusMap & m);
234  void assignUIDs();
235  void registerExperiment(PeakMap & exp, std::vector<std::vector<std::pair<String, double> > > labels);
236  void registerExperiment(ExperimentalSettings & es, std::vector<DataProcessing>& dp, std::vector<std::vector<std::pair<String, double> > > labels = (std::vector<std::vector<std::pair<String, double> > >()));
237 
238 private:
240  std::vector<MetaInfo> bibliographic_reference_;
241  std::vector<ConsensusMap> consensus_maps_;
242  std::vector<FeatureMap > feature_maps_;
243  std::vector<Assay> assays_;
244  std::vector<DataProcessing> data_processings_;
245  //~ std::map<String,ConsensusFeature::Ratio > ratio_calculations_;
246  };
247 
248 } // namespace OpenMS
249 
250 #endif // OPENMS_METADATA_MSQUANTIFICATIONS_H
Assay(const Assay &rhs)
Definition: MSQuantifications.h:135
A more convenient string class.
Definition: String.h:57
AnalysisSummary()
Definition: MSQuantifications.h:97
std::vector< ConsensusMap > consensus_maps_
Definition: MSQuantifications.h:241
Representation of controlled vocabulary term list.
Definition: CVTermList.h:53
CVTermList cv_params_
Definition: MSQuantifications.h:124
Definition: MSQuantifications.h:128
std::vector< DataProcessing > data_processings_
Definition: MSQuantifications.h:244
A container for features.
Definition: FeatureMap.h:94
A container for consensus elements.
Definition: ConsensusMap.h:72
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
String uid_
Definition: MSQuantifications.h:159
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
MetaInfo user_params_
Definition: MSQuantifications.h:123
AnalysisSummary & operator=(const AnalysisSummary &rhs)
Definition: MSQuantifications.h:112
QUANT_TYPES quant_type_
Definition: MSQuantifications.h:125
virtual ~AnalysisSummary()
Definition: MSQuantifications.h:108
std::vector< ExperimentalSettings > raw_files_
Definition: MSQuantifications.h:161
Definition: MSQuantifications.h:52
Assay()
Definition: MSQuantifications.h:131
AnalysisSummary analysis_summary_
Definition: MSQuantifications.h:239
std::vector< FeatureMap > feature_maps_
Definition: MSQuantifications.h:242
QUANT_TYPES
Definition: MSQuantifications.h:61
virtual ~Assay()
Definition: MSQuantifications.h:143
std::vector< Assay > assays_
Definition: MSQuantifications.h:243
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
Definition: MSQuantifications.h:95
std::vector< MetaInfo > bibliographic_reference_
Definition: MSQuantifications.h:240
std::map< size_t, FeatureMap > feature_maps_
Definition: MSQuantifications.h:162
A Type-Name-Value tuple class.
Definition: MetaInfo.h:67
std::vector< std::pair< String, double > > mods_
Definition: MSQuantifications.h:160
Description of the experimental settings.
Definition: ExperimentalSettings.h:59
Assay & operator=(const Assay &rhs)
Definition: MSQuantifications.h:147
AnalysisSummary(const AnalysisSummary &rhs)
Definition: MSQuantifications.h:101

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:02 using doxygen 1.8.13