OpenMS  2.8.0
MSQuantifications.h
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31 // $Maintainer: Mathias Walzer$
32 // $Authors: Mathias Walzer$
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34 
35 #pragma once
36 
41 //~ #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 
186  MSQuantifications() = default;
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 
192  MSQuantifications(const MSQuantifications & source) = default;
193 
196 
198  ~MSQuantifications() override;
199 
201  MSQuantifications & operator=(const MSQuantifications & source) = default;
202 
205 
207  bool operator==(const MSQuantifications & rhs) const;
208 
210  bool operator!=(const MSQuantifications & rhs) const;
211 
225  // void load(const String & filename, bool trim_lines = false, Int first_n = -1);
226 
227  const std::vector<DataProcessing> getDataProcessingList() const;
228  const std::vector<Assay> & getAssays() const;
229  std::vector<Assay> & getAssays();
230  // std::map<String, ConsensusFeature::Ratio> & getRatios(); // TODO : implement
231  const std::vector<ConsensusMap> & getConsensusMaps() const;
232  std::vector<ConsensusMap> & getConsensusMaps();
233  void setConsensusMaps(const std::vector<ConsensusMap> & );
234  const std::vector<FeatureMap > & getFeatureMaps() const;
237  void setDataProcessingList(std::vector<DataProcessing> & dpl);
240  void assignUIDs();
241  void registerExperiment(PeakMap & exp, std::vector<std::vector<std::pair<String, double> > > labels);
242  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> > >()));
243 
244 private:
246  std::vector<MetaInfo> bibliographic_reference_;
247  std::vector<ConsensusMap> consensus_maps_;
248  std::vector<FeatureMap > feature_maps_;
249  std::vector<Assay> assays_;
250  std::vector<DataProcessing> data_processings_;
251  //~ std::map<String,ConsensusFeature::Ratio > ratio_calculations_;
252  };
253 
254 } // namespace OpenMS
255 
Representation of controlled vocabulary term list.
Definition: CVTermList.h:54
A container for consensus elements.
Definition: ConsensusMap.h:90
Description of the experimental settings.
Definition: ExperimentalSettings.h:62
A container for features.
Definition: FeatureMap.h:106
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
Definition: MSQuantifications.h:54
MSQuantifications & operator=(MSQuantifications &&) &=default
Move assignment operator.
std::vector< ConsensusMap > & getConsensusMaps()
std::vector< ConsensusMap > consensus_maps_
Definition: MSQuantifications.h:247
const std::vector< Assay > & getAssays() const
~MSQuantifications() override
Destructor.
std::vector< MetaInfo > bibliographic_reference_
Definition: MSQuantifications.h:246
MSQuantifications(MSQuantifications &&)=default
Move constructor.
bool operator!=(const MSQuantifications &rhs) const
Equality operator.
const std::vector< FeatureMap > & getFeatureMaps() const
MSQuantifications(const MSQuantifications &source)=default
Copy constructor.
void setDataProcessingList(std::vector< DataProcessing > &dpl)
const AnalysisSummary & getAnalysisSummary() const
QUANT_TYPES
Definition: MSQuantifications.h:61
@ LABELFREE
Definition: MSQuantifications.h:61
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 > > >()))
Detailed Constructor.
void setAnalysisSummaryQuantType(QUANT_TYPES r)
MSQuantifications & operator=(const MSQuantifications &source)=default
Assignment operator.
bool operator==(const MSQuantifications &rhs) const
Equality operator.
AnalysisSummary & getAnalysisSummary()
MSQuantifications()=default
Constructor.
void registerExperiment(PeakMap &exp, std::vector< std::vector< std::pair< String, double > > > labels)
std::vector< FeatureMap > feature_maps_
Definition: MSQuantifications.h:248
void setConsensusMaps(const std::vector< ConsensusMap > &)
AnalysisSummary analysis_summary_
Definition: MSQuantifications.h:245
void addConsensusMap(ConsensusMap &m)
std::vector< Assay > assays_
Definition: MSQuantifications.h:249
std::vector< DataProcessing > data_processings_
Definition: MSQuantifications.h:250
std::vector< Assay > & getAssays()
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 > > >()))
const std::vector< ConsensusMap > & getConsensusMaps() const
const std::vector< DataProcessing > getDataProcessingList() const
Loads data from a text file.
A Type-Name-Value tuple class.
Definition: MetaInfo.h:69
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Definition: MSQuantifications.h:96
AnalysisSummary()
Definition: MSQuantifications.h:97
CVTermList cv_params_
Definition: MSQuantifications.h:124
AnalysisSummary & operator=(const AnalysisSummary &rhs)
Definition: MSQuantifications.h:112
virtual ~AnalysisSummary()
Definition: MSQuantifications.h:108
MetaInfo user_params_
Definition: MSQuantifications.h:123
AnalysisSummary(const AnalysisSummary &rhs)
Definition: MSQuantifications.h:101
QUANT_TYPES quant_type_
Definition: MSQuantifications.h:125
Definition: MSQuantifications.h:129
std::vector< std::pair< String, double > > mods_
Definition: MSQuantifications.h:160
std::vector< ExperimentalSettings > raw_files_
Definition: MSQuantifications.h:161
Assay(const Assay &rhs)
Definition: MSQuantifications.h:135
String uid_
Definition: MSQuantifications.h:159
virtual ~Assay()
Definition: MSQuantifications.h:143
Assay()
Definition: MSQuantifications.h:131
Assay & operator=(const Assay &rhs)
Definition: MSQuantifications.h:147
std::map< size_t, FeatureMap > feature_maps_
Definition: MSQuantifications.h:162