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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 
41 //~ #include <OpenMS/KERNEL/ConsensusFeature.h>
45 
46 #include <vector>
47 #include <map>
48 
49 namespace OpenMS
50 {
51  class OPENMS_DLLAPI MSQuantifications :
53  {
54 public:
56 
57  typedef CVTermList ParamGroupList; // userparams are exclusively inside the CVTermList's MetaInfoInterface
59 
60  enum QUANT_TYPES {MS1LABEL = 0, MS2LABEL, LABELFREE, SIZE_OF_QUANT_TYPES}; // derived from processing applied
61  static const std::string NamesOfQuantTypes[SIZE_OF_QUANT_TYPES];
62 
64  //~ InputFiles: //~ searchdb abbildung version,releasedate,#entries,dbname über paramgrouplist
65  //~ struct ParamGroupList
66  //~ {
67  //~ ParamGroupList()
68  //~ {
69  //~ }
70 
71  //~ ParamGroupList(const ParamGroupList& rhs)
72  //~ : cv_params(rhs.cv_params)
73  //~ {
74  //~ }
75 
76  //~ ~ParamGroupList()
77  //~ {
78  //~ }
79 
80  //~ ParamGroupList& operator = (const ParamGroupList& rhs)
81  //~ {
82  //~ if (&rhs != this)
83  //~ {
84  //~ cv_params = rhs.cv_params;
85  //~ user_params = rhs.user_params;
86  //~ }
87  //~ return *this;
88  //~ }
89 
90  //~ MetaInfoInterface user_params;
91  //~ CVTermList cv_params;
92  //~ };
93 
95  {
97  {
98  }
99 
101  cv_params_(rhs.cv_params_)
102  {
103  user_params_ = rhs.user_params_;
104  quant_type_ = rhs.quant_type_;
105  }
106 
108  {
109  }
110 
112  {
113  if (&rhs != this)
114  {
115  cv_params_ = rhs.cv_params_;
116  user_params_ = rhs.user_params_;
117  quant_type_ = rhs.quant_type_;
118  }
119  return *this;
120  }
121 
125  };
126 
127  struct Assay
128  {
130  {
131  }
132 
133  Assay(const Assay & rhs)
134  {
135  uid_ = rhs.uid_;
136  mods_ = rhs.mods_;
137  raw_files_ = rhs.raw_files_;
138  feature_maps_ = rhs.feature_maps_;
139  }
140 
141  virtual ~Assay()
142  {
143  }
144 
145  Assay & operator=(const Assay & rhs)
146  {
147  if (&rhs != this)
148  {
149  uid_ = rhs.uid_;
150  mods_ = rhs.mods_;
151  raw_files_ = rhs.raw_files_;
152  feature_maps_ = rhs.feature_maps_;
153  }
154  return *this;
155  }
156 
158  std::vector<std::pair<String, DoubleReal> > mods_;
159  std::vector<ExperimentalSettings> raw_files_;
160  std::map<size_t, FeatureMap<> > feature_maps_; // iTRAQ needs no FeatureMaps so ExperimentalSettings are not directly mapped to FeatureMaps
161  };
162 
163  // TODO handle referencing from consensusmaps to featuremaps/rawfiles
164  // TODO add ContactPerson or something to (Consensus)FeatureMap or DataProcessing (see below)
165  // 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
166  //~ if(DataProcessing::NamesOfProcessingAction[*it] == String("Quantitation"))
167  //~ {
168  //~ if (processing.getSoftware().getName()==String("SILACAnalyzer"))
169  //~ {
170  //~ experiment_type = MS1LABEL;
171  //~ }
172  //~ else if (processing.getSoftware().getName()==String("ITRAQAnalyzer"))
173  //~ {
174  //~ experiment_type = MS2LABEL;
175  //~ }
176  //~ else
177  //~ {
178  //~ experiment_type = LABELFREE;
179  //~ }
180  //~ }
181  //~ QUANT_TYPES experiment_type = MS1LABEL;
182 
185 
188 
190  MSQuantifications(const MSQuantifications & source);
191 
193  MSQuantifications & operator=(const MSQuantifications & source);
194 
196  bool operator==(const MSQuantifications & rhs) const;
197 
199  bool operator!=(const MSQuantifications & rhs) const;
200 
214  // void load(const String & filename, bool trim_lines = false, Int first_n = -1);
215 
216  const std::vector<DataProcessing> getDataProcessingList() const;
217  const std::vector<Assay> & getAssays() const;
218  std::vector<Assay> & getAssays();
219  // std::map<String, ConsensusFeature::Ratio> & getRatios(); // TODO : implement
220  const std::vector<ConsensusMap> & getConsensusMaps() const;
221  std::vector<ConsensusMap> & getConsensusMaps();
222  void setConsensusMaps(const std::vector<ConsensusMap> & );
223  const std::vector<FeatureMap<> > & getFeatureMaps() const;
224  const AnalysisSummary & getAnalysisSummary() const;
225  AnalysisSummary & getAnalysisSummary();
226  void setDataProcessingList(std::vector<DataProcessing> & dpl);
227  void setAnalysisSummaryQuantType(QUANT_TYPES r);
228  void addConsensusMap(ConsensusMap & m);
229  void assignUIDs();
230  void registerExperiment(MSExperiment<Peak1D> & exp, std::vector<std::vector<std::pair<String, DoubleReal> > > labels);
231 
232 private:
234  std::vector<MetaInfo> bibliographic_reference_;
235  std::vector<ConsensusMap> consensus_maps_;
236  std::vector<FeatureMap<> > feature_maps_;
237  std::vector<Assay> assays_;
238  std::vector<DataProcessing> data_processings_;
239  //~ std::map<String,ConsensusFeature::Ratio > ratio_calculations_;
240  };
241 
242 } // namespace OpenMS
243 
244 #endif // OPENMS_METADATA_MSQUANTIFICATIONS_H
Assay(const Assay &rhs)
Definition: MSQuantifications.h:133
A more convenient string class.
Definition: String.h:56
AnalysisSummary()
Definition: MSQuantifications.h:96
std::vector< ConsensusMap > consensus_maps_
Definition: MSQuantifications.h:235
Representation of controlled vocabulary term list.
Definition: CVTermList.h:54
CVTermList cv_params_
Definition: MSQuantifications.h:123
Definition: MSQuantifications.h:127
std::vector< DataProcessing > data_processings_
Definition: MSQuantifications.h:238
A container for consensus elements.
Definition: ConsensusMap.h:60
String uid_
Definition: MSQuantifications.h:157
MetaInfo user_params_
Definition: MSQuantifications.h:122
AnalysisSummary & operator=(const AnalysisSummary &rhs)
Definition: MSQuantifications.h:111
QUANT_TYPES quant_type_
Definition: MSQuantifications.h:124
virtual ~AnalysisSummary()
Definition: MSQuantifications.h:107
std::vector< ExperimentalSettings > raw_files_
Definition: MSQuantifications.h:159
Definition: MSQuantifications.h:51
Assay()
Definition: MSQuantifications.h:129
AnalysisSummary analysis_summary_
Definition: MSQuantifications.h:233
std::map< size_t, FeatureMap<> > feature_maps_
Definition: MSQuantifications.h:160
QUANT_TYPES
Definition: MSQuantifications.h:60
virtual ~Assay()
Definition: MSQuantifications.h:141
std::vector< Assay > assays_
Definition: MSQuantifications.h:237
Definition: MSQuantifications.h:94
std::vector< std::pair< String, DoubleReal > > mods_
Definition: MSQuantifications.h:158
std::vector< MetaInfo > bibliographic_reference_
Definition: MSQuantifications.h:234
std::vector< FeatureMap<> > feature_maps_
Definition: MSQuantifications.h:236
A Type-Name-Value tuple class.
Definition: MetaInfo.h:67
Description of the experimental settings.
Definition: ExperimentalSettings.h:59
Assay & operator=(const Assay &rhs)
Definition: MSQuantifications.h:145
AnalysisSummary(const AnalysisSummary &rhs)
Definition: MSQuantifications.h:100

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:18 using doxygen 1.8.5