OpenMS  3.0.0
ConsensusFeature.h
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34 
35 #pragma once
36 
40 
41 #include <OpenMS/CONCEPT/Types.h>
43 #include <OpenMS/OpenMSConfig.h>
44 
45 #include <set>
46 
47 namespace OpenMS
48 {
49  class FeatureMap;
50  class Peak2D;
51 
69  class OPENMS_DLLAPI ConsensusFeature :
70  public BaseFeature
71  {
72 public:
74 
75  typedef std::set<FeatureHandle, FeatureHandle::IndexLess> HandleSetType;
76  typedef HandleSetType::const_iterator const_iterator;
77  typedef HandleSetType::iterator iterator;
78  typedef HandleSetType::const_reverse_iterator const_reverse_iterator;
79  typedef HandleSetType::reverse_iterator reverse_iterator;
81 
83  struct SizeLess
84  {
85  inline bool operator()(ConsensusFeature const& left, ConsensusFeature const& right) const
86  {
87  return left.size() < right.size();
88  }
89 
90  inline bool operator()(ConsensusFeature const& left, UInt64 const& right) const
91  {
92  return left.size() < right;
93  }
94 
95  inline bool operator()(UInt64 const& left, ConsensusFeature const& right) const
96  {
97  return left < right.size();
98  }
99 
100  inline bool operator()(const UInt64& left, const UInt64& right) const
101  {
102  return left < right;
103  }
104 
105  };
106 
108  struct MapsLess
109  {
110  inline bool operator()(ConsensusFeature const& left, ConsensusFeature const& right) const
111  {
112  return std::lexicographical_compare(left.begin(), left.end(), right.begin(), right.end(), FeatureHandle::IndexLess());
113  }
114 
115  };
116 
118  struct Ratio
119  {
121  {
122  }
123 
124  Ratio(const Ratio& rhs)
125  {
126  ratio_value_ = rhs.ratio_value_;
127  denominator_ref_ = rhs.denominator_ref_;
128  numerator_ref_ = rhs.numerator_ref_;
129  description_ = rhs.description_;
130  }
131 
132  virtual ~Ratio()
133  {
134  }
135 
136  Ratio& operator=(const Ratio& rhs)
137  {
138  if (&rhs != this)
139  {
140  ratio_value_ = rhs.ratio_value_;
141  denominator_ref_ = rhs.denominator_ref_;
142  numerator_ref_ = rhs.numerator_ref_;
143  description_ = rhs.description_;
144  }
145  return *this;
146  }
147 
148  double ratio_value_;
151  std::vector<String> description_;
152  //TODO ratio cv info
153  };
154 
156 
159 
161  ConsensusFeature(const ConsensusFeature& rhs) = default;
162 
164  ConsensusFeature(ConsensusFeature&& rhs) = default;
165 
167  explicit ConsensusFeature(const BaseFeature& feature);
168 
175  ConsensusFeature(UInt64 map_index, const Peak2D& element, UInt64 element_index);
176 
183  ConsensusFeature(UInt64 map_index, const BaseFeature& element);
184 
186  ConsensusFeature& operator=(const ConsensusFeature& rhs) = default;
187 
189  ConsensusFeature& operator=(ConsensusFeature&& rhs) = default;
190 
192  ~ConsensusFeature() override;
194 
195 
197 
198 
202  void insert(const ConsensusFeature& cf);
203  void insert(ConsensusFeature&& cf);
204 
211  void insert(const FeatureHandle& handle);
212  void insert(FeatureHandle&& handle);
213 
215  void insert(const HandleSetType& handle_set);
216  void insert(HandleSetType&& handle_set);
217 
224  void insert(UInt64 map_index, const Peak2D& element, UInt64 element_index);
225 
232  void insert(UInt64 map_index, const BaseFeature& element);
233 
235  const HandleSetType& getFeatures() const;
236 
238  std::vector<FeatureHandle> getFeatureList() const;
239 
241  void setFeatures(HandleSetType h);
243 
245 
246  DRange<2> getPositionRange() const;
249  DRange<1> getIntensityRange() const;
250 
252 
262  void computeConsensus();
263 
273  void computeMonoisotopicConsensus();
274 
288  void computeDechargeConsensus(const FeatureMap& fm, bool intensity_weighted_averaging = false);
289 
297  void addRatio(const Ratio& r);
298 
306  void setRatios(std::vector<Ratio>& rs);
307 
311  std::vector<Ratio> getRatios() const;
312 
316  std::vector<Ratio>& getRatios();
317 
319 
320  Size size() const;
321 
322  const_iterator begin() const;
323 
324  iterator begin();
325 
326  const_iterator end() const;
327 
328  iterator end();
329 
330  const_reverse_iterator rbegin() const;
331 
332  reverse_iterator rbegin();
333 
334  const_reverse_iterator rend() const;
335 
336  reverse_iterator rend();
337 
338  void clear();
339 
340  bool empty() const;
342 
343 private:
344 
346  std::vector<Ratio> ratios_;
347 
348 
349  };
350 
352  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ConsensusFeature& cons);
353 
354 } // namespace OpenMS
355 
OpenMS::ConsensusFeature::Ratio::~Ratio
virtual ~Ratio()
Definition: ConsensusFeature.h:132
OpenMS::ConsensusFeature::MapsLess
Compare by the sets of consensus elements (lexicographically)
Definition: ConsensusFeature.h:108
OpenMS::UInt64
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
DRange.h
Types.h
OpenMS::ConsensusFeature::Ratio::ratio_value_
double ratio_value_
Definition: ConsensusFeature.h:148
OpenMS::Peak2D
A 2-dimensional raw data point or peak.
Definition: Peak2D.h:54
OpenMS::ConsensusFeature::handles_
HandleSetType handles_
Definition: ConsensusFeature.h:345
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::BaseFeature
A basic LC-MS feature.
Definition: BaseFeature.h:58
OpenMS::DRange< 2 >
OpenMS::ConsensusFeature::iterator
HandleSetType::iterator iterator
Definition: ConsensusFeature.h:77
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::ConsensusFeature::Ratio::Ratio
Ratio(const Ratio &rhs)
Definition: ConsensusFeature.h:124
OpenMS::ConsensusFeature::HandleSetType
std::set< FeatureHandle, FeatureHandle::IndexLess > HandleSetType
Type definitions.
Definition: ConsensusFeature.h:75
OpenMS::FeatureHandle::IndexLess
Comparator by map and unique id.
Definition: FeatureHandle.h:140
FeatureHandle.h
OpenMS::ConsensusFeature::SizeLess::operator()
bool operator()(ConsensusFeature const &left, UInt64 const &right) const
Definition: ConsensusFeature.h:90
OpenMS::ConsensusFeature::const_reverse_iterator
HandleSetType::const_reverse_iterator const_reverse_iterator
Definition: ConsensusFeature.h:78
OpenMS::ConsensusFeature::end
const_iterator end() const
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ConsensusFeature::Ratio::Ratio
Ratio()
Definition: ConsensusFeature.h:120
BaseFeature.h
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::ConsensusFeature::Ratio::operator=
Ratio & operator=(const Ratio &rhs)
Definition: ConsensusFeature.h:136
OpenMS::ConsensusFeature::const_iterator
HandleSetType::const_iterator const_iterator
Definition: ConsensusFeature.h:76
OpenMS::ConsensusFeature::SizeLess::operator()
bool operator()(UInt64 const &left, ConsensusFeature const &right) const
Definition: ConsensusFeature.h:95
OpenMS::ConsensusFeature::MapsLess::operator()
bool operator()(ConsensusFeature const &left, ConsensusFeature const &right) const
Definition: ConsensusFeature.h:110
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS::ConsensusFeature::ratios_
std::vector< Ratio > ratios_
Definition: ConsensusFeature.h:346
OpenMS::ConsensusFeature::reverse_iterator
HandleSetType::reverse_iterator reverse_iterator
Definition: ConsensusFeature.h:79
OpenMS::Constants::h
const double h
Definition: Constants.h:162
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::ConsensusFeature::begin
const_iterator begin() const
OpenMS::FeatureHandle
Representation of a Peak2D, RichPeak2D or Feature .
Definition: FeatureHandle.h:57
OpenMS::ConsensusFeature::size
Size size() const
OpenMS::ConsensusFeature::SizeLess::operator()
bool operator()(const UInt64 &left, const UInt64 &right) const
Definition: ConsensusFeature.h:100
OpenMS::ConsensusFeature::Ratio::numerator_ref_
String numerator_ref_
Definition: ConsensusFeature.h:150
String.h
OpenMS::ConsensusFeature::Ratio::description_
std::vector< String > description_
Definition: ConsensusFeature.h:151
OpenMS::ConsensusFeature::Ratio
slim struct to feed the need for systematically storing of ratios (
Definition: ConsensusFeature.h:118
OpenMS::ConsensusFeature::Ratio::denominator_ref_
String denominator_ref_
Definition: ConsensusFeature.h:149
OpenMS::ConsensusFeature::SizeLess
Compare by size(), the number of consensus elements.
Definition: ConsensusFeature.h:83
OpenMS::ConsensusFeature::SizeLess::operator()
bool operator()(ConsensusFeature const &left, ConsensusFeature const &right) const
Definition: ConsensusFeature.h:85