OpenMS  2.5.0
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  std::binary_function<ConsensusFeature, ConsensusFeature, bool>
85  {
86  inline bool operator()(ConsensusFeature const& left, ConsensusFeature const& right) const
87  {
88  return left.size() < right.size();
89  }
90 
91  inline bool operator()(ConsensusFeature const& left, UInt64 const& right) const
92  {
93  return left.size() < right;
94  }
95 
96  inline bool operator()(UInt64 const& left, ConsensusFeature const& right) const
97  {
98  return left < right.size();
99  }
100 
101  inline bool operator()(const UInt64& left, const UInt64& right) const
102  {
103  return left < right;
104  }
105 
106  };
107 
109  struct MapsLess :
110  std::binary_function<ConsensusFeature, ConsensusFeature, bool>
111  {
112  inline bool operator()(ConsensusFeature const& left, ConsensusFeature const& right) const
113  {
114  return std::lexicographical_compare(left.begin(), left.end(), right.begin(), right.end(), FeatureHandle::IndexLess());
115  }
116 
117  };
118 
120  struct Ratio
121  {
123  {
124  }
125 
126  Ratio(const Ratio& rhs)
127  {
128  ratio_value_ = rhs.ratio_value_;
129  denominator_ref_ = rhs.denominator_ref_;
130  numerator_ref_ = rhs.numerator_ref_;
131  description_ = rhs.description_;
132  }
133 
134  virtual ~Ratio()
135  {
136  }
137 
138  Ratio& operator=(const Ratio& rhs)
139  {
140  if (&rhs != this)
141  {
142  ratio_value_ = rhs.ratio_value_;
143  denominator_ref_ = rhs.denominator_ref_;
144  numerator_ref_ = rhs.numerator_ref_;
145  description_ = rhs.description_;
146  }
147  return *this;
148  }
149 
150  double ratio_value_;
153  std::vector<String> description_;
154  //TODO ratio cv info
155  };
156 
158 
161 
163  ConsensusFeature(const ConsensusFeature& rhs) = default;
164 
166  ConsensusFeature(ConsensusFeature&& rhs) = default;
167 
169  explicit ConsensusFeature(const BaseFeature& feature);
170 
177  ConsensusFeature(UInt64 map_index, const Peak2D& element, UInt64 element_index);
178 
185  ConsensusFeature(UInt64 map_index, const BaseFeature& element);
186 
188  ConsensusFeature& operator=(const ConsensusFeature& rhs) = default;
189 
191  ConsensusFeature& operator=(ConsensusFeature&& rhs) = default;
192 
194  ~ConsensusFeature() override;
196 
197 
199 
200 
204  void insert(const ConsensusFeature& cf);
205 
212  void insert(const FeatureHandle& handle);
213 
215  void insert(const HandleSetType& handle_set);
216 
223  void insert(UInt64 map_index, const Peak2D& element, UInt64 element_index);
224 
231  void insert(UInt64 map_index, const BaseFeature& element);
232 
234  const HandleSetType& getFeatures() const;
235 
237  std::vector<FeatureHandle> getFeatureList() const;
238 
240  void setFeatures(HandleSetType h);
242 
244 
245  DRange<2> getPositionRange() const;
248  DRange<1> getIntensityRange() const;
249 
251 
261  void computeConsensus();
262 
272  void computeMonoisotopicConsensus();
273 
287  void computeDechargeConsensus(const FeatureMap& fm, bool intensity_weighted_averaging = false);
288 
296  void addRatio(const Ratio& r);
297 
305  void setRatios(std::vector<Ratio>& rs);
306 
310  std::vector<Ratio> getRatios() const;
311 
315  std::vector<Ratio>& getRatios();
316 
318 
319  Size size() const;
320 
321  const_iterator begin() const;
322 
323  iterator begin();
324 
325  const_iterator end() const;
326 
327  iterator end();
328 
329  const_reverse_iterator rbegin() const;
330 
331  reverse_iterator rbegin();
332 
333  const_reverse_iterator rend() const;
334 
335  reverse_iterator rend();
336 
337  void clear();
338 
339  bool empty() const;
341 
342 private:
343 
345  std::vector<Ratio> ratios_;
346 
347 
348  };
349 
351  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ConsensusFeature& cons);
352 
353 } // namespace OpenMS
354 
OpenMS::ConsensusFeature::Ratio::~Ratio
virtual ~Ratio()
Definition: ConsensusFeature.h:134
OpenMS::ConsensusFeature::MapsLess
Compare by the sets of consensus elements (lexicographically)
Definition: ConsensusFeature.h:109
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:150
OpenMS::Peak2D
A 2-dimensional raw data point or peak.
Definition: Peak2D.h:54
OpenMS::ConsensusFeature::handles_
HandleSetType handles_
Definition: ConsensusFeature.h:344
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::BaseFeature
A basic LC-MS feature.
Definition: BaseFeature.h:56
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:126
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:91
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:46
OpenMS::ConsensusFeature::Ratio::Ratio
Ratio()
Definition: ConsensusFeature.h:122
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:138
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:96
OpenMS::ConsensusFeature::MapsLess::operator()
bool operator()(ConsensusFeature const &left, ConsensusFeature const &right) const
Definition: ConsensusFeature.h:112
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS::ConsensusFeature::ratios_
std::vector< Ratio > ratios_
Definition: ConsensusFeature.h:345
OpenMS::ConsensusFeature::reverse_iterator
HandleSetType::reverse_iterator reverse_iterator
Definition: ConsensusFeature.h:79
OpenMS::Constants::h
const double h
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
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:101
OpenMS::ConsensusFeature::Ratio::numerator_ref_
String numerator_ref_
Definition: ConsensusFeature.h:152
String.h
OpenMS::ConsensusFeature::Ratio::description_
std::vector< String > description_
Definition: ConsensusFeature.h:153
OpenMS::ConsensusFeature::Ratio
slim struct to feed the need for systematically storing of ratios (
Definition: ConsensusFeature.h:120
OpenMS::ConsensusFeature::Ratio::denominator_ref_
String denominator_ref_
Definition: ConsensusFeature.h:151
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:86