OpenMS  2.6.0
BaseFeature.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser, Chris Bielow $
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34 
35 #pragma once
36 
39 
40 namespace OpenMS
41 {
42  class FeatureHandle;
43  class PeptideIdentification;
44 
56  class OPENMS_DLLAPI BaseFeature :
57  public RichPeak2D
58  {
59 public:
61 
62  typedef float QualityType;
65  typedef Int ChargeType;
67  typedef float WidthType;
68 
71  {
76  SIZE_OF_ANNOTATIONSTATE
77  };
78 
79  static const std::string NamesOfAnnotationState[SIZE_OF_ANNOTATIONSTATE];
80 
82 
86  BaseFeature();
88 
90  BaseFeature(const BaseFeature& feature) = default;
91 
93  BaseFeature(BaseFeature&& feature) = default;
94 
96  BaseFeature(const BaseFeature& rhs, UInt64 map_index);
97 
99  explicit BaseFeature(const Peak2D& point);
100 
102  explicit BaseFeature(const RichPeak2D& point);
103 
105  explicit BaseFeature(const FeatureHandle& fh);
106 
108  ~BaseFeature() override;
110 
112 
113  QualityType getQuality() const;
116  void setQuality(QualityType q);
118  struct QualityLess :
119  std::binary_function<BaseFeature, BaseFeature, bool>
120  {
121  bool operator()(const BaseFeature& left, const BaseFeature& right) const
122  {
123  return left.getQuality() < right.getQuality();
124  }
125 
126  bool operator()(const BaseFeature& left, const QualityType& right) const
127  {
128  return left.getQuality() < right;
129  }
130 
131  bool operator()(const QualityType& left, const BaseFeature& right) const
132  {
133  return left < right.getQuality();
134  }
135 
136  bool operator()(const QualityType& left, const QualityType& right) const
137  {
138  return left < right;
139  }
140 
141  };
143 
145  WidthType getWidth() const;
147  void setWidth(WidthType fwhm);
148 
150  const ChargeType& getCharge() const;
151 
153  void setCharge(const ChargeType& ch);
154 
156  BaseFeature& operator=(const BaseFeature& rhs) = default;
157 
159  BaseFeature& operator=(BaseFeature&& rhs) & = default;
160 
162  bool operator==(const BaseFeature& rhs) const;
163 
165  bool operator!=(const BaseFeature& rhs) const;
166 
168  const std::vector<PeptideIdentification>& getPeptideIdentifications() const;
169 
171  std::vector<PeptideIdentification>& getPeptideIdentifications();
172 
174  void setPeptideIdentifications(const std::vector<PeptideIdentification>& peptides);
175 
177  AnnotationState getAnnotationState() const;
178 
179 protected:
180 
183 
186 
189 
191  std::vector<PeptideIdentification> peptides_;
192  };
193 
194 } // namespace OpenMS
195 
OpenMS::BaseFeature::width_
WidthType width_
Width (FWHM) for the feature. The default value is 0.0, a feature finding algorithm can compute this ...
Definition: BaseFeature.h:188
OpenMS::UInt64
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
OpenMS::BaseFeature::ChargeType
Int ChargeType
Type of charge values.
Definition: BaseFeature.h:65
OpenMS::BaseFeature::FEATURE_ID_MULTIPLE_DIVERGENT
Definition: BaseFeature.h:75
OpenMS::BaseFeature::FEATURE_ID_NONE
Definition: BaseFeature.h:72
OpenMS::BaseFeature::AnnotationState
AnnotationState
state of identification, use getIDState() to query it
Definition: BaseFeature.h:70
OpenMS::Peak2D
A 2-dimensional raw data point or peak.
Definition: Peak2D.h:54
OpenMS::BaseFeature::FEATURE_ID_SINGLE
Definition: BaseFeature.h:73
OpenMS::BaseFeature
A basic LC-MS feature.
Definition: BaseFeature.h:56
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::RichPeak2D
A 2-dimensional raw data point or peak with meta information.
Definition: RichPeak2D.h:52
OpenMS::BaseFeature::WidthType
float WidthType
Type of feature width/FWHM (RT)
Definition: BaseFeature.h:67
OpenMS::BaseFeature::FEATURE_ID_MULTIPLE_SAME
Definition: BaseFeature.h:74
OpenMS::BaseFeature::quality_
QualityType quality_
Overall quality measure of the feature.
Definition: BaseFeature.h:182
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::BaseFeature::QualityLess::operator()
bool operator()(const QualityType &left, const QualityType &right) const
Definition: BaseFeature.h:136
OpenMS::BaseFeature::QualityLess::operator()
bool operator()(const QualityType &left, const BaseFeature &right) const
Definition: BaseFeature.h:131
int
RichPeak2D.h
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::FeatureHandle
Representation of a Peak2D, RichPeak2D or Feature .
Definition: FeatureHandle.h:57
OpenMS::BaseFeature::peptides_
std::vector< PeptideIdentification > peptides_
PeptideIdentifications belonging to the feature.
Definition: BaseFeature.h:191
float
OpenMS::BaseFeature::QualityLess::operator()
bool operator()(const BaseFeature &left, const BaseFeature &right) const
Definition: BaseFeature.h:121
OpenMS::BaseFeature::charge_
ChargeType charge_
Charge of the peptide represented by this feature. The default value is 0, which represents an unknow...
Definition: BaseFeature.h:185
OpenMS::BaseFeature::QualityLess
Compare by quality.
Definition: BaseFeature.h:118
PeptideIdentification.h
OpenMS::BaseFeature::QualityLess::operator()
bool operator()(const BaseFeature &left, const QualityType &right) const
Definition: BaseFeature.h:126
OpenMS::BaseFeature::getQuality
QualityType getQuality() const
Non-mutable access to the overall quality.