OpenMS  2.5.0
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 
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  ~BaseFeature() override;
107 
109 
110  QualityType getQuality() const;
113  void setQuality(QualityType q);
115  struct QualityLess :
116  std::binary_function<BaseFeature, BaseFeature, bool>
117  {
118  bool operator()(const BaseFeature& left, const BaseFeature& right) const
119  {
120  return left.getQuality() < right.getQuality();
121  }
122 
123  bool operator()(const BaseFeature& left, const QualityType& right) const
124  {
125  return left.getQuality() < right;
126  }
127 
128  bool operator()(const QualityType& left, const BaseFeature& right) const
129  {
130  return left < right.getQuality();
131  }
132 
133  bool operator()(const QualityType& left, const QualityType& right) const
134  {
135  return left < right;
136  }
137 
138  };
140 
142  WidthType getWidth() const;
144  void setWidth(WidthType fwhm);
145 
147  const ChargeType& getCharge() const;
148 
150  void setCharge(const ChargeType& ch);
151 
153  BaseFeature& operator=(const BaseFeature& rhs) = default;
154 
156  BaseFeature& operator=(BaseFeature&& rhs) & = default;
157 
159  bool operator==(const BaseFeature& rhs) const;
160 
162  bool operator!=(const BaseFeature& rhs) const;
163 
165  const std::vector<PeptideIdentification>& getPeptideIdentifications() const;
166 
168  std::vector<PeptideIdentification>& getPeptideIdentifications();
169 
171  void setPeptideIdentifications(const std::vector<PeptideIdentification>& peptides);
172 
174  AnnotationState getAnnotationState() const;
175 
176 protected:
177 
180 
183 
186 
188  std::vector<PeptideIdentification> peptides_;
189  };
190 
191 } // namespace OpenMS
192 
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:185
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:179
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::BaseFeature::QualityLess::operator()
bool operator()(const QualityType &left, const QualityType &right) const
Definition: BaseFeature.h:133
OpenMS::BaseFeature::QualityLess::operator()
bool operator()(const QualityType &left, const BaseFeature &right) const
Definition: BaseFeature.h:128
int
RichPeak2D.h
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
OpenMS::BaseFeature::peptides_
std::vector< PeptideIdentification > peptides_
Peptide PeptideIdentifications belonging to the feature.
Definition: BaseFeature.h:188
float
OpenMS::BaseFeature::QualityLess::operator()
bool operator()(const BaseFeature &left, const BaseFeature &right) const
Definition: BaseFeature.h:118
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:182
OpenMS::BaseFeature::QualityLess
Compare by quality.
Definition: BaseFeature.h:115
PeptideIdentification.h
OpenMS::BaseFeature::QualityLess::operator()
bool operator()(const BaseFeature &left, const QualityType &right) const
Definition: BaseFeature.h:123
OpenMS::BaseFeature::getQuality
QualityType getQuality() const
Non-mutable access to the overall quality.