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BaseFeature.h
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34 
35 #ifndef OPENMS_KERNEL_BASEFEATURE_H
36 #define OPENMS_KERNEL_BASEFEATURE_H
37 
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);
91 
93  explicit BaseFeature(const Peak2D& point);
94 
96  explicit BaseFeature(const RichPeak2D& point);
97 
99  ~BaseFeature();
101 
103 
104  QualityType getQuality() const;
107  void setQuality(QualityType q);
109  struct QualityLess :
110  std::binary_function<BaseFeature, BaseFeature, bool>
111  {
112  bool operator()(const BaseFeature& left, const BaseFeature& right) const
113  {
114  return left.getQuality() < right.getQuality();
115  }
116 
117  bool operator()(const BaseFeature& left, const QualityType& right) const
118  {
119  return left.getQuality() < right;
120  }
121 
122  bool operator()(const QualityType& left, const BaseFeature& right) const
123  {
124  return left < right.getQuality();
125  }
126 
127  bool operator()(const QualityType& left, const QualityType& right) const
128  {
129  return left < right;
130  }
131 
132  };
134 
136  WidthType getWidth() const;
138  void setWidth(WidthType fwhm);
139 
141  const ChargeType& getCharge() const;
142 
144  void setCharge(const ChargeType& ch);
145 
147  BaseFeature& operator=(const BaseFeature& rhs);
148 
150  bool operator==(const BaseFeature& rhs) const;
151 
153  bool operator!=(const BaseFeature& rhs) const;
154 
156  const std::vector<PeptideIdentification>& getPeptideIdentifications() const;
157 
159  std::vector<PeptideIdentification>& getPeptideIdentifications();
160 
162  void setPeptideIdentifications(const std::vector<PeptideIdentification>& peptides);
163 
165  AnnotationState getAnnotationState() const;
166 
167 protected:
168 
170  QualityType quality_;
171 
173  ChargeType charge_;
174 
176  WidthType width_;
177 
179  std::vector<PeptideIdentification> peptides_;
180  };
181 
182 } // namespace OpenMS
183 
184 #endif // OPENMS_KERNEL_BASEFEATURE_H
bool operator()(const BaseFeature &left, const QualityType &right) const
Definition: BaseFeature.h:117
Definition: BaseFeature.h:72
A 2-dimensional raw data point or peak.
Definition: Peak2D.h:55
Int ChargeType
Type of charge values.
Definition: BaseFeature.h:65
Compare by quality.
Definition: BaseFeature.h:109
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
QualityType getQuality() const
Non-mutable access to the overall quality.
A basic LC-MS feature.
Definition: BaseFeature.h:56
bool operator()(const QualityType &left, const BaseFeature &right) const
Definition: BaseFeature.h:122
QualityType quality_
Overall quality measure of the feature.
Definition: BaseFeature.h:170
bool operator()(const QualityType &left, const QualityType &right) const
Definition: BaseFeature.h:127
Definition: BaseFeature.h:73
WidthType width_
Width (FWHM) for the feature. The default value is 0.0, a feature finding algorithm can compute this ...
Definition: BaseFeature.h:176
bool operator()(const BaseFeature &left, const BaseFeature &right) const
Definition: BaseFeature.h:112
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
A 2-dimensional raw data point or peak with meta information.
Definition: RichPeak2D.h:53
float WidthType
Type of feature width/FWHM (RT)
Definition: BaseFeature.h:67
AnnotationState
state of identification, use getIDState() to query it
Definition: BaseFeature.h:70
std::vector< PeptideIdentification > peptides_
Peptide PeptideIdentifications belonging to the feature.
Definition: BaseFeature.h:179
int Int
Signed integer type.
Definition: Types.h:103
ChargeType charge_
Charge of the peptide represented by this feature. The default value is 0, which represents an unknow...
Definition: BaseFeature.h:173

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:21:59 using doxygen 1.8.13