OpenMS  2.8.0
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 
40 
41 #include <optional>
42 
43 namespace OpenMS
44 {
45  class FeatureHandle;
46 
58  class OPENMS_DLLAPI BaseFeature : public RichPeak2D
59  {
60 public:
64  typedef float QualityType;
66  typedef Int ChargeType;
68  typedef float WidthType;
69 
72  {
77  SIZE_OF_ANNOTATIONSTATE
78  };
79 
80  static const std::string NamesOfAnnotationState[SIZE_OF_ANNOTATIONSTATE];
82 
87 
89  BaseFeature(const BaseFeature& feature) = default;
90 
94  BaseFeature(BaseFeature&& feature) noexcept
95  : RichPeak2D(std::move(feature))
96  {
97  quality_ = feature.quality_;
98  charge_ = feature.charge_;
99  width_ = feature.width_;
100  // Note: will terminate program if move assignment throws because of noexcept
101  // but we can't recover in that case anyways and we need to mark it noexcept for the move.
102  peptides_ = std::move(feature.peptides_);
103  primary_id_ = std::move(feature.primary_id_);
104  id_matches_ = std::move(feature.id_matches_);
105  }
106 
108  BaseFeature(const BaseFeature& rhs, UInt64 map_index);
109 
111  explicit BaseFeature(const Peak2D& point);
112 
114  explicit BaseFeature(const RichPeak2D& point);
115 
117  explicit BaseFeature(const FeatureHandle& fh);
118 
120  ~BaseFeature() override;
122 
130  struct QualityLess
131  {
132  bool operator()(const BaseFeature& left, const BaseFeature& right) const
133  {
134  return left.getQuality() < right.getQuality();
135  }
136 
137  bool operator()(const BaseFeature& left, const QualityType& right) const
138  {
139  return left.getQuality() < right;
140  }
141 
142  bool operator()(const QualityType& left, const BaseFeature& right) const
143  {
144  return left < right.getQuality();
145  }
146 
147  bool operator()(const QualityType& left, const QualityType& right) const
148  {
149  return left < right;
150  }
151 
152  };
154 
158  void setWidth(WidthType fwhm);
159 
161  const ChargeType& getCharge() const;
162 
164  void setCharge(const ChargeType& ch);
165 
167  BaseFeature& operator=(const BaseFeature& rhs) = default;
168 
170  BaseFeature& operator=(BaseFeature&& rhs) & = default;
171 
173  bool operator==(const BaseFeature& rhs) const;
174 
176  bool operator!=(const BaseFeature& rhs) const;
177 
181  const std::vector<PeptideIdentification>& getPeptideIdentifications() const;
182 
184  std::vector<PeptideIdentification>& getPeptideIdentifications();
185 
187  void setPeptideIdentifications(const std::vector<PeptideIdentification>& peptides);
188 
192 
195 
199  bool hasPrimaryID() const;
200 
207 
210 
213 
215  const std::set<IdentificationData::ObservationMatchRef>& getIDMatches() const;
216 
218  std::set<IdentificationData::ObservationMatchRef>& getIDMatches();
219 
222 
230 
231 protected:
232 
235 
238 
241 
243  std::vector<PeptideIdentification> peptides_;
244 
246  std::optional<IdentificationData::IdentifiedMolecule> primary_id_;
247 
249  std::set<IdentificationData::ObservationMatchRef> id_matches_;
250  };
251 
252 } // namespace OpenMS
A basic LC-MS feature.
Definition: BaseFeature.h:59
void setPeptideIdentifications(const std::vector< PeptideIdentification > &peptides)
sets the PeptideIdentification vector
std::optional< IdentificationData::IdentifiedMolecule > primary_id_
primary ID (peptide, RNA, compound) assigned to this feature
Definition: BaseFeature.h:246
void setQuality(QualityType q)
Set the overall quality.
BaseFeature & operator=(BaseFeature &&rhs) &=default
Move Assignment operator.
void sortPeptideIdentifications()
sorts PeptideIdentifications, assuming they have the same scoreType.
void clearPrimaryID()
clear any primary ID that was assigned
WidthType width_
Width (FWHM) for the feature. The default value is 0.0, a feature finding algorithm can compute this ...
Definition: BaseFeature.h:240
bool operator==(const BaseFeature &rhs) const
Equality operator.
QualityType getQuality() const
const ChargeType & getCharge() const
Non-mutable access to charge state.
AnnotationState getAnnotationState() const
state of peptide identifications attached to this feature. If one ID has multiple hits,...
BaseFeature(const BaseFeature &rhs, UInt64 map_index)
Copy constructor with a new map_index.
ChargeType charge_
Charge of the peptide represented by this feature. The default value is 0, which represents an unknow...
Definition: BaseFeature.h:237
bool hasPrimaryID() const
float QualityType
Definition: BaseFeature.h:64
float WidthType
Type of feature width/FWHM (RT)
Definition: BaseFeature.h:68
std::set< IdentificationData::ObservationMatchRef > & getIDMatches()
mutable access to the set of matches (e.g. PSMs) with IDs for this feature
BaseFeature(const BaseFeature &feature)=default
Copy constructor.
std::vector< PeptideIdentification > & getPeptideIdentifications()
returns a mutable reference to the PeptideIdentification vector
const std::set< IdentificationData::ObservationMatchRef > & getIDMatches() const
immutable access to the set of matches (e.g. PSMs) with IDs for this feature
WidthType getWidth() const
Non-mutable access to the features width (full width at half max, FWHM)
Int ChargeType
Type of charge values.
Definition: BaseFeature.h:66
void setWidth(WidthType fwhm)
Set the width of the feature (FWHM)
const IdentificationData::IdentifiedMolecule & getPrimaryID() const
Return the primary ID (peptide, RNA, compound) assigned to this feature.
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
void addIDMatch(IdentificationData::ObservationMatchRef ref)
add an ID match (e.g. PSM) for this feature
bool operator!=(const BaseFeature &rhs) const
Inequality operator.
QualityType quality_
Overall quality measure of the feature.
Definition: BaseFeature.h:234
BaseFeature(const RichPeak2D &point)
Constructor from raw data point with meta information.
void setCharge(const ChargeType &ch)
Set charge state.
std::set< IdentificationData::ObservationMatchRef > id_matches_
set of observation matches (e.g. PSMs) with IDs for this feature
Definition: BaseFeature.h:249
BaseFeature(BaseFeature &&feature) noexcept
Definition: BaseFeature.h:94
~BaseFeature() override
Destructor.
AnnotationState
state of identification, use getAnnotationState() to query it
Definition: BaseFeature.h:72
@ FEATURE_ID_MULTIPLE_SAME
Definition: BaseFeature.h:75
@ FEATURE_ID_SINGLE
Definition: BaseFeature.h:74
@ FEATURE_ID_NONE
Definition: BaseFeature.h:73
@ FEATURE_ID_MULTIPLE_DIVERGENT
Definition: BaseFeature.h:76
std::vector< PeptideIdentification > peptides_
PeptideIdentifications belonging to the feature.
Definition: BaseFeature.h:243
BaseFeature & operator=(const BaseFeature &rhs)=default
Assignment operator.
void updateIDReferences(const IdentificationData::RefTranslator &trans)
Update ID references (primary ID, matches) for this feature.
BaseFeature(const Peak2D &point)
Constructor from raw data point.
BaseFeature(const FeatureHandle &fh)
Constructor from a featurehandle.
void setPrimaryID(const IdentificationData::IdentifiedMolecule &id)
set the primary ID (peptide, RNA, compound) for this feature
Representation of a Peak2D, RichPeak2D or Feature .
Definition: FeatureHandle.h:60
A 2-dimensional raw data point or peak.
Definition: Peak2D.h:55
A 2-dimensional raw data point or peak with meta information.
Definition: RichPeak2D.h:56
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
int Int
Signed integer type.
Definition: Types.h:102
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Compare by quality.
Definition: BaseFeature.h:131
bool operator()(const BaseFeature &left, const BaseFeature &right) const
Definition: BaseFeature.h:132
bool operator()(const QualityType &left, const QualityType &right) const
Definition: BaseFeature.h:147
bool operator()(const BaseFeature &left, const QualityType &right) const
Definition: BaseFeature.h:137
bool operator()(const QualityType &left, const BaseFeature &right) const
Definition: BaseFeature.h:142
Variant type holding Peptide/Compound/Oligo references and convenience functions.
Definition: IdentifiedMolecule.h:55
Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi...
Definition: MetaData.h:46
structure that maps references of corresponding objects after copying
Definition: IdentificationData.h:192