OpenMS
BaseFeature.h
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1 // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Hendrik Weisser $
6 // $Authors: Hendrik Weisser, Chris Bielow $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
15 
16 #include <optional>
17 
18 namespace OpenMS
19 {
20  class FeatureHandle;
21 
33  class OPENMS_DLLAPI BaseFeature : public RichPeak2D
34  {
35 public:
39  typedef float QualityType;
41  typedef Int ChargeType;
43  typedef float WidthType;
44 
47  {
52  SIZE_OF_ANNOTATIONSTATE
53  };
54 
55  static const std::string NamesOfAnnotationState[SIZE_OF_ANNOTATIONSTATE];
57 
62 
64  BaseFeature(const BaseFeature& feature) = default;
65 
69  BaseFeature(BaseFeature&& feature) noexcept
70  : RichPeak2D(std::move(feature))
71  {
72  quality_ = feature.quality_;
73  charge_ = feature.charge_;
74  width_ = feature.width_;
75  // Note: will terminate program if move assignment throws because of noexcept
76  // but we can't recover in that case anyways and we need to mark it noexcept for the move.
77  peptides_ = std::move(feature.peptides_);
78  primary_id_ = std::move(feature.primary_id_);
79  id_matches_ = std::move(feature.id_matches_);
80  }
81 
83  BaseFeature(const BaseFeature& rhs, UInt64 map_index);
84 
86  explicit BaseFeature(const Peak2D& point);
87 
89  explicit BaseFeature(const RichPeak2D& point);
90 
92  explicit BaseFeature(const FeatureHandle& fh);
93 
95  ~BaseFeature() override;
97 
105  struct QualityLess
106  {
107  bool operator()(const BaseFeature& left, const BaseFeature& right) const
108  {
109  return left.getQuality() < right.getQuality();
110  }
111 
112  bool operator()(const BaseFeature& left, const QualityType& right) const
113  {
114  return left.getQuality() < right;
115  }
116 
117  bool operator()(const QualityType& left, const BaseFeature& right) const
118  {
119  return left < right.getQuality();
120  }
121 
122  bool operator()(const QualityType& left, const QualityType& right) const
123  {
124  return left < right;
125  }
126 
127  };
129 
133  void setWidth(WidthType fwhm);
134 
136  const ChargeType& getCharge() const;
137 
139  void setCharge(const ChargeType& ch);
140 
142  BaseFeature& operator=(const BaseFeature& rhs) = default;
143 
145  BaseFeature& operator=(BaseFeature&& rhs) & = default;
146 
148  bool operator==(const BaseFeature& rhs) const;
149 
151  bool operator!=(const BaseFeature& rhs) const;
152 
157 
160 
163 
167 
170 
174  bool hasPrimaryID() const;
175 
182 
185 
188 
190  const std::set<IdentificationData::ObservationMatchRef>& getIDMatches() const;
191 
193  std::set<IdentificationData::ObservationMatchRef>& getIDMatches();
194 
197 
205 
206 protected:
207 
210 
213 
216 
219 
221  std::optional<IdentificationData::IdentifiedMolecule> primary_id_;
222 
224  std::set<IdentificationData::ObservationMatchRef> id_matches_;
225  };
226 
227 } // namespace OpenMS
A basic LC-MS feature.
Definition: BaseFeature.h:34
std::optional< IdentificationData::IdentifiedMolecule > primary_id_
primary ID (peptide, RNA, compound) assigned to this feature
Definition: BaseFeature.h:221
void setQuality(QualityType q)
Set the overall quality.
BaseFeature & operator=(BaseFeature &&rhs) &=default
Move Assignment operator.
void setPeptideIdentifications(const PeptideIdentificationList &peptides)
sets the PeptideIdentification vector
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:215
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,...
PeptideIdentificationList & getPeptideIdentifications()
returns a mutable reference to the PeptideIdentification vector
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:212
bool hasPrimaryID() const
float QualityType
Definition: BaseFeature.h:39
float WidthType
Type of feature width/FWHM (RT)
Definition: BaseFeature.h:43
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.
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:41
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.
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:209
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:224
BaseFeature(BaseFeature &&feature) noexcept
Definition: BaseFeature.h:69
~BaseFeature() override
Destructor.
PeptideIdentificationList peptides_
PeptideIdentifications belonging to the feature.
Definition: BaseFeature.h:218
AnnotationState
state of identification, use getAnnotationState() to query it
Definition: BaseFeature.h:47
@ FEATURE_ID_MULTIPLE_SAME
Definition: BaseFeature.h:50
@ FEATURE_ID_SINGLE
Definition: BaseFeature.h:49
@ FEATURE_ID_NONE
Definition: BaseFeature.h:48
@ FEATURE_ID_MULTIPLE_DIVERGENT
Definition: BaseFeature.h:51
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
const PeptideIdentificationList & getPeptideIdentifications() const
Representation of a Peak2D, RichPeak2D or Feature .
Definition: FeatureHandle.h:34
A 2-dimensional raw data point or peak.
Definition: Peak2D.h:29
Container for peptide identifications from multiple spectra.
Definition: PeptideIdentificationList.h:66
A 2-dimensional raw data point or peak with meta information.
Definition: RichPeak2D.h:30
int Int
Signed integer type.
Definition: Types.h:72
uint64_t UInt64
Unsigned integer type (64bit)
Definition: Types.h:47
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
Compare by quality.
Definition: BaseFeature.h:106
bool operator()(const BaseFeature &left, const BaseFeature &right) const
Definition: BaseFeature.h:107
bool operator()(const QualityType &left, const QualityType &right) const
Definition: BaseFeature.h:122
bool operator()(const BaseFeature &left, const QualityType &right) const
Definition: BaseFeature.h:112
bool operator()(const QualityType &left, const BaseFeature &right) const
Definition: BaseFeature.h:117
Variant type holding Peptide/Compound/Oligo references and convenience functions.
Definition: IdentifiedMolecule.h:29
Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi...
Definition: MetaData.h:20
structure that maps references of corresponding objects after copying
Definition: IdentificationData.h:184