OpenMS  2.4.0
MetaboliteSpectralMatching.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Erhan Kenar $
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34 
35 #pragma once
36 
38 #include <OpenMS/KERNEL/Feature.h>
40 #include <OpenMS/FORMAT/MzTab.h>
46 
47 
48 #include <vector>
49 #include <algorithm>
50 
51 namespace OpenMS
52 {
53 
54  struct OPENMS_DLLAPI PrecursorMassComparator
55  {
56  bool operator() (const MSSpectrum& a, const MSSpectrum& b)
57  {
58  return a.getPrecursors()[0].getMZ() < b.getPrecursors()[0].getMZ();
59  }
60 
62 
63  class OPENMS_DLLAPI SpectralMatch
64  {
65  public:
67  SpectralMatch();
68 
70  ~SpectralMatch();
71 
74 
76  SpectralMatch& operator=(const SpectralMatch&);
77 
78  double getObservedPrecursorMass() const;
79  void setObservedPrecursorMass(const double&);
80 
81  double getObservedPrecursorRT() const;
82  void setObservedPrecursorRT(const double&);
83 
84  double getFoundPrecursorMass() const;
85  void setFoundPrecursorMass(const double&);
86 
87  Int getFoundPrecursorCharge() const;
88  void setFoundPrecursorCharge(const Int&);
89 
90  double getMatchingScore() const;
91  void setMatchingScore(const double&);
92 
93  Size getObservedSpectrumIndex() const;
94  void setObservedSpectrumIndex(const Size&);
95 
96  Size getMatchingSpectrumIndex() const;
97  void setMatchingSpectrumIndex(const Size&);
98 
99  String getPrimaryIdentifier() const;
100  void setPrimaryIdentifier(const String&);
101 
102  String getSecondaryIdentifier() const;
103  void setSecondaryIdentifier(const String&);
104 
105  String getCommonName() const;
106  void setCommonName(const String&);
107 
108  String getSumFormula() const;
109  void setSumFormula(const String&);
110 
111  String getInchiString() const;
112  void setInchiString(const String&);
113 
114  String getSMILESString() const;
115  void setSMILESString(const String&);
116 
117  String getPrecursorAdduct() const;
118  void setPrecursorAdduct(const String&);
119 
120 
121  private:
129 
130  // further meta information
138 
139  };
140 
141  struct OPENMS_DLLAPI SpectralMatchScoreComparator
142  {
143  bool operator() (const SpectralMatch& a, const SpectralMatch& b)
144  {
145  return a.getMatchingScore() > b.getMatchingScore();
146  }
147 
149 
150  class OPENMS_DLLAPI MetaboliteSpectralMatching :
151  public DefaultParamHandler,
152  public ProgressLogger
153  {
154  public:
157 
159  ~MetaboliteSpectralMatching() override;
160 
162  double computeHyperScore(MSSpectrum, MSSpectrum, const double&, const double&);
163 
165  void run(PeakMap &, PeakMap &, MzTab &);
166 
167  protected:
168  void updateMembers_() override;
169 
170  private:
172  void exportMzTab_(const std::vector<SpectralMatch>&, MzTab&);
173 
178 
180  };
181 
182 }
183 
A more convenient string class.
Definition: String.h:57
Definition: MetaboliteSpectralMatching.h:141
Int found_precursor_charge_
Definition: MetaboliteSpectralMatching.h:125
Definition: MetaboliteSpectralMatching.h:150
double found_precursor_mass_
Definition: MetaboliteSpectralMatching.h:124
Definition: MetaboliteSpectralMatching.h:63
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
String primary_id_
Definition: MetaboliteSpectralMatching.h:131
struct OpenMS::SpectralMatchScoreComparator SpectralMatchScoreGreater
double observed_precursor_mass_
Definition: MetaboliteSpectralMatching.h:122
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
String ion_mode_
Definition: MetaboliteSpectralMatching.h:177
String secondary_id_
Definition: MetaboliteSpectralMatching.h:132
Definition: MetaboliteSpectralMatching.h:54
double getMatchingScore() const
Size observed_spectrum_idx_
Definition: MetaboliteSpectralMatching.h:127
struct OpenMS::PrecursorMassComparator PrecursorMZLess
String inchi_string_
Definition: MetaboliteSpectralMatching.h:135
String precursor_adduct_
Definition: MetaboliteSpectralMatching.h:137
double precursor_mz_error_
Definition: MetaboliteSpectralMatching.h:174
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
Size matching_spectrum_idx_
Definition: MetaboliteSpectralMatching.h:128
String common_name_
Definition: MetaboliteSpectralMatching.h:133
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
double matching_score_
Definition: MetaboliteSpectralMatching.h:126
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
double observed_precursor_rt_
Definition: MetaboliteSpectralMatching.h:123
int Int
Signed integer type.
Definition: Types.h:102
String report_mode_
Definition: MetaboliteSpectralMatching.h:179
String smiles_string_
Definition: MetaboliteSpectralMatching.h:136
double fragment_mz_error_
Definition: MetaboliteSpectralMatching.h:175
String sum_formula_
Definition: MetaboliteSpectralMatching.h:134
Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/.
Definition: MzTab.h:699
String mz_error_unit_
Definition: MetaboliteSpectralMatching.h:176