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CompNovoIonScoringBase.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
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10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
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15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
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20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35
36 #pragma once
37
38 // OpenMS includes
39 #include <OpenMS/KERNEL/StandardTypes.h>
40 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
41 #include <OpenMS/KERNEL/MSExperiment.h>
42
43 // stl includes
44 #include <vector>
45
46 namespace OpenMS
47 {
53 class OPENMS_DLLAPI CompNovoIonScoringBase :
54 public DefaultParamHandler
55 {
56
57 public:
58
59 enum IsotopeType
60 {
61 PARENT = 0,
62 CHILD = 1,
63 LONE = 2
64 };
65
66 struct OPENMS_DLLAPI IonScore
67 {
68 IonScore();
69
70 IonScore(const IonScore & rhs);
71
72 virtual ~IonScore();
73
74 IonScore & operator=(const IonScore & rhs);
75
76
77 double score;
78 double s_bion;
79 double s_yion;
80 double s_witness;
81 double position;
82 double s_isotope_pattern_1;
83 Int is_isotope_1_mono;
84 double s_isotope_pattern_2;
85 };
86
87
91 CompNovoIonScoringBase();
93
95 CompNovoIonScoringBase(const CompNovoIonScoringBase & source);
96
98 ~CompNovoIonScoringBase() override;
100
102 CompNovoIonScoringBase & operator=(const CompNovoIonScoringBase & source);
103
107 double scoreIsotopes(const PeakSpectrum & CID_spec, PeakSpectrum::ConstIterator it, Size charge);
109
110 protected:
111
113 void updateMembers_() override;
114
115
116 IsotopeType classifyIsotopes_(const PeakSpectrum & spec, PeakSpectrum::ConstIterator it);
117
118 double scoreIsotopes_(const PeakSpectrum & spec, PeakSpectrum::ConstIterator it, Map<double, IonScore> & CID_nodes, Size charge = 1);
119
120 virtual void scoreWitnessSet_(Size charge, double precursor_weight, Map<double, IonScore> & CID_nodes, const PeakSpectrum & CID_orig_spec) = 0;
121
122 void addSingleChargedIons_(Map<double, IonScore> & ion_scores, PeakSpectrum & CID_spec);
123
124 void initIsotopeDistributions_();
125
127 Map<Size, std::vector<double> > isotope_distributions_;
128
129 double fragment_mass_tolerance_;
130
131 public:
132
133 };
134
135 }
136
OpenMS::CompNovoIonScoringBase::IonScore::s_isotope_pattern_1
double s_isotope_pattern_1
isotope pattern score charge 1
Definition: CompNovoIonScoringBase.h:82
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::CompNovoIonScoringBase::IsotopeType
IsotopeType
Definition: CompNovoIonScoringBase.h:59
OpenMS::CompNovoIonScoringBase
run with CompNovoIonScoringBase
Definition: CompNovoIonScoringBase.h:53
StandardTypes.h
OpenMS::CompNovoIonScoringBase::isotope_distributions_
Map< Size, std::vector< double > > isotope_distributions_
Definition: CompNovoIonScoringBase.h:127
OpenMS::CompNovoIonScoringBase::IonScore::score
double score
Definition: CompNovoIonScoringBase.h:77
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS::CompNovoIonScoringBase::IonScore::s_isotope_pattern_2
double s_isotope_pattern_2
"" charge 2
Definition: CompNovoIonScoringBase.h:84
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::CompNovoIonScoringBase::IonScore
Definition: CompNovoIonScoringBase.h:66
DefaultParamHandler.h
OpenMS::MSSpectrum::ConstIterator
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:104
OpenMS::CompNovoIonScoringBase::fragment_mass_tolerance_
double fragment_mass_tolerance_
Definition: CompNovoIonScoringBase.h:129
OpenMS::CompNovoIonScoringBase::IonScore::is_isotope_1_mono
Int is_isotope_1_mono
0 means not tested, 1 mean is, -1 is tail of isotopes
Definition: CompNovoIonScoringBase.h:83
OpenMS::CompNovoIonScoringBase::IonScore::s_witness
double s_witness
Definition: CompNovoIonScoringBase.h:80
OpenMS::CompNovoIonScoringBase::IonScore::s_yion
double s_yion
Definition: CompNovoIonScoringBase.h:79
OpenMS::CompNovoIonScoringBase::IonScore::position
double position
Definition: CompNovoIonScoringBase.h:81
int
OpenMS::CompNovoIonScoringBase::IonScore::s_bion
double s_bion
Definition: CompNovoIonScoringBase.h:78
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127