| OpenMS 2.5.0

DeNovoIonScoring.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Sandro Andreotti, Andreas Bertsch$
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
38 #include <OpenMS/KERNEL/StandardTypes.h>
39 #include <vector>
40
41 namespace OpenMS
42 {
50 class OPENMS_DLLAPI DeNovoIonScoring :
51 public DefaultParamHandler
52 {
53 public:
59 class IonScore
60 {
61 public:
63 double score;
64
66 double position;
67
69 SignedSize index;
70
71
72 IonScore() :
73 score(0),
74 position(0.0),
75 index(-1)
76 {
77 }
78
79 IonScore(const IonScore & rhs) :
80 score(rhs.score),
81 position(rhs.score),
82 index(rhs.index)
83 {
84 }
85
86 virtual ~IonScore()
87 {
88 }
89
90 IonScore & operator=(const IonScore & rhs)
91 {
92 if (this != &rhs)
93 {
94 score = rhs.score;
95 position = rhs.position;
96 index = rhs.index;
97 }
98 return *this;
99 }
100
101 };
102
103
107 DeNovoIonScoring();
109
111 ~DeNovoIonScoring() override;
112
114 DeNovoIonScoring(const DeNovoIonScoring & rhs);
116
118 DeNovoIonScoring & operator=(const DeNovoIonScoring & rhs);
119
120 virtual void getIonScores(std::vector<IonScore> & ion_scores, const PeakSpectrum & spec) = 0;
121
122 virtual void getIonScores(std::vector<std::vector<IonScore> > & ion_scores, const PeakMap & exp) = 0;
123 };
124
125 } // namespace OpenMS
126
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::DeNovoIonScoring::IonScore::score
double score
score
Definition: DeNovoIonScoring.h:63
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
seqan::position
Size< TNeedle >::Type position(const PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:561
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::DeNovoIonScoring::IonScore::index
SignedSize index
index of peak in the spectrum, -1 if not in spectrum
Definition: DeNovoIonScoring.h:69
StandardTypes.h
OpenMS::DeNovoIonScoring
Base class for ion scoring implementation for de novo algorithms.
Definition: DeNovoIonScoring.h:50
OpenMS::DeNovoIonScoring::IonScore::IonScore
IonScore(const IonScore &rhs)
Definition: DeNovoIonScoring.h:79
OpenMS::DeNovoIonScoring::IonScore::operator=
IonScore & operator=(const IonScore &rhs)
Definition: DeNovoIonScoring.h:90
OpenMS::DeNovoIonScoring::IonScore::IonScore
IonScore()
Definition: DeNovoIonScoring.h:72
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::DeNovoIonScoring::IonScore::~IonScore
virtual ~IonScore()
Definition: DeNovoIonScoring.h:86
DefaultParamHandler.h
OpenMS::DeNovoIonScoring::IonScore
IonScore.
Definition: DeNovoIonScoring.h:59
OpenMS::DeNovoIonScoring::IonScore::position
double position
position of the ion
Definition: DeNovoIonScoring.h:66