| OpenMS 2.5.0

ILPDCWrapper.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37
38 #include <OpenMS/DATASTRUCTURES/Map.h>
39 #include <OpenMS/DATASTRUCTURES/String.h>
40
41 #include <vector>
42 #include <set>
43
44 namespace OpenMS
45 {
46
47 class MassExplainer;
48 class FeatureMap;
49 class ChargePair;
50
51 class OPENMS_DLLAPI ILPDCWrapper
52 {
53
54 public:
55 typedef std::vector<ChargePair> PairsType;
56 typedef PairsType::size_type PairsIndex;
57
59 ILPDCWrapper();
60
62 virtual ~ILPDCWrapper();
63
68 double compute(const FeatureMap fm, PairsType& pairs, Size verbose_level) const;
69
70 private:
71
73 double computeSlice_(const FeatureMap fm,
74 PairsType& pairs,
75 const PairsIndex margin_left,
76 const PairsIndex margin_right,
77 const Size verbose_level) const;
78
80 double computeSliceOld_(const FeatureMap fm,
81 PairsType& pairs,
82 const PairsIndex margin_left,
83 const PairsIndex margin_right,
84 const Size verbose_level) const;
85
87 double getLogScore_(const PairsType::value_type& pair, const FeatureMap& fm) const;
88
89 typedef Map<String, std::set<Size> > FeatureType_;
90
91 // add another charge annotation variant for a feature
92 void updateFeatureVariant_(FeatureType_& f_set, const String& rota_l, const Size& v) const;
93
94
95
96 }; // !class
97
98 } // !namespace
99
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ILPDCWrapper::PairsType
std::vector< ChargePair > PairsType
Definition: ILPDCWrapper.h:55
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::ILPDCWrapper::FeatureType_
Map< String, std::set< Size > > FeatureType_
Definition: ILPDCWrapper.h:89
OpenMS::ILPDCWrapper::PairsIndex
PairsType::size_type PairsIndex
Definition: ILPDCWrapper.h:56
String.h
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS::ILPDCWrapper
Definition: ILPDCWrapper.h:51
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Map.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127