| OpenMS 2.5.0

MassExplainer.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 #include <OpenMS/DATASTRUCTURES/Adduct.h>
38
39 #include <OpenMS/CONCEPT/Types.h>
40 #include <OpenMS/CONCEPT/LogStream.h>
41
42 #include <OpenMS/DATASTRUCTURES/String.h>
43 #include <OpenMS/OpenMSConfig.h>
44
45 namespace OpenMS
46 {
47 class Compomer;
48
55 class OPENMS_DLLAPI MassExplainer
56 {
57
58 public:
59
60 typedef Adduct::AdductsType AdductsType; //vector<Adduct>
61 typedef std::vector<Compomer>::const_iterator CompomerIterator;
62
64
65 MassExplainer();
67
69 MassExplainer(AdductsType adduct_base);
70
72 MassExplainer(Int q_min, Int q_max, Int max_span, double thresh_logp);
73
75 MassExplainer(AdductsType adduct_base, Int q_min, Int q_max, Int max_span, double thresh_logp, Size max_neutrals);
76
77
78 private:
81 void init_(bool init_thresh_p);
82 public:
84 MassExplainer& operator=(const MassExplainer& rhs);
85
87 virtual ~MassExplainer();
89
90
92 void compute();
93
94
95 //@name Accessors
97
99 void setAdductBase(AdductsType adduct_base);
101 AdductsType getAdductBase() const;
102
104 const Compomer& getCompomerById(Size id) const;
106
107
115 SignedSize query(const Int net_charge,
116 const float mass_to_explain,
117 const float mass_delta,
118 const float thresh_log_p,
119 std::vector<Compomer>::const_iterator& firstExplanation,
120 std::vector<Compomer>::const_iterator& lastExplanation) const;
121 protected:
122
124 bool compomerValid_(const Compomer& cmp);
125
127 Adduct createAdduct_(const String& formula, const Int charge, const double p) const;
128
130 std::vector<Compomer> explanations_;
132 AdductsType adduct_base_;
134 Int q_min_;
136 Int q_max_;
138 Int max_span_;
140 double thresh_p_;
142 Size max_neutrals_;
143
144 };
145
146
147 } // namespace OpenMS
148
OpenMS::MassExplainer::AdductsType
Adduct::AdductsType AdductsType
Definition: MassExplainer.h:60
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::String
A more convenient string class.
Definition: String.h:58
Adduct.h
OpenMS::MassExplainer::max_span_
Int max_span_
maximal span (in terms of charge) for co-features, e.g. a cluster with q={3,6} has span=4 ...
Definition: MassExplainer.h:138
OpenMS::MassExplainer::explanations_
std::vector< Compomer > explanations_
store possible explanations (as formula) for a certain ChargeDifference and MassDifference ...
Definition: MassExplainer.h:130
Types.h
OpenMS::MassExplainer::adduct_base_
AdductsType adduct_base_
all allowed adducts, whose combination explains the mass difference
Definition: MassExplainer.h:132
OpenMS::MassExplainer::thresh_p_
double thresh_p_
minimum required probability of a compound (all other compounds are discarded)
Definition: MassExplainer.h:140
String.h
OpenMS::Adduct
Definition: Adduct.h:44
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MassExplainer::max_neutrals_
Size max_neutrals_
Maximum number of neutral(q=0) adducts.
Definition: MassExplainer.h:142
LogStream.h
OpenMS::MassExplainer::q_min_
Int q_min_
minimal expected charge
Definition: MassExplainer.h:134
OpenMS::MassExplainer
computes empirical formulas for given mass differences using a set of allowed elements ...
Definition: MassExplainer.h:55
OpenMS::Compomer
Holds information on an edge connecting two features from a (putative) charge ladder.
Definition: Compomer.h:58
int
OpenMS::Adduct::AdductsType
std::vector< Adduct > AdductsType
Definition: Adduct.h:48
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::MassExplainer::q_max_
Int q_max_
maximal expected charge
Definition: MassExplainer.h:136
OpenMS::MassExplainer::CompomerIterator
std::vector< Compomer >::const_iterator CompomerIterator
Definition: MassExplainer.h:61