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MassExplainer.h
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34 
35 #ifndef OPENMS_DATASTRUCTURES_MASSEXPLAINER_H
36 #define OPENMS_DATASTRUCTURES_MASSEXPLAINER_H
37 
39 
40 namespace OpenMS
41 {
42  class Compomer;
43  class Adduct;
44 
51  class OPENMS_DLLAPI MassExplainer
52  {
53 
54 public:
55 
56  typedef Adduct::AdductsType AdductsType; //vector<Adduct>
57  typedef std::vector<Compomer>::const_iterator CompomerIterator;
58 
60 
61  MassExplainer();
63 
65  MassExplainer(AdductsType adduct_base);
66 
68  MassExplainer(Int q_min, Int q_max, Int max_span, DoubleReal thresh_logp);
69 
71  MassExplainer(AdductsType adduct_base, Int q_min, Int q_max, Int max_span, DoubleReal thresh_logp, Size max_neutrals);
72 
73 
74 private:
77  void init_(bool init_thresh_p);
78 public:
80  MassExplainer & operator=(const MassExplainer & rhs);
81 
83  virtual ~MassExplainer();
85 
86 
88  void compute();
89 
90 
91  //@name Accessors
93 
95  void setAdductBase(AdductsType adduct_base);
97  AdductsType getAdductBase() const;
98 
100  const Compomer & getCompomerById(Size id) const;
102 
103 
111  SignedSize query(const Int net_charge,
112  const float mass_to_explain,
113  const float mass_delta,
114  const float thresh_log_p,
115  std::vector<Compomer>::const_iterator & firstExplanation,
116  std::vector<Compomer>::const_iterator & lastExplanation) const;
117 protected:
118 
120  bool compomerValid_(const Compomer & cmp);
121 
123  Adduct createAdduct_(const String & formula, const Int charge, const DoubleReal p) const;
124 
126  std::vector<Compomer> explanations_;
139 
140  };
141 
142 
143 } // namespace OpenMS
144 
145 #endif // OPENMS_DATASTRUCTURES_MASSEXPLAINER_H
A more convenient string class.
Definition: String.h:56
Holds information on an edge connecting two features from a (putative) charge ladder.
Definition: Compomer.h:58
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:151
std::vector< Adduct > AdductsType
Definition: Adduct.h:50
Size max_neutrals_
Maximum number of neutral(q=0) adducts.
Definition: MassExplainer.h:138
std::vector< Compomer > explanations_
store possible explanations (as formula) for a certain ChargeDifference and MassDifference ...
Definition: MassExplainer.h:126
computes empirical formulas for given mass differences using a set of allowed elements ...
Definition: MassExplainer.h:51
Definition: Adduct.h:46
std::vector< Compomer >::const_iterator CompomerIterator
Definition: MassExplainer.h:57
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
DoubleReal thresh_p_
minimum required probability of a compound (all other compounds are discarded)
Definition: MassExplainer.h:136
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:134
Int q_max_
maximal expected charge
Definition: MassExplainer.h:132
AdductsType adduct_base_
all allowed adducts, whose combination explains the mass difference
Definition: MassExplainer.h:128
Adduct::AdductsType AdductsType
Definition: MassExplainer.h:56
int Int
Signed integer type.
Definition: Types.h:100
Int q_min_
minimal expected charge
Definition: MassExplainer.h:130

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:16 using doxygen 1.8.5