OpenMS  3.0.0
EnzymaticDigestionLogModel.h
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31 // $Maintainer: Chris Bielow, Xiao Liang $
32 // $Authors: Marc Sturm, Chris Bielow, Xiao Liang $
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
40 
41 #include <string>
42 #include <vector>
43 #include <map>
44 
45 namespace OpenMS
46 {
58  class OPENMS_DLLAPI EnzymaticDigestionLogModel
59  {
60 public:
63 
66 
69 
71  String getEnzymeName() const;
72 
74  void setEnzyme(const String name);
75 
77  void digest(const AASequence& protein, std::vector<AASequence>& output) const;
78 
80  Size peptideCount(const AASequence& protein);
81 
83  double getLogThreshold() const;
84 
87  void setLogThreshold(double threshold);
88 
89 protected:
90  // define a binding site by position and AA
91  struct BindingSite_
92  {
95 
97  position(), AAname() {}
98 
99  BindingSite_(const Size& p, const String& name) :
100  position(p), AAname(name) {}
101 
102  bool operator<(const BindingSite_& rhs) const
103  {
104  return (position < rhs.position) || ((position == rhs.position) && (AAname < rhs.AAname));
105  }
106 
107  bool operator==(const BindingSite_& rhs) const
108  {
109  return position == rhs.position && AAname == rhs.AAname;
110  }
111 
112  };
113 
114  // define the log likelihood for missed and cleavage model
116  {
117  double p_cleave;
118  double p_miss;
119 
121  p_cleave(0), p_miss(0) {}
122  CleavageModel_(const double& p_c, const double& p_m) :
123  p_cleave(p_c), p_miss(p_m) {}
124  };
125 
127  void nextCleavageSite_(const AASequence& sequence, AASequence::ConstIterator& p) const;
128 
130  bool isCleavageSite_(const AASequence& sequence, const AASequence::ConstIterator& p) const;
131 
134 
138  std::map<BindingSite_, CleavageModel_> model_data_;
139  };
140 
141 } // namespace OpenMS
142 
OpenMS::EnzymaticDigestionLogModel::BindingSite_::BindingSite_
BindingSite_()
Definition: EnzymaticDigestionLogModel.h:96
OpenMS::AASequence::ConstIterator
ConstIterator for AASequence.
Definition: AASequence.h:121
OpenMS::EnzymaticDigestionLogModel::CleavageModel_
Definition: EnzymaticDigestionLogModel.h:115
OpenMS::EnzymaticDigestionLogModel
Class for the Log L model of enzymatic digestion of proteins.
Definition: EnzymaticDigestionLogModel.h:58
Types.h
OpenMS::EnzymaticDigestionLogModel::BindingSite_::operator<
bool operator<(const BindingSite_ &rhs) const
Definition: EnzymaticDigestionLogModel.h:102
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::EnzymaticDigestionLogModel::BindingSite_::position
Size position
Definition: EnzymaticDigestionLogModel.h:93
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::EnzymaticDigestionLogModel::CleavageModel_::CleavageModel_
CleavageModel_()
Definition: EnzymaticDigestionLogModel.h:120
OpenMS::EnzymaticDigestionLogModel::log_model_threshold_
double log_model_threshold_
Threshold to decide if position is cleaved or missed (only for the model)
Definition: EnzymaticDigestionLogModel.h:136
OpenMS::EnzymaticDigestionLogModel::CleavageModel_::p_cleave
double p_cleave
Definition: EnzymaticDigestionLogModel.h:117
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::EnzymaticDigestionLogModel::CleavageModel_::CleavageModel_
CleavageModel_(const double &p_c, const double &p_m)
Definition: EnzymaticDigestionLogModel.h:122
OpenMS::EnzymaticDigestionLogModel::enzyme_
const DigestionEnzyme * enzyme_
Used enzyme.
Definition: EnzymaticDigestionLogModel.h:133
OpenMS::EnzymaticDigestionLogModel::BindingSite_::AAname
String AAname
Definition: EnzymaticDigestionLogModel.h:94
OpenMS::EnzymaticDigestionLogModel::BindingSite_
Definition: EnzymaticDigestionLogModel.h:91
OpenMS::EnzymaticDigestionLogModel::BindingSite_::operator==
bool operator==(const BindingSite_ &rhs) const
Definition: EnzymaticDigestionLogModel.h:107
OpenMS::DigestionEnzyme
Base class for digestion enzymes.
Definition: DigestionEnzyme.h:52
AASequence.h
DigestionEnzyme.h
OpenMS::EnzymaticDigestionLogModel::CleavageModel_::p_miss
double p_miss
Definition: EnzymaticDigestionLogModel.h:118
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::EnzymaticDigestionLogModel::BindingSite_::BindingSite_
BindingSite_(const Size &p, const String &name)
Definition: EnzymaticDigestionLogModel.h:99
OpenMS::EnzymaticDigestionLogModel::model_data_
std::map< BindingSite_, CleavageModel_ > model_data_
Holds the cleavage model.
Definition: EnzymaticDigestionLogModel.h:138