OpenMS  3.0.0
EnzymaticDigestion.h
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31 // $Maintainer: Chris Bielow, Xiao Liang $
32 // $Authors: Marc Sturm, Chris Bielow $
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
39 
40 #include <string>
41 #include <vector>
42 
43 #include <functional> // for std::function
44 #include <memory> // unique_ptr
45 
46 #include <boost/regex_fwd.hpp> // forward declaration of boost::regex
47 
48 namespace OpenMS
49 {
50  class StringView;
51 
66  class OPENMS_DLLAPI EnzymaticDigestion
67  {
68 public:
71  { // note: the value of the first three items is important, since some engines just report the number of required termini (0, 1, 2)
72  SPEC_NONE = 0,
73  SPEC_SEMI = 1,
74  SPEC_FULL = 2,
75  SPEC_UNKNOWN = 3,
76  SPEC_NOCTERM = 8,
77  SPEC_NONTERM = 9,
78  SIZE_OF_SPECIFICITY = 10
79  };
81  static const std::string NamesOfSpecificity[SIZE_OF_SPECIFICITY];
82 
84  static const std::string NoCleavage;
85 
87  static const std::string UnspecificCleavage;
88 
91 
94 
96  EnzymaticDigestion& operator=(const EnzymaticDigestion& rhs);
97 
99  virtual ~EnzymaticDigestion();
100 
102  Size getMissedCleavages() const;
103 
105  void setMissedCleavages(Size missed_cleavages);
106 
108  String getEnzymeName() const;
109 
111  virtual void setEnzyme(const DigestionEnzyme* enzyme);
112 
114  Specificity getSpecificity() const;
115 
117  void setSpecificity(Specificity spec);
118 
121  static Specificity getSpecificityByName(const String& name);
122 
134  Size digestUnmodified(const StringView& sequence, std::vector<StringView>& output, Size min_length = 1, Size max_length = 0) const;
135 
149  Size digestUnmodified(const StringView& sequence, std::vector<std::pair<Size,Size>>& output, Size min_length = 1, Size max_length = 0) const;
150 
162  bool isValidProduct(const String& protein, int pep_pos, int pep_length, bool ignore_missed_cleavages = true) const;
163 
171  bool filterByMissedCleavages(const String& sequence, const std::function<bool(const Int)>& filter) const;
172 
173 protected:
174 
181  bool isValidProduct_(const String& sequence,
182  int pos,
183  int length,
184  bool ignore_missed_cleavages,
185  bool allow_nterm_protein_cleavage,
186  bool allow_random_asp_pro_cleavage) const;
202  std::vector<int> tokenize_(const String& sequence, int start = 0, int end = -1) const;
203 
212  Size digestAfterTokenize_(const std::vector<int>& fragment_positions, const StringView& sequence, std::vector<StringView>& output, Size min_length = 0, Size max_length = -1) const;
213  Size digestAfterTokenize_(const std::vector<int>& fragment_positions, const StringView& sequence, std::vector<std::pair<Size,Size>>& output, Size min_length = 0, Size max_length = -1) const;
214 
223  Size countMissedCleavages_(const std::vector<int>& cleavage_positions, Size seq_start, Size seq_end) const;
224 
227 
231  std::unique_ptr<boost::regex> re_; // use PImpl, since #include cost is huge
232 
235  };
236 
237 } // namespace OpenMS
238 
239 
OpenMS::EnzymaticDigestion::Specificity
Specificity
when querying for valid digestion products, this determines if the specificity of the two peptide end...
Definition: EnzymaticDigestion.h:70
Types.h
OpenMS::EnzymaticDigestion::specificity_
Specificity specificity_
specificity of enzyme
Definition: EnzymaticDigestion.h:234
OpenMS::EnzymaticDigestion::missed_cleavages_
Size missed_cleavages_
Number of missed cleavages.
Definition: EnzymaticDigestion.h:226
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::EnzymaticDigestion
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:66
OpenMS::EnzymaticDigestion::UnspecificCleavage
static const std::string UnspecificCleavage
Name for unspecific cleavage.
Definition: EnzymaticDigestion.h:87
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::EnzymaticDigestion::re_
std::unique_ptr< boost::regex > re_
Regex for tokenizing (huge speedup by making this a member instead of stack object in tokenize_())
Definition: EnzymaticDigestion.h:231
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::StringView
StringView provides a non-owning view on an existing string.
Definition: StringView.h:55
OpenMS::DigestionEnzyme
Base class for digestion enzymes.
Definition: DigestionEnzyme.h:52
OpenMS::EnzymaticDigestion::NoCleavage
static const std::string NoCleavage
Name for no cleavage.
Definition: EnzymaticDigestion.h:84
DigestionEnzyme.h
OpenMS::EnzymaticDigestion::enzyme_
const DigestionEnzyme * enzyme_
Used enzyme.
Definition: EnzymaticDigestion.h:229