OpenMS  2.6.0
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 <boost/regex.hpp>
41 #include <string>
42 #include <vector>
43 
44 #include <functional> // for std::function
45 
46 namespace OpenMS
47 {
62  class OPENMS_DLLAPI EnzymaticDigestion
63  {
64 public:
67  { // note: the value of the first three items is important, since some engines just report the number of required termini (0, 1, 2)
68  SPEC_NONE = 0,
69  SPEC_SEMI = 1,
70  SPEC_FULL = 2,
71  SPEC_UNKNOWN = 3,
72  SPEC_NOCTERM = 8,
73  SPEC_NONTERM = 9,
74  SIZE_OF_SPECIFICITY = 10
75  };
77  static const std::string NamesOfSpecificity[SIZE_OF_SPECIFICITY];
78 
80  static const std::string NoCleavage;
81 
83  static const std::string UnspecificCleavage;
84 
87 
89  virtual ~EnzymaticDigestion();
90 
92  Size getMissedCleavages() const;
93 
95  void setMissedCleavages(Size missed_cleavages);
96 
98  String getEnzymeName() const;
99 
101  virtual void setEnzyme(const DigestionEnzyme* enzyme);
102 
104  Specificity getSpecificity() const;
105 
107  void setSpecificity(Specificity spec);
108 
111  static Specificity getSpecificityByName(const String& name);
112 
124  Size digestUnmodified(const StringView& sequence, std::vector<StringView>& output, Size min_length = 1, Size max_length = 0) const;
125 
139  Size digestUnmodified(const StringView& sequence, std::vector<std::pair<Size,Size>>& output, Size min_length = 1, Size max_length = 0) const;
140 
152  bool isValidProduct(const String& sequence, int pos, int length, bool ignore_missed_cleavages = true) const;
153 
161  bool filterByMissedCleavages(const String& sequence, const std::function<bool(const Int)>& filter) const;
162 
163 protected:
164 
171  bool isValidProduct_(const String& sequence,
172  int pos,
173  int length,
174  bool ignore_missed_cleavages,
175  bool allow_nterm_protein_cleavage,
176  bool allow_random_asp_pro_cleavage) const;
192  std::vector<int> tokenize_(const String& sequence, int start = 0, int end = -1) const;
193 
202  Size digestAfterTokenize_(const std::vector<int>& fragment_positions, const StringView& sequence, std::vector<StringView>& output, Size min_length = 0, Size max_length = -1) const;
203  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;
204 
213  Size countMissedCleavages_(const std::vector<int>& cleavage_positions, Size seq_start, Size seq_end) const;
214 
217 
221  boost::regex re_;
222 
225  };
226 
227 } // namespace OpenMS
228 
229 
OpenMS::EnzymaticDigestion::Specificity
Specificity
when querying for valid digestion products, this determines if the specificity of the two peptide end...
Definition: EnzymaticDigestion.h:66
Types.h
OpenMS::EnzymaticDigestion::specificity_
Specificity specificity_
specificity of enzyme
Definition: EnzymaticDigestion.h:224
OpenMS::EnzymaticDigestion::missed_cleavages_
Size missed_cleavages_
Number of missed cleavages.
Definition: EnzymaticDigestion.h:216
OpenMS::String
A more convenient string class.
Definition: String.h:59
OpenMS::EnzymaticDigestion
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:62
OpenMS::EnzymaticDigestion::UnspecificCleavage
static const std::string UnspecificCleavage
Name for unspecific cleavage.
Definition: EnzymaticDigestion.h:83
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
int
OpenMS::EnzymaticDigestion::re_
boost::regex re_
Regex for tokenizing (huge speedup by making this a member instead of stack object in tokenize_())
Definition: EnzymaticDigestion.h:221
OpenMS::StringView
StringView provides a non-owning view on an existing string.
Definition: String.h:489
OpenMS::DigestionEnzyme
Abstract base class for digestion enzymes.
Definition: DigestionEnzyme.h:52
OpenMS::EnzymaticDigestion::NoCleavage
static const std::string NoCleavage
Name for no cleavage.
Definition: EnzymaticDigestion.h:80
DigestionEnzyme.h
OpenMS::EnzymaticDigestion::enzyme_
const DigestionEnzyme * enzyme_
Used enzyme.
Definition: EnzymaticDigestion.h:219