| OpenMS 2.5.0

EnzymaticDigestion.h
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Chris Bielow, Xiao Liang $
32 // $Authors: Marc Sturm, Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/Types.h>
38 #include <OpenMS/CHEMISTRY/DigestionEnzyme.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:
66 enum Specificity
67 {
68 SPEC_FULL,
69 SPEC_SEMI,
70 SPEC_NONE,
71 SIZE_OF_SPECIFICITY
72 };
74 static const std::string NamesOfSpecificity[SIZE_OF_SPECIFICITY];
75
77 static const std::string NoCleavage;
78
80 static const std::string UnspecificCleavage;
81
83 EnzymaticDigestion();
84
86 virtual ~EnzymaticDigestion();
87
89 Size getMissedCleavages() const;
90
92 void setMissedCleavages(Size missed_cleavages);
93
95 String getEnzymeName() const;
96
98 virtual void setEnzyme(const DigestionEnzyme* enzyme);
99
101 Specificity getSpecificity() const;
102
104 void setSpecificity(Specificity spec);
105
108 static Specificity getSpecificityByName(const String& name);
109
121 Size digestUnmodified(const StringView& sequence, std::vector<StringView>& output, Size min_length = 1, Size max_length = 0) const;
122
136 Size digestUnmodified(const StringView& sequence, std::vector<std::pair<Size,Size>>& output, Size min_length = 1, Size max_length = 0) const;
137
149 bool isValidProduct(const String& sequence, int pos, int length, bool ignore_missed_cleavages = true) const;
150
158 bool filterByMissedCleavages(const String& sequence, std::function<bool(const Int)> filter) const;
159
160 protected:
161
168 bool isValidProduct_(const String& sequence,
169 int pos,
170 int length,
171 bool ignore_missed_cleavages,
172 bool allow_nterm_protein_cleavage,
173 bool allow_random_asp_pro_cleavage) const;
189 std::vector<int> tokenize_(const String& sequence, int start = 0, int end = -1) const;
190
199 Size digestAfterTokenize_(const std::vector<int>& fragment_positions, const StringView& sequence, std::vector<StringView>& output, Size min_length = 0, Size max_length = -1) const;
200 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;
201
210 Size countMissedCleavages_(const std::vector<int>& cleavage_positions, Size seq_start, Size seq_end) const;
211
213 Size missed_cleavages_;
214
216 const DigestionEnzyme* enzyme_;
218 boost::regex re_;
219
221 Specificity specificity_;
222 };
223
224 } // namespace OpenMS
225
226
OpenMS::EnzymaticDigestion::Specificity
Specificity
when querying for valid digestion products, this determines if the specificity of the two peptide end...
Definition: EnzymaticDigestion.h:66
DigestionEnzyme.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::DigestionEnzyme
Abstract base class for digestion enzymes.
Definition: DigestionEnzyme.h:52
Types.h
OpenMS::StringView
StringView provides a non-owning view on an existing string.
Definition: String.h:488
OpenMS::EnzymaticDigestion::SPEC_NONE
no requirements on start / end
Definition: EnzymaticDigestion.h:70
OpenMS::EnzymaticDigestion
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:62
OpenMS::EnzymaticDigestion::specificity_
Specificity specificity_
specificity of enzyme
Definition: EnzymaticDigestion.h:221
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::EnzymaticDigestion::SPEC_FULL
fully enzyme specific, e.g., tryptic (ends with KR, AA-before is KR), or peptide is at protein termin...
Definition: EnzymaticDigestion.h:68
OpenMS::EnzymaticDigestion::missed_cleavages_
Size missed_cleavages_
Number of missed cleavages.
Definition: EnzymaticDigestion.h:213
int
OpenMS::EnzymaticDigestion::NoCleavage
static const std::string NoCleavage
Name for no cleavage.
Definition: EnzymaticDigestion.h:77
OpenMS::EnzymaticDigestion::enzyme_
const DigestionEnzyme * enzyme_
Used enzyme.
Definition: EnzymaticDigestion.h:216
OpenMS::EnzymaticDigestion::SPEC_SEMI
semi specific, i.e., one of the two cleavage sites must fulfill requirements
Definition: EnzymaticDigestion.h:69
OpenMS::EnzymaticDigestion::UnspecificCleavage
static const std::string UnspecificCleavage
Name for unspecific cleavage.
Definition: EnzymaticDigestion.h:80
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:218
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127