OpenMS  3.0.0
RNaseDigestion.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser, Samuel Wein $
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34 
35 #pragma once
36 
40 
41 #include <boost/regex.hpp>
42 
43 namespace OpenMS
44 {
52  class OPENMS_DLLAPI RNaseDigestion: public EnzymaticDigestion
53  {
54  public:
56  void setEnzyme(const DigestionEnzyme* enzyme) override;
57 
59  void setEnzyme(const String& name);
60 
66  void digest(const NASequence& rna, std::vector<NASequence>& output,
67  Size min_length = 0, Size max_length = 0) const;
68 
75  void digest(IdentificationData& id_data, Size min_length = 0,
76  Size max_length = 0) const;
77 
78  protected:
81  std::vector<boost::regex> cuts_after_regexes_;
82  std::vector<boost::regex> cuts_before_regexes_;
83 
87  std::vector<std::pair<Size, Size>> getFragmentPositions_(
88  const NASequence& rna, Size min_length, Size max_length)
89  const;
90  };
91 
92 } // namespace OpenMS
93 
OpenMS::RNaseDigestion::three_prime_gain_
const Ribonucleotide * three_prime_gain_
3' mod added by the enzyme
Definition: RNaseDigestion.h:80
EnzymaticDigestion.h
OpenMS::NASequence
Representation of a nucleic acid sequence.
Definition: NASequence.h:61
OpenMS::Ribonucleotide
Representation of a ribonucleotide (modified or unmodified)
Definition: Ribonucleotide.h:51
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::RNaseDigestion::five_prime_gain_
const Ribonucleotide * five_prime_gain_
5' mod added by the enzyme
Definition: RNaseDigestion.h:79
OpenMS::EnzymaticDigestion
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:66
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
NASequence.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::RNaseDigestion::cuts_after_regexes_
std::vector< boost::regex > cuts_after_regexes_
a vector of reg. exp. for enzyme cutting pattern
Definition: RNaseDigestion.h:81
OpenMS::RNaseDigestion::cuts_before_regexes_
std::vector< boost::regex > cuts_before_regexes_
a vector reg. exp. for enzyme cutting pattern
Definition: RNaseDigestion.h:82
OpenMS::IdentificationData
Representation of spectrum identification results and associated data.
Definition: IdentificationData.h:94
OpenMS::DigestionEnzyme
Base class for digestion enzymes.
Definition: DigestionEnzyme.h:52
IdentificationData.h
OpenMS::RNaseDigestion
Class for the enzymatic digestion of RNAs.
Definition: RNaseDigestion.h:52