OpenMS  3.0.0
Tagger.h
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31 // $Maintainer: Eugen Netz $
32 // $Authors: Timo Sachsenberg, Eugen Netz $
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34 
35 #pragma once
36 
38 #include <map>
39 
40 namespace OpenMS
41 {
42  class MSSpectrum;
43 
52  class OPENMS_DLLAPI Tagger
53  {
54  public:
69  Tagger(size_t min_tag_length, double ppm, size_t max_tag_length = 65535, size_t min_charge = 1, size_t max_charge = 1, const StringList& fixed_mods = StringList(), const StringList& var_mods = StringList());
70 
81  void getTag(const std::vector<double>& mzs, std::vector<std::string>& tags) const;
82 
93  void getTag(const MSSpectrum& spec, std::vector<std::string>& tags) const;
94 
103  void setMaxCharge(size_t max_charge);
104 
105  private:
106  double min_gap_;
107  double max_gap_;
108  double ppm_;
111  size_t min_charge_;
112  size_t max_charge_;
113  std::map<double, char> mass2aa_;
114 
116  char getAAByMass_(double m) const;
118  void getTag_(std::string& tag, const std::vector<double>& mzs, const size_t i, std::vector<std::string>& tags, const size_t charge) const;
119  };
120 }
OpenMS::Tagger::min_charge_
size_t min_charge_
minimal fragment charge
Definition: Tagger.h:111
OpenMS::Tagger
Calculate sequence tags from m/z values.
Definition: Tagger.h:52
OpenMS::Tagger::max_tag_length_
size_t max_tag_length_
maximum tag length
Definition: Tagger.h:110
OpenMS::Tagger::max_charge_
size_t max_charge_
maximal fragment charge
Definition: Tagger.h:112
OpenMS::Tagger::min_tag_length_
size_t min_tag_length_
minimum tag length
Definition: Tagger.h:109
OpenMS::Tagger::ppm_
double ppm_
tolerance
Definition: Tagger.h:108
ListUtils.h
OpenMS::Tagger::max_gap_
double max_gap_
will be set to highest residue mass in ResidueDB
Definition: Tagger.h:107
OpenMS::Tagger::mass2aa_
std::map< double, char > mass2aa_
mapping of residue masses to their one letter codes
Definition: Tagger.h:113
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Tagger::min_gap_
double min_gap_
will be set to smallest residue mass in ResidueDB
Definition: Tagger.h:106
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66