| OpenMS 2.5.0

Tagger.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Eugen Netz $
32 // $Authors: Timo Sachsenberg, Eugen Netz $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/ListUtils.h>
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_;
109 size_t min_tag_length_;
110 size_t max_tag_length_;
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_gap_
double min_gap_
will be set to smallest residue mass in ResidueDB
Definition: Tagger.h:106
OpenMS::Tagger::max_tag_length_
size_t max_tag_length_
maximum tag length
Definition: Tagger.h:110
OpenMS::Tagger
Calculate sequence tags from m/z values.
Definition: Tagger.h:52
OpenMS::Tagger::ppm_
double ppm_
tolerance
Definition: Tagger.h:108
OpenMS::Tagger::max_gap_
double max_gap_
will be set to highest residue mass in ResidueDB
Definition: Tagger.h:107
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::Tagger::max_charge_
size_t max_charge_
maximal fragment charge
Definition: Tagger.h:112
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Tagger::mass2aa_
std::map< double, char > mass2aa_
mapping of residue masses to their one letter codes
Definition: Tagger.h:113
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
ListUtils.h
OpenMS::Tagger::min_tag_length_
size_t min_tag_length_
minimum tag length
Definition: Tagger.h:109
OpenMS::Tagger::min_charge_
size_t min_charge_
minimal fragment charge
Definition: Tagger.h:111