OpenMS  3.0.0
RNPxlModificationsGenerator.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
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34 
35 #pragma once
36 
41 #include <vector>
42 #include <map>
43 #include <set>
44 
45 namespace OpenMS
46 {
47  class AASequence;
48 
49  struct OPENMS_DLLAPI RNPxlModificationMassesResult
50  {
51  std::map<String, double> mod_masses;
52  std::map<String, std::set<String> > mod_combinations;
53  };
54 
55  class OPENMS_DLLAPI RNPxlModificationsGenerator
56  {
57  public:
58  static RNPxlModificationMassesResult initModificationMassesRNA(StringList target_nucleotides,
59  StringList nt_groups,
60  std::set<char> can_xl,
61  StringList mappings,
62  StringList modifications,
63  String sequence_restriction,
64  bool cysteine_adduct,
65  Int max_length = 4);
66  private:
67  static bool notInSeq(String res_seq, String query);
68  static void generateTargetSequences(const String& res_seq, Size param_pos, const std::map<char, std::vector<char> >& map_source2target, StringList& target_sequences);
69  };
70 }
71 
72 
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::RNPxlModificationMassesResult::mod_combinations
std::map< String, std::set< String > > mod_combinations
empirical formula -> nucleotide formula(s) (formulas if modifications lead to ambiguities)
Definition: RNPxlModificationsGenerator.h:52
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
ListUtils.h
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::RNPxlModificationsGenerator
Definition: RNPxlModificationsGenerator.h:55
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
EmpiricalFormula.h
String.h
OpenMS::RNPxlModificationMassesResult::mod_masses
std::map< String, double > mod_masses
empirical formula -> mass
Definition: RNPxlModificationsGenerator.h:51
StandardTypes.h
OpenMS::RNPxlModificationMassesResult
Definition: RNPxlModificationsGenerator.h:49