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RNPxlModificationsGenerator.h
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34 
35 #ifndef OPENMS_ANALYSIS_RNPXL_RNPXLMODIFICATIONSGENERATOR_H
36 #define OPENMS_ANALYSIS_RNPXL_RNPXLMODIFICATIONSGENERATOR_H
37 
38 #include <vector>
39 #include <map>
40 #include <set>
42 
43 namespace OpenMS
44 {
45  struct OPENMS_DLLAPI RNPxlModificationMassesResult
46  {
47  std::map<String, double> mod_masses; // empirical formula -> mass
48  std::map<String, std::set<String> > mod_combinations; // empirical formula -> nucleotide formula(s) (formulas if modifications lead to ambiguities)
49  std::map<Size, String> mod_formula_idx;
50  };
51 
52  class OPENMS_DLLAPI RNPxlModificationsGenerator
53  {
54  public:
55  static RNPxlModificationMassesResult initModificationMassesRNA(StringList target_nucleotides, StringList mappings, StringList restrictions, StringList modifications, String sequence_restriction, bool cysteine_adduct, Int max_length = 4);
56  private:
57  static bool notInSeq(String res_seq, String query);
58  static void generateTargetSequences(const String& res_seq, Size pos, const std::map<char, std::vector<char> >& map_source2target, StringList& target_sequences);
59  };
60 }
61 
62 #endif // OPENMS_ANALYSIS_RNPXL_RNPXLMODIFICATIONSGENERATOR_H
std::map< Size, String > mod_formula_idx
Definition: RNPxlModificationsGenerator.h:49
A more convenient string class.
Definition: String.h:57
Definition: RNPxlModificationsGenerator.h:45
Definition: RNPxlModificationsGenerator.h:52
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::map< String, std::set< String > > mod_combinations
Definition: RNPxlModificationsGenerator.h:48
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:74
std::map< String, double > mod_masses
Definition: RNPxlModificationsGenerator.h:47
int Int
Signed integer type.
Definition: Types.h:96

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:32 using doxygen 1.8.9.1