OpenMS  3.0.0
ModifiedNASequenceGenerator.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
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34 
35 #pragma once
36 
40 #include <vector>
41 #include <map>
42 #include <set>
43 
44 namespace OpenMS
45 {
46  /*
47  * @brief This class applies fixed and variable modifications to (unmodified)
48  * nucleic acid sequences, combinatorically generating modified sequences.
49  *
50  */
51  class OPENMS_DLLAPI ModifiedNASequenceGenerator
52  {
53  public:
55 
57  static void applyFixedModifications(
58  const std::set<ConstRibonucleotidePtr>& fixed_mods,
59  NASequence& sequence);
60 
62  static void applyVariableModifications(
63  const std::set<ConstRibonucleotidePtr>& var_mods,
64  const NASequence& seq, Size max_variable_mods_per_NASequence,
65  std::vector<NASequence>& all_modified_NASequences,
66  bool keep_original = true);
67 
68  protected:
70  static void recurseAndGenerateVariableModifiedSequences_(
71  const std::vector<int>& subset_indices,
72  const std::map<int, std::vector<ConstRibonucleotidePtr>>& map_compatibility,
73  int depth,
74  const NASequence& current_NASequence,
75  std::vector<NASequence>& modified_NASequences);
76 
80  static void applyAtMostOneVariableModification_(
81  const std::set<ConstRibonucleotidePtr>& var_mods,
82  const NASequence& seq,
83  std::vector<NASequence>& all_modified_NASequences,
84  bool keep_original = true);
85  };
86 }
87 
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::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
NASequence.h
Ribonucleotide.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ModifiedNASequenceGenerator
Definition: ModifiedNASequenceGenerator.h:51
StandardTypes.h