OpenMS
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 
58  const std::set<ConstRibonucleotidePtr>& fixed_mods,
59  NASequence& sequence);
60 
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:
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 
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 
Definition: ModifiedNASequenceGenerator.h:52
static void applyFixedModifications(const std::set< ConstRibonucleotidePtr > &fixed_mods, NASequence &sequence)
Applies fixed modifications to a single NASequence.
static void recurseAndGenerateVariableModifiedSequences_(const std::vector< int > &subset_indices, const std::map< int, std::vector< ConstRibonucleotidePtr >> &map_compatibility, int depth, const NASequence &current_NASequence, std::vector< NASequence > &modified_NASequences)
Recursively generate all combinatorial placements at compatible sites.
static void applyAtMostOneVariableModification_(const std::set< ConstRibonucleotidePtr > &var_mods, const NASequence &seq, std::vector< NASequence > &all_modified_NASequences, bool keep_original=true)
static void applyVariableModifications(const std::set< ConstRibonucleotidePtr > &var_mods, const NASequence &seq, Size max_variable_mods_per_NASequence, std::vector< NASequence > &all_modified_NASequences, bool keep_original=true)
Applies variable modifications to a single NASequence. If keep_original is set the original (e....
Representation of a nucleic acid sequence.
Definition: NASequence.h:60
Representation of a ribonucleotide (modified or unmodified)
Definition: Ribonucleotide.h:52
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48