OpenMS  2.4.0
ModifiedPeptideGenerator.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  class OPENMS_DLLAPI ModifiedPeptideGenerator
47  {
48  /*
49  * @brief Modifications can be generated and applied to AASequences.
50  */
51 
52  public
53 :
54  // Applies fixed modifications to a single peptide
55  static void applyFixedModifications(const std::vector<ResidueModification>::const_iterator& fixed_mods_begin, const std::vector<ResidueModification>::const_iterator& fixed_mods_end, AASequence& peptide);
56 
57  // Applies variable modifications to a single peptide. If keep_original is set the original (e.g. unmodified version) is also returned
58  static void applyVariableModifications(const std::vector<ResidueModification>::const_iterator& var_mods_begin, const std::vector<ResidueModification>::const_iterator& var_mods_end, const AASequence& peptide, Size max_variable_mods_per_peptide, std::vector<AASequence>& all_modified_peptides, bool keep_original=true);
59 
60  protected:
61  // Recursively generate all combinatoric placements at compatible sites
62  static void recurseAndGenerateVariableModifiedPeptides_(const std::vector<int>& subset_indices, const std::map<int, std::vector<ResidueModification> >& map_compatibility, int depth, const AASequence& current_peptide, std::vector<AASequence>& modified_peptides);
63 
64  // Fast implementation of modification placement. No combinatoric placement is needed in this case - just every site is modified once by each compatible modification. Already modified residues are skipped
65  static void applyAtMostOneVariableModification_(const std::vector<ResidueModification>::const_iterator& var_mods_begin, const std::vector<ResidueModification>::const_iterator& var_mods_end, const AASequence& peptide, std::vector<AASequence>& all_modified_peptides, bool keep_original=true);
66 
67  };
68 }
69 
70 
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Definition: ModifiedPeptideGenerator.h:46
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127