| OpenMS 2.5.0

ModifiedNASequenceGenerator.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/CHEMISTRY/NASequence.h>
39 #include <OpenMS/CHEMISTRY/Ribonucleotide.h>
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, combinatorially generating modified sequences.
49 *
50 */
51 class OPENMS_DLLAPI ModifiedNASequenceGenerator
52 {
53 public:
54 using ConstRibonucleotidePtr = const Ribonucleotide*;
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::Ribonucleotide
Representation of a ribonucleotide (modified or unmodified)
Definition: Ribonucleotide.h:51
Ribonucleotide.h
NASequence.h
StandardTypes.h
OpenMS::ModifiedNASequenceGenerator
Definition: ModifiedNASequenceGenerator.h:51
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::NASequence
Representation of a nucleic acid sequence.
Definition: NASequence.h:62
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127