| OpenMS 2.5.0

RNPxlModificationsGenerator.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/DATASTRUCTURES/String.h>
39 #include <OpenMS/DATASTRUCTURES/ListUtils.h>
40 #include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
41 #include <vector>
42 #include <map>
43 #include <set>
44 #include <iostream>
45
46 namespace OpenMS
47 {
48 class AASequence;
49
50 struct OPENMS_DLLAPI RNPxlModificationMassesResult
51 {
52 std::map<String, double> mod_masses;
53 std::map<String, std::set<String> > mod_combinations;
54 };
55
56 class OPENMS_DLLAPI RNPxlModificationsGenerator
57 {
58 public:
59 static RNPxlModificationMassesResult initModificationMassesRNA(StringList target_nucleotides,
60 StringList nt_groups,
61 std::set<char> can_xl,
62 StringList mappings,
63 StringList modifications,
64 String sequence_restriction,
65 bool cysteine_adduct,
66 Int max_length = 4);
67 private:
68 static bool notInSeq(String res_seq, String query);
69 static void generateTargetSequences(const String& res_seq, Size param_pos, const std::map<char, std::vector<char> >& map_source2target, StringList& target_sequences);
70 };
71 }
72
73
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::RNPxlModificationsGenerator
Definition: RNPxlModificationsGenerator.h:56
StandardTypes.h
String.h
OpenMS::RNPxlModificationMassesResult::mod_masses
std::map< String, double > mod_masses
empirical formula -> mass
Definition: RNPxlModificationsGenerator.h:52
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::RNPxlModificationMassesResult::mod_combinations
std::map< String, std::set< String > > mod_combinations
empirical formula -> nucleotide formula(s) (formulas if modifications lead to ambiguities) ...
Definition: RNPxlModificationsGenerator.h:53
EmpiricalFormula.h
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
int
OpenMS::RNPxlModificationMassesResult
Definition: RNPxlModificationsGenerator.h:50
ListUtils.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127