OpenMS  3.0.0
ModificationDefinitionsSet.h
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35 
36 #pragma once
37 
40 #include <OpenMS/CONCEPT/Types.h> // for "UInt"
42 #include <OpenMS/DATASTRUCTURES/ListUtils.h> // for "StringList"
45 
46 #include <set>
47 
48 namespace OpenMS
49 {
58  class OPENMS_DLLAPI ModificationDefinitionsSet
59  {
60 public:
61 
67 
70 
72  ModificationDefinitionsSet(const StringList& fixed_modifications, const StringList& variable_modifications);
73 
75  virtual ~ModificationDefinitionsSet();
77 
81  void setMaxModifications(Size max_mod);
83 
85  Size getMaxModifications() const;
86 
88  Size getNumberOfModifications() const;
89 
91  Size getNumberOfFixedModifications() const;
92 
94  Size getNumberOfVariableModifications() const;
95 
97  void addModification(const ModificationDefinition& mod_def);
98 
100  void setModifications(const std::set<ModificationDefinition>& mod_defs);
101 
108  void setModifications(const String& fixed_modifications, const String& variable_modifications);
109 
111  void setModifications(const StringList& fixed_modifications, const StringList& variable_modifications);
112 
114  std::set<ModificationDefinition> getModifications() const;
115 
117  const std::set<ModificationDefinition>& getFixedModifications() const;
118 
120  const std::set<ModificationDefinition>& getVariableModifications() const;
121 
123  std::set<String> getModificationNames() const;
124 
126  void getModificationNames(StringList& fixed_modifications, StringList& variable_modifications) const;
127 
129  std::set<String> getFixedModificationNames() const;
130 
132  std::set<String> getVariableModificationNames() const;
134 
138  ModificationDefinitionsSet& operator=(const ModificationDefinitionsSet& element);
141 
145  bool isCompatible(const AASequence& peptide) const;
147 
149  bool operator==(const ModificationDefinitionsSet& rhs) const;
150 
152  bool operator!=(const ModificationDefinitionsSet& rhs) const;
154 
169  void findMatches(std::multimap<double, ModificationDefinition>& matches, double mass, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY, bool consider_fixed = true, bool consider_variable = true, bool is_delta = true, double tolerance = 0.01) const;
170 
172  void inferFromPeptides(const std::vector<PeptideIdentification>& peptides);
173 
174 protected:
175 
176  std::set<ModificationDefinition> variable_mods_;
177 
178  std::set<ModificationDefinition> fixed_mods_;
179 
181 
183  static void addMatches_(std::multimap<double, ModificationDefinition>& matches, double mass, const String& residue, ResidueModification::TermSpecificity term_spec, const std::set<ModificationDefinition>& source, bool is_delta, double tolerance);
184 
185  };
186 
187 } // namespace OpenMS
188 
Types.h
OpenMS::ModificationDefinition
Representation of modification definition.
Definition: ModificationDefinition.h:52
OpenMS::ModificationDefinitionsSet
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:58
OpenMS::String
A more convenient string class.
Definition: String.h:58
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::ResidueModification::NUMBER_OF_TERM_SPECIFICITY
Definition: ResidueModification.h:104
OpenMS::ModificationDefinitionsSet::variable_mods_
std::set< ModificationDefinition > variable_mods_
Definition: ModificationDefinitionsSet.h:176
ListUtils.h
OpenMS::ModificationDefinitionsSet::fixed_mods_
std::set< ModificationDefinition > fixed_mods_
Definition: ModificationDefinitionsSet.h:178
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ResidueModification::TermSpecificity
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:97
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
AASequence.h
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::ModificationDefinitionsSet::max_mods_per_peptide_
Size max_mods_per_peptide_
Definition: ModificationDefinitionsSet.h:180
String.h
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
PeptideIdentification.h
ModificationDefinition.h
StringListUtils.h