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ModificationDefinitionsSet.h
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35 
36 #ifndef OPENMS_CHEMISTRY_MODIFICATIONDEFINITIONSSET_H
37 #define OPENMS_CHEMISTRY_MODIFICATIONDEFINITIONSSET_H
38 
41 #include <OpenMS/CONCEPT/Types.h> // for "UInt"
43 #include <OpenMS/DATASTRUCTURES/ListUtils.h> // for "StringList"
46 
47 #include <set>
48 
49 namespace OpenMS
50 {
59  class OPENMS_DLLAPI ModificationDefinitionsSet
60  {
61 public:
62 
68 
71 
73  ModificationDefinitionsSet(const StringList& fixed_modifications, const StringList& variable_modifications);
74 
76  virtual ~ModificationDefinitionsSet();
78 
82  void setMaxModifications(Size max_mod);
84 
86  Size getMaxModifications() const;
87 
89  Size getNumberOfModifications() const;
90 
92  Size getNumberOfFixedModifications() const;
93 
95  Size getNumberOfVariableModifications() const;
96 
98  void addModification(const ModificationDefinition& mod_def);
99 
101  void setModifications(const std::set<ModificationDefinition>& mod_defs);
102 
109  void setModifications(const String& fixed_modifications, const String& variable_modifications);
110 
112  void setModifications(const StringList& fixed_modifications, const StringList& variable_modifications);
113 
115  std::set<ModificationDefinition> getModifications() const;
116 
118  const std::set<ModificationDefinition>& getFixedModifications() const;
119 
121  const std::set<ModificationDefinition>& getVariableModifications() const;
122 
124  std::set<String> getModificationNames() const;
125 
127  void getModificationNames(StringList& fixed_modifications, StringList& variable_modifications) const;
128 
130  std::set<String> getFixedModificationNames() const;
131 
133  std::set<String> getVariableModificationNames() const;
135 
139  ModificationDefinitionsSet& operator=(const ModificationDefinitionsSet& element);
142 
146  bool isCompatible(const AASequence& peptide) const;
148 
150  bool operator==(const ModificationDefinitionsSet& rhs) const;
151 
153  bool operator!=(const ModificationDefinitionsSet& rhs) const;
155 
170  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;
171 
173  void inferFromPeptides(const std::vector<PeptideIdentification>& peptides);
174 
175 protected:
176 
177  std::set<ModificationDefinition> variable_mods_;
178 
179  std::set<ModificationDefinition> fixed_mods_;
180 
182 
184  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);
185 
186  };
187 
188 } // namespace OpenMS
189 
190 #endif
std::set< ModificationDefinition > fixed_mods_
Definition: ModificationDefinitionsSet.h:179
A more convenient string class.
Definition: String.h:57
Definition: ResidueModification.h:103
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
Representation of a peptide/protein sequence.
Definition: AASequence.h:108
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:59
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:96
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:74
Representation of modification definition.
Definition: ModificationDefinition.h:53
std::set< ModificationDefinition > variable_mods_
Definition: ModificationDefinitionsSet.h:177
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
Size max_mods_per_peptide_
Definition: ModificationDefinitionsSet.h:181

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:02 using doxygen 1.8.13