| OpenMS 2.5.0

ModificationDefinitionsSet.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
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34 //
35
36 #pragma once
37
38 #include <OpenMS/CHEMISTRY/AASequence.h>
39 #include <OpenMS/CHEMISTRY/ModificationDefinition.h>
40 #include <OpenMS/CONCEPT/Types.h> // for "UInt"
41 #include <OpenMS/DATASTRUCTURES/String.h>
42 #include <OpenMS/DATASTRUCTURES/ListUtils.h> // for "StringList"
43 #include <OpenMS/DATASTRUCTURES/StringListUtils.h>
44 #include <OpenMS/METADATA/PeptideIdentification.h>
45
46 #include <set>
47
48 namespace OpenMS
49 {
58 class OPENMS_DLLAPI ModificationDefinitionsSet
59 {
60 public:
61
65 ModificationDefinitionsSet();
67
69 ModificationDefinitionsSet(const ModificationDefinitionsSet& rhs);
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
180 Size max_mods_per_peptide_;
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
OpenMS::String
A more convenient string class.
Definition: String.h:58
AASequence.h
OpenMS::ModificationDefinitionsSet::max_mods_per_peptide_
Size max_mods_per_peptide_
Definition: ModificationDefinitionsSet.h:180
OpenMS::ModificationDefinitionsSet::variable_mods_
std::set< ModificationDefinition > variable_mods_
Definition: ModificationDefinitionsSet.h:176
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
ModificationDefinition.h
Types.h
OpenMS::ModificationDefinitionsSet::fixed_mods_
std::set< ModificationDefinition > fixed_mods_
Definition: ModificationDefinitionsSet.h:178
StringListUtils.h
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::ModificationDefinition
Representation of modification definition.
Definition: ModificationDefinition.h:52
String.h
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::ModificationDefinitionsSet
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:58
OpenMS::ResidueModification::TermSpecificity
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:95
OpenMS::ResidueModification::NUMBER_OF_TERM_SPECIFICITY
Definition: ResidueModification.h:102
ListUtils.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806