81 void setMaxModifications(
Size max_mod);
85 Size getMaxModifications()
const;
88 Size getNumberOfModifications()
const;
91 Size getNumberOfFixedModifications()
const;
94 Size getNumberOfVariableModifications()
const;
100 void setModifications(
const std::set<ModificationDefinition>& mod_defs);
108 void setModifications(
const String& fixed_modifications,
const String& variable_modifications);
111 void setModifications(
const StringList& fixed_modifications,
const StringList& variable_modifications);
114 std::set<ModificationDefinition> getModifications()
const;
117 const std::set<ModificationDefinition>& getFixedModifications()
const;
120 const std::set<ModificationDefinition>& getVariableModifications()
const;
123 std::set<String> getModificationNames()
const;
126 void getModificationNames(
StringList& fixed_modifications,
StringList& variable_modifications)
const;
129 std::set<String> getFixedModificationNames()
const;
132 std::set<String> getVariableModificationNames()
const;
145 bool isCompatible(
const AASequence& peptide)
const;
172 void inferFromPeptides(
const std::vector<PeptideIdentification>& peptides);
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);