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void | readFromOBOFile (const String &filename) |
| Adds modifications from a given file in OBO format. More...
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void | getAllSearchModifications (std::vector< String > &modifications) const |
| Collects all modifications that can be used for identification searches. More...
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Size | getNumberOfModifications () const |
| Returns the number of modifications read from the unimod.xml file. More...
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const ResidueModification * | getModification (Size index) const |
| Returns the modification with the given index. note: out-of-bounds check is only performed in debug mode. More...
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void | searchModifications (std::set< const ResidueModification * > &mods, const String &mod_name, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const |
| Collects all modifications which have the given name as synonym. More...
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const ResidueModification * | searchModificationsFast (const String &mod_name, bool &multiple_matches, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const |
| Returns the modification which has the given name as synonym (fast version) More...
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const ResidueModification * | getModification (const String &mod_name, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const |
| Returns the modification with the given name. More...
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bool | has (const String &modification) const |
| Returns true if the modification exists. More...
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const ResidueModification * | addModification (std::unique_ptr< ResidueModification > new_mod) |
| Add a new modification to ModificationsDB. If the modification already exists (based on its fullID) it is not added. The function returns a pointer to the modification in the ModificationDB (which can be differ from input if mod was already present). More...
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Size | findModificationIndex (const String &mod_name) const |
| Returns the index of the modification in the mods_ vector; a unique name must be given. More...
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void | searchModificationsByDiffMonoMass (std::vector< String > &mods, double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) |
| Collects all modifications with matching delta mass. More...
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void | searchModificationsByDiffMonoMass (std::vector< const ResidueModification * > &mods, double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) |
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const ResidueModification * | getBestModificationByDiffMonoMass (double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) |
| Returns the best matching modification for the given delta mass and residue. More...
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void | getAllSearchModifications (std::vector< String > &modifications) const |
| Collects all modifications that can be used for identification searches. More...
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