ModificationsDB Member List

This is the complete list of members for ModificationsDB, including all inherited members.

AASequence class	ModificationsDB	friend
addModification(std::unique_ptr< ResidueModification > new_mod)	ModificationsDB
addModification(const ResidueModification &new_mod)	ModificationsDB
addNewModification_(const ResidueModification &new_mod)	ModificationsDB	private
CrossLinksDB class	ModificationsDB	friend
findModificationIndex(const String &mod_name) const	ModificationsDB
getAllSearchModifications(std::vector< String > &modifications) const	ModificationsDB
getBestModificationByDiffMonoMass(double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)	ModificationsDB
getInstance()	ModificationsDB	static
getModification(Size index) const	ModificationsDB
getModification(const String &mod_name, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const	ModificationsDB
getNumberOfModifications() const	ModificationsDB
has(const String &modification) const	ModificationsDB
initializeModificationsDB(OpenMS::String unimod_file="CHEMISTRY/unimod.xml", OpenMS::String custommod_file="CHEMISTRY/custom_mods.xml", OpenMS::String psimod_file="CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file="CHEMISTRY/XLMOD.obo")	ModificationsDB	static
is_instantiated_	ModificationsDB	protectedstatic
isInstantiated()	ModificationsDB	static
modification_names_	ModificationsDB	protected
ModificationsDB(const OpenMS::String &unimod_file="CHEMISTRY/unimod.xml", const OpenMS::String &custommod_file="CHEMISTRY/custom_mods.xml", const OpenMS::String &psimod_file="CHEMISTRY/PSI-MOD.obo", const OpenMS::String &xlmod_file="CHEMISTRY/XLMOD.obo")	ModificationsDB	explicitprivate
ModificationsDB(const ModificationsDB &residue_db)	ModificationsDB	private
mods_	ModificationsDB	protected
operator=(const ModificationsDB &aa)	ModificationsDB	private
readFromOBOFile(const String &filename)	ModificationsDB	private
readFromUnimodXMLFile(const String &filename)	ModificationsDB	private
Residue class	ModificationsDB	friend
residuesMatch_(const char residue, const ResidueModification *curr_mod) const	ModificationsDB	protected
searchModification(const ResidueModification &mod_in) const	ModificationsDB
searchModifications(std::set< const ResidueModification * > &mods, const String &mod_name, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const	ModificationsDB
searchModificationsByDiffMonoMass(std::vector< String > &mods, double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)	ModificationsDB
searchModificationsByDiffMonoMass(std::vector< const ResidueModification * > &mods, double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)	ModificationsDB
searchModificationsByDiffMonoMassSorted(std::vector< String > &mods, double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)	ModificationsDB
searchModificationsByDiffMonoMassSorted(std::vector< const ResidueModification * > &mods, double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)	ModificationsDB
searchModificationsFast(const String &mod_name, bool &multiple_matches, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const	ModificationsDB
writeTSV(const String &filename)	ModificationsDB
~ModificationsDB()	ModificationsDB	privatevirtual