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ModificationsDB Member List

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

AASequence classModificationsDBfriend
addModification(std::unique_ptr< ResidueModification > new_mod)ModificationsDB
addModification(const ResidueModification &new_mod)ModificationsDB
addNewModification_(const ResidueModification &new_mod)ModificationsDBprivate
CrossLinksDB classModificationsDBfriend
findModificationIndex(const String &mod_name) constModificationsDB
getAllSearchModifications(std::vector< String > &modifications) constModificationsDB
getBestModificationByDiffMonoMass(double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)ModificationsDB
getInstance()ModificationsDBstatic
getModification(Size index) constModificationsDB
getModification(const String &mod_name, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) constModificationsDB
getNumberOfModifications() constModificationsDB
has(const String &modification) constModificationsDB
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")ModificationsDBstatic
is_instantiated_ModificationsDBprotectedstatic
isInstantiated()ModificationsDBstatic
modification_names_ModificationsDBprotected
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")ModificationsDBexplicitprivate
ModificationsDB(const ModificationsDB &residue_db)ModificationsDBprivate
mods_ModificationsDBprotected
operator=(const ModificationsDB &aa)ModificationsDBprivate
readFromOBOFile(const String &filename)ModificationsDBprivate
readFromUnimodXMLFile(const String &filename)ModificationsDBprivate
Residue classModificationsDBfriend
residuesMatch_(const char residue, const ResidueModification *curr_mod) constModificationsDBprotected
searchModification(const ResidueModification &mod_in) constModificationsDB
searchModifications(std::set< const ResidueModification * > &mods, const String &mod_name, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) constModificationsDB
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) constModificationsDB
writeTSV(const String &filename)ModificationsDB
~ModificationsDB()ModificationsDBprivatevirtual