Class ProteaseManager


  • public final class ProteaseManager
    extends java.lang.Object
    Registry and utility methods for Proteases.
    Author:
    Mark Schreiber
    • Constructor Detail

      • ProteaseManager

        public ProteaseManager()
    • Method Detail

      • createProtease

        public static Protease createProtease​(SymbolList cleaveRes,
                                              boolean endoProtease,
                                              SymbolList notCleaveRes,
                                              java.lang.String name)
                                       throws IllegalSymbolException,
                                              BioException
        Creates and registers a new Protease. In future the Protease can be recovered using the getProteaseByName() method.
        Parameters:
        cleaveRes - the cleavege residues
        endoProtease - is it an endo protease?
        notCleaveRes - the exceptions to the cleavage residues
        name - the name of the Protease
        Returns:
        a reference to the new Protease
        Throws:
        IllegalSymbolException - if the cleaveRes or notCleaveRes are not from the PROTEIN alphabet
        BioException - if a Protease with the same name already exists.
      • registerProtease

        public static void registerProtease​(Protease prot)
                                     throws BioException
        Registers a protease and ensures its flyweight status
        Parameters:
        prot - the Protease to register
        Throws:
        BioException - if a Protease with the same name is already registered.
      • getProteaseByName

        public static Protease getProteaseByName​(java.lang.String proteaseName)
                                          throws BioException
        Gets a Protease instance by name.
        Parameters:
        proteaseName - the name of a registered Protease (case sensistive)
        Returns:
        a fly-weight Protease instance
        Throws:
        BioException - if no protease is registered by that name
      • getNames

        public static java.util.Set getNames()
        Returns:
        an unmodifiable Set of all the registered Protease names (Strings).
      • getAllProteases

        public static java.util.Set getAllProteases()
        Returns:
        an unmodifiable set of all the registered Protease objects.
      • registered

        public static boolean registered​(java.lang.String proteaseName)
        Has a Protease been registered with that name?
        Parameters:
        proteaseName - the query
        Returns:
        true if one has, false otherwise
      • getInstance

        public static ProteaseManager getInstance()
        Returns:
        a reference to the singleton instance of the ProteaseManager
      • getTrypsin

        public static Protease getTrypsin()
        Returns:
        a flywieght instance of Trypsin
      • getLys_C

        public static Protease getLys_C()
        Returns:
        a flywieght instance of Lys-C
      • getArg_C

        public static Protease getArg_C()
        Returns:
        a flywieght instance of Arg-C
      • getAsp_N

        public static Protease getAsp_N()
        Returns:
        a flywieght instance of Asp-N
      • getGlu_C_bicarbonate

        public static Protease getGlu_C_bicarbonate()
        Returns:
        a flywieght instance of Glu_C_bicarbonate
      • getGlu_C_phosphate

        public static Protease getGlu_C_phosphate()
        Returns:
        a flywieght instance of Glu_C_phosphate
      • getChymotrypsin

        public static Protease getChymotrypsin()
        Returns:
        a flywieght instance of Chymotrypsin
      • getCNBr

        public static Protease getCNBr()
        Returns:
        a flywieght instance of CNBr