Class ProteaseManager

Method Details

• createProtease

  public static Protease createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, 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.

• createProtease

  public static Protease createProtease(SymbolList cleaveRes, boolean endoProtease, String name) throws IllegalSymbolException, BioException

  Throws:

  IllegalSymbolException

  BioException

• createProtease

  public static Protease createProtease(String cleaveRes, boolean endoProtease, String notCleaveRes, String name) throws BioException, IllegalSymbolException

  Throws:

  BioException

  IllegalSymbolException

• createProtease

  public static Protease createProtease(String cleaveRes, boolean endoProtease, String name) throws BioException, IllegalSymbolException

  Throws:

  BioException

  IllegalSymbolException

• 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(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 Set getNames()

  Returns:

  an unmodifiable Set of all the registered Protease names (Strings).

• getAllProteases

  public static Set getAllProteases()

  Returns:

  an unmodifiable set of all the registered Protease objects.

• registered

  public static boolean registered(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