public final class ProteaseManager
extends Object 

Author:

Mark Schreiber

• Field Summary

  Fields

  Modifier and Type	Field and Description
  static String	ARG_C
  static String	ASP_N
  static String	CHYMOTRYP
  static String	CNBr
  static String	GLU_C_BICARB
  static String	GLU_C_PHOS
  static String	LYS_C
  static String	TRYPSIN

• Constructor Summary

  Constructors

  Constructor and Description
  ProteaseManager ()

• Method Summary

  All Methods

  Modifier and Type	Method and Description
  static Protease	createProtease (String cleaveRes, boolean endoProtease, String name)
  static Protease	createProtease (String cleaveRes, boolean endoProtease, String notCleaveRes, String name)
  static Protease	createProtease (SymbolList cleaveRes, boolean endoProtease, String name)
  static Protease	createProtease (SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name) Creates and registers a new Protease.
  static Set	getAllProteases ()
  static Protease	getArg_C ()
  static Protease	getAsp_N ()
  static Protease	getChymotrypsin ()
  static Protease	getCNBr ()
  static Protease	getGlu_C_bicarbonate ()
  static Protease	getGlu_C_phosphate ()
  static ProteaseManager	getInstance ()
  static Protease	getLys_C ()
  static Set	getNames ()
  static Protease	getProteaseByName (String proteaseName) Gets a Protease instance by name.
  static Protease	getTrypsin ()
  static boolean	registered (String proteaseName) Has a Protease been registered with that name?
  static void	registerProtease (Protease prot) Registers a protease and ensures its flyweight status

  • Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

• Field Detail

  • TRYPSIN

    public static final String TRYPSIN 

    See Also:

    Constant Field Values

  • LYS_C

    public static final String LYS_C 

    See Also:

    Constant Field Values

  • ARG_C

    public static final String ARG_C 

    See Also:

    Constant Field Values

  • ASP_N

    public static final String ASP_N 

    See Also:

    Constant Field Values

  • GLU_C_BICARB

    public static final String GLU_C_BICARB 

    See Also:

    Constant Field Values

  • GLU_C_PHOS

    public static final String GLU_C_PHOS 

    See Also:

    Constant Field Values

  • CHYMOTRYP

    public static final String CHYMOTRYP 

    See Also:

    Constant Field Values

  • CNBr

    public static final String CNBr 

    See Also:

    Constant Field Values

• Constructor Detail

  • ProteaseManager

    public ProteaseManager()

• Method Detail

  • 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