## org.biojava.bio.proteomics
Class ProteaseManager

    java.lang.Object
      org.biojava.bio.proteomics.ProteaseManager

    public final class ProteaseManager

extends Object

Registry and utility methods for Proteases.

Author:
  Mark Schreiber

Field Summary
`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
`ProteaseManager()`

Method Summary
`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