Package 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

Fields

Modifier and Type	Field	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	Description
ProteaseManager()

Method Summary

Modifier and Type	Method	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