Package org.biojava.bio.proteomics

Class Protease

java.lang.Object

org.biojava.bio.proteomics.Protease

All Implemented Interfaces:

Serializable

public class Protease
extends Object
implements Serializable

The protease class stores parameters needed by Digest to digest a protein sequence. A custom protease can be created or one derived from the attributes set in the ProteaseManager.xml resource.

Author:

Michael Jones, Mark Schreiber (refactoring to ProteaseManager)

See Also:

Serialized Form

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

Modifier	Constructor	Description
	Protease(String cleavageRes, boolean endoProtease)	Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
	Protease(String cleaveRes, boolean endoProtease, String notCleaveRes)	Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
	Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes)	Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
protected	Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name)

Method Summary

Modifier and Type	Method	Description
SymbolList	getCleaveageResidues()	The list of residues that the protease will cleave at.
String	getName()	Gets the name of this Protease
SymbolList	getNotCleaveResidues()	The list of residues that will prevent cleavage if they follow the cleavage residue.
static Protease	getProteaseByName(String proteaseName)	Retrieves a reference to the named Protease.
static String[]	getProteaseList()	Get the list of Protease names defined in the ProteaseManager (Internally calls ProteaseManager.
boolean	isEndoProtease()
protected Object	readResolve()	Prevent duplication of the object during Serialization

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

Protease

protected Protease(SymbolList cleaveRes,
                   boolean endoProtease,
                   SymbolList notCleaveRes,
                   String name)
            throws IllegalSymbolException

Throws:

IllegalSymbolException

Protease

public Protease(SymbolList cleaveRes,
                boolean endoProtease,
                SymbolList notCleaveRes)
         throws IllegalSymbolException,
                BioException

Deprecated.

Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())

Throws:

IllegalSymbolException

BioException

Protease

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

Deprecated.

Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())

Throws:

IllegalSymbolException

BioException

Protease

public Protease(String cleavageRes,
                boolean endoProtease)
         throws IllegalSymbolException,
                BioException

Deprecated.

Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())

Throws:

IllegalSymbolException

BioException

Method Detail

getCleaveageResidues

public SymbolList getCleaveageResidues()

The list of residues that the protease will cleave at.

Returns:

the residues as a SymbolList

getName

public String getName()

Gets the name of this Protease

Returns:

the name as a String

getNotCleaveResidues

public SymbolList getNotCleaveResidues()

The list of residues that will prevent cleavage if they follow the cleavage residue.

isEndoProtease

public boolean isEndoProtease()

getProteaseList

public static String[] getProteaseList()

Get the list of Protease names defined in the ProteaseManager (Internally calls ProteaseManager.

Returns:

A String array of protease names

getProteaseByName

public static final Protease getProteaseByName(String proteaseName)
                                        throws BioException

Retrieves a reference to the named Protease. (Internally calls ProteaseManager.getProteaseByName())

Parameters:

proteaseName - A protease name that is registered in the ProteaseManager (case sensitive)

Returns:

A Protease instance for the given protease name

Throws:

BioException

readResolve

protected Object readResolve()
                      throws ObjectStreamException

Prevent duplication of the object during Serialization

Throws:

ObjectStreamException