org.biojava.bio.proteomics
Class Protease

java.lang.Object
  extended by 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
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
  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
 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


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