All Implemented Interfaces:

Serializable

public class Protease
extends Object
implements Serializable 

Author:

Michael Jones, Mark Schreiber (refactoring to ProteaseManager)

See Also:

Serialized Form

• 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

  Modifier	Constructor and 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

  All Methods

  Modifier and Type	Method and 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