Class Protease

  • All Implemented Interfaces:
    java.io.Serializable

    public class Protease
    extends java.lang.Object
    implements java.io.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 java.lang.String ARG_C  
      static java.lang.String ASP_N  
      static java.lang.String CHYMOTRYP  
      static java.lang.String CNBr  
      static java.lang.String GLU_C_BICARB  
      static java.lang.String GLU_C_PHOS  
      static java.lang.String LYS_C  
      static java.lang.String TRYPSIN  
    • Constructor Summary

      Constructors 
      Modifier Constructor Description
        Protease​(java.lang.String cleavageRes, boolean endoProtease)
      Deprecated.
      Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
        Protease​(java.lang.String cleaveRes, boolean endoProtease, java.lang.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, java.lang.String name)  
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      SymbolList getCleaveageResidues()
      The list of residues that the protease will cleave at.
      java.lang.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​(java.lang.String proteaseName)
      Retrieves a reference to the named Protease.
      static java.lang.String[] getProteaseList()
      Get the list of Protease names defined in the ProteaseManager (Internally calls ProteaseManager.
      boolean isEndoProtease()  
      protected java.lang.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
    • Method Detail

      • getCleaveageResidues

        public SymbolList getCleaveageResidues()
        The list of residues that the protease will cleave at.
        Returns:
        the residues as a SymbolList
      • getName

        public java.lang.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 java.lang.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​(java.lang.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 java.lang.Object readResolve()
                                        throws java.io.ObjectStreamException
        Prevent duplication of the object during Serialization
        Throws:
        java.io.ObjectStreamException