Package org.biojava.bio.proteomics
Class Protease
java.lang.Object
org.biojava.bio.proteomics.Protease
- All Implemented Interfaces:
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:
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Field Summary
Fields -
Constructor Summary
ConstructorsModifierConstructorDescriptionDeprecated.Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())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 TypeMethodDescriptionThe list of residues that the protease will cleave at.getName()
Gets the name of this ProteaseThe list of residues that will prevent cleavage if they follow the cleavage residue.static final Protease
getProteaseByName
(String proteaseName) Retrieves a reference to the named Protease.static String[]
Get the list of Protease names defined in the ProteaseManager (Internally calls ProteaseManager.boolean
protected Object
Prevent duplication of the object during Serialization
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Field Details
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TRYPSIN
- See Also:
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LYS_C
- See Also:
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ARG_C
- See Also:
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ASP_N
- See Also:
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GLU_C_BICARB
- See Also:
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GLU_C_PHOS
- See Also:
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CHYMOTRYP
- See Also:
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CNBr
- See Also:
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Constructor Details
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Protease
protected Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name) throws IllegalSymbolException - Throws:
IllegalSymbolException
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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
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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
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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
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Method Details
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getCleaveageResidues
The list of residues that the protease will cleave at.- Returns:
- the residues as a SymbolList
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getName
Gets the name of this Protease- Returns:
- the name as a String
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getNotCleaveResidues
The list of residues that will prevent cleavage if they follow the cleavage residue. -
isEndoProtease
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getProteaseList
Get the list of Protease names defined in the ProteaseManager (Internally calls ProteaseManager.- Returns:
- A String array of protease names
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getProteaseByName
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
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readResolve
Prevent duplication of the object during Serialization- Throws:
ObjectStreamException
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