Package org.biojava.bio.proteomics
Class ProteaseManager
java.lang.Object
org.biojava.bio.proteomics.ProteaseManager
Registry and utility methods for Proteases.
- Author:
- Mark Schreiber
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic Protease
createProtease
(String cleaveRes, boolean endoProtease, String name) static Protease
createProtease
(String cleaveRes, boolean endoProtease, String notCleaveRes, String name) static Protease
createProtease
(SymbolList cleaveRes, boolean endoProtease, String name) static Protease
createProtease
(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name) Creates and registers a new Protease.static Set
static Protease
getArg_C()
static Protease
getAsp_N()
static Protease
static Protease
getCNBr()
static Protease
static Protease
static ProteaseManager
static Protease
getLys_C()
static Set
getNames()
static Protease
getProteaseByName
(String proteaseName) Gets a Protease instance by name.static Protease
static boolean
registered
(String proteaseName) Has a Protease been registered with that name?static void
registerProtease
(Protease prot) Registers a protease and ensures its flyweight status
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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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ProteaseManager
public ProteaseManager()
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Method Details
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createProtease
public static Protease createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name) throws IllegalSymbolException, BioException Creates and registers a new Protease. In future the Protease can be recovered using the getProteaseByName() method.- Parameters:
cleaveRes
- the cleavege residuesendoProtease
- is it an endo protease?notCleaveRes
- the exceptions to the cleavage residuesname
- the name of the Protease- Returns:
- a reference to the new Protease
- Throws:
IllegalSymbolException
- if the cleaveRes or notCleaveRes are not from the PROTEIN alphabetBioException
- if a Protease with the same name already exists.
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createProtease
public static Protease createProtease(SymbolList cleaveRes, boolean endoProtease, String name) throws IllegalSymbolException, BioException - Throws:
IllegalSymbolException
BioException
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createProtease
public static Protease createProtease(String cleaveRes, boolean endoProtease, String notCleaveRes, String name) throws BioException, IllegalSymbolException - Throws:
BioException
IllegalSymbolException
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createProtease
public static Protease createProtease(String cleaveRes, boolean endoProtease, String name) throws BioException, IllegalSymbolException - Throws:
BioException
IllegalSymbolException
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registerProtease
Registers a protease and ensures its flyweight status- Parameters:
prot
- the Protease to register- Throws:
BioException
- if a Protease with the same name is already registered.
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getProteaseByName
Gets a Protease instance by name.- Parameters:
proteaseName
- the name of a registered Protease (case sensistive)- Returns:
- a fly-weight Protease instance
- Throws:
BioException
- if no protease is registered by that name
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getNames
- Returns:
- an unmodifiable Set of all the registered Protease names (Strings).
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getAllProteases
- Returns:
- an unmodifiable set of all the registered Protease objects.
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registered
Has a Protease been registered with that name?- Parameters:
proteaseName
- the query- Returns:
- true if one has, false otherwise
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getInstance
- Returns:
- a reference to the singleton instance of the ProteaseManager
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getTrypsin
- Returns:
- a flywieght instance of Trypsin
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getLys_C
- Returns:
- a flywieght instance of Lys-C
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getArg_C
- Returns:
- a flywieght instance of Arg-C
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getAsp_N
- Returns:
- a flywieght instance of Asp-N
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getGlu_C_bicarbonate
- Returns:
- a flywieght instance of Glu_C_bicarbonate
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getGlu_C_phosphate
- Returns:
- a flywieght instance of Glu_C_phosphate
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getChymotrypsin
- Returns:
- a flywieght instance of Chymotrypsin
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getCNBr
- Returns:
- a flywieght instance of CNBr
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