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java.lang.Objectorg.biojava.bio.proteomics.ProteaseManager
Registry and utility methods for Proteases.
Field Summary | |
static java.lang.String |
ARG_C
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static java.lang.String |
ASP_N
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static java.lang.String |
CHYMOTRYP
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static java.lang.String |
CNBr
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static java.lang.String |
GLU_C_BICARB
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static java.lang.String |
GLU_C_PHOS
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static java.lang.String |
LYS_C
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static java.lang.String |
TRYPSIN
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Constructor Summary | |
ProteaseManager()
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Method Summary | |
static Protease |
createProtease(java.lang.String cleaveRes,
boolean endoProtease,
java.lang.String name)
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static Protease |
createProtease(java.lang.String cleaveRes,
boolean endoProtease,
java.lang.String notCleaveRes,
java.lang.String name)
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static Protease |
createProtease(SymbolList cleaveRes,
boolean endoProtease,
java.lang.String name)
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static Protease |
createProtease(SymbolList cleaveRes,
boolean endoProtease,
SymbolList notCleaveRes,
java.lang.String name)
Creates and registers a new Protease. |
static java.util.Set |
getAllProteases()
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static Protease |
getArg_C()
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static Protease |
getAsp_N()
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static Protease |
getChymotrypsin()
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static Protease |
getCNBr()
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static Protease |
getGlu_C_bicarbonate()
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static Protease |
getGlu_C_phosphate()
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static ProteaseManager |
getInstance()
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static Protease |
getLys_C()
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static java.util.Set |
getNames()
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static Protease |
getProteaseByName(java.lang.String proteaseName)
Gets a Protease instance by name. |
static Protease |
getTrypsin()
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static boolean |
registered(java.lang.String proteaseName)
Has a Protease been registered with that name? |
static void |
registerProtease(Protease prot)
Registers a protease and ensures its flyweight status |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
public static final java.lang.String TRYPSIN
public static final java.lang.String LYS_C
public static final java.lang.String ARG_C
public static final java.lang.String ASP_N
public static final java.lang.String GLU_C_BICARB
public static final java.lang.String GLU_C_PHOS
public static final java.lang.String CHYMOTRYP
public static final java.lang.String CNBr
Constructor Detail |
public ProteaseManager()
Method Detail |
public static Protease createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, java.lang.String name) throws IllegalSymbolException, BioException
cleaveRes
- the cleavege residuesendoProtease
- is it an endo protease?notCleaveRes
- the exceptions to the cleavage residuesname
- the name of the Protease
IllegalSymbolException
- if the cleaveRes or notCleaveRes are not
from the PROTEIN alphabet
BioException
- if a Protease with the same name already exists.public static Protease createProtease(SymbolList cleaveRes, boolean endoProtease, java.lang.String name) throws IllegalSymbolException, BioException
IllegalSymbolException
BioException
public static Protease createProtease(java.lang.String cleaveRes, boolean endoProtease, java.lang.String notCleaveRes, java.lang.String name) throws BioException, IllegalSymbolException
BioException
IllegalSymbolException
public static Protease createProtease(java.lang.String cleaveRes, boolean endoProtease, java.lang.String name) throws BioException, IllegalSymbolException
BioException
IllegalSymbolException
public static void registerProtease(Protease prot) throws BioException
prot
- the Protease to register
BioException
- if a Protease with the same name is already registered.public static Protease getProteaseByName(java.lang.String proteaseName) throws BioException
proteaseName
- the name of a registered Protease (case sensistive)
BioException
- if no protease is registered by that namepublic static java.util.Set getNames()
public static java.util.Set getAllProteases()
public static boolean registered(java.lang.String proteaseName)
proteaseName
- the query
public static ProteaseManager getInstance()
public static Protease getTrypsin()
public static Protease getLys_C()
public static Protease getArg_C()
public static Protease getAsp_N()
public static Protease getGlu_C_bicarbonate()
public static Protease getGlu_C_phosphate()
public static Protease getChymotrypsin()
public static Protease getCNBr()
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