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java.lang.Objectorg.biojava.bio.proteomics.Protease
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.
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 | |
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Protease(java.lang.String cleavageRes,
boolean endoProtease)
Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease()) |
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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()) |
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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)
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Method Summary | |
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()
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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 |
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 |
protected Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, java.lang.String name) throws IllegalSymbolException
public Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes) throws IllegalSymbolException, BioException
public Protease(java.lang.String cleaveRes, boolean endoProtease, java.lang.String notCleaveRes) throws IllegalSymbolException, BioException
public Protease(java.lang.String cleavageRes, boolean endoProtease) throws IllegalSymbolException, BioException
Method Detail |
public SymbolList getCleaveageResidues()
public java.lang.String getName()
public SymbolList getNotCleaveResidues()
public boolean isEndoProtease()
public static java.lang.String[] getProteaseList()
public static final Protease getProteaseByName(java.lang.String proteaseName) throws BioException
proteaseName
- A protease name that is registered in the ProteaseManager (case sensitive)
BioException
protected java.lang.Object readResolve() throws java.io.ObjectStreamException
java.io.ObjectStreamException
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