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java.lang.Objectorg.biojava.bio.proteomics.Protease
public class 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 | |
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static String |
ARG_C
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static String |
ASP_N
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static String |
CHYMOTRYP
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static String |
CNBr
|
static String |
GLU_C_BICARB
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static String |
GLU_C_PHOS
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static String |
LYS_C
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static String |
TRYPSIN
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Constructor Summary | |
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Protease(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(String cleaveRes,
boolean endoProtease,
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,
String name)
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Method Summary | |
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SymbolList |
getCleaveageResidues()
The list of residues that the protease will cleave at. |
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(String proteaseName)
Retrieves a reference to the named Protease. |
static String[] |
getProteaseList()
Get the list of Protease names defined in the ProteaseManager (Internally calls ProteaseManager. |
boolean |
isEndoProtease()
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protected Object |
readResolve()
Prevent duplication of the object during Serialization |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final String TRYPSIN
public static final String LYS_C
public static final String ARG_C
public static final String ASP_N
public static final String GLU_C_BICARB
public static final String GLU_C_PHOS
public static final String CHYMOTRYP
public static final String CNBr
Constructor Detail |
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protected Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name) throws IllegalSymbolException
IllegalSymbolException
public Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes) throws IllegalSymbolException, BioException
IllegalSymbolException
BioException
public Protease(String cleaveRes, boolean endoProtease, String notCleaveRes) throws IllegalSymbolException, BioException
IllegalSymbolException
BioException
public Protease(String cleavageRes, boolean endoProtease) throws IllegalSymbolException, BioException
IllegalSymbolException
BioException
Method Detail |
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public SymbolList getCleaveageResidues()
public String getName()
public SymbolList getNotCleaveResidues()
public boolean isEndoProtease()
public static String[] getProteaseList()
public static final Protease getProteaseByName(String proteaseName) throws BioException
proteaseName
- A protease name that is registered in the ProteaseManager (case sensitive)
BioException
protected Object readResolve() throws ObjectStreamException
ObjectStreamException
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