Package org.biojava.bio.proteomics
Class Protease
- java.lang.Object
-
- org.biojava.bio.proteomics.Protease
-
- All Implemented Interfaces:
java.io.Serializable
public class Protease extends java.lang.Object implements java.io.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:
- Serialized Form
-
-
Field Summary
Fields Modifier and Type Field Description static java.lang.String
ARG_C
static java.lang.String
ASP_N
static java.lang.String
CHYMOTRYP
static java.lang.String
CNBr
static java.lang.String
GLU_C_BICARB
static java.lang.String
GLU_C_PHOS
static java.lang.String
LYS_C
static java.lang.String
TRYPSIN
-
Constructor Summary
Constructors Modifier Constructor Description Protease(java.lang.String cleavageRes, boolean endoProtease)
Deprecated.Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())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())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)
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description SymbolList
getCleaveageResidues()
The list of residues that the protease will cleave at.java.lang.String
getName()
Gets the name of this ProteaseSymbolList
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()
protected java.lang.Object
readResolve()
Prevent duplication of the object during Serialization
-
-
-
Field Detail
-
TRYPSIN
public static final java.lang.String TRYPSIN
- See Also:
- Constant Field Values
-
LYS_C
public static final java.lang.String LYS_C
- See Also:
- Constant Field Values
-
ARG_C
public static final java.lang.String ARG_C
- See Also:
- Constant Field Values
-
ASP_N
public static final java.lang.String ASP_N
- See Also:
- Constant Field Values
-
GLU_C_BICARB
public static final java.lang.String GLU_C_BICARB
- See Also:
- Constant Field Values
-
GLU_C_PHOS
public static final java.lang.String GLU_C_PHOS
- See Also:
- Constant Field Values
-
CHYMOTRYP
public static final java.lang.String CHYMOTRYP
- See Also:
- Constant Field Values
-
CNBr
public static final java.lang.String CNBr
- See Also:
- Constant Field Values
-
-
Constructor Detail
-
Protease
protected Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, java.lang.String name) throws IllegalSymbolException
- Throws:
IllegalSymbolException
-
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
-
Protease
public Protease(java.lang.String cleaveRes, boolean endoProtease, java.lang.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
-
Protease
public Protease(java.lang.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
-
-
Method Detail
-
getCleaveageResidues
public SymbolList getCleaveageResidues()
The list of residues that the protease will cleave at.- Returns:
- the residues as a SymbolList
-
getName
public java.lang.String getName()
Gets the name of this Protease- Returns:
- the name as a String
-
getNotCleaveResidues
public SymbolList getNotCleaveResidues()
The list of residues that will prevent cleavage if they follow the cleavage residue.
-
isEndoProtease
public boolean isEndoProtease()
-
getProteaseList
public static java.lang.String[] getProteaseList()
Get the list of Protease names defined in the ProteaseManager (Internally calls ProteaseManager.- Returns:
- A String array of protease names
-
getProteaseByName
public static final Protease getProteaseByName(java.lang.String proteaseName) throws BioException
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
-
readResolve
protected java.lang.Object readResolve() throws java.io.ObjectStreamException
Prevent duplication of the object during Serialization- Throws:
java.io.ObjectStreamException
-
-