org.expasy.mzjava.proteomics.mol.digest

Enum Protease

java.lang.Object

java.lang.Enum<Protease>

org.expasy.mzjava.proteomics.mol.digest.Protease

All Implemented Interfaces:

Serializable, Comparable<Protease>, CleavageSiteFinder

public enum Protease
extends Enum<Protease>
implements CleavageSiteFinder

http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

The bottom of the page has a table of the rules.

Author:

fnikitin, Oliver Horlacher

Enum Constant Summary

Enum Constants

Enum Constant and Description
ARG_C
ASP_N
BNPS_SKATOLE
CASPASE_1
CASPASE_10
CASPASE_2
CASPASE_3
CASPASE_4
CASPASE_5
CASPASE_6
CASPASE_7
CASPASE_8
CASPASE_9
CHYMOTRYPSIN_FYL
CHYMOTRYPSIN_FYLW
CHYMOTRYPSIN_HIGH_SPEC
CHYMOTRYPSIN_LOW_SPEC
CNBR
ENTEROKINASE
GLU_C_BICARBONATE
GLU_C_PHOSPHATE
LYS_C
PEPSINE_PH_1_3
PEPSINE_PH_GT_2
PROTEINASE_K
THERMOLYSINE
TRYPSIN

Method Summary

Methods

Modifier and Type	Method and Description
int	countCleavageSites(SymbolSequence<AminoAcid> aaSeq) Get the number of potential cleavage sites
void	find(SymbolSequence<AminoAcid> aaSeq, gnu.trove.list.TIntList sites) Find potential cleavage sites over the given amino-acid sequence
CleavageSiteMatcher	getCleavageSiteMatcher() Get the cleavage site matcher
static Protease	valueOf(String name) Returns the enum constant of this type with the specified name.
static Protease[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

TRYPSIN

public static final Protease TRYPSIN

CASPASE_1

public static final Protease CASPASE_1

CASPASE_2

public static final Protease CASPASE_2

CASPASE_3

public static final Protease CASPASE_3

CASPASE_4

public static final Protease CASPASE_4

CASPASE_5

public static final Protease CASPASE_5

CASPASE_6

public static final Protease CASPASE_6

CASPASE_7

public static final Protease CASPASE_7

CASPASE_8

public static final Protease CASPASE_8

CASPASE_9

public static final Protease CASPASE_9

CASPASE_10

public static final Protease CASPASE_10

CHYMOTRYPSIN_FYLW

public static final Protease CHYMOTRYPSIN_FYLW

CHYMOTRYPSIN_FYL

public static final Protease CHYMOTRYPSIN_FYL

CHYMOTRYPSIN_HIGH_SPEC

public static final Protease CHYMOTRYPSIN_HIGH_SPEC

CHYMOTRYPSIN_LOW_SPEC

public static final Protease CHYMOTRYPSIN_LOW_SPEC

ENTEROKINASE

public static final Protease ENTEROKINASE

LYS_C

public static final Protease LYS_C

ARG_C

public static final Protease ARG_C

CNBR

public static final Protease CNBR

ASP_N

public static final Protease ASP_N

BNPS_SKATOLE

public static final Protease BNPS_SKATOLE

GLU_C_BICARBONATE

public static final Protease GLU_C_BICARBONATE

GLU_C_PHOSPHATE

public static final Protease GLU_C_PHOSPHATE

PEPSINE_PH_1_3

public static final Protease PEPSINE_PH_1_3

PEPSINE_PH_GT_2

public static final Protease PEPSINE_PH_GT_2

PROTEINASE_K

public static final Protease PROTEINASE_K

THERMOLYSINE

public static final Protease THERMOLYSINE

Method Detail

values

public static Protease[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (Protease c : Protease.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static Protease valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

find

public void find(SymbolSequence<AminoAcid> aaSeq,
        gnu.trove.list.TIntList sites)

Description copied from interface: CleavageSiteFinder

Find potential cleavage sites over the given amino-acid sequence

Specified by:

find in interface CleavageSiteFinder

countCleavageSites

public int countCleavageSites(SymbolSequence<AminoAcid> aaSeq)

Description copied from interface: CleavageSiteFinder

Get the number of potential cleavage sites

Specified by:

countCleavageSites in interface CleavageSiteFinder

getCleavageSiteMatcher

public CleavageSiteMatcher getCleavageSiteMatcher()

Description copied from interface: CleavageSiteFinder

Get the cleavage site matcher

Specified by:

getCleavageSiteMatcher in interface CleavageSiteFinder