com.hfg.bio

Class Protease

java.lang.Object

com.hfg.bio.Protease

All Implemented Interfaces:

java.lang.Comparable

public class Protease
extends java.lang.Object
implements java.lang.Comparable

Chemical or biological proteolytic agent which can be used to theoretically digest a Protein.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	Protease.SlidingWindow

Field Summary

Fields

Modifier and Type	Field and Description
static Protease	ASP_N
static Protease	ASP_N_DE
static Protease	CHYMOTRYPSIN
static Protease	GLU_C
static Protease	LYS_C
static Protease	TRYPSIN

Constructor Summary

Constructors

Constructor and Description
Protease(java.lang.String inName)

Method Summary

Modifier and Type	Method and Description
int	compareTo(java.lang.Object inObj2)
java.util.List<DigestFragment>	digest(Protein inProtein, DigestSettings inSettings)
boolean	equals(java.lang.Object inObj2)
java.lang.String	getExcludedP1PrimeResidues()
java.lang.String	getExcludedP1Residues()
java.lang.String	getP1PrimeSpecificity()
java.lang.String	getP1Specificity()
int	hashCode()
boolean	isCleavageSite(char inP1Residue, char inP1PrimeResidue)
Protease	lock()
java.lang.String	name()
Protease	setExcludedP1PrimeResidues(java.lang.String inValue)
Protease	setExcludedP1Residues(java.lang.String inValue)
Protease	setP1PrimeSpecificity(java.lang.String inValue)
Protease	setP1Specificity(java.lang.String inValue)
java.lang.String	toString()
static Protease	valueOf(java.lang.String inName)
static Protease[]	values()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

TRYPSIN

public static final Protease TRYPSIN

LYS_C

public static final Protease LYS_C

CHYMOTRYPSIN

public static final Protease CHYMOTRYPSIN

GLU_C

public static final Protease GLU_C

ASP_N

public static final Protease ASP_N

ASP_N_DE

public static final Protease ASP_N_DE

Constructor Detail

Protease

public Protease(java.lang.String inName)

Method Detail

values

public static Protease[] values()

valueOf

public static Protease valueOf(java.lang.String inName)

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

equals

public boolean equals(java.lang.Object inObj2)

Overrides:

equals in class java.lang.Object

compareTo

public int compareTo(java.lang.Object inObj2)

Specified by:

compareTo in interface java.lang.Comparable

name

public java.lang.String name()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

setP1Specificity

public Protease setP1Specificity(java.lang.String inValue)

getP1Specificity

public java.lang.String getP1Specificity()

setExcludedP1PrimeResidues

public Protease setExcludedP1PrimeResidues(java.lang.String inValue)

getExcludedP1PrimeResidues

public java.lang.String getExcludedP1PrimeResidues()

setP1PrimeSpecificity

public Protease setP1PrimeSpecificity(java.lang.String inValue)

getP1PrimeSpecificity

public java.lang.String getP1PrimeSpecificity()

setExcludedP1Residues

public Protease setExcludedP1Residues(java.lang.String inValue)

getExcludedP1Residues

public java.lang.String getExcludedP1Residues()

lock

public Protease lock()

digest

public java.util.List<DigestFragment> digest(Protein inProtein,
                                             DigestSettings inSettings)

isCleavageSite

public boolean isCleavageSite(char inP1Residue,
                              char inP1PrimeResidue)