com.hfg.bio.molbio

Class RestrictionEnzyme

java.lang.Object

com.hfg.bio.seq.pattern.SeqPattern<NucleicAcid,T>

com.hfg.bio.seq.pattern.NucleotidePattern<RestrictionSite>

com.hfg.bio.molbio.RestrictionEnzyme

All Implemented Interfaces:

Cloneable

public class RestrictionEnzyme
extends NucleotidePattern<RestrictionSite>

Restriction enzyme is an endonuclease used for cutting DNA/RNA at specific locations.

Field Summary

Fields

Modifier and Type	Field and Description
static RestrictionEnzyme	AarI
static RestrictionEnzyme	AatII
static RestrictionEnzyme	Acc65I
static RestrictionEnzyme	AccI
static RestrictionEnzyme	AciI
static RestrictionEnzyme	AcII
static RestrictionEnzyme	AcuI
static RestrictionEnzyme	AfeI
static RestrictionEnzyme	AflII
static RestrictionEnzyme	AflIII
static RestrictionEnzyme	AgeI
static RestrictionEnzyme	AhdI
static RestrictionEnzyme	AleI
static RestrictionEnzyme	AluI
static RestrictionEnzyme	AlwI
static RestrictionEnzyme	AlwNI
static RestrictionEnzyme	ApaI
static RestrictionEnzyme	ApaLI
static RestrictionEnzyme	ApoI
static RestrictionEnzyme	AscI
static RestrictionEnzyme	AseI
static RestrictionEnzyme	AsiSI
static RestrictionEnzyme	AvaI
static RestrictionEnzyme	AvaII
static RestrictionEnzyme	AvrII
static RestrictionEnzyme	BaeGI
static RestrictionEnzyme	BaeI
static RestrictionEnzyme	BamHI
static RestrictionEnzyme	BanI
static RestrictionEnzyme	BanII
static RestrictionEnzyme	BbsI
static RestrictionEnzyme	BbvCI
static RestrictionEnzyme	BbvI
static RestrictionEnzyme	BccI
static RestrictionEnzyme	BceAI
static RestrictionEnzyme	BcgI
static RestrictionEnzyme	BciVI
static RestrictionEnzyme	BclI
static RestrictionEnzyme	BfaI
static RestrictionEnzyme	BglI
static RestrictionEnzyme	BglII
static RestrictionEnzyme	BlpI
static RestrictionEnzyme	BmgBI
static RestrictionEnzyme	BmrI
static RestrictionEnzyme	BmtI
static RestrictionEnzyme	BpmI
static RestrictionEnzyme	Bpu10I
static RestrictionEnzyme	BpuEI
static RestrictionEnzyme	BsaAI
static RestrictionEnzyme	BsaBI
static RestrictionEnzyme	BsaHI
static RestrictionEnzyme	BsaI
static RestrictionEnzyme	BsaJI
static RestrictionEnzyme	BsaWI
static RestrictionEnzyme	BsaXI
static RestrictionEnzyme	BseRI
static RestrictionEnzyme	BseYI
static RestrictionEnzyme	BsgI
static RestrictionEnzyme	BsiEI
static RestrictionEnzyme	BsiHKAI
static RestrictionEnzyme	BsiWI
static RestrictionEnzyme	BslI
static RestrictionEnzyme	BsmAI
static RestrictionEnzyme	BsmBI
static RestrictionEnzyme	BsmFI
static RestrictionEnzyme	BsmI
static RestrictionEnzyme	Bsp1286I
static RestrictionEnzyme	BspCNI
static RestrictionEnzyme	BspEI
static RestrictionEnzyme	BspHI
static RestrictionEnzyme	BspMI
static RestrictionEnzyme	BsrBI
static RestrictionEnzyme	BsrDI
static RestrictionEnzyme	BsrFI
static RestrictionEnzyme	BsrGI
static RestrictionEnzyme	BsrI
static RestrictionEnzyme	BssHII
static RestrictionEnzyme	BssKI
static RestrictionEnzyme	BssSI
static RestrictionEnzyme	BstAPI
static RestrictionEnzyme	BstBI
static RestrictionEnzyme	BstEII
static RestrictionEnzyme	BstNI
static RestrictionEnzyme	BstUI
static RestrictionEnzyme	BstXI
static RestrictionEnzyme	BstYI
static RestrictionEnzyme	BstZ17I
static RestrictionEnzyme	Bsu36I
static RestrictionEnzyme	BtgI
static RestrictionEnzyme	BtgZI
static RestrictionEnzyme	BtsCI
static RestrictionEnzyme	BtsI
static RestrictionEnzyme	BtsIMutI
static RestrictionEnzyme	Cac8I
static RestrictionEnzyme	ClaI
static RestrictionEnzyme	CspCI
static RestrictionEnzyme	CviAII
static RestrictionEnzyme	CviKI_1
static RestrictionEnzyme	CviQI
static RestrictionEnzyme	DdeI
static RestrictionEnzyme	DpnI
static RestrictionEnzyme	DraI
static RestrictionEnzyme	DraIII
static RestrictionEnzyme	DrdI
static RestrictionEnzyme	EaeI
static RestrictionEnzyme	EagI
static RestrictionEnzyme	EarI
static RestrictionEnzyme	EciI
static RestrictionEnzyme	Eco53kI
static RestrictionEnzyme	EcoNI
static RestrictionEnzyme	EcoO109I
static RestrictionEnzyme	EcoP15I
static RestrictionEnzyme	EcoRI
static RestrictionEnzyme	EcoRV
static RestrictionEnzyme	FatI
static RestrictionEnzyme	FauI
static RestrictionEnzyme	Fnu4HI
static RestrictionEnzyme	FokI
static RestrictionEnzyme	FseI
static RestrictionEnzyme	FspEI
static RestrictionEnzyme	FspI
static RestrictionEnzyme	HaeII
static RestrictionEnzyme	HaeIII
static RestrictionEnzyme	HgaI
static RestrictionEnzyme	HhaI
static RestrictionEnzyme	HincII
static RestrictionEnzyme	HindIII
static RestrictionEnzyme	HinfI
static RestrictionEnzyme	HinP1I
static RestrictionEnzyme	HpaI
static RestrictionEnzyme	HphI
static RestrictionEnzyme	Hpy166II
static RestrictionEnzyme	Hpy188I
static RestrictionEnzyme	Hpy188III
static RestrictionEnzyme	Hpy99I
static RestrictionEnzyme	HpyAV
static RestrictionEnzyme	HpyCH4III
static RestrictionEnzyme	HpyCH4IV
static RestrictionEnzyme	HpyCH4V
static RestrictionEnzyme	I_CeuI
static RestrictionEnzyme	I_SceI
static RestrictionEnzyme	KasI
static RestrictionEnzyme	KpnI
static RestrictionEnzyme	LpnPI
static RestrictionEnzyme	MboI
static RestrictionEnzyme	MboII
static RestrictionEnzyme	MfeI
static RestrictionEnzyme	MluCI
static RestrictionEnzyme	MluI
static RestrictionEnzyme	MlyI
static RestrictionEnzyme	MmeI
static RestrictionEnzyme	MnlI
static RestrictionEnzyme	MscI
static RestrictionEnzyme	MseI
static RestrictionEnzyme	MslI
static RestrictionEnzyme	MspA1I
static RestrictionEnzyme	MspI
static RestrictionEnzyme	MspJI
static RestrictionEnzyme	MwoI
static RestrictionEnzyme	NaeI
static RestrictionEnzyme	NarI
static RestrictionEnzyme	NciI
static RestrictionEnzyme	NcoI
static RestrictionEnzyme	NdeI
static RestrictionEnzyme	NgoMIV
static RestrictionEnzyme	NheI
static RestrictionEnzyme	NlaIII
static RestrictionEnzyme	NlaIV
static RestrictionEnzyme	NmeAIII
static RestrictionEnzyme	NotI
static RestrictionEnzyme	NruI
static RestrictionEnzyme	NsiI
static RestrictionEnzyme	NspI
static RestrictionEnzyme	Nt_AlwI
static RestrictionEnzyme	Nt_BbvCI
static RestrictionEnzyme	Nt_BsmAI
static RestrictionEnzyme	Nt_BspQI
static RestrictionEnzyme	Nt_BstNBI
static RestrictionEnzyme	Nt_CviPII
static RestrictionEnzyme	PacI
static RestrictionEnzyme	PciI
static RestrictionEnzyme	PflMI
static RestrictionEnzyme	PI_PspI
static RestrictionEnzyme	PI_SceI
static RestrictionEnzyme	PleI
static RestrictionEnzyme	PluTI
static RestrictionEnzyme	PmeI
static RestrictionEnzyme	PmlI
static RestrictionEnzyme	PpuMI
static RestrictionEnzyme	PshAI
static RestrictionEnzyme	PsiI
static RestrictionEnzyme	PspGI
static RestrictionEnzyme	PspOMI
static RestrictionEnzyme	PspXI
static RestrictionEnzyme	PstI
static RestrictionEnzyme	PvuI
static RestrictionEnzyme	PvuII
static RestrictionEnzyme	RsaI
static RestrictionEnzyme	RsrII
static RestrictionEnzyme	SacI
static RestrictionEnzyme	SacII
static RestrictionEnzyme	SalI
static RestrictionEnzyme	SapI
static RestrictionEnzyme	Sau96I
static RestrictionEnzyme	SbfI
static RestrictionEnzyme	ScaI
static RestrictionEnzyme	ScrFI
static RestrictionEnzyme	SexAI
static RestrictionEnzyme	SfaNI
static RestrictionEnzyme	SfcI
static RestrictionEnzyme	SfiI
static RestrictionEnzyme	SfoI
static RestrictionEnzyme	SgrAI
static RestrictionEnzyme	SmaI
static RestrictionEnzyme	SmlI
static RestrictionEnzyme	SnaBI
static RestrictionEnzyme	SpeI
static RestrictionEnzyme	SphI
static RestrictionEnzyme	SrfI
static RestrictionEnzyme	SspI
static RestrictionEnzyme	StuI
static RestrictionEnzyme	StyI
static RestrictionEnzyme	SwaI
static RestrictionEnzyme	TaqAI
static RestrictionEnzyme	TfiI
static RestrictionEnzyme	TseI
static RestrictionEnzyme	Tsp45I
static RestrictionEnzyme	TspRI
static RestrictionEnzyme	Tth111I
static RestrictionEnzyme	XbaI
static RestrictionEnzyme	XcmI
static RestrictionEnzyme	XhoI
static RestrictionEnzyme	XmaI
static RestrictionEnzyme	XmnI
static RestrictionEnzyme	ZraI

Fields inherited from class com.hfg.bio.seq.pattern.SeqPattern

PROSITE_COUNT_PATTERN

Constructor Summary

Constructors

Constructor and Description
RestrictionEnzyme()

Method Summary

Modifier and Type	Method and Description
protected RestrictionSite	createMatch(String inSeq, SeqLocation inLocation)
int[]	getFwdStrandCutSiteIndices() Returns the forward strand cut site indices relative to the start of the motif.
String	getRecognitionSequence()
int[]	getRevStrandCutSiteIndices() Returns the reverse strand cut site indices relative to the start of the motif.
boolean	isPalindromic()
RestrictionEnzyme	lock()
RestrictionEnzyme	register() Puts the AminoAcid into the Set of unique RestrictionEnzymes returned by RestrictionEnzyme.values().
protected void	setIsPalindromic(boolean inValue)
RestrictionEnzyme	setName(String inValue)
RestrictionEnzyme	setRecognitionSequence(String inValue)
String	toString()
static RestrictionEnzyme	valueOf(String inString) Returns the RestrictionEnzyme whose name matches the specified String.
static RestrictionEnzyme[]	values()

Methods inherited from class com.hfg.bio.seq.pattern.NucleotidePattern

clone, convertStringToRegExp, getBioSequenceType, getStrandsToSearch, setIgnoreGaps, setMaxMismatches, setStrandsToSearch, setStrandsToSearch

Methods inherited from class com.hfg.bio.seq.pattern.SeqPattern

containsMismatchRestrictions, containsPositionAmbiguity, containsRanges, getIgnoreGaps, getMaxLength, getMaxMismatches, getPrositePattern, getPrositePatternPositions, isCaseSensitive, isLocked, isRestrictedToSeqEnd, isRestrictedToSeqStart, matcher, matcher, name, setIsCaseSensitive, setPrositePattern

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

AarI

public static final RestrictionEnzyme AarI

AatII

public static final RestrictionEnzyme AatII

AcII

public static final RestrictionEnzyme AcII

AccI

public static final RestrictionEnzyme AccI

Acc65I

public static final RestrictionEnzyme Acc65I

AciI

public static final RestrictionEnzyme AciI

AcuI

public static final RestrictionEnzyme AcuI

AfeI

public static final RestrictionEnzyme AfeI

AflII

public static final RestrictionEnzyme AflII

AflIII

public static final RestrictionEnzyme AflIII

AgeI

public static final RestrictionEnzyme AgeI

AhdI

public static final RestrictionEnzyme AhdI

AleI

public static final RestrictionEnzyme AleI

AluI

public static final RestrictionEnzyme AluI

AlwI

public static final RestrictionEnzyme AlwI

AlwNI

public static final RestrictionEnzyme AlwNI

ApaI

public static final RestrictionEnzyme ApaI

ApaLI

public static final RestrictionEnzyme ApaLI

ApoI

public static final RestrictionEnzyme ApoI

AscI

public static final RestrictionEnzyme AscI

AseI

public static final RestrictionEnzyme AseI

AsiSI

public static final RestrictionEnzyme AsiSI

AvaI

public static final RestrictionEnzyme AvaI

AvaII

public static final RestrictionEnzyme AvaII

AvrII

public static final RestrictionEnzyme AvrII

BaeI

public static final RestrictionEnzyme BaeI

BaeGI

public static final RestrictionEnzyme BaeGI

BamHI

public static final RestrictionEnzyme BamHI

BanI

public static final RestrictionEnzyme BanI

BanII

public static final RestrictionEnzyme BanII

BbsI

public static final RestrictionEnzyme BbsI

BbvI

public static final RestrictionEnzyme BbvI

BbvCI

public static final RestrictionEnzyme BbvCI

BccI

public static final RestrictionEnzyme BccI

BceAI

public static final RestrictionEnzyme BceAI

BcgI

public static final RestrictionEnzyme BcgI

BciVI

public static final RestrictionEnzyme BciVI

BclI

public static final RestrictionEnzyme BclI

BfaI

public static final RestrictionEnzyme BfaI

BglI

public static final RestrictionEnzyme BglI

BglII

public static final RestrictionEnzyme BglII

BlpI

public static final RestrictionEnzyme BlpI

BmgBI

public static final RestrictionEnzyme BmgBI

BmrI

public static final RestrictionEnzyme BmrI

BmtI

public static final RestrictionEnzyme BmtI

BpmI

public static final RestrictionEnzyme BpmI

BpuEI

public static final RestrictionEnzyme BpuEI

Bpu10I

public static final RestrictionEnzyme Bpu10I

BsaI

public static final RestrictionEnzyme BsaI

BsaAI

public static final RestrictionEnzyme BsaAI

BsaBI

public static final RestrictionEnzyme BsaBI

BsaHI

public static final RestrictionEnzyme BsaHI

BsaJI

public static final RestrictionEnzyme BsaJI

BsaXI

public static final RestrictionEnzyme BsaXI

BseRI

public static final RestrictionEnzyme BseRI

BsaWI

public static final RestrictionEnzyme BsaWI

BseYI

public static final RestrictionEnzyme BseYI

BsgI

public static final RestrictionEnzyme BsgI

BsiEI

public static final RestrictionEnzyme BsiEI

BsiHKAI

public static final RestrictionEnzyme BsiHKAI

BsiWI

public static final RestrictionEnzyme BsiWI

BslI

public static final RestrictionEnzyme BslI

BsmI

public static final RestrictionEnzyme BsmI

BsmAI

public static final RestrictionEnzyme BsmAI

BsmBI

public static final RestrictionEnzyme BsmBI

BsmFI

public static final RestrictionEnzyme BsmFI

Bsp1286I

public static final RestrictionEnzyme Bsp1286I

BspCNI

public static final RestrictionEnzyme BspCNI

BspEI

public static final RestrictionEnzyme BspEI

BspHI

public static final RestrictionEnzyme BspHI

BspMI

public static final RestrictionEnzyme BspMI

BsrI

public static final RestrictionEnzyme BsrI

BsrBI

public static final RestrictionEnzyme BsrBI

BsrDI

public static final RestrictionEnzyme BsrDI

BsrFI

public static final RestrictionEnzyme BsrFI

BsrGI

public static final RestrictionEnzyme BsrGI

BssHII

public static final RestrictionEnzyme BssHII

BssKI

public static final RestrictionEnzyme BssKI

BssSI

public static final RestrictionEnzyme BssSI

BstAPI

public static final RestrictionEnzyme BstAPI

BstBI

public static final RestrictionEnzyme BstBI

BstEII

public static final RestrictionEnzyme BstEII

BstNI

public static final RestrictionEnzyme BstNI

BstUI

public static final RestrictionEnzyme BstUI

BstXI

public static final RestrictionEnzyme BstXI

BstYI

public static final RestrictionEnzyme BstYI

BstZ17I

public static final RestrictionEnzyme BstZ17I

Bsu36I

public static final RestrictionEnzyme Bsu36I

BtgI

public static final RestrictionEnzyme BtgI

BtgZI

public static final RestrictionEnzyme BtgZI

BtsI

public static final RestrictionEnzyme BtsI

BtsCI

public static final RestrictionEnzyme BtsCI

BtsIMutI

public static final RestrictionEnzyme BtsIMutI

Cac8I

public static final RestrictionEnzyme Cac8I

ClaI

public static final RestrictionEnzyme ClaI

CspCI

public static final RestrictionEnzyme CspCI

CviAII

public static final RestrictionEnzyme CviAII

CviKI_1

public static final RestrictionEnzyme CviKI_1

CviQI

public static final RestrictionEnzyme CviQI

DdeI

public static final RestrictionEnzyme DdeI

DpnI

public static final RestrictionEnzyme DpnI

DraI

public static final RestrictionEnzyme DraI

DraIII

public static final RestrictionEnzyme DraIII

DrdI

public static final RestrictionEnzyme DrdI

EaeI

public static final RestrictionEnzyme EaeI

EagI

public static final RestrictionEnzyme EagI

EarI

public static final RestrictionEnzyme EarI

EciI

public static final RestrictionEnzyme EciI

Eco53kI

public static final RestrictionEnzyme Eco53kI

EcoO109I

public static final RestrictionEnzyme EcoO109I

EcoNI

public static final RestrictionEnzyme EcoNI

EcoP15I

public static final RestrictionEnzyme EcoP15I

EcoRI

public static final RestrictionEnzyme EcoRI

EcoRV

public static final RestrictionEnzyme EcoRV

FatI

public static final RestrictionEnzyme FatI

FauI

public static final RestrictionEnzyme FauI

Fnu4HI

public static final RestrictionEnzyme Fnu4HI

FokI

public static final RestrictionEnzyme FokI

FseI

public static final RestrictionEnzyme FseI

FspI

public static final RestrictionEnzyme FspI

FspEI

public static final RestrictionEnzyme FspEI

HaeII

public static final RestrictionEnzyme HaeII

HaeIII

public static final RestrictionEnzyme HaeIII

HgaI

public static final RestrictionEnzyme HgaI

HhaI

public static final RestrictionEnzyme HhaI

HincII

public static final RestrictionEnzyme HincII

HindIII

public static final RestrictionEnzyme HindIII

HinfI

public static final RestrictionEnzyme HinfI

HinP1I

public static final RestrictionEnzyme HinP1I

HpaI

public static final RestrictionEnzyme HpaI

HphI

public static final RestrictionEnzyme HphI

Hpy99I

public static final RestrictionEnzyme Hpy99I

Hpy166II

public static final RestrictionEnzyme Hpy166II

Hpy188I

public static final RestrictionEnzyme Hpy188I

Hpy188III

public static final RestrictionEnzyme Hpy188III

HpyAV

public static final RestrictionEnzyme HpyAV

HpyCH4III

public static final RestrictionEnzyme HpyCH4III

HpyCH4IV

public static final RestrictionEnzyme HpyCH4IV

HpyCH4V

public static final RestrictionEnzyme HpyCH4V

I_CeuI

public static final RestrictionEnzyme I_CeuI

I_SceI

public static final RestrictionEnzyme I_SceI

KasI

public static final RestrictionEnzyme KasI

KpnI

public static final RestrictionEnzyme KpnI

LpnPI

public static final RestrictionEnzyme LpnPI

MboI

public static final RestrictionEnzyme MboI

MboII

public static final RestrictionEnzyme MboII

MfeI

public static final RestrictionEnzyme MfeI

MluI

public static final RestrictionEnzyme MluI

MluCI

public static final RestrictionEnzyme MluCI

MlyI

public static final RestrictionEnzyme MlyI

MmeI

public static final RestrictionEnzyme MmeI

MnlI

public static final RestrictionEnzyme MnlI

MscI

public static final RestrictionEnzyme MscI

MseI

public static final RestrictionEnzyme MseI

MslI

public static final RestrictionEnzyme MslI

MspI

public static final RestrictionEnzyme MspI

MspA1I

public static final RestrictionEnzyme MspA1I

MspJI

public static final RestrictionEnzyme MspJI

MwoI

public static final RestrictionEnzyme MwoI

NaeI

public static final RestrictionEnzyme NaeI

NarI

public static final RestrictionEnzyme NarI

NciI

public static final RestrictionEnzyme NciI

NcoI

public static final RestrictionEnzyme NcoI

NdeI

public static final RestrictionEnzyme NdeI

NgoMIV

public static final RestrictionEnzyme NgoMIV

NheI

public static final RestrictionEnzyme NheI

NlaIII

public static final RestrictionEnzyme NlaIII

NlaIV

public static final RestrictionEnzyme NlaIV

NmeAIII

public static final RestrictionEnzyme NmeAIII

NotI

public static final RestrictionEnzyme NotI

NruI

public static final RestrictionEnzyme NruI

NsiI

public static final RestrictionEnzyme NsiI

NspI

public static final RestrictionEnzyme NspI

Nt_AlwI

public static final RestrictionEnzyme Nt_AlwI

Nt_BbvCI

public static final RestrictionEnzyme Nt_BbvCI

Nt_BsmAI

public static final RestrictionEnzyme Nt_BsmAI

Nt_BspQI

public static final RestrictionEnzyme Nt_BspQI

Nt_BstNBI

public static final RestrictionEnzyme Nt_BstNBI

Nt_CviPII

public static final RestrictionEnzyme Nt_CviPII

PacI

public static final RestrictionEnzyme PacI

PciI

public static final RestrictionEnzyme PciI

PflMI

public static final RestrictionEnzyme PflMI

PI_PspI

public static final RestrictionEnzyme PI_PspI

PI_SceI

public static final RestrictionEnzyme PI_SceI

PleI

public static final RestrictionEnzyme PleI

PluTI

public static final RestrictionEnzyme PluTI

PmeI

public static final RestrictionEnzyme PmeI

PmlI

public static final RestrictionEnzyme PmlI

PpuMI

public static final RestrictionEnzyme PpuMI

PshAI

public static final RestrictionEnzyme PshAI

PsiI

public static final RestrictionEnzyme PsiI

PspGI

public static final RestrictionEnzyme PspGI

PspOMI

public static final RestrictionEnzyme PspOMI

PspXI

public static final RestrictionEnzyme PspXI

PstI

public static final RestrictionEnzyme PstI

PvuI

public static final RestrictionEnzyme PvuI

PvuII

public static final RestrictionEnzyme PvuII

RsaI

public static final RestrictionEnzyme RsaI

RsrII

public static final RestrictionEnzyme RsrII

SacI

public static final RestrictionEnzyme SacI

SacII

public static final RestrictionEnzyme SacII

SalI

public static final RestrictionEnzyme SalI

SapI

public static final RestrictionEnzyme SapI

Sau96I

public static final RestrictionEnzyme Sau96I

SbfI

public static final RestrictionEnzyme SbfI

ScaI

public static final RestrictionEnzyme ScaI

ScrFI

public static final RestrictionEnzyme ScrFI

SexAI

public static final RestrictionEnzyme SexAI

SfaNI

public static final RestrictionEnzyme SfaNI

SfcI

public static final RestrictionEnzyme SfcI

SfiI

public static final RestrictionEnzyme SfiI

SfoI

public static final RestrictionEnzyme SfoI

SgrAI

public static final RestrictionEnzyme SgrAI

SmaI

public static final RestrictionEnzyme SmaI

SmlI

public static final RestrictionEnzyme SmlI

SnaBI

public static final RestrictionEnzyme SnaBI

SpeI

public static final RestrictionEnzyme SpeI

SphI

public static final RestrictionEnzyme SphI

SrfI

public static final RestrictionEnzyme SrfI

SspI

public static final RestrictionEnzyme SspI

StuI

public static final RestrictionEnzyme StuI

StyI

public static final RestrictionEnzyme StyI

SwaI

public static final RestrictionEnzyme SwaI

TaqAI

public static final RestrictionEnzyme TaqAI

TfiI

public static final RestrictionEnzyme TfiI

TseI

public static final RestrictionEnzyme TseI

Tsp45I

public static final RestrictionEnzyme Tsp45I

TspRI

public static final RestrictionEnzyme TspRI

Tth111I

public static final RestrictionEnzyme Tth111I

XbaI

public static final RestrictionEnzyme XbaI

XcmI

public static final RestrictionEnzyme XcmI

XhoI

public static final RestrictionEnzyme XhoI

XmaI

public static final RestrictionEnzyme XmaI

XmnI

public static final RestrictionEnzyme XmnI

ZraI

public static final RestrictionEnzyme ZraI

Constructor Detail

RestrictionEnzyme

public RestrictionEnzyme()

Method Detail

setName

public RestrictionEnzyme setName(String inValue)

Overrides:

setName in class SeqPattern<NucleicAcid,RestrictionSite>

toString

public String toString()

Overrides:

toString in class SeqPattern<NucleicAcid,RestrictionSite>

setRecognitionSequence

public RestrictionEnzyme setRecognitionSequence(String inValue)

getRecognitionSequence

public String getRecognitionSequence()

getFwdStrandCutSiteIndices

public int[] getFwdStrandCutSiteIndices()

Returns the forward strand cut site indices relative to the start of the motif.

Returns:

Usually one but possibly two cut site indices on the forward strand.

getRevStrandCutSiteIndices

public int[] getRevStrandCutSiteIndices()

Returns the reverse strand cut site indices relative to the start of the motif.

Returns:

Usually one but possibly two cut site indices on the reverse strand.

isPalindromic

public boolean isPalindromic()

lock

public RestrictionEnzyme lock()

Overrides:

lock in class SeqPattern<NucleicAcid,RestrictionSite>

register

public RestrictionEnzyme register()

Puts the AminoAcid into the Set of unique RestrictionEnzymes returned by RestrictionEnzyme.values().

valueOf

public static RestrictionEnzyme valueOf(String inString)

Returns the RestrictionEnzyme whose name matches the specified String.

Parameters:

inString - the name for the RestrictionEnzyme to retrieve

Returns:

the RestrictionEnzyme whose name matches the specified String

values

public static RestrictionEnzyme[] values()

createMatch

protected RestrictionSite createMatch(String inSeq,
                                      SeqLocation inLocation)

Overrides:

createMatch in class NucleotidePattern<RestrictionSite>

setIsPalindromic

protected void setIsPalindromic(boolean inValue)