org.biojava.bio.molbio
Class RestrictionEnzymeManager

java.lang.Object
  org.biojava.bio.molbio.RestrictionEnzymeManager

public final class RestrictionEnzymeManager

extends Object

RestrictionEnzymeManager manages collections of static RestrictionEnzyme instances. A properties file should be placed in the CLASSPATH containing a key "rebase.data.file" and a corresponding value of a REBASE file (standard REBASE format #31 conventionally named withrefm.### where ### is the version number). This file will be loaded by the RestrictionEnzymeManager ClassLoader. The properties are loaded as a ResourceBundle, so the file should be named "RestrictionEnzymeManager.properties".

Since:

1.3

Author:

Keith James

Field Summary

static String	REBASE_DATA_KEY REBASE_DATA_KEY the ResourceBundle key which specifies the location of the REBASE flat file.
static String	REBASE_TAG_COMM REBASE_TAG_COMM the REBASE tag containing the commercial suppliers.
static String	REBASE_TAG_ISZR REBASE_TAG_ISZR the REBASE tag containing the enzyme isoschizomers.
static String	REBASE_TAG_METH REBASE_TAG_METH the REBASE tag containing the methylation site.
static String	REBASE_TAG_NAME REBASE_TAG_NAME the REBASE tag containing the enzyme name.
static String	REBASE_TAG_ORGN REBASE_TAG_ORGN the REBASE tag containing the organism.
static String	REBASE_TAG_REFS REBASE_TAG_REFS the REBASE tag containing the references.
static String	REBASE_TAG_SITE REBASE_TAG_SITE the REBASE tag containing the enzyme site.
static String	REBASE_TAG_SRCE REBASE_TAG_SRCE the REBASE tag containing the source.

Method Summary

static Set	getAllEnzymes() getAllEnzymes returns an unmodifable set of all available enzymes.
static Annotation	getAnnotation(RestrictionEnzyme enzyme) getAnnotation returns an immutable, static annotation describing the enzyme.
static RestrictionEnzyme	getEnzyme(String name) getEnzyme returns an enzyme by name.
static Set	getIsoschizomers(String name) getIsoschizomers returns an unmodifable set of the isoschizomers of this enzyme.
static Set	getNCutters(int n) getNCutters returns an unmodifable set of all enzymes with a cut site of size n.
static Pattern[]	getPatterns(RestrictionEnzyme enzyme) getPatterns returns two Pattern objects for an enzyme, one matches the forward strand and one the reverse.
static void	register(RestrictionEnzyme enzyme, Set isoschizomers) register regisiters a new RestrictionEnzyme with the manager.

Methods inherited from class java.lang.Object

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

Field Detail

REBASE_DATA_KEY

public static final String REBASE_DATA_KEY

REBASE_DATA_KEY the ResourceBundle key which specifies the location of the REBASE flat file.

See Also:

Constant Field Values

REBASE_TAG_NAME

public static final String REBASE_TAG_NAME

REBASE_TAG_NAME the REBASE tag containing the enzyme name.

See Also:

Constant Field Values

REBASE_TAG_ISZR

public static final String REBASE_TAG_ISZR

REBASE_TAG_ISZR the REBASE tag containing the enzyme isoschizomers.

See Also:

Constant Field Values

REBASE_TAG_SITE

public static final String REBASE_TAG_SITE

REBASE_TAG_SITE the REBASE tag containing the enzyme site.

See Also:

Constant Field Values

REBASE_TAG_METH

public static final String REBASE_TAG_METH

REBASE_TAG_METH the REBASE tag containing the methylation site.

See Also:

Constant Field Values

REBASE_TAG_ORGN

public static final String REBASE_TAG_ORGN

REBASE_TAG_ORGN the REBASE tag containing the organism.

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Constant Field Values

REBASE_TAG_SRCE

public static final String REBASE_TAG_SRCE

REBASE_TAG_SRCE the REBASE tag containing the source.

See Also:

Constant Field Values

REBASE_TAG_COMM

public static final String REBASE_TAG_COMM

REBASE_TAG_COMM the REBASE tag containing the commercial suppliers.

See Also:

Constant Field Values

REBASE_TAG_REFS

public static final String REBASE_TAG_REFS

REBASE_TAG_REFS the REBASE tag containing the references.

See Also:

Constant Field Values

Method Detail

getAllEnzymes

public static Set getAllEnzymes()

getAllEnzymes returns an unmodifable set of all available enzymes.

Returns:

a Set of RestrictionEnzymes.

getEnzyme

public static RestrictionEnzyme getEnzyme(String name)

getEnzyme returns an enzyme by name.

Parameters:

name - a String such as EcoRI, case sensitive.

Returns:

a RestrictionEnzyme.

getIsoschizomers

public static Set getIsoschizomers(String name)

getIsoschizomers returns an unmodifable set of the isoschizomers of this enzyme.

Parameters:

name - a String such as EcoRI, case sensitive.

Returns:

a Set of RestrictionEnzymes.

getNCutters

public static Set getNCutters(int n)

getNCutters returns an unmodifable set of all enzymes with a cut site of size n.

Parameters:

n - an int cut site size.

Returns:

a Set of RestrictionEnzymes.

getPatterns

public static Pattern[] getPatterns(RestrictionEnzyme enzyme)

getPatterns returns two Pattern objects for an enzyme, one matches the forward strand and one the reverse. This enables searching of both strands of a sequence without reverse-complementing it. As Pattern objects are thread-safe these may be used for all searches.

Parameters:

enzyme - a RestrictionEnzyme.

Returns:

a Pattern [] array with the forward strand Pattern at index 0 and the reverse at index 1.

getAnnotation

public static Annotation getAnnotation(RestrictionEnzyme enzyme)

getAnnotation returns an immutable, static annotation describing the enzyme. This is suitable for adding to Features which represent restriction sites. The annotation produced currently contains one key "dbxref" in line with the GenBank/EMBL qualifier for the "misc_binding" feature key. The key has a corresponding value "REBASE:<enzyme name>".

Parameters:

enzyme - a RestrictionEnzyme.

Returns:

an Annotation.

register

public static void register(RestrictionEnzyme enzyme,
                            Set isoschizomers)

register regisiters a new RestrictionEnzyme with the manager. It does not check that the isoschizomers are known to the manager. If there are custom isoschizomers in the Set, they should be also be registered.

Parameters:

enzyme - a RestrictionEnzyme to register.

isoschizomers - a Set of RestrictionEnzymes which are isoschizomers.