org.biojava.bio.molbio

Class RestrictionMapper

java.lang.Object

org.biojava.bio.molbio.RestrictionMapper

All Implemented Interfaces:

SequenceAnnotator

public class RestrictionMapper
extends Object
implements SequenceAnnotator

RestrictionMapper is a class for annotating Sequences with Features which represent restriction sites. Calling annotate(Sequence sequence) will annotate the Sequence with the sites of any RestrictionEnzymes which have been added to the RestrictionMapper. The returned Sequence is a ViewSequence wrapping the original.

The Features created are RestrictionSites which have a flyweight Annotation containing a single String property "dbxref" whose value is "REBASE:" plus name of the enzyme (e.g. EcoRI).

The mapper will by default map only those sites which have both their recognition sites and their cut sites within the Sequence. This behaviour may be changed to map all sites which have their recognition sites within the Sequence using the setMapAll(boolean on) method.

The current implementation requires that RestrictionEnzymes to be searched must first be registered with the RestrictionEnzymeManager.

Since:

1.3

Author:

Keith James

Field Summary

Fields

Modifier and Type	Field and Description
static String	SITE_FEATURE_SOURCE SITE_FEATURE_SOURCE the source String used by RestrictionMapper when creating restriction site Features.
static String	SITE_FEATURE_TYPE SITE_FEATURE_TYPE the type String used by RestrictionMapper when creating restriction site Features.

Constructor Summary

Constructors

Constructor and Description
RestrictionMapper(ExecutorService xser) Creates a new RestrictionMapper which will use the specified ExecutorService.
RestrictionMapper(ThreadPool threadPool) Creates a new RestrictionMapper which will use the specified ThreadPool.

Method Summary

Methods

Modifier and Type	Method and Description
void	addEnzyme(RestrictionEnzyme enzyme) addEnzyme adds an enzyme to be searched for in the Sequence.
Sequence	annotate(Sequence sequence) annotate adds Features which represent restriction sites.
void	clearEnzymes() clearEnzymes removes all enzymes from those to be searched for in the Sequence.
boolean	getMapAll() getMapAll returns whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it.
void	removeEnzyme(RestrictionEnzyme enzyme) removeEnzyme removes an enzyme from those to be searched for in the Sequence.
void	setMapAll(boolean on) setMapAll sets whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it.

Methods inherited from class java.lang.Object

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

Field Detail

SITE_FEATURE_SOURCE

public static final String SITE_FEATURE_SOURCE

SITE_FEATURE_SOURCE the source String used by RestrictionMapper when creating restriction site Features. This is the String which is returned when a Feature's getSource() method is called.

See Also:

Constant Field Values

SITE_FEATURE_TYPE

public static final String SITE_FEATURE_TYPE

SITE_FEATURE_TYPE the type String used by RestrictionMapper when creating restriction site Features. This is the String which is returned when a Feature's getType() method is called.

See Also:

Constant Field Values

Constructor Detail

RestrictionMapper

public RestrictionMapper(ThreadPool threadPool)

Creates a new RestrictionMapper which will use the specified ThreadPool. Do not share one pool between a number of RestrictionMappers because annotate(Sequence sequence) waits for all threads in the pool to finish work before returning and this will lead to a race condition between mappers. One mapper could end up waiting for another mapper's threads before returning.

Parameters:

threadPool - a ThreadPool.

RestrictionMapper

public RestrictionMapper(ExecutorService xser)

Creates a new RestrictionMapper which will use the specified ExecutorService.

Parameters:

xser - a ExecutorService, e.g. ExecutorService.newCachedThreadPool()

Since:

1.8.1

Method Detail

annotate

public Sequence annotate(Sequence sequence)

annotate adds Features which represent restriction sites.

Specified by:

annotate in interface SequenceAnnotator

Parameters:

sequence - a Sequence.

Returns:

a Sequence view with restriction sites marked.

getMapAll

public boolean getMapAll()

getMapAll returns whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it. The default is false, indicating only sites which can actually be cut are mapped.

Returns:

a boolean.

setMapAll

public void setMapAll(boolean on)

setMapAll sets whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it. The default is false, indicating only sites which can actually be cut are mapped.

Parameters:

on - a boolean.

addEnzyme

public void addEnzyme(RestrictionEnzyme enzyme)

addEnzyme adds an enzyme to be searched for in the Sequence.

Parameters:

enzyme - a RestrictionEnzyme.

removeEnzyme

public void removeEnzyme(RestrictionEnzyme enzyme)

removeEnzyme removes an enzyme from those to be searched for in the Sequence.

Parameters:

enzyme - a RestrictionEnzyme.

clearEnzymes

public void clearEnzymes()

clearEnzymes removes all enzymes from those to be searched for in the Sequence.