Package org.biojava.bio.seq.impl

Class SimpleRestrictionSite

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.impl.SimpleFeature

org.biojava.bio.seq.impl.SimpleStrandedFeature

org.biojava.bio.seq.impl.SimpleRestrictionSite

All Implemented Interfaces:

Serializable, Annotatable, RestrictionSite, Feature, FeatureHolder, RealizingFeatureHolder, StrandedFeature, Changeable

public class SimpleRestrictionSite
extends SimpleStrandedFeature
implements RestrictionSite

SimpleRestrictionSite represents the recognition site of a restriction enzyme.

Since:

1.3

Author:

Keith James

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Nested classes/interfaces inherited from interface org.biojava.bio.seq.Feature

Feature.ByLocationComparator, Feature.Template

Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder

FeatureHolder.EmptyFeatureHolder

Nested classes/interfaces inherited from interface org.biojava.bio.molbio.RestrictionSite

RestrictionSite.Template

Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature

StrandedFeature.Strand, StrandedFeature.Template

Field Summary

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Fields inherited from interface org.biojava.bio.seq.Feature

byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERM

Fields inherited from interface org.biojava.bio.seq.FeatureHolder

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Fields inherited from interface org.biojava.bio.seq.StrandedFeature

NEGATIVE, POSITIVE, STRAND, UNKNOWN

Constructor Summary

Constructors

Constructor	Description
SimpleRestrictionSite(Sequence sourceSeq, FeatureHolder parent, RestrictionSite.Template template)	Creates a new SimpleRestrictionSite.

Method Summary

Modifier and Type	Method	Description
RestrictionEnzyme	getEnzyme()	getEnzyme returns the enzyme which cuts at this site.
int	getPosition()	getPosition returns the common, forward strand cut site.
String	toString()

Methods inherited from class org.biojava.bio.seq.impl.SimpleStrandedFeature

fillTemplate, getStrand, getSymbols, makeTemplate, setStrand

Methods inherited from class org.biojava.bio.seq.impl.SimpleFeature

containsFeature, countFeatures, createFeature, equals, featureHolderAllocated, features, fillTemplate, filter, filter, getAnnotation, getChangeSupport, getFeatureHolder, getLocation, getParent, getSchema, getSequence, getSource, getSourceTerm, getType, getTypeTerm, hashCode, realizeFeature, removeFeature, setLocation, setSource, setSourceTerm, setType, setTypeTerm

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.seq.Feature

features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm

Methods inherited from interface org.biojava.bio.seq.FeatureHolder

containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature

Methods inherited from interface org.biojava.bio.seq.StrandedFeature

getStrand, getSymbols, setStrand

Constructor Detail

SimpleRestrictionSite

public SimpleRestrictionSite(Sequence sourceSeq,
                             FeatureHolder parent,
                             RestrictionSite.Template template)

Creates a new SimpleRestrictionSite.

Parameters:

sourceSeq - a Sequence.

parent - a FeatureHolder.

template - a RestrictionSite.Template.

Method Detail

getPosition

public int getPosition()

Description copied from interface: RestrictionSite

getPosition returns the common, forward strand cut site. Note that some enzymes cut in more than one position. Such supplementary sites may be calculated by retrieving the RestrictionEnzyme instance and using its methods to calculate the position.

Specified by:

getPosition in interface RestrictionSite

Returns:

an int indicating the base immediately before the cleavage site on the forward strand.

getEnzyme

public RestrictionEnzyme getEnzyme()

Description copied from interface: RestrictionSite

getEnzyme returns the enzyme which cuts at this site. A sequence which is the target for several different enzymes is expected to have a corresponding RestrictionSite feature for each.

Specified by:

getEnzyme in interface RestrictionSite

Returns:

a RestrictionEnzyme.

toString

public String toString()

Overrides:

toString in class SimpleStrandedFeature