org.biojava.bio.molbio

Interface RestrictionSite

All Superinterfaces:

Annotatable, Changeable, Feature, FeatureHolder, StrandedFeature

All Known Implementing Classes:

SimpleRestrictionSite

public interface RestrictionSite
extends StrandedFeature

RestrictionSite represents the recognition site of a restriction enzyme.

Since:

1.3

Author:

Keith James

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	RestrictionSite.Template Template for construction of RestrictionSites.

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

StrandedFeature.Strand

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

Feature.ByLocationComparator

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

FeatureHolder.EmptyFeatureHolder

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

Annotatable.AnnotationForwarder

Field Summary

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

NEGATIVE, POSITIVE, STRAND, UNKNOWN

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.Annotatable

ANNOTATION

Method Summary

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

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

getStrand, getSymbols, setStrand

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.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Method Detail

getPosition

int getPosition()

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.

Returns:

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

getEnzyme

RestrictionEnzyme getEnzyme()

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.

Returns:

a RestrictionEnzyme.