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
static class RestrictionSite.Template
          Template for construction of RestrictionSites.
 
Nested classes inherited from class org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand
 
Nested classes inherited from class org.biojava.bio.seq.Feature
Feature.ByLocationComparator
 
Nested classes inherited from class org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
 
Nested classes inherited from class org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
 
Field Summary
 
Fields inherited from interface org.biojava.bio.seq.StrandedFeature
NEGATIVE, POSITIVE, UNKNOWN
 
Fields inherited from interface org.biojava.bio.seq.Feature
byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, TYPE
 
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
 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
 
Methods inherited from interface org.biojava.bio.seq.Feature
features, getLocation, getParent, getSequence, getSource, getType, makeTemplate, setLocation, setSource, setType
 
Methods inherited from interface org.biojava.bio.seq.FeatureHolder
containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 
Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
 

Method Detail

getPosition

public 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

public 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.