org.biojava.bio.seq.impl
Class SimpleRestrictionSite

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by org.biojava.bio.seq.impl.SimpleFeature
          extended by org.biojava.bio.seq.impl.SimpleStrandedFeature
              extended by 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.molbio.RestrictionSite
RestrictionSite.Template
 
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
 
Constructor Summary
SimpleRestrictionSite(Sequence sourceSeq, FeatureHolder parent, RestrictionSite.Template template)
          Creates a new SimpleRestrictionSite.
 
Method Summary
 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.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.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 
Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

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