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
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 interface org.biojava.bio.seq.Feature |
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm |
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
.
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