public class SimpleRestrictionSite extends SimpleStrandedFeature implements RestrictionSite
SimpleRestrictionSite represents the recognition site
of a restriction enzyme.RestrictionSite.TemplateStrandedFeature.StrandFeature.ByLocationComparatorFeatureHolder.EmptyFeatureHolderAnnotatable.AnnotationForwarderNEGATIVE, POSITIVE, STRAND, UNKNOWNbyLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERMEMPTY_FEATURE_HOLDER, FEATURES, SCHEMAANNOTATION| Constructor and Description |
|---|
SimpleRestrictionSite(Sequence sourceSeq,
FeatureHolder parent,
RestrictionSite.Template template)
Creates a new
SimpleRestrictionSite. |
| 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. |
String |
toString() |
fillTemplate, getStrand, getSymbols, makeTemplate, setStrandcontainsFeature, 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, setTypeTermaddChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListenerclone, finalize, getClass, notify, notifyAll, wait, wait, waitgetStrand, getSymbols, setStrandfeatures, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTermcontainsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeaturegetAnnotationaddChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListenerpublic SimpleRestrictionSite(Sequence sourceSeq, FeatureHolder parent, RestrictionSite.Template template)
SimpleRestrictionSite.sourceSeq - a Sequence.parent - a FeatureHolder.template - a RestrictionSite.Template.public int getPosition()
RestrictionSitegetPosition 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.getPosition in interface RestrictionSiteint indicating the base immediately
before the cleavage site on the forward strand.public RestrictionEnzyme getEnzyme()
RestrictionSitegetEnzyme 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.getEnzyme in interface RestrictionSiteRestrictionEnzyme.public String toString()
toString in class SimpleStrandedFeatureCopyright © 2014 BioJava. All rights reserved.