|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
public interface RestrictionSite
RestrictionSite
represents the recognition site of a
restriction enzyme.
Nested Class Summary | |
---|---|
static class |
RestrictionSite.Template
Template for construction of
RestrictionSite s. |
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 | |
---|---|
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 |
---|
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.
int
indicating the base immediately
before the cleavage site on the forward strand.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.
RestrictionEnzyme
.
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |