Package org.biojava.bio.molbio
Interface RestrictionSite
- All Superinterfaces:
Annotatable
,Changeable
,Feature
,FeatureHolder
,StrandedFeature
- All Known Implementing Classes:
SimpleRestrictionSite
RestrictionSite
represents the recognition site of a
restriction enzyme.- Since:
- 1.3
- Author:
- Keith James
-
Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic class
Template
for construction ofRestrictionSite
s.Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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.seq.StrandedFeature
StrandedFeature.Strand
-
Field Summary
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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.seq.StrandedFeature
NEGATIVE, POSITIVE, STRAND, UNKNOWN
-
Method Summary
Modifier and TypeMethodDescriptiongetEnzyme
returns the enzyme which cuts at this site.int
getPosition
returns the common, forward strand cut site.Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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.seq.StrandedFeature
getStrand, getSymbols, setStrand
-
Method Details
-
getPosition
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 theRestrictionEnzyme
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
getEnzyme
returns the enzyme which cuts at this site. A sequence which is the target for several different enzymes is expected to have a correspondingRestrictionSite
feature for each.- Returns:
- a
RestrictionEnzyme
.
-