Package 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
SimpleRestrictionSite
represents the recognition site
of a restriction enzyme.- Since:
- 1.3
- Author:
- Keith James
- See Also:
-
Nested Class Summary
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, Feature.Template
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
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, StrandedFeature.Template
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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
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Constructor Summary
ConstructorsConstructorDescriptionSimpleRestrictionSite
(Sequence sourceSeq, FeatureHolder parent, RestrictionSite.Template template) Creates a newSimpleRestrictionSite
. -
Method Summary
Modifier and TypeMethodDescriptiongetEnzyme
returns the enzyme which cuts at this site.int
getPosition
returns the common, forward strand cut site.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.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
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Constructor Details
-
SimpleRestrictionSite
public SimpleRestrictionSite(Sequence sourceSeq, FeatureHolder parent, RestrictionSite.Template template) Creates a newSimpleRestrictionSite
.- Parameters:
sourceSeq
- aSequence
.parent
- aFeatureHolder
.template
- aRestrictionSite.Template
.
-
-
Method Details
-
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 theRestrictionEnzyme
instance and using its methods to calculate the position.- Specified by:
getPosition
in interfaceRestrictionSite
- Returns:
- an
int
indicating the base immediately before the cleavage site on the forward strand.
-
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 correspondingRestrictionSite
feature for each.- Specified by:
getEnzyme
in interfaceRestrictionSite
- Returns:
- a
RestrictionEnzyme
.
-
toString
- Overrides:
toString
in classSimpleStrandedFeature
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