Package org.biojava.bio.seq.impl
Class SimpleStrandedFeature
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.impl.SimpleFeature
org.biojava.bio.seq.impl.SimpleStrandedFeature
- All Implemented Interfaces:
Serializable
,Annotatable
,Feature
,FeatureHolder
,RealizingFeatureHolder
,StrandedFeature
,Changeable
- Direct Known Subclasses:
SimpleFramedFeature
,SimpleHomologyFeature
,SimpleRemoteFeature
,SimpleRestrictionSite
,SimpleSimilarityPairFeature
A no-frills implementation of StrandedFeature.
- Author:
- Matthew Pocock, Thomas Down
- See Also:
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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.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
ConstructorsConstructorDescriptionSimpleStrandedFeature
(Sequence sourceSeq, FeatureHolder parent, StrandedFeature.Template template) -
Method Summary
Modifier and TypeMethodDescriptionprotected void
Retrieve the strand that this feature lies upon.Return a list of symbols that are contained in this feature.Create a new Template that could be used to generate a feature identical to this one.void
setStrand
(StrandedFeature.Strand strand) Set the strand that this feature lies upon.toString()
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, setLocation, setSource, setSourceTerm, setType, setTypeTerm
Methods inherited from interface org.biojava.bio.seq.FeatureHolder
containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature
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Constructor Details
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SimpleStrandedFeature
public SimpleStrandedFeature(Sequence sourceSeq, FeatureHolder parent, StrandedFeature.Template template) throws IllegalArgumentException - Throws:
IllegalArgumentException
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Method Details
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getStrand
Description copied from interface:StrandedFeature
Retrieve the strand that this feature lies upon.This will be one of StrandedFeature.POSITIVE or NEGATIVE.
- Specified by:
getStrand
in interfaceStrandedFeature
- Returns:
- one of the Strand constants
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getSymbols
Description copied from interface:Feature
Return a list of symbols that are contained in this feature.The symbols may not be contiguous in the original sequence, but they will be concatenated together in the resulting SymbolList.
The order of the Symbols within the resulting symbol list will be according to the concept of ordering within the location object.
If the feature location is modified then this does not modify any SymbolList produced by earlier invocations of this method.
- Specified by:
getSymbols
in interfaceFeature
- Specified by:
getSymbols
in interfaceStrandedFeature
- Overrides:
getSymbols
in classSimpleFeature
- Returns:
- a SymbolList containing each symbol of the parent sequence contained within this feature in the order they appear in the parent
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setStrand
Description copied from interface:StrandedFeature
Set the strand that this feature lies upon.This will be one of StrandedFeature.POSITIVE or NEGATIVE.
- Specified by:
setStrand
in interfaceStrandedFeature
- Parameters:
strand
- aStrand
.- Throws:
ChangeVetoException
- if the strand may not be changed.
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makeTemplate
Description copied from interface:Feature
Create a new Template that could be used to generate a feature identical to this one. The fields of the template can be edited without changing the feature.- Specified by:
makeTemplate
in interfaceFeature
- Overrides:
makeTemplate
in classSimpleFeature
- Returns:
- a new Template that would make a feature like this one
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fillTemplate
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toString
- Overrides:
toString
in classSimpleFeature
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