Interface StrandedFeature
- All Superinterfaces:
Annotatable
,Changeable
,Feature
,FeatureHolder
- All Known Subinterfaces:
ComponentFeature
,FramedFeature
,HomologyFeature
,RemoteFeature
,RestrictionSite
,RichFeature
,SimilarityPairFeature
- All Known Implementing Classes:
SimpleFramedFeature
,SimpleHomologyFeature
,SimpleRemoteFeature
,SimpleRestrictionSite
,SimpleRichFeature
,SimpleSimilarityPairFeature
,SimpleStrandedFeature
Strandedness only applies to some types of sequence, such as DNA. Any
implementation should blow chunks to avoid being added to a sequence for
which strand is a foreign concept.
Strand is intrinsicly part of all RichFeatures
We strongly recommend using this interface.
- Author:
- Matthew Pocock
- See Also:
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Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic final class
Class to represent the 'strandedness' of a feature.static class
Template class for parameterizing the creation of a newStrandedFeature
.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
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final StrandedFeature.Strand
Flag to indicate that a feature is on the negative strand.static final StrandedFeature.Strand
Flag to indicate that a feature is on the positive strand.static final ChangeType
The strand of this feature is being altered.static final StrandedFeature.Strand
Flag to indicate that a feature has an unknown strand.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
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Method Summary
Modifier and TypeMethodDescriptionRetrieve the strand that this feature lies upon.Return a list of symbols that are contained in this feature.void
setStrand
(StrandedFeature.Strand strand) Set the strand that this feature lies upon.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
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Field Details
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STRAND
The strand of this feature is being altered. -
POSITIVE
Flag to indicate that a feature is on the positive strand. -
NEGATIVE
Flag to indicate that a feature is on the negative strand. -
UNKNOWN
Flag to indicate that a feature has an unknown strand.
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Method Details
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getStrand
Retrieve the strand that this feature lies upon.This will be one of StrandedFeature.POSITIVE or NEGATIVE.
- Returns:
- one of the Strand constants
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setStrand
Set the strand that this feature lies upon.This will be one of StrandedFeature.POSITIVE or NEGATIVE.
- Parameters:
strand
- aStrand
.- Throws:
ChangeVetoException
- if the strand may not be changed.
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getSymbols
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 is on the negative strand then the SymbolList will be reverse-complemented as appropriate.
- Specified by:
getSymbols
in interfaceFeature
- 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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