Package org.biojava.bio.seq
Interface FramedFeature
- All Superinterfaces:
Annotatable,Changeable,Feature,FeatureHolder,StrandedFeature
- All Known Implementing Classes:
SimpleFramedFeature
Title: FramedFeature.
Description: An feature that includes the concept of frame by extending stranded.
Copyright: Copyright (c) 2001
- Version:
- 1.0
- Author:
- Mark Schreiber
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Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic classA singleton to hold the frame informationstatic classNested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarderNested classes/interfaces inherited from interface org.biojava.bio.seq.Feature
Feature.ByLocationComparatorNested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolderNested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand -
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final FramedFeature.ReadingFramestatic final FramedFeature.ReadingFramestatic final FramedFeature.ReadingFrameFields inherited from interface org.biojava.bio.Annotatable
ANNOTATIONFields inherited from interface org.biojava.bio.seq.Feature
byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERMFields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMAFields inherited from interface org.biojava.bio.seq.StrandedFeature
NEGATIVE, POSITIVE, STRAND, UNKNOWN -
Method Summary
Modifier and TypeMethodDescriptionreturn the reading frame of the feature.Retrieve the strand that this feature lies upon.Methods inherited from interface org.biojava.bio.Annotatable
getAnnotationMethods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListenerMethods inherited from interface org.biojava.bio.seq.Feature
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTermMethods inherited from interface org.biojava.bio.seq.FeatureHolder
containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeatureMethods inherited from interface org.biojava.bio.seq.StrandedFeature
getSymbols, setStrand
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Field Details
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FRAME_0
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FRAME_1
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FRAME_2
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Method Details
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getReadingFrame
return the reading frame of the feature. -
getStrand
Description copied from interface:StrandedFeatureRetrieve the strand that this feature lies upon.This will be one of StrandedFeature.POSITIVE or NEGATIVE.
- Specified by:
getStrandin interfaceStrandedFeature- Returns:
- the Strand that the feature is found on
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