Package org.biojava.bio.seq
Interface FramedFeature
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- All Superinterfaces:
Annotatable
,Changeable
,Feature
,FeatureHolder
,StrandedFeature
- All Known Implementing Classes:
SimpleFramedFeature
public interface FramedFeature extends StrandedFeature
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 Classes Modifier and Type Interface Description static class
FramedFeature.ReadingFrame
A singleton to hold the frame informationstatic class
FramedFeature.Template
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Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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Nested classes/interfaces inherited from interface org.biojava.bio.seq.Feature
Feature.ByLocationComparator
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Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
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Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand
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Field Summary
Fields Modifier and Type Field Description static FramedFeature.ReadingFrame
FRAME_0
static FramedFeature.ReadingFrame
FRAME_1
static FramedFeature.ReadingFrame
FRAME_2
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Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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Fields inherited from interface org.biojava.bio.seq.Feature
byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERM
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Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA
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Fields inherited from interface org.biojava.bio.seq.StrandedFeature
NEGATIVE, POSITIVE, STRAND, UNKNOWN
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description FramedFeature.ReadingFrame
getReadingFrame()
return the reading frame of the feature.StrandedFeature.Strand
getStrand()
Retrieve the strand that this feature lies upon.-
Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
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Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Methods inherited from interface org.biojava.bio.seq.Feature
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm
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Methods inherited from interface org.biojava.bio.seq.FeatureHolder
containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature
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Methods inherited from interface org.biojava.bio.seq.StrandedFeature
getSymbols, setStrand
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Field Detail
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FRAME_0
static final FramedFeature.ReadingFrame FRAME_0
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FRAME_1
static final FramedFeature.ReadingFrame FRAME_1
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FRAME_2
static final FramedFeature.ReadingFrame FRAME_2
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Method Detail
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getReadingFrame
FramedFeature.ReadingFrame getReadingFrame()
return the reading frame of the feature.
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getStrand
StrandedFeature.Strand 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:
- the Strand that the feature is found on
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