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
-
Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic class
A singleton to hold the frame informationstatic class
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
Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final FramedFeature.ReadingFrame
static final FramedFeature.ReadingFrame
static final FramedFeature.ReadingFrame
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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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
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
getSymbols, setStrand
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Field Details
-
FRAME_0
-
FRAME_1
-
FRAME_2
-
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Method Details
-
getReadingFrame
return the reading frame of the feature. -
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
-