Package org.biojava.bio.seq.impl
Class SimpleFramedFeature
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.impl.SimpleFeature
org.biojava.bio.seq.impl.SimpleStrandedFeature
org.biojava.bio.seq.impl.SimpleFramedFeature
- All Implemented Interfaces:
Serializable
,Annotatable
,Feature
,FeatureHolder
,Frame
,FramedFeature
,RealizingFeatureHolder
,StrandedFeature
,Changeable
Title: SimpleFramedFeature.
Description: A no frills implementation of FramedFeature.
Copyright: Copyright (c) 2001.
- Version:
- 1.0
- Author:
- Mark Schreiber
- 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.FramedFeature
FramedFeature.ReadingFrame, FramedFeature.Template
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.FramedFeature
FRAME_0, FRAME_1, FRAME_2
Fields inherited from interface org.biojava.bio.seq.StrandedFeature
NEGATIVE, POSITIVE, STRAND, UNKNOWN
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Constructor Summary
ConstructorsConstructorDescriptionSimpleFramedFeature
(Sequence sourceSeq, FeatureHolder parent, FramedFeature.Template template) -
Method Summary
Methods inherited from class org.biojava.bio.seq.impl.SimpleStrandedFeature
fillTemplate, getStrand, getSymbols, setStrand
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
Methods inherited from interface org.biojava.bio.seq.FramedFeature
getStrand
Methods inherited from interface org.biojava.bio.seq.StrandedFeature
getSymbols, setStrand
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Constructor Details
-
SimpleFramedFeature
public SimpleFramedFeature(Sequence sourceSeq, FeatureHolder parent, FramedFeature.Template template) throws IllegalAlphabetException - Throws:
IllegalAlphabetException
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Method Details
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getReadingFrame
Description copied from interface:FramedFeature
return the reading frame of the feature.- Specified by:
getReadingFrame
in interfaceFramedFeature
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getFrame
Description copied from interface:Frame
A method to get the frame information of the implementing object -
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 classSimpleStrandedFeature
- 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 classSimpleStrandedFeature
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