Uses of Class
org.biojava.bio.seq.Feature.Template

Packages that use Feature.Template

Package	Description
org.biojava.bio.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program.xff	Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.homol	The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.io.agave	Classes for converting between AGAVE XML and BioJava objects.
org.biojava.bio.seq.io.game	Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.projection	Code for projecting Feature objects and systematically altering their properties.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.

Uses of Feature.Template in org.biojava.bio.molbio

Subclasses of Feature.Template in org.biojava.bio.molbio

Modifier and Type	Class and Description
static class	RestrictionSite.Template Template for construction of RestrictionSites.

Uses of Feature.Template in org.biojava.bio.program.xff

Methods in org.biojava.bio.program.xff that return Feature.Template

Modifier and Type	Method and Description
protected Feature.Template	StrandedFeatureHandler.createFeatureTemplate()
protected Feature.Template	FeatureHandler.createFeatureTemplate() Create a new template of the appropriate type.
protected Feature.Template	FeatureHandler.getFeatureTemplate() Get the template for the feature being constructed.

Uses of Feature.Template in org.biojava.bio.seq

Subclasses of Feature.Template in org.biojava.bio.seq

Modifier and Type	Class and Description
static class	ComponentFeature.Template Template for constructing a new ComponentFeature.
static class	FramedFeature.Template
static class	RemoteFeature.Template
static class	StrandedFeature.Template Template class for parameterizing the creation of a new StrandedFeature.

Methods in org.biojava.bio.seq that return Feature.Template

Modifier and Type	Method and Description
Feature.Template	Feature.makeTemplate() Create a new Template that could be used to generate a feature identical to this one.

Methods in org.biojava.bio.seq with parameters of type Feature.Template

Modifier and Type	Method and Description
Feature	SimpleAssembly.createFeature(Feature.Template temp)
Feature	NewSimpleAssembly.createFeature(Feature.Template temp)
Feature	LazyFeatureHolder.createFeature(Feature.Template template)
Feature	FeatureHolder.createFeature(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.
Feature	FeatureHolder.EmptyFeatureHolder.createFeature(Feature.Template f)
Feature	CircularView.createFeature(Feature.Template template) Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence).
Feature	AbstractFeatureHolder.createFeature(Feature.Template temp)
Feature	SimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
Feature	RealizingFeatureHolder.realizeFeature(FeatureHolder parent, Feature.Template template) Realize a feature template.
Feature	NewSimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
Feature	SimpleFeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template temp)
Feature	FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template) Install a feature on the specified sequence.

Constructors in org.biojava.bio.seq with parameters of type Feature.Template

Constructor and Description
RemoteFeature.Template(Feature.Template theTemplate) Creates a RemoteFeature.Template that has the same values as the template passed in.

Uses of Feature.Template in org.biojava.bio.seq.homol

Subclasses of Feature.Template in org.biojava.bio.seq.homol

Modifier and Type	Class and Description
static class	HomologyFeature.Template
static class	SimilarityPairFeature.Template Template for construction of SimilarityPairFeatures.

Uses of Feature.Template in org.biojava.bio.seq.impl

Methods in org.biojava.bio.seq.impl that return Feature.Template

Modifier and Type	Method and Description
static Feature.Template	TemplateUtils.instantiateTemplate(Feature feat) This attempts to divine the 'best' template class for a feature and return a new instance readly for pupulating.
Feature.Template	SimpleStrandedFeature.makeTemplate()
Feature.Template	SimpleSimilarityPairFeature.makeTemplate()
Feature.Template	SimpleRemoteFeature.makeTemplate()
Feature.Template	SimpleHomologyFeature.makeTemplate()
Feature.Template	SimpleFramedFeature.makeTemplate()
Feature.Template	SimpleFeature.makeTemplate()
static Feature.Template	TemplateUtils.makeTemplate(Feature feat)

Methods in org.biojava.bio.seq.impl with parameters of type Feature.Template

Modifier and Type	Method and Description
Feature	ViewSequence.createFeature(Feature.Template template)
Feature	SubSequence.createFeature(Feature.Template templ)
Feature	SimpleSequence.createFeature(Feature.Template template)
Feature	SimpleGappedSequence.createFeature(Feature.Template templ)
Feature	SimpleFeature.createFeature(Feature.Template temp)
Feature	RevCompSequence.createFeature(Feature.Template ft) createFeature() will call createFeature() on the underlying Sequence.
Feature	LazyFilterFeatureHolder.createFeature(Feature.Template temp)
Feature	DummySequence.createFeature(Feature.Template template)
Feature	SimpleSequence.createFeature(FeatureHolder fh, Feature.Template template) Deprecated. Please use new 1-arg createFeature instead.
protected void	SimpleFeature.fillTemplate(Feature.Template ft)
static void	TemplateUtils.populate(Feature.Template templ, Feature feat) This attempts to populate the fields of a template using the publically accessible information in a feature.
Feature	ViewSequence.realizeFeature(FeatureHolder parent, Feature.Template template)
Feature	SimpleSequence.realizeFeature(FeatureHolder parent, Feature.Template template)
Feature	SimpleFeature.realizeFeature(FeatureHolder fh, Feature.Template templ)

Constructors in org.biojava.bio.seq.impl with parameters of type Feature.Template

Constructor and Description
SimpleFeature(Sequence sourceSeq, FeatureHolder parent, Feature.Template template) Create a SimpleFeature on the given sequence.

Uses of Feature.Template in org.biojava.bio.seq.io

Methods in org.biojava.bio.seq.io that return Feature.Template

Modifier and Type	Method and Description
Feature.Template	EmblLikeLocationParser.parseLocation(String location, Feature.Template theTemplate) Deprecated. parseLocation creates a Location from the String and returns a stranded location.

Methods in org.biojava.bio.seq.io with parameters of type Feature.Template

Modifier and Type	Method and Description
Feature.Template	EmblLikeLocationParser.parseLocation(String location, Feature.Template theTemplate) Deprecated. parseLocation creates a Location from the String and returns a stranded location.
void	SwissprotFileFormer.startFeature(Feature.Template templ) Deprecated. Null implementation.
void	SequenceBuilderFilter.startFeature(Feature.Template templ)
void	SequenceBuilderBase.startFeature(Feature.Template templ)
void	SeqIOListener.startFeature(Feature.Template templ) Notify the listener that a new feature object is starting.
void	SeqIOFilter.startFeature(Feature.Template templ)
void	SeqIOAdapter.startFeature(Feature.Template templ)
void	ProteinRefSeqFileFormer.startFeature(Feature.Template templ) Deprecated.
void	GenbankFileFormer.startFeature(Feature.Template templ) Deprecated.
void	EmblFileFormer.startFeature(Feature.Template templ) Deprecated.

Uses of Feature.Template in org.biojava.bio.seq.io.agave

Fields in org.biojava.bio.seq.io.agave declared as Feature.Template

Modifier and Type	Field and Description
protected Feature.Template	StAXFeatureHandler.featureTemplate

Methods in org.biojava.bio.seq.io.agave that return Feature.Template

Modifier and Type	Method and Description
protected Feature.Template	StAXFeatureHandler.createTemplate() generates a very basic Template for the feature with SmallAnnotation in the annotation field.

Uses of Feature.Template in org.biojava.bio.seq.io.game

Fields in org.biojava.bio.seq.io.game declared as Feature.Template

Modifier and Type	Field and Description
protected Feature.Template	StAXFeatureHandler.featureTemplate

Methods in org.biojava.bio.seq.io.game that return Feature.Template

Modifier and Type	Method and Description
protected Feature.Template	StAXFeatureHandler.createTemplate() generates a very basic Template for the feature with SmallAnnotation in the annotation field.
protected Feature.Template	GAMEFeatureSpanHandler.createTemplate()
protected Feature.Template	GAMEFeatureSetHandler.createTemplate()
protected Feature.Template	GAMEAnnotationHandler.createTemplate()

Uses of Feature.Template in org.biojava.bio.seq.projection

Methods in org.biojava.bio.seq.projection that return Feature.Template

Modifier and Type	Method and Description
Feature.Template	ProjectedFeature.makeTemplate()
Feature.Template	ProjectionEngine.revertTemplate(Feature.Template templ, ProjectionContext ctxt) Revert a template so that it can be used on the original feature-space.
Feature.Template	ProjectionEngine.TemplateProjector.revertTemplate(ProjectionContext ctxt, Feature.Template projTempl)

Methods in org.biojava.bio.seq.projection with parameters of type Feature.Template

Modifier and Type	Method and Description
Feature	ReparentContext.createFeature(Feature.Template projTempl)
Feature	ProjectionContext.createFeature(Feature.Template projTempl) Create a projected feature with properties matching the template.
Feature	ProjectedFeatureHolder.createFeature(Feature.Template templ)
Feature	ProjectedFeature.createFeature(Feature.Template temp)
Feature	ReparentContext.createFeature(Feature f, Feature.Template projTempl)
Feature	ProjectionContext.createFeature(Feature projParent, Feature.Template projTempl) Create a new projected feature.
Feature.Template	ProjectionEngine.revertTemplate(Feature.Template templ, ProjectionContext ctxt) Revert a template so that it can be used on the original feature-space.
Feature.Template	ProjectionEngine.TemplateProjector.revertTemplate(ProjectionContext ctxt, Feature.Template projTempl)

Uses of Feature.Template in org.biojavax.bio.seq

Subclasses of Feature.Template in org.biojavax.bio.seq

Modifier and Type	Class and Description
static class	RichFeature.Template Added-value extension of Feature.Template including bits we're interested in, eg. featureRelationshipSet for relationships with other features, and rankedCrossRefs for lookups into other databases.

Methods in org.biojavax.bio.seq that return Feature.Template

Modifier and Type	Method and Description
Feature.Template	SimpleRichFeature.makeTemplate() Create a new Template that could be used to generate a feature identical to this one.

Methods in org.biojavax.bio.seq with parameters of type Feature.Template

Modifier and Type	Method and Description
Feature	ThinRichSequence.createFeature(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.
Feature	SimpleRichFeature.createFeature(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.

Constructors in org.biojavax.bio.seq with parameters of type Feature.Template

Constructor and Description
SimpleRichFeature(FeatureHolder parent, Feature.Template templ) Creates a new instance of SimpleRichFeature based on a template.

Uses of Feature.Template in org.biojavax.bio.seq.io

Methods in org.biojavax.bio.seq.io with parameters of type Feature.Template

Modifier and Type	Method and Description
void	SimpleRichSequenceBuilder.startFeature(Feature.Template templ) Notify the listener that a new feature object is starting.
void	RichSeqIOAdapter.startFeature(Feature.Template templ)
void	DebuggingRichSeqIOListener.startFeature(Feature.Template templ)