Uses of Class org.biojava.bio.seq.Feature.Template (BioJava-1.5-beta API)

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

Packages that use Feature.Template
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.das | Development client for the Distributed Annotation System.
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
`static class` | `RestrictionSite.Template` `Template` for construction of `RestrictionSite`s.

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

Methods in org.biojava.bio.program.das with parameters of type Feature.Template
`Feature` | `DASSequence.createFeature(Feature.Template temp)`
`Feature` | `DASSequence.realizeFeature(FeatureHolder dest, Feature.Template temp)`

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

Methods in org.biojava.bio.program.xff that return Feature.Template
`protected Feature.Template` | `FeatureHandler.createFeatureTemplate()` Create a new template of the appropriate type.
`protected Feature.Template` | `StrandedFeatureHandler.createFeatureTemplate()`
`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
`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
`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
`Feature` | `SimpleAssembly.createFeature(Feature.Template temp)`
`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` | `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` | `SimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)`
`Feature` | `NewSimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)`
`Feature` | `RealizingFeatureHolder.realizeFeature(FeatureHolder parent, Feature.Template template)` Realize a feature template.
`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
`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
`static class` | `HomologyFeature.Template`
`static class` | `SimilarityPairFeature.Template` `Template` for construction of `SimilarityPairFeature`s.

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

Methods in org.biojava.bio.seq.impl that return Feature.Template
`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` | `SimpleHomologyFeature.makeTemplate()`
`Feature.Template` | `SimpleFeature.makeTemplate()`
`Feature.Template` | `SimpleSimilarityPairFeature.makeTemplate()`
`Feature.Template` | `SimpleStrandedFeature.makeTemplate()`
`Feature.Template` | `SimpleFramedFeature.makeTemplate()`
`Feature.Template` | `SimpleRemoteFeature.makeTemplate()`
`static Feature.Template` | `TemplateUtils.makeTemplate(Feature feat)`

Methods in org.biojava.bio.seq.impl with parameters of type Feature.Template
`Feature` | `SimpleGappedSequence.createFeature(Feature.Template templ)`
`Feature` | `RevCompSequence.createFeature(Feature.Template ft)` createFeature() will call createFeature() on the underlying Sequence.
`Feature` | `SimpleSequence.createFeature(Feature.Template template)`
`Feature` | `SimpleFeature.createFeature(Feature.Template temp)`
`Feature` | `DummySequence.createFeature(Feature.Template template)`
`Feature` | `ViewSequence.createFeature(Feature.Template template)`
`Feature` | `SubSequence.createFeature(Feature.Template templ)`
`Feature` | `LazyFilterFeatureHolder.createFeature(Feature.Template temp)`
`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` | `SimpleSequence.realizeFeature(FeatureHolder parent, Feature.Template template)`
`Feature` | `SimpleFeature.realizeFeature(FeatureHolder fh, Feature.Template templ)`
`Feature` | `ViewSequence.realizeFeature(FeatureHolder parent, Feature.Template template)`

Constructors in org.biojava.bio.seq.impl with parameters of type Feature.Template
`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
`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
`Feature.Template` | `EmblLikeLocationParser.parseLocation(String location, Feature.Template theTemplate)` Deprecated. `parseLocation` creates a `Location` from the String and returns a stranded location.
`void` | `SequenceBuilderFilter.startFeature(Feature.Template templ)`
`void` | `SeqIOFilter.startFeature(Feature.Template templ)`
`void` | `SequenceBuilderBase.startFeature(Feature.Template templ)`
`void` | `SwissprotFileFormer.startFeature(Feature.Template templ)` Deprecated. Null implementation.
`void` | `GenbankFileFormer.startFeature(Feature.Template templ)` Deprecated.
`void` | `SeqIOListener.startFeature(Feature.Template templ)` Notify the listener that a new feature object is starting.
`void` | `EmblFileFormer.startFeature(Feature.Template templ)` Deprecated.
`void` | `ProteinRefSeqFileFormer.startFeature(Feature.Template templ)` Deprecated.
`void` | `SeqIOAdapter.startFeature(Feature.Template templ)`

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

Fields in org.biojava.bio.seq.io.agave declared as Feature.Template
`protected Feature.Template` | `StAXFeatureHandler.featureTemplate`

Methods in org.biojava.bio.seq.io.agave that return Feature.Template
`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
`protected Feature.Template` | `StAXFeatureHandler.featureTemplate`

Methods in org.biojava.bio.seq.io.game that return Feature.Template
`protected Feature.Template` | `StAXFeatureHandler.createTemplate()` generates a very basic Template for the feature with SmallAnnotation in the annotation field.
`protected Feature.Template` | `GAMEFeatureSetHandler.createTemplate()`
`protected Feature.Template` | `GAMEFeatureSpanHandler.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
`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
`Feature` | `ProjectedFeature.createFeature(Feature.Template temp)`
`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` | `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
`static class` | `RichFeature.Template` Added-value extension of Feature.Template including bits we're interested in, eg.

Methods in org.biojavax.bio.seq that return Feature.Template
`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
`Feature` | `SimpleRichFeature.createFeature(Feature.Template ft)` Create a new Feature, and add it to this FeatureHolder.
`Feature` | `ThinRichSequence.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
`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
`void` | `SimpleRichSequenceBuilder.startFeature(Feature.Template templ)` Notify the listener that a new feature object is starting.
`void` | `DebuggingRichSeqIOListener.startFeature(Feature.Template templ)`
`void` | `RichSeqIOAdapter.startFeature(Feature.Template templ)`

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