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Packages that use Feature.Template | |
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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 |
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Subclasses of Feature.Template in org.biojava.bio.molbio | |
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static class |
RestrictionSite.Template
Template for construction of
RestrictionSite s. |
Uses of Feature.Template in org.biojava.bio.program.das |
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Methods in org.biojava.bio.program.das with parameters of type Feature.Template | |
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Feature |
DASSequence.createFeature(Feature.Template temp)
|
Feature |
DASSequence.realizeFeature(FeatureHolder dest,
Feature.Template temp)
|
Uses of Feature.Template in org.biojava.bio.program.xff |
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Methods in org.biojava.bio.program.xff that return Feature.Template | |
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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 |
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Subclasses of Feature.Template in org.biojava.bio.seq | |
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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 | |
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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 | |
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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 | |
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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 |
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Subclasses of Feature.Template in org.biojava.bio.seq.homol | |
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static class |
HomologyFeature.Template
|
static class |
SimilarityPairFeature.Template
Template for construction of
SimilarityPairFeature s. |
Uses of Feature.Template in org.biojava.bio.seq.impl |
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Methods in org.biojava.bio.seq.impl that return Feature.Template | |
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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 | |
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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 | |
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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 |
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Methods in org.biojava.bio.seq.io that return Feature.Template | |
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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 | |
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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 |
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Fields in org.biojava.bio.seq.io.agave declared as Feature.Template | |
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protected Feature.Template |
StAXFeatureHandler.featureTemplate
|
Methods in org.biojava.bio.seq.io.agave that return Feature.Template | |
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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 |
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Fields in org.biojava.bio.seq.io.game declared as Feature.Template | |
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protected Feature.Template |
StAXFeatureHandler.featureTemplate
|
Methods in org.biojava.bio.seq.io.game that return Feature.Template | |
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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 |
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Methods in org.biojava.bio.seq.projection that return Feature.Template | |
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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 | |
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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 |
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Subclasses of Feature.Template in org.biojavax.bio.seq | |
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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 | |
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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 | |
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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 | |
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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 |
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Methods in org.biojavax.bio.seq.io with parameters of type Feature.Template | |
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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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