Uses of Class
org.biojava.bio.seq.Feature.Template
Packages that use Feature.Template
Package
Description
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
Event-driven parsing system for the Extensible Feature Format (XFF).
Classes and interfaces for defining biological sequences and informatics
objects.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes for converting between AGAVE XML and BioJava objects.
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Code for projecting Feature objects and systematically altering their
properties.
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of Feature.Template in org.biojava.bio.molbio
Subclasses of Feature.Template in org.biojava.bio.molbioModifier and TypeClassDescriptionstatic class
Template
for construction ofRestrictionSite
s. -
Uses of Feature.Template in org.biojava.bio.program.xff
Methods in org.biojava.bio.program.xff that return Feature.TemplateModifier and TypeMethodDescriptionprotected 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.seqModifier and TypeClassDescriptionstatic class
Template for constructing a new ComponentFeature.static class
static class
static class
Template class for parameterizing the creation of a newStrandedFeature
.Methods in org.biojava.bio.seq that return Feature.TemplateModifier and TypeMethodDescriptionFeature.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.TemplateModifier and TypeMethodDescriptionAbstractFeatureHolder.createFeature
(Feature.Template temp) 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).FeatureHolder.createFeature
(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.FeatureHolder.EmptyFeatureHolder.createFeature
(Feature.Template f) LazyFeatureHolder.createFeature
(Feature.Template template) NewSimpleAssembly.createFeature
(Feature.Template temp) SimpleAssembly.createFeature
(Feature.Template temp) FeatureRealizer.realizeFeature
(Sequence seq, FeatureHolder parent, Feature.Template template) Install a feature on the specified sequence.NewSimpleAssembly.realizeFeature
(FeatureHolder fh, Feature.Template temp) RealizingFeatureHolder.realizeFeature
(FeatureHolder parent, Feature.Template template) Realize a feature template.SimpleAssembly.realizeFeature
(FeatureHolder fh, Feature.Template temp) SimpleFeatureRealizer.realizeFeature
(Sequence seq, FeatureHolder parent, Feature.Template temp) Constructors in org.biojava.bio.seq with parameters of type Feature.TemplateModifierConstructorDescriptionTemplate
(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.homolModifier and TypeClassDescriptionstatic class
static class
Template
for construction ofSimilarityPairFeature
s. -
Uses of Feature.Template in org.biojava.bio.seq.impl
Methods in org.biojava.bio.seq.impl that return Feature.TemplateModifier and TypeMethodDescriptionstatic 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.SimpleFeature.makeTemplate()
SimpleFramedFeature.makeTemplate()
SimpleHomologyFeature.makeTemplate()
SimpleRemoteFeature.makeTemplate()
SimpleSimilarityPairFeature.makeTemplate()
SimpleStrandedFeature.makeTemplate()
static Feature.Template
TemplateUtils.makeTemplate
(Feature feat) Methods in org.biojava.bio.seq.impl with parameters of type Feature.TemplateModifier and TypeMethodDescriptionDummySequence.createFeature
(Feature.Template template) LazyFilterFeatureHolder.createFeature
(Feature.Template temp) RevCompSequence.createFeature
(Feature.Template ft) createFeature() will call createFeature() on the underlying Sequence.SimpleFeature.createFeature
(Feature.Template temp) SimpleGappedSequence.createFeature
(Feature.Template templ) SimpleSequence.createFeature
(Feature.Template template) SimpleSequence.createFeature
(FeatureHolder fh, Feature.Template template) Deprecated.Please use new 1-arg createFeature instead.SubSequence.createFeature
(Feature.Template templ) ViewSequence.createFeature
(Feature.Template template) 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.SimpleFeature.realizeFeature
(FeatureHolder fh, Feature.Template templ) SimpleSequence.realizeFeature
(FeatureHolder parent, Feature.Template template) ViewSequence.realizeFeature
(FeatureHolder parent, Feature.Template template) Constructors in org.biojava.bio.seq.impl with parameters of type Feature.TemplateModifierConstructorDescriptionSimpleFeature
(Sequence sourceSeq, FeatureHolder parent, Feature.Template template) Create aSimpleFeature
on the given sequence. -
Uses of Feature.Template in org.biojava.bio.seq.io
Methods in org.biojava.bio.seq.io that return Feature.TemplateModifier and TypeMethodDescriptionEmblLikeLocationParser.parseLocation
(String location, Feature.Template theTemplate) Deprecated.parseLocation
creates aLocation
from the String and returns a stranded location.Methods in org.biojava.bio.seq.io with parameters of type Feature.TemplateModifier and TypeMethodDescriptionEmblLikeLocationParser.parseLocation
(String location, Feature.Template theTemplate) Deprecated.parseLocation
creates aLocation
from the String and returns a stranded location.void
EmblFileFormer.startFeature
(Feature.Template templ) Deprecated.void
GenbankFileFormer.startFeature
(Feature.Template templ) Deprecated.void
ProteinRefSeqFileFormer.startFeature
(Feature.Template templ) Deprecated.void
SeqIOAdapter.startFeature
(Feature.Template templ) void
SeqIOFilter.startFeature
(Feature.Template templ) void
SeqIOListener.startFeature
(Feature.Template templ) Notify the listener that a new feature object is starting.void
SequenceBuilderBase.startFeature
(Feature.Template templ) void
SequenceBuilderFilter.startFeature
(Feature.Template templ) void
SwissprotFileFormer.startFeature
(Feature.Template templ) Deprecated.Null implementation. -
Uses of Feature.Template in org.biojava.bio.seq.io.agave
Fields in org.biojava.bio.seq.io.agave declared as Feature.TemplateMethods in org.biojava.bio.seq.io.agave that return Feature.TemplateModifier and TypeMethodDescriptionprotected 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.TemplateMethods in org.biojava.bio.seq.io.game that return Feature.TemplateModifier and TypeMethodDescriptionprotected Feature.Template
GAMEAnnotationHandler.createTemplate()
protected Feature.Template
GAMEFeatureSetHandler.createTemplate()
protected Feature.Template
GAMEFeatureSpanHandler.createTemplate()
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.projection
Methods in org.biojava.bio.seq.projection that return Feature.TemplateModifier and TypeMethodDescriptionProjectedFeature.makeTemplate()
ProjectionEngine.revertTemplate
(Feature.Template templ, ProjectionContext ctxt) Revert a template so that it can be used on the original feature-space.ProjectionEngine.TemplateProjector.revertTemplate
(ProjectionContext ctxt, Feature.Template projTempl) Methods in org.biojava.bio.seq.projection with parameters of type Feature.TemplateModifier and TypeMethodDescriptionProjectedFeature.createFeature
(Feature.Template temp) ProjectedFeatureHolder.createFeature
(Feature.Template templ) ProjectionContext.createFeature
(Feature.Template projTempl) Create a projected feature with properties matching the template.ProjectionContext.createFeature
(Feature projParent, Feature.Template projTempl) Create a new projected feature.final Feature
ReparentContext.createFeature
(Feature.Template projTempl) final Feature
ReparentContext.createFeature
(Feature f, Feature.Template projTempl) ProjectionEngine.revertTemplate
(Feature.Template templ, ProjectionContext ctxt) Revert a template so that it can be used on the original feature-space.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.seqModifier and TypeClassDescriptionstatic class
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.TemplateModifier and TypeMethodDescriptionSimpleRichFeature.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.TemplateModifier and TypeMethodDescriptionSimpleRichFeature.createFeature
(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.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.TemplateModifierConstructorDescriptionSimpleRichFeature
(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.TemplateModifier and TypeMethodDescriptionvoid
DebuggingRichSeqIOListener.startFeature
(Feature.Template templ) void
RichSeqIOAdapter.startFeature
(Feature.Template templ) void
SimpleRichSequenceBuilder.startFeature
(Feature.Template templ) Notify the listener that a new feature object is starting.