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 RestrictionSites.
 

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 SimilarityPairFeatures.
 

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)