Uses of Interface
org.biojava.nbio.core.sequence.features.FeatureInterface

Packages that use FeatureInterface

Package	Description
org.biojava.nbio.core.sequence.features
org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.sequence.template

Uses of FeatureInterface in org.biojava.nbio.core.sequence.features

Classes in org.biojava.nbio.core.sequence.features that implement FeatureInterface

Modifier and Type	Class	Description
class	AbstractFeature<S extends AbstractSequence<C>,C extends Compound>	A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user Ideally well defined features should have a class to describe attributes of that feature
class	FeatureDbReferenceInfo<S extends AbstractSequence<C>,C extends Compound>	It is DBReferenceInfo which implements FeatureInterface.
class	QualityFeature<S extends AbstractSequence<C>,C extends Compound>	DNA Sequences produced by modern sequencers usually have quality informaion attached to them.
class	QuantityFeature<S extends AbstractSequence<C>,C extends Compound>	It is common to have a numerical value or values associated with a feature.
class	TextFeature<S extends AbstractSequence<C>,C extends Compound>	A implmentation of AbstractFeature

Fields in org.biojava.nbio.core.sequence.features with type parameters of type FeatureInterface

Modifier and Type	Field	Description
static Comparator<FeatureInterface<?,?>>	AbstractFeature.LENGTH	Sort features by length.
static Comparator<FeatureInterface<?,?>>	AbstractFeature.LOCATION_LENGTH	Sort features by start position and then longest length.
static Comparator<FeatureInterface<?,?>>	AbstractFeature.TYPE	Sort features by type

Methods in org.biojava.nbio.core.sequence.features that return FeatureInterface

Modifier and Type	Method	Description
FeatureInterface<S,C>	AbstractFeature.getParentFeature()	Get the parent Feature
FeatureInterface<S,C>	FeatureDbReferenceInfo.getParentFeature()
FeatureInterface<S,C>	FeatureInterface.getParentFeature()	Get the parent feature

Methods in org.biojava.nbio.core.sequence.features that return types with arguments of type FeatureInterface

Modifier and Type	Method	Description
List<FeatureInterface<S,C>>	AbstractFeature.getChildrenFeatures()	Get the children features
List<FeatureInterface<S,C>>	FeatureDbReferenceInfo.getChildrenFeatures()
List<FeatureInterface<S,C>>	FeatureInterface.getChildrenFeatures()	Get the features contained by this feature

Methods in org.biojava.nbio.core.sequence.features with parameters of type FeatureInterface

Modifier and Type	Method	Description
void	AbstractFeature.setParentFeature(FeatureInterface<S,C> feature)	A feature can be the child or contained by a parent feature.
void	FeatureDbReferenceInfo.setParentFeature(FeatureInterface<S,C> feature)
void	FeatureInterface.setParentFeature(FeatureInterface<S,C> feature)	Set the parent feature

Method parameters in org.biojava.nbio.core.sequence.features with type arguments of type FeatureInterface

Modifier and Type	Method	Description
void	AbstractFeature.setChildrenFeatures(List<FeatureInterface<S,C>> features)	Set the children features
void	FeatureDbReferenceInfo.setChildrenFeatures(List<FeatureInterface<S,C>> features)
void	FeatureInterface.setChildrenFeatures(List<FeatureInterface<S,C>> features)	Set the children features

Uses of FeatureInterface in org.biojava.nbio.core.sequence.io

Methods in org.biojava.nbio.core.sequence.io with parameters of type FeatureInterface

Modifier and Type	Method	Description
protected String	GenericInsdcHeaderFormat._write_feature(FeatureInterface<AbstractSequence<C>,C> feature, int record_length)	Write a single SeqFeature object to features table.

Uses of FeatureInterface in org.biojava.nbio.core.sequence.template

Methods in org.biojava.nbio.core.sequence.template that return types with arguments of type FeatureInterface

Modifier and Type	Method	Description
List<FeatureInterface<AbstractSequence<C>,C>>	AbstractSequence.getFeatures()
List<FeatureInterface<AbstractSequence<C>,C>>	AbstractSequence.getFeatures(int bioSequencePosition)	Return features at a sequence position
List<FeatureInterface<AbstractSequence<C>,C>>	AbstractSequence.getFeatures(String featureType, int bioSequencePosition)	Return features at a sequence position by type
List<FeatureInterface<AbstractSequence<C>,C>>	AbstractSequence.getFeaturesByType(String type)

Methods in org.biojava.nbio.core.sequence.template with parameters of type FeatureInterface

Modifier and Type	Method	Description
void	AbstractSequence.addFeature(int bioStart, int bioEnd, FeatureInterface<AbstractSequence<C>,C> feature)	Method to help set the proper details for a feature as it relates to a sequence where the feature needs to have a location on the sequence
void	AbstractSequence.addFeature(FeatureInterface<AbstractSequence<C>,C> feature)	Add a feature to this sequence.
void	AbstractSequence.removeFeature(FeatureInterface<AbstractSequence<C>,C> feature)	Remove a feature from the sequence