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

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

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

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

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

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

Modifier and Type	Method and Description
void	AbstractFeature.setChildrenFeatures(List<FeatureInterface<S,C>> features) Set the children features
void	FeatureInterface.setChildrenFeatures(List<FeatureInterface<S,C>> features) Set the children features
void	FeatureDbReferenceInfo.setChildrenFeatures(List<FeatureInterface<S,C>> 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 and 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 and 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 and Description
void	AbstractSequence.addFeature(FeatureInterface<AbstractSequence<C>,C> feature) Add a feature to this sequence.
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.removeFeature(FeatureInterface<AbstractSequence<C>,C> feature) Remove a feature from the sequence