Uses of Interface
org.biojava.nbio.core.sequence.features.FeatureInterface
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Packages that use FeatureInterface Package Description org.biojava.nbio.core.sequence.features org.biojava.nbio.core.sequence.io org.biojava.nbio.core.sequence.template -
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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 featureclass
FeatureDbReferenceInfo<S extends AbstractSequence<C>,C extends Compound>
It isDBReferenceInfo
which implementsFeatureInterface
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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 AbstractFeatureFields 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 typeMethods in org.biojava.nbio.core.sequence.features that return FeatureInterface Modifier and Type Method Description FeatureInterface<S,C>
AbstractFeature. getParentFeature()
Get the parent FeatureFeatureInterface<S,C>
FeatureDbReferenceInfo. getParentFeature()
FeatureInterface<S,C>
FeatureInterface. getParentFeature()
Get the parent featureMethods 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 featuresList<FeatureInterface<S,C>>
FeatureDbReferenceInfo. getChildrenFeatures()
List<FeatureInterface<S,C>>
FeatureInterface. getChildrenFeatures()
Get the features contained by this featureMethods 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 featureMethod 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 featuresvoid
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 positionList<FeatureInterface<AbstractSequence<C>,C>>
AbstractSequence. getFeatures(String featureType, int bioSequencePosition)
Return features at a sequence position by typeList<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 sequencevoid
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
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