Uses of Class
org.jbei.ice.storage.model.SequenceFeature

Packages that use SequenceFeature

Package	Description
org.jbei.ice.lib.entry.sequence.composers.formatters	Formatters for various sequence file formats.
org.jbei.ice.storage.hibernate.dao
org.jbei.ice.storage.model	Data models for ice objects.

Uses of SequenceFeature in org.jbei.ice.lib.entry.sequence.composers.formatters

Methods in org.jbei.ice.lib.entry.sequence.composers.formatters with parameters of type SequenceFeature

Modifier and Type	Method and Description
int	SequenceFeatureComparator.compare(SequenceFeature sf1, SequenceFeature sf2)
protected int	SequenceFeatureComparator.compareEnds(SequenceFeature sf1, SequenceFeature sf2)
protected org.biojavax.RichAnnotation	GenbankFormatter.getAnnotations(SequenceFeature sequenceFeature) Convert SequenceFeature into a RichAnnotation.
protected String	GenbankFormatter.getFeatureType(SequenceFeature sequenceFeature) Retrieve feature type from given SequenceFeature.
protected org.biojavax.bio.seq.RichLocation.Strand	GenbankFormatter.getStrand(SequenceFeature sequenceFeature) Get the strand of the SequenceFeature feature.
void	SBOLVisitor.visit(SequenceFeature feature)
void	SBOL2Visitor.visit(SequenceFeature feature)

Uses of SequenceFeature in org.jbei.ice.storage.hibernate.dao

Methods in org.jbei.ice.storage.hibernate.dao that return SequenceFeature

Modifier and Type	Method and Description
SequenceFeature	SequenceFeatureDAO.get(long id)

Methods in org.jbei.ice.storage.hibernate.dao that return types with arguments of type SequenceFeature

Modifier and Type	Method and Description
List<SequenceFeature>	SequenceFeatureDAO.getByFeature(Feature feature)
List<SequenceFeature>	SequenceFeatureDAO.getEntrySequenceFeatures(Entry entry)
List<SequenceFeature>	SequenceFeatureDAO.getSequenceFeatures(String userId, List<Group> groups, String nameFilter, int start, int limit)

Method parameters in org.jbei.ice.storage.hibernate.dao with type arguments of type SequenceFeature

Modifier and Type	Method and Description
Sequence	SequenceDAO.updateSequence(Sequence sequence, Set<SequenceFeature> newFeatures) Updates an existing feature with a new set of features

Uses of SequenceFeature in org.jbei.ice.storage.model

Methods in org.jbei.ice.storage.model that return SequenceFeature

Modifier and Type	Method and Description
SequenceFeature	AnnotationLocation.getSequenceFeature()
SequenceFeature	SequenceFeatureAttribute.getSequenceFeature()

Methods in org.jbei.ice.storage.model that return types with arguments of type SequenceFeature

Modifier and Type	Method and Description
Set<SequenceFeature>	Sequence.getSequenceFeatures()

Methods in org.jbei.ice.storage.model with parameters of type SequenceFeature

Modifier and Type	Method and Description
void	AnnotationLocation.setSequenceFeature(SequenceFeature sequenceFeature)
void	SequenceFeatureAttribute.setSequenceFeature(SequenceFeature sequenceFeature)

Method parameters in org.jbei.ice.storage.model with type arguments of type SequenceFeature

Modifier and Type	Method and Description
void	Sequence.setSequenceFeatures(Set<SequenceFeature> features)

Constructors in org.jbei.ice.storage.model with parameters of type SequenceFeature

Constructor and Description
AnnotationLocation(int genbankStart, int end, SequenceFeature sequenceFeature)