Uses of Class
org.jbei.ice.lib.dto.DNAFeature

Packages that use DNAFeature

Package	Description
org.jbei.ice.lib.bulkupload
org.jbei.ice.lib.dto	Value Objects classes.
org.jbei.ice.lib.entry.sequence.annotation
org.jbei.ice.lib.parsers.genbank
org.jbei.ice.lib.search.blast	BLAST search classes.
org.jbei.ice.services.rest
org.jbei.ice.storage.model	Data models for ice objects.

Uses of DNAFeature in org.jbei.ice.lib.bulkupload

Methods in org.jbei.ice.lib.bulkupload with parameters of type DNAFeature

Modifier and Type	Method and Description
int	DNAFeatureComparator.compare(DNAFeature sf1, DNAFeature sf2)
protected int	DNAFeatureComparator.compareEnds(DNAFeature sf1, DNAFeature sf2)

Uses of DNAFeature in org.jbei.ice.lib.dto

Methods in org.jbei.ice.lib.dto that return types with arguments of type DNAFeature

Modifier and Type	Method and Description
List<DNAFeature>	FeaturedDNASequence.getFeatures()
List<DNAFeature>	DNAFeatures.getFeatures()

Method parameters in org.jbei.ice.lib.dto with type arguments of type DNAFeature

Modifier and Type	Method and Description
void	FeaturedDNASequence.setFeatures(List<DNAFeature> features)

Constructor parameters in org.jbei.ice.lib.dto with type arguments of type DNAFeature

Constructor and Description
FeaturedDNASequence(String sequence, List<DNAFeature> features)
FeaturedDNASequence(String sequence, String name, boolean isCircular, List<DNAFeature> features, String identifier)

Uses of DNAFeature in org.jbei.ice.lib.entry.sequence.annotation

Methods in org.jbei.ice.lib.entry.sequence.annotation that return types with arguments of type DNAFeature

Modifier and Type	Method and Description
Results<DNAFeature>	Annotations.filter(int offset, int limit, String filter)

Method parameters in org.jbei.ice.lib.entry.sequence.annotation with type arguments of type DNAFeature

Modifier and Type	Method and Description
void	Annotations.curate(List<DNAFeature> features) Curates a specified set of annotations.

Uses of DNAFeature in org.jbei.ice.lib.parsers.genbank

Methods in org.jbei.ice.lib.parsers.genbank that return types with arguments of type DNAFeature

Modifier and Type	Method and Description
List<DNAFeature>	FeaturesTag.getFeatures()

Method parameters in org.jbei.ice.lib.parsers.genbank with type arguments of type DNAFeature

Modifier and Type	Method and Description
void	FeaturesTag.setFeatures(List<DNAFeature> features)

Uses of DNAFeature in org.jbei.ice.lib.search.blast

Methods in org.jbei.ice.lib.search.blast that return types with arguments of type DNAFeature

Modifier and Type	Method and Description
static List<DNAFeature>	BlastPlus.processFeaturesBlastOutput(String blastOutput) Process the output of the blast run for features into a list of feature objects Expected format for the output (per line) is feature_id, label, type, qstart, qend, sstart, send, sstrand Therefore line[0] is feature_id, line[1] is label etc Since we are only interested in features that have a full match (covers entire feature) some matches are manually eliminated.
static List<DNAFeature>	BlastPlus.runCheckFeatures(BlastQuery query) Run a blast query against the sequence features blast database.

Uses of DNAFeature in org.jbei.ice.services.rest

Method parameters in org.jbei.ice.services.rest with type arguments of type DNAFeature

Modifier and Type	Method and Description
javax.ws.rs.core.Response	AnnotationResource.curate(List<DNAFeature> list) Curate available annotations to include or exclude them from auto-annotation feature

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

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

Modifier and Type	Method and Description
DNAFeature	Feature.toDataTransferObject()
DNAFeature	SequenceFeature.toDataTransferObject()