Uses of Class
util.bio.parsers.gff.Gff3Feature

Packages that use Gff3Feature

util.bio.annotation	For representing gene annotation.
util.bio.parsers.gff	GFF2 and GFF3 parsers.

Uses of Gff3Feature in util.bio.annotation

Methods in util.bio.annotation with parameters of type Gff3Feature

boolean[]

ExportIntergenicRegions.maskBoolean(Gff3Feature[] features) Uses a boolean[] to score whether a base is part of an annotation (true) or not (false).

Constructors in util.bio.annotation with parameters of type Gff3Feature

Translation(Gff3Feature f)

Transcript(Gff3Feature f)

GenericFeature(Gff3Feature f)

ExonIntron(Gff3Feature f)

Uses of Gff3Feature in util.bio.parsers.gff

Methods in util.bio.parsers.gff that return Gff3Feature

Gff3Feature[][]	Gff3Parser.getChromSplitFeatures() Returns the features split by chromosome.
Gff3Feature[]	Gff3Parser.getFeatures()

Methods in util.bio.parsers.gff with parameters of type Gff3Feature

static void	Gff3Feature.saveGFF3TextFile(Gff3Feature[] g, java.io.File newGFF3File) Prints an array of GFF3Features as a plain text file
void	DmelRel4Extractor.buildGenericFeature(Gff3Feature f)
void	DmelRel4Extractor.buildGeneGrp(Gff3Feature f) Creates a new gene group, call this last after having loaded the exons, transcripts, and translations.