[Biojava-l] BioJava Gene Hierarchies

[Daniel Di Giulio]

Hello,

I'm currently using BioJava to upgrade a eukaryotic gene finder program
(EVIGAN) to be compatible with the GFF3 formats.  Your BioJava genome
package is very useful, but I had a question about implementing a sort of
gene hierarchy from parsed files.  Essentially, I would like to be able to
read in a GFF3 file of a region of interest, parse out the CDS segments, and
then create a hierarchy of genes from the attribute tags, which I can then
employ later in my program.  It seems as if the
org.biojava3.genome.parsers.gff class is good for this, but there doesn't
seem to be a data structure for organizing related "Feature" objects into a
higher grouping based on similar attributes.  Does anyone know of a way to
implement this, or a package within BioJava which could be useful?

Thanks a lot,
Daniel