[Bioperl-l] AssemblyIO (ace), singlets, and Contigs

[Chad Matsalla]

Greetings all,

I have a question with regards to AssemblyIO and parsing phrap's .ace
files.

I'm using a Java Swing-based application that retrieves complex objects
from Perl-based web services. I do this so that I can have the
'advantages' of Swing and the power of Bioperl at the same time.

The AssemblyIO system works perfectly but I would like a singlet to be a
Bio::Assembly::Contig object rather then a Bio::Seq.

UML describing my Assembly object can be found here:
http://www.dieselwurks.com/bioinformatics/assembly.pdf
My web service 'converts' a Bio::Assembly::Scaffold into my Assembly
object and sends it to a Swing client that renders it.

Using that object model one can, in Perl or in Java, loop through the
Contigs in an Assembly and perform operations on them without caring
what kind of Contig it is. For example, I draw cartoons in SVG and
getting Contigs and singlets from the Assembly object separately is...
irritating.

I volunteer to do this change but I wanted to see if anybody objected to
this.

Chad Matsalla