pluggable feature diagram generator with direct access to sequence objects

[jprocter]

The existing /src/plone4bio.base/src/plone4bio/base/png/perl/graphics-cmd.pl based feature diagram does not represent all the metadata available from a rich sequence feature object (such as one retrieved from a biosql datasource).

A mechanism could be provided for people deploying plone4bio to easily substitute the default feature diagram implementation for their own, which has access to the the plone4bio sequence object directly (rather than a flatfile representation such as GenBank?).

[jprocter]

I would also recommend enhancing the existing flatfile generator to honour all the annotation data supported by the bio-* bindings to biosql.

See this page for details:  http://www.biosql.org/wiki/Annotation_Mapping

[jprocter]

comment from Peter C (biopython) - bioperl scripts could access biosql entry via the BioPerl? binding.

[m]

We postpone the solution to this problem in the future: at the moment there are non reliable Python alternative to the Perl graphics module. Code we have tested has been either lacking features or too slow.