Bioperl: Module collections...
Steve A. Chervitz
Sat, 1 Aug 1998 11:52:46 -0700 (PDT)
On Sat, 1 Aug 1998, Ewan Birney wrote:
> On Fri, 31 Jul 1998, Steve A. Chervitz wrote:
> > The name change should coincide with a functionality change, namely,
> > adding a feature description mechanism. We'll have to hear from ChrisD
> > and Ian about their progress along these lines.
> In my opinion the feature description stuff *should not* be in the Seq
> object (the 'light-weight' sequence object) but in the heavyweight
> sequence object (what I call the 'Entry' object). My game plan has
> PreSeq.pm -> Seq.pm (light weight object) from Chris
> Entry.pm -> Ian's object adapted from his GSC objects that
> has features (and taxonomy and the kitchen sink...).
> I think this is a much cleaner way of breaking up the problem than
> simply having a single heavy weight object. Entry.pm can have alot of
> 'magic' whereas Seq.pm should be lean and mean. (Of course Entry.pm
> should contain Seq.pm)...
> From this point of view PreSeq can become Seq now, which is what I
> reckon. Other votes? (before Wednesday by any chance?)
I want to call your attention to some changes that I have made to PreSeq.pm
which we might want to add to the version that becomes "Seq.pm". Some of
my changes were designed for integration into my Bio::Root hierarchy or
were related to autoloading and should *not* go into Seq.pm. However, I
made a number of bug fixes and other functionality enhancements that should
be considered. All of my changes are documented in the module itself
> > > b) Stevec's Blast module
> > >
> > > This use's Steves Bio::Root::Global (at least) and ??
> > > Bio::Root::Object
> > >
> > > Steve - can we get rid of these things? (Do you want to?)
> > >
> > Well, my modules rely on these so they are a necessary part of my Blast
> > distribution as it currently stands. You could put my Bio::Root directory
> > under CVS as well (it's bundled with my Blast distribution). Removing
> > them from my design would take a fair bit of non-trivial de-engineering
> > that I would hesitate to do (but would consider if people complained loud
> > enough :).
> Consider one complaint lodged ;) - but I am certainly not obsessive about
> it. I don't think we can really try to coordinate everything through
> Bio::Root which means Bio::Root *really* is Bio::SteveC::Root ;) --->
> Lets work with the entire Root and Object (Root and Branch?) of the
> Blast.pm and see if we can trim it later on (with your blessing ;)).
> For the moment shall we put the entire Blast stuff into the repository
> as it stands, then you can do a checkout, merge and commit for the new
> stuff, or does it make more sense to wait and perhaps for you to attach
> the directories yourself once we have made the CVS system? Your choice...
I vote for adding it as it stands and modifying as necesary later.
> > > Stevec - do you want to write bioperl.pod and the README (you seem the
> > > natural person for it as leader etc...)?
> > I can come up with a draft. Do you have some ideas in mind for what these
> > documents should say?
> I think bioperl.pod should be like the perl.pod in the distribution -
> a) A header of links into the other Bio:: classes (split into
> two groups - Core distribution and contributed)
> b) Introduction to bioperl like --->
> bioperl uses perl (and here is where to get it?)
> bioperl is not an executable it is an extension of perl
> The main objects (and docs) with a breif description
> of how they fit together
> The core group and other html resources.
> c) some light hearted jokes about doing the Camel genome in the
How about also including some guidelines for various things:
* Module documentation
* Creating and submitting a new module
* Exception handling
* Argument handling
* Handling of constants
Some of these things are stylistic issues and could be phrased as
suggestions. Enforcing standards would be very non-Perl but having some
shared conventions would make code sharing/reuse/maintenance easier.
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