[Bioperl-l] strand() question

[Steve Chervitz]

The documentation in GenericHit incorrectly refers you to see  
SearchUtils. It should instead point you at the interface module which  
GenericHit implements: Bio::Search::Hit::HitI::strand(). Here's a link  
to the corresponding HTML version for this method:
http://doc.bioperl.org/releases/bioperl-1.2/Bio/Search/Hit/ 
HitI.html#POD25

I fixed this and similar documentation bugs in GenericHit on the main  
trunk.

This brings up the issue of what to do with method documentation in an  
interface module and corresponding implementation modules. The approach  
I've been favoring is to refer to the interface documentation from the  
implementing module and include only implementation-specific docs in  
the implementing module's method POD.

The alternative approach is to cut-and-paste the method POD from the  
interface into the impl, but this leads to redundancy and  
synchronization problems and more maintenance work.

It would be nice to maintain documentation in a single location and  
simply refer to it. The HTML links would solve the problem nicely... if  
they worked. The POD syntax I've been using doesn't seem to work when  
the HTML docs are generated. Here's an example:

=head2 strand

See documentation in  
L<Bio::Search::Hit::HitI::strand()|Bio::Search::Hit::HitI>

=cut

I'm not that familiar with Pdoc, but it seems like this sort of thing  
should be possible. Anyone have any tips?

Steve

On Tuesday, Jun 10, 2003, at 04:41 US/Pacific, Brian Osborne wrote:

> Annette,
>
> Check out the SearchIO HOWTO, it might answer your questions:
>
> http://bioperl.org/HOWTOs/html/SearchIO.html
>
> If not there will be someone on the list how can provide further
> clarification.
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of hackstam
> Sent: Monday, June 09, 2003 3:03 PM
> To: Bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] strand() question
>
> Sorry if this is not the right place to ask this question
> but I am having problems locating the documentation on the
> strand function in Bio::Search::Hit::GenericHit.  Could
> someone please tell me what are the output values and there
> meaning?  Thanks in advance for any help.
> Annette
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