Return-value for methods; seed funding

[Georg Fuellen]

SteveB wrote,
> My suggested modification (probably can't show up until Bio::Seq) would be
> for revcom to return an object with the required modification.  

I think it's just awkward to have to create the modified object first 
and then access its data. For me (and, I think, the average user),
revcom is an accessor modifying data on the fly, and that's how it's
implemented at the moment. This also saves space.

Related problem: accessing the sequence without modification: getting
the sequence data as string/array VERSUS getting the sequence as a new object.
SteveB wrote,
> Suggestions for a new method name better than "get_seq_obj($end,$beg)"?
SteveC wrote,
> How about "newseq()"?

Intuitively, newseq() implies ``a new sequence'', not a new object.

Both problems may be solved easily I hope.

Consider
-- -----------

$seq->slice(seq($beg,$end))       returns modified object
$seq->slice($beg,$end)            same as current get_seq() -- returns sequence
$seq->slice(inplace($beg,$end))   modifies the object itself -- this saves time+space

Same for revcom:

$seq->revcom(seq($beg,$end))      returns modified object
$seq->revcom($beg,$end)           same as current revcom() -- returns sequence
$seq->revcom(inplace($beg,$end))  modifies the object itself -- this saves time+space

The implementation should be straightforward doing a pattern match
on the argument.

Most importantly, everyone in the core group, take a look NOW at
the UnivAln POD -- are there more things you don't like ?
The revcom-issue should have come up much earlier. URL is
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/UnivAln/UnivAln.pm.html
I've spend a lot of time writing it -- please take the time to read it !

SteveB wrote,
> > We should do whatever it takes to get some seed funding from the Perl
> > Institute... ;-) Other than that, I see few benefits that WE may get from
> > THEM, or am I wrong ?!
>
> The problem is not funding but manpower and expertise.  (Funding would
> only be an issue if we wanted to hire a programmer, which I do not think
> is realistic).

Actually, such funding is not the same as the ``seed funding'' that I wish to see.
The latter would give us a big push in terms of acceptance and credability;
the amount of funding is not the main issue. But it would open a lot more
possibilities.

best wishes,
georg