Reverse Complement utility, Bio::Alg, return value problem
Wed, 6 Aug 1997 09:34:36 +0000 (GMT)
I agree w/ SteveC -re- a web driver (see today's post).
I've already got a little experience using Bio::UnivAln with
CGI.pm and PGPLOT, see
(the script is kinda dated, e.g. I've now got a much better grip of PGPLOT)
Do you think this is on the right track ?
Anyway, we should keep in mind that for the GUI, we're probably
going to have Java applets, too -- and then we can also demonstrate that Perl is
an excellent glue for all this.
> You might want a different name than Bio::Alg, since this name to me
> implies that the module *provides* the algorithms rather than simply
> wraps around them. Perhaps AlgManager? AlgWrapper?
I agree; IMO AlgMgr is best.
(SteveC: If you think your GCG.pm is worth looking at, pls mail it
or point to it.)
> > > 3) Regarding return-values, pls let me know soon about your opinion.
> > > Btw, in my post I should have used get_seq() instead of slice(), so that
> > > we have
> > > $myseq->get_seq(seq($beg,$end)) returns modified object
> > I'm confused. Is seq an exported function?
I'd like to follow the PDL example; I think they export the inplace()
function, and seq() [and possibly some other, similar functions]
could be handled the same way.
> > When you say "returns modified object," do you mean modifies the current
> > object or creates a new object and returns that?
creates a new object and returns that. You modify the current object
> > > $myseq->get_seq($beg,$end) same as current get_seq() -- returns sequence
> > > $myseq->get_seq(inplace($beg,$end)) modifies the object itself -- ithis saves time+space
> > >
> > > And for revcom:
> > > $myseq->revcom(seq($beg,$end)) returns modified object
> > > $myseq->revcom($beg,$end) same as current revcom() -- returns sequence
> > > $myseq->revcom(inplace($beg,$end)) modifies the object itself -- this saves time+space
> > >
> I'm also confused about how the seq() and inplace() calls within the
> get_seq() and revcom() calls are being used. Either of these might be
> more obvious:
The analog $myseq->get_seq($myseq->seq($beg,$end)) [which slices and returns
a new object containing the slice] doesn't look nice to me.
This runs into problems if for some utilities you later add a 3rd parameter
(and need to move 'inplace' one step further towards the end of the parameter