Return-value for methods; seed funding

[Steve A. Chervitz]

Georg,

> > $seq->revcom(seq($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.
> 
> The last sentence should read 
> The implementation should be straightforward by setting an appropriate flag --
> the PDL module uses inplace() in such a way, as far as I remember.

In UnivAln, your documentation would suggest the following:

$seq->inplace(1);
$seq->revcom($beg,$end);
$seq->inplace(0);

This seems reasonable, since you could imagine having multiple 
manipulations between the two calls to inplace().


As for other comments on the UnivAln.pm module, I would recommend 
soliciting your users as much as possible. I haven't had much of a chance 
to use it much (yet), so my input will be limited. 

Here are a few observations:

1) In the "Object Manipulation" section:
   line 69: if ($str =~ /[AaTtRr]+/) {return 1;} else {return 0;}
  change to: 
   line 69: if ($str =~ /[AaGgRr]+/) {return 1;} else {return 0;}

   Similarly for line 283 (in the "Access by Selector Function" section).

2) Also in the "Object Manipulation" section:
   for the examples of the methods that can return a string or an array  
   (gap_free_sites, reverse, complement, revcom), it would be clearer to 
   have something like:

   @alnSlice OR $alnString = $aln->reverse(1,3);
   @alnSlice OR $alnString = $aln->complement(1,3);
   etc...
   
   It's not valid Perl but this is obvious and it gets the idea across.

3) Wording change on line 740 (in the Appendix):
   'considered possibly dangerous' --> 'intended for internal use only'

4) When we decide on the best way to handle how reverse/complement/revcom 
   are to deal with slices, it would be nice for PreSeq and UnivAln to 
   employ the same strategy.


That's all for now. I too must sleep |^)

SteveC