[Bioperl-l] Perl/Tk and clustalw

[Remo Sanges]

On 28-May-04, at PM 11:52, Nathan Haigh wrote:

> Here's part of the code that I refer to:
>
> sub seq_align {
>      my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
>      my $aln = $factory->align($seq_array_ref);     # returns a 
> simplealign
> object
>
>      $aln->set_displayname_flat();                  # don't include
> start-stop in seq name
>      $aln->map_chars('\.','-');                     # GCG uses . for 
> gaps,
> but the aln object has - set as gaps
>      return $aln;
> }

It seems that there are some problems in Tk under Windows....
You can try:

-some evaluation of your align object before to call functions.

-to put a little delay before start to work on align object.
Keep in mind that with Tk you should not use 'sleep'!

Read perldoc Tk::after  for what to use in Tk.
There is "after" and "repeat".

$Tk_obj->after(50);
is the simplest use to get a 50 msec delay.


Remo


---------------------------------------------------------
Remo Sanges - Ph.D. student
Gene Expression Core Lab - BioGeM
CODE Bionformatic Project - Tigem
Via Pietro Castellino 111
80131 Naples - Italy
tel: +390816132 - 339 - 303
fax: +390816132 - 262
sanges at biogem.it
rsanges at tigem.it
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