[Bioperl-l] PAML parser

[Chris Fields]

Normally when you parse a report you use a loop to iterate through  
results:

while (my $result = $parser->next_result) {
   # do work here
}

So returning undef is necessary to end the loop.  This type of loop  
construct is common in BioPerl (and in Perl in general).

There is a HOWTO for PAML:

http://www.bioperl.org/wiki/HOWTO:PAML

Chris

On Jul 21, 2006, at 4:04 AM, Michael Han wrote:

> Hi,
>
> I have some questions about the PAML parser  
> (Bio::Tools::Phylo::PAML in CVS HEAD). Maybe some of you could help.
>
> If you call next_result, $self->_parse_summary might be called,  
> which loops over $self->_readline .
>
> Later in next_result when "while (defined ($_=$self->_readline))"  
> is used isn't the filepointer/filehandle
> already at the end of the output file and should return undef  
> breaking the parsing?
>
> I added a crude seek($self->{_filehandle},0,0) after the  
> _parse_summary and it seemed to work, but I wonder if I missed  
> something obvious.
>
> thanks,
>
> Mike
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign