[Bioperl-l] bug in Bio::SearchIO::Writer::HTMLResultWriter ?

[Smithies, Russell]

Not wanting to be picky...
But $result_>database_name (for blast results) returns the description of the database rather than just the name.
Eg. "hs.fna (Human mRNA Refseqs)" instead of  "hs.fna"
I've had a hunt but can't see where the code for getting the database_name is.
Any ideas?

Thanx,

--Russell

> -----Original Message-----
> From: Jason Stajich [mailto:jason.stajich at gmail.com] On Behalf Of Jason
> Stajich
> Sent: Friday, 3 April 2009 2:09 p.m.
> To: Smithies, Russell
> Cc: 'bioperl-l'
> Subject: Re: [Bioperl-l] bug in Bio::SearchIO::Writer::HTMLResultWriter ?
> 
> looking at the code - it doesn't seem to accept resetting the default
> value.
> sub end_report {
>      return "</BODY>\n</HTML>\n";
> }
> 
> sub footer {
>      my ($self) = @_;
>      return "<hr><h5>Produced by Bioperl module ".ref($self)." on
> $DATE<br>Revision: $Revision</h5>\n"
> 
> }
> 
> So just adjusting it to mirror what is happening for title and the
> rest would be necessary.
> 
> -jason
> On Apr 2, 2009, at 5:46 PM, Smithies, Russell wrote:
> 
> > I'm re-formatting some blast output into nice html webpages but am
> > finding $self->end_report() and $self->footer() don't seem to be
> > working.
> > The other methods ($self->start_report, $self->introduction, $self-
> > >title) all work fine.
> > Am I doing something wrong or is there a trick to it?
> >
> > Here's some test code:
> > ==================================
> >
> > #!perl -w
> >
> > use Bio::SearchIO;
> > use Bio::SearchIO::Writer::HTMLResultWriter;
> > use CGI qw(:standard);
> >
> >
> > my $in = Bio::SearchIO->new(-format => "blast",-file   => shift
> > @ARGV, );
> >
> > my $index = Bio::SearchIO::Writer::HTMLResultWriter->new();
> >
> > $index->start_report( \&my_start_report );
> > $index->title( \&my_title );
> > $index->footer(\&my_footer);
> > $index->end_report(\&my_end_report);
> >
> > my $out = Bio::SearchIO->new(-writer => $index, -file =>
> > ">blast.htm");
> >
> > $out->write_result($in->next_result);
> >
> >
> > sub my_start_report{
> > 	return h1('this is my header');
> > }
> >
> > sub my_title{
> > 	return h1('this is my title');
> > }
> >
> > sub my_footer{
> >    my ($self) = @_;
> >    return h2('this is a footer');
> > }
> >
> > sub my_end_report {
> >    return h2('this is the end');
> > }
> >
> > =================================
> >
> > Thanx,
> >
> >
> > Russell Smithies
> >
> > Bioinformatics Applications Developer
> > T +64 3 489 9085
> > E  russell.smithies at agresearch.co.nz
> >
> > Invermay  Research Centre
> > Puddle Alley,
> > Mosgiel,
> > New Zealand
> > T  +64 3 489 3809
> > F  +64 3 489 9174
> > www.agresearch.co.nz
> >
> >
> >
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> 
> Jason Stajich
> jason at bioperl.org
> 
>