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

Smithies, Russell Russell.Smithies at agresearch.co.nz
Thu Apr 2 20:46:39 EDT 2009

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 );

my $out = Bio::SearchIO->new(-writer => $index, -file => ">blast.htm");


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');



Russell Smithies 

Bioinformatics Applications Developer 
T +64 3 489 9085 
E  russell.smithies at agresearch.co.nz 

Invermay  Research Centre 
Puddle Alley, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  

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