Raw content of Bio::EnsEMBL::Utils::Eprof
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Utils::Eprof - Bespoke Ensembl profiler
=head1 SYNOPSIS
use Bio::EnsEMBL::Utils::Eprof( 'eprof_start', 'eprof_end',
'eprof_dump' );
&eprof_start('function-a');
# ... do something
&eprof_end('function-a');
&eprof_dump( \*STDERR );
# there is an object based set for above as well, for running
# multiple concurrent profilers
=head1 DESCRIPTION
This is an Ensembl profiler as we broke the Perl profilers.
=head1 METHODS
=cut
package Bio::EnsEMBL::Utils::Eprof;
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Utils::EprofStack;
use base('Exporter');
our @EXPORT_OK =
( 'eprof_start', 'eprof_end', 'eprof_dump', 'eprof_reset' );
my $global;
sub new {
my ($proto) = @_;
my $class = ref($proto) || $proto;
my $self = bless( { '_tags' => {} }, $class );
return $self;
}
=head2 eprof_start
Title : eprof_start
Usage :
Function:
Example :
Returns :
Args :
=cut
sub eprof_start {
my ($tag) = @_;
if ( !defined($global) ) {
$global = Bio::EnsEMBL::Utils::Eprof->new();
}
$global->start($tag);
}
=head2 eprof_end
Title : eprof_end
Usage :
Function:
Example :
Returns :
Args :
=cut
sub eprof_end {
my ($tag) = @_;
if ( !defined($global) ) {
$global = Bio::EnsEMBL::Utils::Eprof->new();
}
$global->end($tag);
}
sub eprof_dump {
my ($fh) = @_;
if ( !defined($global) ) { return }
$global->dump($fh);
}
=head2 eprof_reset
Title : eprof_reset
Usage :
Function:
Example :
Returns :
Args :
=cut
sub eprof_reset { undef($global) }
=head2 dump
Title : dump
Usage :
Function:
Example :
Returns :
Args :
=cut
sub dump {
my ( $self, $fh ) = @_;
my @tags = sort {
$self->_tags()->{$a}->total_time()
<=> $self->_tags()->{$b}->total_time()
} keys %{ $self->_tags() };
foreach my $tag (@tags) {
my $st = $self->_tags->{$tag};
if ( $st->number() == 0 ) { next }
my $STD = '---';
if ( $st->number() > 1 ) {
my $SS =
$st->total_time_time() -
$st->total_time()*$st->total_time()/$st->number();
if ( $SS > 0 ) {
$STD = sprintf( "%6f",
sqrt( $SS/$st->number()/( $st->number() - 1 ) )
);
}
}
print( $fh sprintf( "Eprof: %20s %6f %6f %d %s [%6f,%6f]\n",
$st->tag(), $st->total_time(),
$st->total_time()/$st->number(), $st->number(),
$STD, $st->min_time(),
$st->max_time() ) );
} ## end foreach my $tag (@tags)
} ## end sub dump
=head2 start
Title : start
Usage : $eprof->start('this_tag');
Function:
Example :
Returns :
Args :
=cut
sub start {
my ( $self, $tag ) = @_;
if ( !defined($tag) ) {
$self->throw("No tag, can't start.");
}
if ( !defined( $self->_tags()->{$tag} ) ) {
$self->_tags()->{$tag} = Bio::EnsEMBL::Utils::EprofStack->new($tag);
}
$self->_tags()->{$tag}->push_stack();
}
=head2 end
Title : end
Usage : $eprof->end('this_tag');
Function:
Example :
Returns :
Args :
=cut
sub end {
my ( $self, $tag ) = @_;
if ( !defined($tag) ) {
$self->throw("No tag, can't end.");
}
if ( !defined( $self->_tags()->{$tag} ) ) {
$self->throw(
sprintf( "Ending with a nonexistant tag '%s'", $tag ) );
}
$self->_tags->{$tag}->pop_stack();
}
=head2 _tags
Title : _tags
Usage : $obj->_tags($newval)
Function:
Returns : value of _tags
Args : newvalue (optional)
=cut
sub _tags {
my ($obj) = @_;
return $obj->{'_tags'};
}
1;
]]>