=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
Questions may also be sent to the Ensembl help desk at
=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
$Bio::EnsEMBL::Utils::Eprof::VERSION = '112.0_52'; # TRIAL
$Bio::EnsEMBL::Utils::Eprof::VERSION = '112.052';
use strict;
use base qw( 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;