view variant_effect_predictor/Bio/EnsEMBL/Utils/Eprof.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=head1 LICENSE

  Copyright (c) 1999-2012 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

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=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 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;