comparison variant_effect_predictor/Bio/EnsEMBL/Root.pm @ 0:2bc9b66ada89 draft default tip

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=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]>.

=head1 AUTHOR

  Originally from Steve Chervitz.  Refactored by Ewan Birney.

=cut

=head1 NAME

Bio::EnsEMBL::Root

=head1 DESCRIPTION

Do not use Bio::EnsEMBL::Root anymore. It is included for backwards
compatibility (every object in EnsEMBL used to inherit from this class)
but will eventually be phased out. The replacement for the _rearrage
method is the rearrange method which can be imported in the following
way:

  use Bio::EnsEMBL::Utils::Argument qw(rearrange);

  # can now call rearrange as a class method (instead as object method)
  my ( $start, $end ) = rearrange( [ 'START', 'END' ], @args );

If you want to use the throw or warn methods the replacement use the
class methods throw and warning from the Bio::EnsEMBL::Utils::Exception
class:

  use Bio::EnsEMBL::Utils::Exception qw(throw warning);

  # can now call throw or warning even without blessed reference
  warning('This is a warning');
  throw('This is an exception');

This module was stolen from BioPerl to avoid problems with moving to
BioPerl 1 from 0.7

=head1 METHODS

=cut

package Bio::EnsEMBL::Root;

use strict;
use vars qw($VERBOSITY);
use Bio::EnsEMBL::Utils::Exception qw( );
use Bio::EnsEMBL::Utils::Argument qw( );


$VERBOSITY = 0;

sub new{
  my($caller,@args) = @_;
  
  my $class = ref($caller) || $caller;
  return bless({}, $class);
}


=head2 throw

  DEPRECATED

=cut

sub throw{
   my ($self,$string) = @_;

   Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
                                        "Bio::EnsEMBL::Root::throw has been deprecated\n".
					"use Bio::EnsEMBL::Utils::Exception qw(throw); \n".
				        "throw('message'); #instead\n".
					"\n---------------------------------------------------\n");

   Bio::EnsEMBL::Utils::Exception->throw($string);


}

=head2 warn

   DEPRECATED 

=cut

sub warn{
    my ($self,$string) = @_;



    Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
                                        "Bio::EnsEMBL::Root::warn has been deprecated\n".
					 "use Bio::EnsEMBL::Utils::Exception qw(warning); \n".
					 "warning('message'); #instead\n".
					 "\n---------------------------------------------------\n");
    
    Bio::EnsEMBL::Utils::Exception->warning($string);

}
				       


		     
=head2 verbose

  DEPRECATED

=cut

sub verbose{
   my ($self,$value) = @_;

    Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
                                        "Bio::EnsEMBL::Root::verbose has been deprecated\n".
					 "use Bio::EnsEMBL::Utils::Exception qw(verbose); \n".
					 "verbose(value); #instead\n".
					 "\n---------------------------------------------------\n");
    
   Bio::EnsEMBL::Utils::Exception->verbose($value);
   
 }

=head2 stack_trace_dump

  DEPRECATED

=cut

sub stack_trace_dump{
   my ($self) = @_;

    Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
                                        "Bio::EnsEMBL::Root::stack_trace_dump has been deprecated\n".
					 "use Bio::EnsEMBL::Utils::Exception qw(stack_trace_dump); \n".
					 "stack_trace_dump(); #instead\n".
					 "\n---------------------------------------------------\n");

   Bio::EnsEMBL::Utils::Exception->stack_trace_dump();

}


=head2 stack_trace

  DEPRECATED

=cut

sub stack_trace{
   my ($self) = @_;

    Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
                                        "Bio::EnsEMBL::Root::stack_trace has been deprecated\n".
					 "use Bio::EnsEMBL::Utils::Exception qw(stack_trace); \n".
					 "stack_trace(); #instead\n".
					 "\n---------------------------------------------------\n");

   Bio::EnsEMBL::Utils::Exception->stack_trace();

}


=head2 _rearrange

  DEPRECATED

=cut

#----------------'
sub _rearrange {
#----------------
    my($self,$order,@param) = @_;

    my $mess = "use Bio::EnsEMBL::Utils::Argument qw(rearrange); \n";
       $mess .= "rearrange(order, list); #instead\n";

    Bio::EnsEMBL::Utils::Exception->deprecate($mess);

   return Bio::EnsEMBL::Utils::Argument->rearrange($order,@param);

}

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