Raw content of Bio::EnsEMBL::Root
<![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>.
=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);
}
1;
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