Raw content of Bio::EnsEMBL::Root =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;