Bio::EnsEMBL Root
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Summary
Bio::EnsEMBL::Root
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Utils::Argument qw ( )
Bio::EnsEMBL::Utils::Exception qw ( )
Synopsis
No synopsis!
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
Methods
_rearrangeDescriptionCode
new
No description
Code
stack_traceDescriptionCode
stack_trace_dumpDescriptionCode
throwDescriptionCode
verboseDescriptionCode
warnDescriptionCode
Methods description
_rearrangecode    nextTop
  DEPRECATED
stack_tracecodeprevnextTop
  DEPRECATED
stack_trace_dumpcodeprevnextTop
  DEPRECATED
throwcodeprevnextTop
  DEPRECATED
verbosecodeprevnextTop
  DEPRECATED
warncodeprevnextTop
   DEPRECATED
Methods code
_rearrangedescriptionprevnextTop
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;
}
newdescriptionprevnextTop
sub new {
  my($caller,@args) = @_;
  
  my $class = ref($caller) || $caller;
  return bless({}, $class);
}
stack_tracedescriptionprevnextTop
sub stack_trace {
   my ($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();
}
stack_trace_dumpdescriptionprevnextTop
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();
}
throwdescriptionprevnextTop
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($string);
}
verbosedescriptionprevnextTop
sub verbose {
   my ($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($value);
}
warndescriptionprevnextTop
sub warn {
    my ($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);
}
General documentation
LICENSETop
  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
CONTACTTop
  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>.
AUTHORTop
  Originally from Steve Chervitz.  Refactored by Ewan Birney.