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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Root.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,200 @@
+=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);
+
+}
+
+1;