Commit ba8ab267 authored by Laura Clarke's avatar Laura Clarke
Browse files

Every module changed here has had Bio::Root::RootI changed to Bio::EnsEMBL::Root

The only modelue with any significant changes other than that is Transcript where moltype
has been changed to alphabet due to another change in Bioperl 1.0
parent e0a3cede
......@@ -47,9 +47,9 @@ package Bio::EnsEMBL::AceDB::Clone;
use vars qw(@ISA);
use strict;
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
@ISA = qw(Bio::EnsEMBL::DB::CloneI Bio::Root::RootI);
@ISA = qw(Bio::EnsEMBL::DB::CloneI Bio::EnsEMBL::Root);
# new() is inherited from Bio::Root::Object
# _initialize is where the heavy stuff will happen when new is called
......
......@@ -41,7 +41,7 @@ use vars qw(@ISA);
use strict;
use Bio::Seq;
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
use Bio::EnsEMBL::AceDB::Obj;
use Bio::EnsEMBL::ContigOverlap;
use Bio::EnsEMBL::ContigOverlapHelper;
......@@ -55,7 +55,7 @@ use Bio::SeqFeature::Generic;
@ISA = qw(Bio::EnsEMBL::DB::RawContigI Bio::Root::RootI);
@ISA = qw(Bio::EnsEMBL::DB::RawContigI Bio::EnsEMBL::Root);
# new() is inherited from Bio::Root::Object
# _initialize is where the heavy stuff will happen when new is called
......
......@@ -62,7 +62,7 @@ use Bio::EnsEMBL::AceDB::Update_Obj;
use Time::Local 'timelocal';
use Ace;
@ISA = qw(Bio::Root::RootI);
@ISA = qw(Bio::EnsEMBL::Root);
sub new {
my($pkg,@args) = @_;
......
......@@ -44,12 +44,12 @@ package Bio::EnsEMBL::AlignBlock;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::RootI
# Object preamble - inherits from Bio::EnsEMBL::Root
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
use Bio::SeqFeatureI;
@ISA = qw(Bio::Root::RootI Bio::SeqFeatureI);
@ISA = qw(Bio::EnsEMBL::Root Bio::SeqFeatureI);
# new() is written here
......
......@@ -44,11 +44,11 @@ package Bio::EnsEMBL::AlignBlockSet;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::RootI
# Object preamble - inherits from Bio::EnsEMBL::Root
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
@ISA = qw(Bio::Root::RootI);
@ISA = qw(Bio::EnsEMBL::Root);
# new() is written here
......
......@@ -55,10 +55,10 @@ package Bio::EnsEMBL::Analysis;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::AnalysisI;
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
# Inherits from the base bioperl object
@ISA = qw(Bio::Root::RootI Bio::EnsEMBL::AnalysisI );
@ISA = qw(Bio::EnsEMBL::Root Bio::EnsEMBL::AnalysisI );
sub new {
......
......@@ -67,11 +67,13 @@ use vars qw(@ISA);
use strict;
@ISA = qw(Bio::Root::RootI);
@ISA = qw(Bio::EnsEMBL::Root);
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my $self = {};
bless $self, $class;
$self->{'_homol'} = [];
return $self; # success - we hope!
......
......@@ -54,9 +54,9 @@ use strict;
# Object preamble - inherits from Bio::Root::Object
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
@ISA = qw ( Bio::Root::RootI );
@ISA = qw ( Bio::EnsEMBL::Root );
=head2 db
......
......@@ -51,7 +51,7 @@ package Bio::EnsEMBL::Archive::DBSQL::DBAdaptor;
use vars qw(@ISA);
use strict;
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
use DBI;
use Bio::EnsEMBL::DBSQL::SQL;
use Bio::EnsEMBL::Archive::DBSQL::VersionedSeqAdaptor;
......@@ -61,7 +61,7 @@ BEGIN {
print STDERR "\n\n**** Loading Archive ******\n\n";
};
@ISA = qw(Bio::Root::RootI);
@ISA = qw(Bio::EnsEMBL::Root);
sub new {
my($class, @args) = @_;
......
......@@ -53,19 +53,20 @@ package Bio::EnsEMBL::Archive::Seq;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::RootI
# Object preamble - inherits from Bio::EnsEMBL::Root
# (inherits for methods like throw and rearrange)
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
@ISA = qw(Bio::Root::RootI);
@ISA = qw(Bio::EnsEMBL::Root);
sub new {
my($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my $self = {};
bless $self, $class;
my ($dbid,$name,$type,$created,$adaptor) = $self->_rearrange([qw(
DBID
NAME
......
......@@ -55,18 +55,19 @@ package Bio::EnsEMBL::Archive::VersionedSeq;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::RootI
# Object preamble - inherits from Bio::EnsEMBL::Root
# (inherits for methods like throw and rearrange)
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
use Bio::PrimarySeqI;
@ISA = qw(Bio::Root::RootI Bio::PrimarySeqI);
@ISA = qw(Bio::EnsEMBL::Root Bio::PrimarySeqI);
sub new {
my($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my $self = {};
bless $self, $class;
$self->{'_future_vseqs'} = [];
$self->{'_relatives'} = [];
......
......@@ -58,12 +58,12 @@ package Bio::EnsEMBL::AssemblyMapper;
use vars qw(@ISA);
use strict;
# Object preamble - inheriets from Bio::Root::RootI
# Object preamble - inheriets from Bio::EnsEMBL::Root
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
use Bio::EnsEMBL::Mapper;
@ISA = qw(Bio::Root::RootI);
@ISA = qw(Bio::EnsEMBL::Root);
sub new {
......
......@@ -45,12 +45,12 @@ The rest of the documentation details each of the object methods. Internal metho
package Bio::EnsEMBL::Chromosome;
use vars qw(@ISA);
use strict;
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
use Bio::EnsEMBL::Species;
@ISA = qw( Bio::Root::RootI );
@ISA = qw( Bio::EnsEMBL::Root );
sub new {
......
......@@ -2,8 +2,8 @@ package Bio::EnsEMBL::ChromosomeStats;
use strict;
use vars qw(@ISA);
use Bio::Root::RootI;
@ISA = qw(Bio::Root::RootI);
use Bio::EnsEMBL::Root;
@ISA = qw(Bio::EnsEMBL::Root);
......
......@@ -46,13 +46,13 @@ package Bio::EnsEMBL::Clone;
use vars qw(@ISA);
use strict;
# Object preamble - inheriets from Bio::Root::RootI
# Object preamble - inheriets from Bio::EnsEMBL::Root
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
use Bio::EnsEMBL::DB::CloneI;
@ISA = qw(Bio::Root::RootI Bio::EnsEMBL::DB::CloneI);
@ISA = qw(Bio::EnsEMBL::Root Bio::EnsEMBL::DB::CloneI);
sub new {
my ($class,$adaptor,@args) = @_;
......
......@@ -44,9 +44,9 @@ use Bio::EnsEMBL::ContigOverlapHelper;
use vars qw(@ISA);
use strict;
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
@ISA = qw(Bio::Root::RootI);
@ISA = qw(Bio::EnsEMBL::Root);
sub new {
my($pkg,@args) = @_;
......
......@@ -48,10 +48,10 @@ use strict;
# Object preamble - inheriets from Bio::Root::Object
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
@ISA = qw(Bio::Root::RootI);
@ISA = qw(Bio::EnsEMBL::Root);
# new() is inherited from Bio::Root::Object
# _initialize is where the heavy stuff will happen when new is called
......
......@@ -79,9 +79,9 @@ use vars ('@ISA');
use strict;
use Bio::EnsEMBL::VirtualGene;
use Bio::SeqI;
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
@ISA = qw( Bio::SeqI Bio::Root::RootI );
@ISA = qw( Bio::EnsEMBL::Root Bio::SeqI );
=head2 primary_seq
......
......@@ -161,10 +161,10 @@ The rest of the documentation details each of the object methods. Internal metho
package Bio::EnsEMBL::DB::ExternalFeatureFactoryI;
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
use vars qw(@ISA);
@ISA = ( 'Bio::Root::RootI');
@ISA = ( 'Bio::EnsEMBL::Root');
=head2 get_Ensembl_SeqFeatures_contig
......
......@@ -42,10 +42,10 @@ use vars qw(@ISA);
use strict;
# Object preamble - inheriets from Bio::Root::Object
use Bio::Root::RootI;
use Bio::EnsEMBL::Root;
@ISA = qw(Bio::Root::RootI);
@ISA = qw(Bio::EnsEMBL::Root);
# new() is inherited from Bio::Root::Object
# _initialize is where the heavy stuff will happen when new is called
......
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