SeqRegionSynonym.pm

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=head1 LICENSE
 
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Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0
 
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distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
 
  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=cut
 
=head1 NAME
 
Bio::EnsEMBL::SeqRegionSynonym -
Object representing an alternatice name.
 
=head1 SYNOPSIS
 
=head1 DESCRIPTION
 
This object holds information about alternative name to
Ensembl seq regions.
 
=head1 METHODS
 
=cut
 
package Bio::EnsEMBL::SeqRegionSynonym;
 
use strict;
use warnings;
no warnings qw(uninitialized);
 
use Bio::EnsEMBL::Storable;
use Bio::Annotation::DBLink;
 
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
 
our @ISA = qw(Bio::EnsEMBL::Storable);
 
=head2 new
 
  Args [...] : list of named parameters 
  Example    : my $srs = new Bio::EnsEMBL::SeqRegionSynonym(
                    -adaptor => $adaptor,
                    -synonym => $alt_name,
                    -external_db_id => 1234
                    -seq_region_id  => 12);
  Description: Creates a new SeqRegionSynonym object
  Returntype : Bio::EnsEMBL::SeqRegionSynonym
  Exceptions : none
  Caller     : Bio::EnsEMBL::SeqRegionSynonymAdaptor
  Status     : At Risk
=cut
 
sub new {
  my ($class, @args) = @_;
  
  my $self = bless {},$class;
 
  my ( $adaptor, $synonym, $ex_db, $seq_region_id, $dbid, $dbname, $db_display_name) =
    rearrange ( ['ADAPTOR','SYNONYM','EXTERNAL_DB_ID','SEQ_REGION_ID','DBID', 'DBNAME', 'DB_DISPLAY_NAME'], @args );
 
  $self->adaptor($adaptor);
 
  if( defined $ex_db ) { $self->external_db_id( $ex_db ) } ;
  if( defined $seq_region_id ) { $self->seq_region_id( $seq_region_id ) } ;
  if (defined $dbid) { $self->{'dbID'} = $dbid} ;
  if (defined $dbname) { $self->{'dbname'} = $dbname };
  if (defined $db_display_name) { $self->{'db_display_name'} = $db_display_name };
 
  if( defined $synonym ) { 
    $self->name( $synonym ) ;
  } else {
    warn "No alternative name given\n";
    return undef;
  }
 
  return $self;
}
 
sub name{
 my $self = shift;
  $self->{'name'} = shift if(@_);
  return $self->{'name'};
}
 
sub external_db_id{
 my $self = shift;
  $self->{'ex_db'} = shift if(@_);
  return $self->{'ex_db'};
}
 
sub seq_region_id{
  my $self = shift;
  $self->{'seq_region_id'} = shift if(@_);
  return $self->{'seq_region_id'};
}
 
sub dbname {
  my $self = shift;
  $self->{'dbname'} = shift if(@_);
  return $self->{'dbname'};
}
 
sub db_display_name {
  my $self = shift;
  $self->{'db_display_name'} = shift if(@_);
  return $self->{'db_display_name'};
}
 
sub summary_as_hash {
  my $self = shift;
  my %summary;
  $summary{name} = $self->name;
  $summary{dbname} = $self->dbname;
 
  return \%summary;
}
 
1;