Genome.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
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
 
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
 
=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::Genome - A generic Genome class.
 
=head1 SYNOPSIS
 
  use Bio::EnsEMBL::Genome;
 
  my $genome = Bio::EnsEMBL::Genome->new
       (-NAME => 'myName',
        -CODE => 'MyCode',
        -DESCRIPTION => 'This is my statistics description.',
        -VALUE => '10023');
 
  print $statistic->name(), "\n";
  print $statistic->code(), "\n";
  print $statistic->description(), "\n";
  print $statistic->value(), "\n";
 
=head1 DESCRIPTION
 
This is a generic genome class used to represent statistics
associated with a genome and species
 
=head1 SEE ALSO
 
Bio::EnsEMBL::DBSQL::GenomeContainer
 
=cut
 
package Bio::EnsEMBL::Genome;
 
use strict;
use warnings;
 
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Scalar::Util qw(weaken isweak);
 
=head2 new
 
  Arg [-NAME]        : string - the name for this statistic
  Arg [-CODE]        : string - the code for this statistic
  Arg [-DESCRIPTION] : string - a description for this statistic
  Arg [-VALUE]       : value  - the value of this statistic
  Example            :   my $genome = Bio::EnsEMBL::Genome->new
                         (-name => 'myName',
                          -CODE => 'MyCode',
                          -DESCRIPTION => 'This is my statistics description.',
                          -VALUE => '10023');  
  Description        : Constructor.  Instantiates a Bio::EnsEMBL::Genome object.
  Returntype         : Bio::EnsEMBL::Genome
  Exceptions         : none
  Caller             : general
  Status             : Stable
 
=cut
 
 
sub new {
  my $caller = shift;
 
  # allow to be called as class or object method
  my $class = ref($caller) || $caller;
 
  my ($dbID, $statistic, $value, $species_id, $code, $name, $desc) =
    rearrange([qw(DBID STATISTIC VALUE SPECIES_ID CODE NAME DESCRIPTION)], @_);
 
  return bless {'dbID'        => $dbID,
                'statistic'   => $statistic,
                'value'       => $value,
                'species_id'  => $species_id,
                'code'        => $code,
                'name'        => $name,
                'description' => $desc}, $class;
}
 
=head2 new_fast
 
  Arg [1]    : hashref to be blessed
  Description: Construct a new Bio::EnsEMBL::Genome using the hashref.
  Exceptions : none
  Returntype : Bio::EnsEMBL::Genome
  Caller     : general, subclass constructors
  Status     : Stable
 
=cut
 
 
sub new_fast {
  my $class = shift;
  my $hashref = shift;
  my $self = bless $hashref, $class;
  weaken($self->{adaptor})  if ( ! isweak($self->{adaptor}) );
  return $self;
}
 
=head2 statistic
 
  Arg [1]    : string $statistic (optional)
  Example    : $statistic = $statistic->name();
  Description: Getter/Setter for the statistic name
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub statistic {
  my $self = shift;
  $self->{'statistic'} = shift if(@_);
  return $self->{'statistic'};
}
 
=head2 code
 
  Arg [1]    : string $code (optional)
  Example    : $code = $genome->code();
  Description: Getter/Setter for code statistic
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub code {
  my $self = shift;
  $self->{'code'} = shift if(@_);
  return $self->{'code'};
}
 
 
=head2 name
 
  Arg [1]    : string $name (optional)
  Example    : $name = $statistic->name();
  Description: Getter/Setter for the name associated to the statistic attribute
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub name {
  my $self = shift;
  $self->{'name'} = shift if(@_);
  return $self->{'name'};
}
 
=head2 description
 
  Arg [1]    : string $description (optional)
  Example    : $description = $statistic->description();
  Description: Getter/Setter for description statistic
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub description {
  my $self = shift;
  $self->{'description'} = shift if(@_);
  return $self->{'description'};
}
 
 
=head2 value
 
  Arg [1]    : string $value (optional)
  Example    : $value = $statistic->value();
  Description: Getter/Setter for value statistic
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub value {
  my $self = shift;
  $self->{'value'} = shift if(@_);
  return $self->{'value'};
}
 
=head2 dbID
 
  Arg [1]    : string $value (optional)
  Example    : $dbID = $statistic->dbID();
  Description: Getter/Setter for statistic internal id
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub dbID {
  my $self = shift;
  $self->{'dbID'} = shift if(@_);
  return $self->{'dbID'};
}
 
=head2 species_id
 
  Arg [1]    : string $value (optional)
  Example    : $species_id = $statistic->dbID();
  Description: Getter/Setter for statistic species id
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub species_id {
  my $self = shift;
  $self->{'species_id'} = shift if(@_);
  return $self->{'species_id'};
}
 
 
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