view variant_effect_predictor/Bio/EnsEMBL/Attribute.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=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]>.

=cut

=head1 NAME

Bio::EnsEMBL::Attribute - A generic Attribute class.

=head1 SYNOPSIS

  use Bio::EnsEMBL::Attribute;

  my $attribute = Bio::EnsEMBL::Attribute->new
       (-CODE => 'myCode',
        -NAME => 'My Attribute',
        -DESCRIPTION => 'This is my attribute description.',
        -VALUE => '10023');

  print $attrib->name(), "\n";
  print $attrib->code(), "\n";
  print $attrib->description(), "\n";
  print $attrib->value(), "\n";

=head1 DESCRIPTION

This is a generic attribute class used to represent attributes
associated with seq_regions (and their Slices) and MiscFeatures.

=head1 SEE ALSO

Bio::EnsEMBL::Slice
Bio::EnsEMBL::MiscFeature
Bio::EnsEMBL::DBSQL::AttributeAdaptor

=cut

package Bio::EnsEMBL::Attribute;

use strict;
use warnings;

use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Scalar::Util qw(weaken isweak);

=head2 new

  Arg [-CODE]        : string - the code for this attribute
  Arg [-NAME]        : string - a human readable name for this attribute
  Arg [-DESCRIPTION] : string - a description for this attribute
  Arg [-VALUE]       : value  - the value of this attribute
  Example            :   my $attribute = Bio::EnsEMBL::Attribute->new
                         (-CODE => 'myCode',
                          -NAME => 'My Attribute',
                          -DESCRIPTION => 'This is my attribute description.',
                          -VALUE => '10023');
  Description        : Constructor.  Instantiates a Bio::EnsEMBL::Attribute object.
  Returntype         : Bio::EnsEMBL::Attribute
  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 ($code, $name, $desc, $value) =
    rearrange([qw(CODE NAME DESCRIPTION VALUE)], @_);

  return bless {'code'    => $code,
                'name'    => $name,
                'description' => $desc,
                'value'   => $value}, $class;
}

=head2 new_fast

  Arg [1]    : hashref to be blessed
  Description: Construct a new Bio::EnsEMBL::Attribute using the hashref.
  Exceptions : none
  Returntype : Bio::EnsEMBL::Attribute
  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 code

  Arg [1]    : string $code (optional)
  Example    : $code = $attribute->code();
  Description: Getter/Setter for code attribute
  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 = $attribute->name();
  Description: Getter/Setter for name 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 = $attribute->description();
  Description: Getter/Setter for description attribute
  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 = $attribute->value();
  Description: Getter/Setter for value attribute
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub value {
  my $self = shift;
  $self->{'value'} = shift if(@_);
  return $self->{'value'};
}


1;