Raw content of Bio::EnsEMBL::MiscSet
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 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
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::MiscSet - This is a set representing a classification of
a group of miscellaneuos features.
=head1 SYNOPSIS
use Bio::EnsEMBL::MiscSet;
my $misc_set = Bio::EnsEMBL::MiscSet->new(
1234, $adaptor, 'tilepath',
'Assembly Tiling Path',
'The tiling path of clones', 1e6
);
my $misc_feature->add_set($misc_set);
=head1 DESCRIPTION
MiscSets represent classsifications or groupings of MiscFeatures.
Features are classified into sets essentially to define what they are
and how they may be used. Generally MiscFeatures are retrieved on
the basis of their associated sets. See Bio::EnsEMBL::MiscFeature,
Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor.
Note that MiscSets and MiscFeatures were formerly known as MapSets and
MapFrags
=head1 METHODS
=cut
package Bio::EnsEMBL::MiscSet;
use strict;
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Storable);
=head2 new
Arg [1] : int $misc_set_id
The internal identifier for this misc set
Arg [2] : string $code
The unique code which identifies this set type
Arg [3] : string $name
The human readable name of this set
Arg [4] : string $desc
The description of this set
Arg [5] : int $max_len
The maximum length of features of this mapset
Example : $set = new Bio::EnsEMBL::MiscSet(1234, 'tilepath',
'Assembly Tiling Path',
'The tiling path of clones',
1e6);
Description: Instantiates a Bio::EnsEMBL::MiscSet
Returntype : Bio::EnsEMBL::MiscSet
Exceptions : none
Caller : MiscFeatureAdaptor
Status : Stable
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my($code, $name, $desc, $max_len) =
rearrange([qw(CODE NAME DESCRIPTION LONGEST_FEATURE)], @_);
$self->{'code'} = $code;
$self->{'name'} = $name;
$self->{'description'} = $desc;
$self->{'longest_feature'} = $max_len;
return $self;
}
=head2 code
Arg [1] : string $newval (optional)
The new value to set the code attribute to
Example : $code = $obj->code()
Description: Getter/Setter for the 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 $newval (optional)
The new value to set the code attribute to
Example : $name = $obj->name()
Description: Getter/Setter for the 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 $newval (optional)
The new value to set the description attribute to
Example : $description = $obj->description()
Description: Getter/Setter for the description attribute
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub description{
my $self = shift;
$self->{'description'} = shift if(@_);
return $self->{'description'};
}
=head2 longest_feature
Arg [1] : int $newval (optional)
The new value to set the longest_feature attribute to
Example : $longest_feature = $obj->longest_feature()
Description: Getter/Setter for the longest_feature attribute
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub longest_feature{
my $self = shift;
$self->{'longest_feature'} = shift if(@_);
return $self->{'longest_feature'};
}
1;
]]>