Raw content of Bio::EnsEMBL::MiscSet =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;