MiscFeature.pm

=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 <dev@ensembl.org>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.

=cut

=head1 NAME

Bio::EnsEMBL::MiscFeature - A miscelaneous feature with arbitrary features and
associations.

=head1 SYNOPSIS

  use Bio::EnsEMBL::MiscFeature;
  use Bio::EnsEMBL::MiscSet;
  use Bio::EnsEMBL::Attribute;

  my $mfeat = Bio::EnsEMBL::MiscFeature->new(
    -START  => 1200,
    -END    => 100_000,
    -STRAND => 1,
    -SLICE  => $slice
  );

  # Can add attributes to the misc feature and associate with various
  # sets
  my $clone_set = Bio::EnsEMBL::MiscSet->new(
    -CODE        => 'clone',
    -NAME        => '1MB clone set',
    -DESCRIPTION => '1MB CloneSet'
  );

  my $tiling_path_set = Bio::EnsEMBL::MiscSet->new(
    -CODE => 'tilingpath',
    -NAME => 'tiling path set'
  );

  my $attrib1 = Bio::EnsEMBL::Attribute->new(
    -VALUE => 'RLX12451',
    -CODE  => 'name',
    -NAME  => 'name'
  );

  my $attrib2 = Bio::EnsEMBL::Attribute->new(
    -VALUE => '4',
    -CODE  => 'version',
    -NAME  => 'version'
  );

  my $attrib3 = Bio::EnsEMBL::Attribute->new(
    -VALUE => 'AL42131.4',
    -CODE  => 'synonym',
    -NAME  => 'synonym'
  );

  # can associate a misc feature with any number of sets