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lib/Bio/Cluster/UniGene.pm  view on Meta::CPAN

		   'Cfa' => "Canine familiaris",
		   'Cin' => "Ciona intestinalis",
		   'Cre' => "Chlamydomonas reinhardtii",
		   'Csa' => "Ciona savignyi",
		   'Csi' => "Citrus sinensis",
		   'Ddi' => "Dictyostelium discoideum",
		   'Dr'  => "Danio rerio",
		   'Dm'  => "Drosophila melanogaster",
		   'Gga' => "Gallus gallus",
		   'Gma' => "Glycine max",
		   'Han' => "Helianthus annus",
		   'Hs'  => "Homo sapiens",
		   'Hma' => "Hydra magnipapillata",
		   'Hv'  => "Hordeum vulgare",
		   'Lco' => "Lotus corniculatus",
		   'Les' => "Lycopersicon esculentum",
		   'Lsa' => "Lactuca sativa",
		   'Mdo' => "Malus x domestica",
                   'Mgr' => "Magnaporthe grisea",
		   'Mm'  => "Mus musculus",
		   'Mtr' => "Medicago truncatula",
                   'Ncr' => "Neurospora crassa",
		   'Oar' => "Ovis aries",
		   'Omy' => "Oncorhynchus mykiss",
		   'Os'  => "Oryza sativa",
		   'Ola' => "Oryzias latipes",
		   'Ppa' => "Physcomitrella patens",
		   'Pta' => "Pinus taeda",
		   'Ptp' => "Populus tremula x Populus tremuloides",
		   'Rn'  => "Rattus norvegicus",
		   'Sbi' => "Sorghum bicolor",
		   'Sma' => "Schistosoma mansoni",
		   'Sof' => "Saccharum officinarum",
		   'Spu' => "Strongylocentrotus purpuratus",
		   'Ssa' => "Salmo salar",
		   'Ssc' => "Sus scrofa",
		   'Str' => "Xenopus tropicalis",
		   'Stu' => "Solanum tuberosum",
		   'Ta'  => "Triticum aestivum",
		   'Tgo' => "Toxoplasma gondii",
                   'Tru' => "Takifugu rubripes",
		   'Vvi' => "Vitis vinifera",
		   'Xl'  => "Xenopus laevis",
		   'Zm'  => "Zea mays",
		   );


=head2 new

 Title   : new
 Usage   : used by ClusterIO
 Returns : a new Bio::Cluster::Unigene object

=cut

sub new {
    # standard new call..
    my($caller,@args) = @_;
    my $self = $caller->SUPER::new(@args);

    my ($ugid,$desc,$mems,$size,$species,$dispid,$id,$ns,$auth,$v,$seqfact) =
	$self->_rearrange([qw(UNIGENE_ID
			      DESCRIPTION
			      MEMBERS
			      SIZE
			      SPECIES
			      DISPLAY_ID
			      OBJECT_ID
			      NAMESPACE
			      AUTHORITY
			      VERSION
			      SEQFACTORY
			      )], @args);

    $self->{'_alphabet'} = 'dna';

    $self->unigene_id($ugid) if $ugid;
    $self->description($desc) if $desc;
    $self->sequences($mems) if $mems;
    $self->size($size) if defined($size);
    $self->display_id($dispid) if $dispid; # overwrites ugid
    $self->object_id($id) if $id;          # overwrites dispid
    $self->namespace($ns || 'UniGene');
    $self->authority($auth || 'NCBI');
    $self->version($v) if defined($v);
    if( ! defined $seqfact ) {
	$seqfact = Bio::Seq::SeqFactory->new
	    (-verbose => $self->verbose(),
	     -type => 'Bio::Seq::RichSeq');
    }
    $self->sequence_factory($seqfact);
    if( (! $species) && (defined $self->unigene_id() &&
			 $self->unigene_id() =~ /^([A-Za-z]+)\.[0-9]/)) {
	# try set a default one depending on the ID
	$species = $species_map{$1};
    }
    $self->species($species);
    return $self;
}


=head1 L<Bio::Cluster::UniGeneI> methods

=cut

=head2 unigene_id

 Title   : unigene_id
 Usage   : unigene_id();
 Function: Returns the unigene_id associated with the object.
 Example : $id = $unigene->unigene_id or $unigene->unigene_id($id)
 Returns : A string
 Args    : None or an id


=cut

sub unigene_id {
	my ($obj,$value) = @_;
	if( defined $value) {
		$obj->{'unigene_id'} = $value;
	}
	return $obj->{'unigene_id'};
}



=head2 title

 Title   : title
 Usage   : title();
 Function: Returns the title associated with the object.
 Example : $title = $unigene->title or $unigene->title($title)
 Returns : A string
 Args    : None or a title


=cut

sub title {
	my ($obj,$value) = @_;