Bio::Cluster ClusterFactory
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Cluster::ClusterFactory - Instantiates a new Bio::ClusterI (or derived class) through a factory
Package variables
No package variables defined.
Included modules
    use Bio::Cluster::ClusterFactory;
# if you don't provide a default type, the factory will try
# some guesswork based on display_id and namespace
my $factory = Bio::Cluster::ClusterFactory->new(-type => 'Bio::Cluster::UniGene');
my $clu = $factory->create_object(-description => 'NAT',
-display_id => 'Hs.2');
This object will build Bio::ClusterI objects generically.
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Cluster::ClusterFactory->new();
Function: Builds a new Bio::Cluster::ClusterFactory object
Returns : Bio::Cluster::ClusterFactory
Args : -type => string, name of a ClusterI derived class.
If not provided, the factory will have to guess
from ID and namespace, which may or may not be
 Title   : create_object
Usage : my $seq = $factory->create_object(<named parameters>);
Function: Instantiates new Bio::ClusterI (or one of its child classes)
This object allows us to genericize the instantiation of cluster objects. Returns : Bio::ClusterI compliant object
The return type is configurable using new(-type =>"...").
Args : initialization parameters specific to the type of cluster
object we want. Typically
-display_id => $name
-description => description of the cluster
-members => arrayref, members of the cluster
 Title   : _guess_type
Usage :
Function: Guesses the right type of Bio::ClusterI implementation
based on initialization parameters for the prospective
Example :
Returns : the type (a string, the module name)
Args : initialization parameters to be passed to the prospective
cluster object
Methods code
sub new {
    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);

    $self->type($self->type) if $self->type;

    return $self;
sub create_object {
   my ($self,@args) = @_;

   my $type = $self->type();
   if(! $type) {
       # we need to guess this
$type = $self->_guess_type(@args); $self->throw("No cluster type set and unable to guess.") unless $type; $self->type($type); } return $type->new(-verbose => $self->verbose, @args);
sub _guess_type {
    my ($self,@args) = @_;
    my $type;

    # we can only guess from a certain number of arguments
my ($dispid, $ns, $members) = $self->_rearrange([qw(DISPLAY_ID NAMESPACE MEMBERS )], @args); # Unigene namespace or ID?
if($ns && (lc($ns) eq "unigene")) { $type = 'Bio::Cluster::UniGene'; } elsif($dispid && ($dispid =~ /^Hs\.[0-9]/)) { $type = 'Bio::Cluster::UniGene'; } # what else could we look for?
return $type; } 1;
General documentation
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.                  - General discussion - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
AUTHOR - Hilmar LappTop
Email hlapp at
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _