Bio-Cluster

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with code and data examples if at all possible.

=head2 Reporting Bugs

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
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Shawn Hoon

Email shawnh@fugu-sg.org

=head1 APPENDIX

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _

=cut


# Let the code begin...

package Bio::ClusterI;
$Bio::ClusterI::VERSION = '1.7.3';
use strict;


use base qw(Bio::Root::RootI);

=head1 Implementation Specific Functions

These functions are the ones that a specific implementation must
define.

=head2 new

  We don't mandate but encourage implementors to support at least the
  following named parameters upon object initialization.

  Argument        Description
  --------        -----------
  -display_id     the display ID or name for the cluster
  -description    the consensus description or name of the cluster
  -members        the array of objects belonging to the family

=cut

=head2 display_id

 Title   : display_id
 Usage   :
 Function: Get the display name or identifier for the cluster
 Returns : a string
 Args    :

=cut

sub display_id{
    shift->throw_not_implemented();
}


=head2 description

 Title   : description
 Usage   : Bio::ClusterI->description("POLYUBIQUITIN")
 Function: get/set for the consensus description of the cluster
 Returns : the description string
 Args    : Optional the description string

=cut

sub description{
    shift->throw_not_implemented();
}

=head2 size

 Title   : size
 Usage   : Bio::ClusterI->size();
 Function: get/set for the size of the family,
           calculated from the number of members
 Returns : the size of the family
 Args    :

=cut

sub size {
    shift->throw_not_implemented();
}

=head2 cluster_score

 Title   : cluster_score
 Usage   : $cluster ->cluster_score(100);
 Function: get/set for cluster_score which
           represent the score in which the clustering
           algorithm assigns to this cluster.
 Returns : a number

=cut

sub cluster_score{
    shift->throw_not_implemented();
}

=head2 get_members

 Title   : get_members
 Usage   : Bio::ClusterI->get_members(($seq1, $seq2));
 Function: retrieve the members of the family by some criteria, for
           example :
           $cluster->get_members(-species => 'homo sapiens');

           Will return all members if no criteria are provided.

 Returns : the array of members
 Args    :

=cut

sub get_members {
    shift->throw_not_implemented();
}

1;



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