Bio-Cluster
view release on metacpan or search on metacpan
lib/Bio/ClusterI.pm view on Meta::CPAN
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;
( run in 1.582 second using v1.01-cache-2.11-cpan-39bf76dae61 )