| Bio::ClusterI(3pm) | User Contributed Perl Documentation | Bio::ClusterI(3pm) |
Bio::ClusterI - Cluster Interface
# see the implementations of this interface for details
my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
-members =>[$seq1,$seq2]);
my @members = $cluster->get_members();
my @sub_members = $cluster->get_members(-species=>"homo sapiens");
This interface is the basic structure for a cluster of bioperl objects. In this case it is up to the implementer to check arguments and initialize whatever new object the implementing class is designed for.
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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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
These functions are the ones that a specific implementation must define.
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
Title : display_id Usage : Function: Get the display name or identifier for the cluster Returns : a string Args :
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
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 :
Title : cluster_score Usage : $cluster ->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. Returns : a number
Title : get_members
Usage : Bio::ClusterI->get_members(($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 :
| 2022-03-27 | perl v5.34.0 |