Bio::Cluster
FamilyI
Summary
Bio::Cluster::FamilyI - Family Interface
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# see the implementations of this interface for details but
# basically
my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
-members =>[$seq1,$seq2]);
my @members = $cluster->get_members();
my @sub_members = $cluster->get_members(-species=>"homo sapiens");
Description
This interface if for a Family object representing a family of
biological objects. A generic implementation for this may be
found a Bio::Cluster::Family.
Methods
Methods description
Title : family_id
Usage : Bio::Cluster::FamilyI->family_id("znfp");
Function: get/set for the family id
Returns : the family id
Args : the family id |
Title : family_score
Usage : Bio::Cluster::FamilyI->family_score(95);
Function: get/set for the score of algorithm used to generate
the family if present
Returns : the score
Args : the score |
Methods code
sub family_id
{ shift->throw_not_implemented(); } | sub family_score
{ shift->throw_not_implemented(); } | General documentation
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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
We dont mandate but encourage implementors to support at least the
following named parameters upon object initialization.
Arguments Description
--------- -----------
-family_id the name of the family
-description the consensus description of the family
-annotation_score the confidence by which the consensus description is
representative of the family
-members the members belonging to the family
-alignment the multiple alignment of the members Title : display_id
Usage :
Function: Get the display name or identifier for the cluster
Returns : a string
Args :
Title : get_members
Usage : Bio::Cluster::FamilyI->get_members();
Function: get the members of the family
Returns : the array of members
Args : the array of members
Title : description
Usage : Bio::Cluster::FamilyI->description("Zinc Finger Protein");
Function: get/set for the description of the family
Returns : the description
Args : the description Title : size
Usage : Bio::Cluster::FamilyI->size();
Function: get/set for the description of the family
Returns : size
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