Bio::Cluster FamilyI
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Summary
Bio::Cluster::FamilyI - Family Interface
Package variables
No package variables defined.
Inherit
Bio::ClusterI
Synopsis
    # 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");
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
family_idDescriptionCode
family_scoreDescriptionCode
Methods description
family_idcode    nextTop
 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
family_scorecodeprevnextTop
 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
family_iddescriptionprevnextTop
sub family_id {
    shift->throw_not_implemented();
}
family_scoredescriptionprevnextTop
sub family_score {
    shift->throw_not_implemented();
}
General documentation
FEEDBACKTop
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.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Shawn HoonTop
Email shawnh@fugu-sg.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
  We don't 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
Methods inherited from Bio::ClusterITop
display_idTop
 Title   : display_id
Usage :
Function: Get the display name or identifier for the cluster
Returns : a string
Args :
get_membersTop
 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
descriptionTop
 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
sizeTop
 Title   : size
Usage : Bio::Cluster::FamilyI->size();
Function: get/set for the description of the family
Returns : size
Args :
cluster_scoreTop
 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