Bio::Cluster FamilyI
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Summary
Bio::Cluster::FamilyI - Family Interface
Package variables
No package variables defined.
Included modules
Bio::ClusterI
Inherit
Bio::ClusterI
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
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/MailList.shtml  - About the mailing lists
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
email or the web:
  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
AUTHOR - Shawn HoonTop
Email shawnh@fugu-sg.org
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
  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
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