Bio ClusterI
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Summary
Bio::ClusterI - Cluster Interface
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Inherit
Bio::Root::RootI
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 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.
Methods
cluster_scoreDescriptionCode
descriptionDescriptionCode
display_idDescriptionCode
get_membersDescriptionCode
sizeDescriptionCode
Methods description
cluster_scorecode    nextTop
 Title   : cluster_score
 Usage   : $cluster ->cluster_score(100);
 Function: get/set for cluster_score which
           represent the score in which the clustering
           algorithm assigns to this cluster.
 Returns : a number
descriptioncodeprevnextTop
 Title   : description
 Usage   : Bio::ClusterI->description("POLYUBIQUITIN")
 Function: get/set for the consensus description of the cluster
 Returns : the description string 
 Args    : Optional the description string
display_idcodeprevnextTop
 Title   : display_id
 Usage   : 
 Function: Get the display name or identifier for the cluster
 Returns : a string
 Args    :
get_memberscodeprevnextTop
 Title   : get_members
 Usage   : Bio::ClusterI->get_members(($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    :
sizecodeprevnextTop
 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    :
Methods code
cluster_scoredescriptionprevnextTop
sub cluster_score {
    shift->throw_not_implemented();
}
descriptiondescriptionprevnextTop
sub description {
    shift->throw_not_implemented();
}
display_iddescriptionprevnextTop
sub display_id {
    shift->throw_not_implemented();
}
get_membersdescriptionprevnextTop
sub get_members {
    shift->throw_not_implemented();
}

1;
}
sizedescriptionprevnextTop
sub size {
    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 _
Implementation Specific FunctionsTop
These functions are the ones that a specific implementation must
define.
newTop
  We dont 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