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

1;
}
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 _
Implementation Specific FunctionsTop
These functions are the ones that a specific implementation must
define.
newTop
  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