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.\" ========================================================================
.\"
.IX Title "Bio::ClusterI 3pm"
.TH Bio::ClusterI 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::ClusterI \- Cluster Interface
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    # 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");
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Shawn Hoon"
.IX Header "AUTHOR - Shawn Hoon"
Email shawnh@fugu\-sg.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SH "Implementation Specific Functions"
.IX Header "Implementation Specific Functions"
These functions are the ones that a specific implementation must
define.
.SS "new"
.IX Subsection "new"
.Vb 2
\&  We don\*(Aqt 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
.Ve
.SS "display_id"
.IX Subsection "display_id"
.Vb 5
\& Title   : display_id
\& Usage   : 
\& Function: Get the display name or identifier for the cluster
\& Returns : a string
\& Args    :
.Ve
.SS "description"
.IX Subsection "description"
.Vb 5
\& 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
.Ve
.SS "size"
.IX Subsection "size"
.Vb 6
\& 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    :
.Ve
.SS "cluster_score"
.IX Subsection "cluster_score"
.Vb 6
\& Title   : cluster_score
\& Usage   : $cluster \->cluster_score(100);
\& Function: get/set for cluster_score which
\&           represent the score in which the clustering
\&           algorithm assigns to this cluster.
\& Returns : a number
.Ve
.SS "get_members"
.IX Subsection "get_members"
.Vb 5
\& Title   : get_members
\& Usage   : Bio::ClusterI\->get_members(($seq1, $seq2));
\& Function: retrieve the members of the family by some criteria, for
\&           example :
\&           $cluster\->get_members(\-species => \*(Aqhomo sapiens\*(Aq); 
\&
\&           Will return all members if no criteria are provided.
\&
\& Returns : the array of members
\& Args    :
.Ve