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.\" ========================================================================
.\"
.IX Title "Bio::Cluster::FamilyI 3pm"
.TH Bio::Cluster::FamilyI 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Cluster::FamilyI \- Family 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 if for a Family object representing a family of 
biological objects. A generic implementation for this may be
found a Bio::Cluster::Family.
.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 _
.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.
\&
\& 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
.Ve
.SS "family_id"
.IX Subsection "family_id"
.Vb 5
\& 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
.Ve
.SS "family_score"
.IX Subsection "family_score"
.Vb 6
\& 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
.Ve
.SH "Methods inherited from Bio::ClusterI"
.IX Header "Methods inherited from Bio::ClusterI"
.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 "get_members"
.IX Subsection "get_members"
.Vb 5
\& 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
.Ve
.SS "description"
.IX Subsection "description"
.Vb 5
\& 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
.Ve
.SS "size"
.IX Subsection "size"
.Vb 5
\& Title   : size
\& Usage   : Bio::Cluster::FamilyI\->size();
\& Function: get/set for the description of the family
\& Returns : size 
\& 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