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=head2 Support

Please direct usage questions or support issues to the mailing list:

I<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.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Shawn Hoon

Email shawnh@fugu-sg.org

=head1 APPENDIX

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".

=cut

# Let the code begin...


package Bio::Cluster::SequenceFamily;

use strict;
use warnings;
use base qw(Bio::Root::Root Bio::Cluster::FamilyI);

=head2 new

 Title   : new
 Usage   : my $family = Bio::Cluster::SequenceFamily->new(
                             -family_id=>"Family_1",
                             -description=>"Family Description Here",
                             -annotation_score=>"100",
                             -members=>\@mem);
 Function: Constructor for SequenceFamily object
 Returns : Bio::Cluster::SequenceFamily object

See L<Bio::Cluster::SequenceFamily>.

=cut

sub new {
    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($id,$description,$version,$annot_score,
    $family_score,$members) = $self->_rearrange([qw(FAMILY_ID DESCRIPTION VERSION
                                                    ANNOTATION_SCORE
                                                    FAMILY_SCORE MEMBERS)],@args);
    $self->{'_members'} = [];
    $id             && $self->family_id($id);
    $description    && $self->description($description);
    $version        && $self->version($version);
    $annot_score    && $self->annotation_score($annot_score);
    $family_score   && $self->family_score($family_score);
    $members        && $self->add_members($members);

    return $self;
}

=head2 version

 Title   : version
 Usage   : $family->version("1.0");
 Function: get/set for version
 Returns : a string version of the family generated.

=cut

sub version{
    my ($self,$value) = @_;
    if($value){
        $self->{'_version'} =$value;
    }
    return $self->{'_version'};
}

=head2 annotation_score

 Title   : annotation_score
 Usage   : $family->annotation_score(100);
 Function: get/set for annotation_score which
           represent the confidence in which the
           consensus description has been assigned
           to the family.
 Returns : Bio::SimpleAlign

See L<Bio::SimpleAlign>

=cut

sub annotation_score{
    my ($self,$score) = @_;
    if($score){
        $self->{'_annotation_score'} = $score;
    }
    return $self->{'_annotation_score'};
}

=head2 alignment

 Title   : alignment
 Usage   : $family->alignment($align);
 Function: get/set for an alignment object representing
           the multiple alignment of the members of the family.
 Returns : Bio::SimpleAlign

See L<Bio::SimpleAlign>

=cut

sub alignment {
    my ($self,$align) = @_;
    if($align){