Provided by: libbio-perl-perl_1.7.2-2_all bug

NAME

       Bio::Cluster::SequenceFamily - Sequence Family object

SYNOPSIS

         use Bio::SeqIO;
         use Bio::Cluster::SequenceFamily;
         use File::Spec;

         my $file =  File::Spec->catfile('t','data','swiss.dat');
         my $seqio= Bio::SeqIO->new(-format => 'swiss',
                                   -file => $file);
         my @mem;
         while(my $seq = $seqio->next_seq){
           push @mem, $seq;
         }

         #create the family
         my $family = Bio::Cluster::SequenceFamily->new(
                 -family_id=>"Family_1",
                 -description=>"Family Description Here",
                 -annotation_score=>"100",
                 -members=>\@mem);

         #access the family

         foreach my $mem ($family->get_members){
           print $mem->display_id."\t".$mem->desc."\n";
         }

         #select members if members have a Bio::Species Object

         my @mem = $family->get_members(-binomial=>"Homo sapiens");
         @mem = $family->get_members(-ncbi_taxid => 9606);
         @mem = $family->get_members(-common_name=>"Human");
         @mem = $family->get_members(-species=>"sapiens");
         @mem = $family->get_members(-genus=>"Homo");

DESCRIPTION

       This is a simple Family object that may hold any group of object. For more specific
       families, one should derive from FamilyI.

FEEDBACK

       Email bioperl-l@bioperl.org for support and feedback.

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists. Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       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 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

AUTHOR - Shawn Hoon

       Email shawnh@fugu-sg.org

APPENDIX

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

   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 Bio::Cluster::SequenceFamily.

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

   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 Bio::SimpleAlign

   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 Bio::SimpleAlign

   tree
        Title   : tree
        Usage   : $family->tree($tree);
        Function: get/set for an tree object representing
                  the phylogenetic tree of the family.
        Returns : Bio::Tree

       See Bio::Tree

Bio::Cluster::FamilyI methods

   family_score
        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

                  This is aliased to cluster_score().

        Returns : the score
        Args    : the score

   family_id
        Title   : family_id
        Usage   : $family->family_id("Family_1");
        Function: get/set for family id

                  This is aliased to display_id().

        Returns : a string specifying identifier of the family

Bio::ClusterI methods

   display_id
        Title   : display_id
        Usage   :
        Function: Get/set the display name or identifier for the cluster
        Returns : a string
        Args    : optional, on set the display ID ( a string)

   description
        Title   : description
        Usage   : $fam->description("POLYUBIQUITIN")
        Function: get/set for the consensus description of the cluster
        Returns : the description string
        Args    : Optional the description string

   get_members
        Title   : get_members
        Usage   : Valid criteria:
                  -common_name
                  -binomial
                  -ncbi_taxid
                  -organelle
                  -genus
                  $family->get_members(-common_name =>"human");
                  $family->get_members(-species     =>"homo sapiens");
                  $family->get_members(-ncbi_taxid  => 9606);
                  For now, multiple critieria are ORed.

                  Will return all members if no criteria are provided.

        Function: get members using methods from L<Bio::Species>
                  the phylogenetic tree of the family.
        Returns : an array of objects that are member of this family.

   size
        Title   : size
        Usage   : $fam->size();
        Function: get/set for the size of the family,
                  calculated from the number of members
        Returns : the size of the family
        Args    :

   cluster_score
        Title   : cluster_score
        Usage   : $fam->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

Implementation specific methods

         These are mostly for adding/removing/changing.

   add_members
        Title   : add_members
        Usage   : $fam->add_member([$seq1,$seq1]);
        Function: add members to a family
        Returns :
        Args    : the member(s) to add, as an array or arrayref

   remove_members
        Title   : remove_members
        Usage   : $fam->remove_members();
        Function: remove all members from a family
        Returns : the previous array of members
        Args    : none

   members
        Title   : members
        Usage   : $members = $fam->members([$seq1,$seq1]);
        Function: Deprecated. Use add_members() or get_members() instead