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


       Bio::Cluster::SequenceFamily - Sequence Family object


         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(
                 -description=>"Family Description Here",

         #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");


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


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AUTHOR - Shawn Hoon



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

        Title   : new
        Usage   : my $family = Bio::Cluster::SequenceFamily->new(
                                    -description=>"Family Description Here",
        Function: Constructor for SequenceFamily object
        Returns : Bio::Cluster::SequenceFamily object

       See Bio::Cluster::SequenceFamily.

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

        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

        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

        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

        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

        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

        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)

        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

        Title   : get_members
        Usage   : Valid criteria:
                  $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.

        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    :

        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.

        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

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

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