Langue: en

Version: 2009-03-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)


Bio::Cluster::SequenceFamily - Sequence Family object


   use Bio::Cluster::SequenceFamily;
   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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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