Bio::Cluster::SequenceFamily(3pm)			User Contributed Perl Documentation			 Bio::Cluster::SequenceFamily(3pm)

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 $mem->display_id."	".$mem->desc."
";
	 }

	 #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://redmine.open-bio.org/projects/bioperl/

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

perl v5.14.2							    2012-03-02					 Bio::Cluster::SequenceFamily(3pm)