Bio::Cluster SequenceFamily
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Summary
Bio::Cluster::SequenceFamily - Sequence Family object
Package variables
No package variables defined.
Included modules
Bio::Cluster::FamilyI
Bio::Root::Root
Inherit
Bio::Cluster::FamilyI Bio::Root::Root
Synopsis
  use Bio::Cluster::SequenceFamily

  use Bio::SeqIO;
  use Bio::Cluster::SequenceFamily;

  my $file =  Bio::Root::IO->catfile('t','data','swiss.dat');
  my $seqio= new Bio::SeqIO('-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.
Methods
add_membersDescriptionCode
alignmentDescriptionCode
annotation_scoreDescriptionCode
cluster_scoreDescriptionCode
descriptionDescriptionCode
display_idDescriptionCode
family_idDescriptionCode
family_scoreDescriptionCode
get_membersDescriptionCode
members
No description
Code
newDescriptionCode
remove_membersDescriptionCode
sizeDescriptionCode
treeDescriptionCode
versionDescriptionCode
Methods description
add_memberscode    nextTop
 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
alignmentcodeprevnextTop
 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
annotation_scorecodeprevnextTop
 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
cluster_scorecodeprevnextTop
 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
descriptioncodeprevnextTop
 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
display_idcodeprevnextTop
 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)
family_idcodeprevnextTop
 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
family_scorecodeprevnextTop
 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
get_memberscodeprevnextTop
 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 Bio::Species
           the phylogenetic tree of the family.
 Returns : an array of objects that are member of this family.
newcodeprevnextTop
 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
remove_memberscodeprevnextTop
 Title   : remove_members
 Usage   : $fam->remove_members();
 Function: remove all members from a family 
 Returns : the previous array of members
 Args    : none
sizecodeprevnextTop
 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    :
treecodeprevnextTop
 Title   : tree
 Usage   : $family->tree($tree);
 Function: get/set for an tree object representing
           the phylogenetic tree of the family. 
 Returns : Bio::Tree
versioncodeprevnextTop
 Title   : version
 Usage   : $family->version("1.0");
 Function: get/set for version
 Returns : a string version of the family generated.
Methods code
add_membersdescriptionprevnextTop
sub add_members {
    my ($self,@mems) = @_;

    my $mem = shift(@mems);
    if(ref($mem) eq "ARRAY"){
	push @{$self->{'_members'}},@{$mem};
    } else {
	push @{$self->{'_members'}},$mem;
    }
    push @{$self->{'_members'}}, @mems;

    return 1;
}
alignmentdescriptionprevnextTop
sub alignment {
	my ($self,$align) = @_;
  if($align){
    $self->{'_alignment'} = $align;
  }
    return $self->{'_alignment'};
}
annotation_scoredescriptionprevnextTop
sub annotation_score {
  my ($self,$score) = @_;
  if($score){
    $self->{'_annotation_score'} = $score;
  }
  return $self->{'_annotation_score'};
}
cluster_scoredescriptionprevnextTop
sub cluster_score {
  my ($self,$score) = @_;
  if($score){
    $self->{'_cluster_score'} = $score;
  }
  return $self->{'_cluster_score'};
}
descriptiondescriptionprevnextTop
sub description {
  my ($self,$desc) = @_;
  if($desc){
    $self->{'_description'} = $desc;
  }
  return $self->{'_description'};
}
display_iddescriptionprevnextTop
sub display_id {
    my ($self,$id) = @_;
    if($id){
	$self->{'_cluster_id'} = $id;
    }
    return $self->{'_cluster_id'};
}
family_iddescriptionprevnextTop
sub family_id {
    return shift->display_id(@_);
}
family_scoredescriptionprevnextTop
sub family_score {
    return shift->cluster_score(@_);
}
get_membersdescriptionprevnextTop
sub get_members {
    my $self = shift;
    my @ret;
    
    if(@_) {
	my %hash = @_;
	foreach my $mem ( @{$self->{'_members'}} ) {
	    foreach my $key ( keys %hash){
		my $method = $key;
		$method=~s/-//g;
		if($mem->can('species')){
		    my $species = $mem->species;
		    $species->can($method) ||
			$self->throw("$method is an invalid criteria");
		    if($species->$method() eq $hash{$key} ){
			push @ret, $mem;
		    }
		}
	    }
	}
	return @ret;
    }
    return @{$self->{'_members'}};
}
membersdescriptionprevnextTop
sub members {
    my $self = shift;
    if(@_) {
	# this is in set mode
	$self->warn("setting members() in ".ref($self)." is deprecated.\n".
		    "Use add_members() instead.");
	return $self->add_members(@_);
    } else {
	# get mode
	$self->warn("members() in ".ref($self)." is deprecated.\n".
		    "Use get_members() instead.");
	return $self->get_members();
    }
}

1;
}
newdescriptionprevnextTop
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 $self;
}
remove_membersdescriptionprevnextTop
sub remove_members {
    my ($self) =  @_;
    my $mems = $self->{'_members'};
    $self->{'_members'} = [];
    return @$mems;
}

#####################################################################
# aliases for naming consistency or other reasons                   #
#####################################################################

*flush_members =\& remove_members;
*add_member =\& add_members;
}
sizedescriptionprevnextTop
sub size {
  my ($self) = @_;

  return scalar(@{$self->{'_members'}});
}
treedescriptionprevnextTop
sub tree {
  my ($self,$tree) = @_;
  if($tree) {
    $self->{'_tree'} = $tree;
  }
  return $self->{'_tree'};
}
versiondescriptionprevnextTop
sub version {
  my ($self,$value) = @_;
  if($value){
    $self->{'_version'} =$value;
  }
  return $self->{'_version'};
}
General documentation
FEEDBACKTop
Mailing ListsTop
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://bio.perl.org/MailList.html  - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
AUTHOR - Shawn Hoon Top
Email shawnh@fugu-sg.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
Bio::Cluster::FamilyI methodsTop
Bio::ClusterI methodsTop
Implementation specific methodsTop
  These are mostly for adding/removing/changing.