Bio::Cluster SequenceFamily
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
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
newDescriptionCode
versionDescriptionCode
annotation_scoreDescriptionCode
alignmentDescriptionCode
treeDescriptionCode
family_scoreDescriptionCode
family_idDescriptionCode
display_idDescriptionCode
descriptionDescriptionCode
get_membersDescriptionCode
sizeDescriptionCode
cluster_scoreDescriptionCode
add_membersDescriptionCode
remove_membersDescriptionCode
members
No description
Code
Methods description
newcode    nextTop
 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
versioncodeprevnextTop
 Title   : version
 Usage   : $family->version("1.0");
 Function: get/set for version
 Returns : a string version of the family generated.
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
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
treecodeprevnextTop
 Title   : tree
 Usage   : $family->tree($tree);
 Function: get/set for an tree object representing
           the phylogenetic tree of the family. 
 Returns : Bio::Tree
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
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
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)
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
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.
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    :
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
add_memberscodeprevnextTop
 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_memberscodeprevnextTop
 Title   : remove_members
 Usage   : $fam->remove_members();
 Function: remove all members from a family 
 Returns : the previous array of members
 Args    : none
Methods code
newdescriptionprevnextTop
sub new {
	my ($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 $self;
}
versiondescriptionprevnextTop
sub version {
  my ($self,$value) = @_;
  if($value){
    $self->{'_version'} =$value;
  }
  return $self->{'_version'};
}
annotation_scoredescriptionprevnextTop
sub annotation_score {
  my ($self,$score) = @_;
  if($score){
    $self->{'_annotation_score'} = $score;
  }
  return $self->{'_annotation_score'};
}
alignmentdescriptionprevnextTop
sub alignment {
	my ($self,$align) = @_;
  if($align){
    $self->{'_alignment'} = $align;
  }
    return $self->{'_alignment'};
}
treedescriptionprevnextTop
sub tree {
  my ($self,$tree) = @_;
  if($tree) {
    $self->{'_tree'} = $tree;
  }
  return $self->{'_tree'};
}
family_scoredescriptionprevnextTop
sub family_score {
    return shift->cluster_score(@_);
}
family_iddescriptionprevnextTop
sub family_id {
    return shift->display_id(@_);
}
display_iddescriptionprevnextTop
sub display_id {
    my ($self,$id) = @_;
    if($id){
	$self->{'_cluster_id'} = $id;
    }
    return $self->{'_cluster_id'};
}
descriptiondescriptionprevnextTop
sub description {
  my ($self,$desc) = @_;
  if($desc){
    $self->{'_description'} = $desc;
  }
  return $self->{'_description'};
}
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'}};
}
sizedescriptionprevnextTop
sub size {
  my ($self) = @_;

  return scalar(@{$self->{'_members'}});
}
cluster_scoredescriptionprevnextTop
sub cluster_score {
  my ($self,$score) = @_;
  if($score){
    $self->{'_cluster_score'} = $score;
  }
  return $self->{'_cluster_score'};
}
add_membersdescriptionprevnextTop
sub add_members {
    my ($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;
}
remove_membersdescriptionprevnextTop
sub remove_members {
    my ($self) =  @_;
    my $mems = $self->{'_members'};
    $self->{'_members'} = [];
    return @$mems;
}
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();
    }
}
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.