Bio::Tree Node
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Tree::Node - A Simple Tree Node
Package variables
No package variables defined.
Included modules
Scalar::Util qw ( weaken isweak )
Inherit
Bio::Root::Root Bio::Tree::NodeI
Synopsis
    use Bio::Tree::Node;
    my $nodeA = new Bio::Tree::Node();
    my $nodeL = new Bio::Tree::Node();
    my $nodeR = new Bio::Tree::Node();

    my $node = new Bio::Tree::Node();
    $node->add_Descendent($nodeL);
    $node->add_Descendent($nodeR);

    print "node is not a leaf \n" if( $node->is_leaf);
Description
Makes a Tree Node suitable for building a Tree.
Methods
BEGIN Code
newDescriptionCode
add_DescendentDescriptionCode
each_DescendentDescriptionCode
remove_DescendentDescriptionCode
remove_all_DescendentsDescriptionCode
ancestorDescriptionCode
branch_lengthDescriptionCode
bootstrapDescriptionCode
descriptionDescriptionCode
idDescriptionCode
internal_idDescriptionCode
_creation_idDescriptionCode
is_LeafDescriptionCode
heightDescriptionCode
invalidate_heightDescriptionCode
add_tag_valueDescriptionCode
remove_tagDescriptionCode
remove_all_tagsDescriptionCode
get_all_tagsDescriptionCode
get_tag_valuesDescriptionCode
has_tagDescriptionCode
node_cleanup
No description
Code
reverse_edgeDescriptionCode
Methods description
newcode    nextTop
 Title   : new
 Usage   : my $obj = new Bio::Tree::Node();
 Function: Builds a new Bio::Tree::Node object
 Returns : Bio::Tree::Node
 Args    : -descendents   => arrayref of descendents (they will be
                             updated s.t. their ancestor point is this
                             node)
           -branch_length => branch length [integer] (optional)
           -bootstrap     => value   bootstrap value (string)
           -description   => description of node
           -id            => human readable id for node
add_DescendentcodeprevnextTop
 Title   : add_Descendent
 Usage   : $node->add_Descendant($node);
 Function: Adds a descendent to a node
 Returns : number of current descendents for this node
 Args    : Bio::Node::NodeI
           boolean flag, true if you want to ignore the fact that you are
           adding a second node with the same unique id (typically memory 
           location reference in this implementation).  default is false and 
           will throw an error if you try and overwrite an existing node.
each_DescendentcodeprevnextTop
 Title   : each_Descendent($sortby)
 Usage   : my @nodes = $node->each_Descendent;
 Function: all the descendents for this Node (but not their descendents
					      i.e. not a recursive fetchall)
 Returns : Array of Bio::Tree::NodeI objects
 Args    : $sortby [optional] "height", "creation", "alpha", "revalpha",
           or coderef to be used to sort the order of children nodes.
remove_DescendentcodeprevnextTop
 Title   : remove_Descendent
 Usage   : $node->remove_Descedent($node_foo);
 Function: Removes a specific node from being a Descendent of this node
 Returns : nothing
 Args    : An array of Bio::Node::NodeI objects which have been previously
           passed to the add_Descendent call of this object.
remove_all_DescendentscodeprevnextTop
 Title   : remove_all_Descendents
 Usage   : $node->remove_All_Descendents()
 Function: Cleanup the node's reference to descendents and reset
           their ancestor pointers to undef, if you don't have a reference
           to these objects after this call they will be cleaned up - so
           a get_nodes from the Tree object would be a safe thing to do first
 Returns : nothing
 Args    : none
ancestorcodeprevnextTop
 Title   : ancestor
 Usage   : $obj->ancestor($newval)
 Function: Set the Ancestor
 Returns : ancestral node
 Args    : newvalue (optional)
branch_lengthcodeprevnextTop
 Title   : branch_length
 Usage   : $obj->branch_length()
 Function: Get/Set the branch length
 Returns : value of branch_length
 Args    : newvalue (optional)
bootstrapcodeprevnextTop
 Title   : bootstrap
 Usage   : $obj->bootstrap($newval)
 Function: Get/Set the bootstrap value
 Returns : value of bootstrap
 Args    : newvalue (optional)
descriptioncodeprevnextTop
 Title   : description
 Usage   : $obj->description($newval)
 Function: Get/Set the description string
 Returns : value of description
 Args    : newvalue (optional)
idcodeprevnextTop
 Title   : id
 Usage   : $obj->id($newval)
 Function: The human readable identifier for the node 
 Returns : value of human readable id
 Args    : newvalue (optional)
"A name can be any string of printable characters except blanks,
colons, semicolons, parentheses, and square brackets. Because you may
want to include a blank in a name, it is assumed that an underscore
character ("_") stands for a blank; any of these in a name will be
converted to a blank when it is read in."
from http://evolution.genetics.washington.edu/phylip/newicktree.html
Also note that these objects now support spaces, ();: because we can
automatically quote the strings if they contain these characters. The
id_output method does this for you so use the id() method to get
the raw string while id_output to get the pre-escaped string.
internal_idcodeprevnextTop
 Title   : internal_id
 Usage   : my $internalid = $node->internal_id
 Function: Returns the internal unique id for this Node
           (a monotonically increasing number for this in-memory implementation
            but could be a database determined unique id in other 
	    implementations)
 Returns : unique id
 Args    : none
_creation_idcodeprevnextTop
 Title   : _creation_id
 Usage   : $obj->_creation_id($newval)
 Function: a private method signifying the internal creation order
 Returns : value of _creation_id
 Args    : newvalue (optional)
is_LeafcodeprevnextTop
 Title   : is_Leaf
 Usage   : if( $node->is_Leaf )
 Function: Get Leaf status
 Returns : boolean
 Args    : none
heightcodeprevnextTop
 Title   : height
 Usage   : my $len = $node->height
 Function: Returns the height of the tree starting at this
           node.  Height is the maximum branchlength to get to the tip.
 Returns : The longest length (weighting branches with branch_length) to a leaf
 Args    : none
invalidate_heightcodeprevnextTop
 Title   : invalidate_height
 Usage   : private helper method
 Function: Invalidate our cached value of the node height in the tree
 Returns : nothing
 Args    : none
add_tag_valuecodeprevnextTop
 Title   : add_tag_value
 Usage   : $node->add_tag_value($tag,$value)
 Function: Adds a tag value to a node 
 Returns : number of values stored for this tag
 Args    : $tag   - tag name
           $value - value to store for the tag
remove_tagcodeprevnextTop
 Title   : remove_tag
 Usage   : $node->remove_tag($tag)
 Function: Remove the tag and all values for this tag
 Returns : boolean representing success (0 if tag does not exist)
 Args    : $tag - tagname to remove
remove_all_tagscodeprevnextTop
 Title   : remove_all_tags
 Usage   : $node->remove_all_tags()
 Function: Removes all tags 
 Returns : None
 Args    : None
get_all_tagscodeprevnextTop
 Title   : get_all_tags
 Usage   : my @tags = $node->get_all_tags()
 Function: Gets all the tag names for this Node
 Returns : Array of tagnames
 Args    : None
get_tag_valuescodeprevnextTop
 Title   : get_tag_values
 Usage   : my @values = $node->get_tag_value($tag)
 Function: Gets the values for given tag ($tag)
 Returns : Array of values or empty list if tag does not exist
 Args    : $tag - tag name
has_tagcodeprevnextTop
 Title   : has_tag
 Usage   : $node->has_tag($tag)
 Function: Boolean test if tag exists in the Node
 Returns : Boolean
 Args    : $tag - tagname
reverse_edgecodeprevnextTop
 Title   : reverse_edge
 Usage   : $node->reverse_edge(child);
 Function: makes child be a parent of node
 Requires: child must be a direct descendent of node
 Returns : 1 on success, 0 on failure
 Args    : Bio::Tree::NodeI that is in the tree
Methods code
BEGINTop
BEGIN {
     $CREATIONORDER = 0;
}
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($children, $branchlen,$id,
      $bootstrap, $desc,$d) = $self->_rearrange([qw(
						    DESCENDENTS
						    BRANCH_LENGTH
						    ID
						    BOOTSTRAP
						    DESC
						    DESCRIPTION
						 )],
					     @args);
  $self->_register_for_cleanup(\&node_cleanup);
  $self->{'_desc'} = {}; # for descendents
  if( defined $d && defined $desc ) { 
      $self->warn("can only accept -desc or -description, not both, accepting -description");
      $desc = $d;
  } elsif( defined $d && ! defined $desc ) {
      $desc = $d;
  }
  defined $desc && $self->description($desc);
  defined $bootstrap && $self->bootstrap($bootstrap);
  defined $id && $self->id($id);
  defined $branchlen && $self->branch_length($branchlen);
  if( defined $children ) {
      if( ref($children) !~ /ARRAY/i ) {
	  $self->warn("Must specify a valid ARRAY reference to initialize a Node's Descendents");
      }
      foreach my $c ( @$children ) { 	
	  $self->add_Descendent($c);
      }
  }
  $self->_creation_id($CREATIONORDER++);
  return $self;
}
add_DescendentdescriptionprevnextTop
sub add_Descendent {
   my ($self,$node,$ignoreoverwrite) = @_;
   return -1 if( ! defined $node );
   
   if( ! ref($node) ||
       ref($node) =~ /HASH/ ||
       ! $node->isa('Bio::Tree::NodeI') ) {
       $self->throw("Trying to add a Descendent who is not a Bio::Tree::NodeI");
       return -1;
   }
   
   $self->{_adding_descendent} = 1;
   # avoid infinite recurse
   $node->ancestor($self) unless $node->{_setting_ancestor}; 
   $self->{_adding_descendent} = 0;
   
   if( $self->{'_desc'}->{$node->internal_id} && ! $ignoreoverwrite ) {
       $self->throw("Going to overwrite a node which is $node that is already stored here, set the ignore overwrite flag (parameter 2) to true to ignore this in the future");
   }
   $self->{'_desc'}->{$node->internal_id} = $node; # is this safely unique - we've tested before at any rate??
   
   $self->invalidate_height();
   
   return scalar keys %{$self->{'_desc'}};
}
each_DescendentdescriptionprevnextTop
sub each_Descendent {
   my ($self, $sortby) = @_;

   # order can be based on branch length (and sub branchlength)   
   $sortby ||= 'none';
   if (ref $sortby eq 'CODE') {
       my @values = sort { $sortby->($a,$b) } values %{$self->{'_desc'}};
       return @values;
   } elsif ($sortby eq 'height') {
       return map { $_->[0] }
       sort { $a->[1] <=> $b->[1] || 
		  $a->[2] <=> $b->[2] } 
       map { [$_, $_->height, $_->internal_id ] } 
       values %{$self->{'_desc'}};
   } elsif( $sortby eq 'alpha' ) {
       my @set;
       for my $v ( values %{$self->{'_desc'}} ) {
	   unless( $v->is_Leaf ) {
	       my @lst = ( sort { $a cmp $b } map { $_->id } 
                          grep { $_->is_Leaf } 
			   $v->get_all_Descendents($sortby));
	       push @set, [$v, $lst[0], $v->internal_id];
	   } else {
	       push @set, [$v, $v->id, $v->internal_id];
	   }
       } 
       return map { $_->[0] }
       sort {$a->[1] cmp $b->[1] || $a->[2] <=> $b->[2] } @set;       
   } elsif( $sortby eq 'revalpha' ) {
       my @set;
       for my $v ( values %{$self->{'_desc'}} ) {
	   if( ! defined $v->id && 
	       ! $v->is_Leaf ) {
	       my ($l) = ( sort { $b cmp $a } map { $_->id } 
			   grep { $_->is_Leaf } 
			   $v->get_all_Descendents($sortby));
	       push @set, [$v, $l, $v->internal_id];
	   } else { 
	       push @set, [$v, $v->id, $v->internal_id];
	   }
       } 
       return map { $_->[0] }
       sort {$b->[1] cmp $a->[1] || $b->[2] <=> $a->[2] } @set;
   } else { # creation
       return map { $_->[0] }
       sort { $a->[1] <=> $b->[1] } 
       map { [$_, $_->internal_id ] }
       values %{$self->{'_desc'}};	   
   }
}
remove_DescendentdescriptionprevnextTop
sub remove_Descendent {
   my ($self,@nodes) = @_;
   my $c= 0;
   foreach my $n ( @nodes ) { 
       if( $self->{'_desc'}->{$n->internal_id} ) {
        $self->{_removing_descendent} = 1;
        $n->ancestor(undef);
        $self->{_removing_descendent} = 0;
	   # should be redundant
	   $self->{'_desc'}->{$n->internal_id}->ancestor(undef);
	   delete $self->{'_desc'}->{$n->internal_id};
	   $c++;
       } else { 
	   if( $self->verbose ) {
	       $self->debug(sprintf("no node %s (%s) listed as a descendent in this node %s (%s)\n",$n->id, $n,$self->id,$self));
	       $self->debug("Descendents are " . join(',', keys %{$self->{'_desc'}})."\n");
	   }
       }
   }
   
   # remove unecessary nodes if we have removed the part 
   # which branches.
   my $a1 = $self->ancestor;   
   if( $a1 ) {
       my $bl = $self->branch_length || 0;
       my @d = $self->each_Descendent;
       if (scalar @d == 1) {
	   $d[0]->branch_length($bl + ($d[0]->branch_length || 0));
	   $a1->add_Descendent($d[0]);
	   $a1->remove_Descendent($self);
       }
   }
   $c;
}
remove_all_DescendentsdescriptionprevnextTop
sub remove_all_Descendents {
   my ($self) = @_;
   # this won't cleanup the nodes themselves if you also have
   # a copy/pointer of them (I think)...
   while( my ($node,$val) = each %{ $self->{'_desc'} } ) {
       $val->ancestor(undef);
   }
   $self->{'_desc'} = {};
   1;
}
ancestordescriptionprevnextTop
sub ancestor {
    my $self = shift;
    if (@_) {
        my $new_ancestor = shift;
        
        # we can set ancestor to undef
        if ($new_ancestor) {
            $self->throw("This is [$new_ancestor], not a Bio::Tree::NodeI")
		unless $new_ancestor->isa('Bio::Tree::NodeI');
        }
        
        my $old_ancestor = $self->{'_ancestor'} || '';
        if (!$old_ancestor || 
	    ($old_ancestor && ( !$new_ancestor || 
			       $new_ancestor ne $old_ancestor)) ) {
            if( $old_ancestor && ! $old_ancestor->{_removing_descendent}) {
		$old_ancestor->remove_Descendent($self);
	    }
            if ($new_ancestor && 
		! $new_ancestor->{_adding_descendent} ) { # avoid infinite recurse
                $self->{_setting_ancestor} = 1;
                $new_ancestor->add_Descendent($self, 1);
                $self->{_setting_ancestor} = 0;
            }
        }
        weaken($self->{'_ancestor'} = $new_ancestor);
    }
    
    return $self->{'_ancestor'};
}
branch_lengthdescriptionprevnextTop
sub branch_length {
    my $self = shift;
    if( @_ ) {
	my $bl = shift;
	if( defined $bl &&
	    $bl =~ s/\[(\d+)\]// ) {
	    $self->bootstrap($1);
	}
	$self->{'_branch_length'} = $bl;
    $self->invalidate_height();
    }
    return $self->{'_branch_length'};
}
bootstrapdescriptionprevnextTop
sub bootstrap {
     my $self = shift;
    if( @_ ) {
	if( $self->has_tag('B') ) {
	    $self->remove_tag('B');
	}
	$self->add_tag_value('B',shift);
    }
    return ($self->get_tag_values('B'))[0];
}
descriptiondescriptionprevnextTop
sub description {
    my $self = shift;
    $self->{'_description'} = shift @_ if @_;
    return $self->{'_description'};
}
iddescriptionprevnextTop
sub id {
    my ($self, $value) = @_;
    if (defined $value) {
        #$self->warn("Illegal characters ();:  and space in the id [$value], converting to _ ")
	# if $value =~ /\(\);:/ and $self->verbose >= 0;
        #$value =~ s/[\(\);:\s]/_/g;
        $self->{'_id'} = $value;
    }
    return $self->{'_id'};
}
internal_iddescriptionprevnextTop
sub internal_id {
   return $_[0]->_creation_id;
}
_creation_iddescriptionprevnextTop
sub _creation_id {
    my $self = shift @_;
    $self->{'_creation_id'} = shift @_ if( @_);
    return $self->{'_creation_id'} || 0;
}
is_LeafdescriptionprevnextTop
sub is_Leaf {
    my ($self) = @_;
    my $isleaf = ! (defined $self->{'_desc'} &&
		 (keys %{$self->{'_desc'}} > 0) );
    return $isleaf;
}
heightdescriptionprevnextTop
sub height {
     my ($self) = @_;
    return $self->{'_height'} if( defined $self->{'_height'} );
    
    return 0 if( $self->is_Leaf );
    my $max = 0;
    foreach my $subnode ( $self->each_Descendent ) { 
	my $bl = $subnode->branch_length;
	$bl = 1 unless (defined $bl && $bl =~ /^\-?\d+(\.\d+)?$/);
	my $s = $subnode->height + $bl;
	if( $s > $max ) { $max = $s; }
    }
    return ($self->{'_height'} = $max);
}
invalidate_heightdescriptionprevnextTop
sub invalidate_height {
     my ($self) = @_;
    
    $self->{'_height'} = undef;
    if( defined $self->ancestor ) {
	$self->ancestor->invalidate_height;
    }
}
add_tag_valuedescriptionprevnextTop
sub add_tag_value {
    my ($self,$tag,$value) = @_;
    if( ! defined $tag || ! defined $value ) {
	$self->warn("cannot call add_tag_value with an undefined value");
    }
    push @{$self->{'_tags'}->{$tag}}, $value;
    return scalar @{$self->{'_tags'}->{$tag}};
}
remove_tagdescriptionprevnextTop
sub remove_tag {
   my ($self,$tag) = @_;
   if( exists $self->{'_tags'}->{$tag} ) {
       $self->{'_tags'}->{$tag} = undef;
       delete $self->{'_tags'}->{$tag};
       return 1;
   }
   return 0;
}
remove_all_tagsdescriptionprevnextTop
sub remove_all_tags {
   my ($self) = @_;
   $self->{'_tags'} = {};
   return;
}
get_all_tagsdescriptionprevnextTop
sub get_all_tags {
   my ($self) = @_;
   my @tags = sort keys %{$self->{'_tags'} || {}};
   return @tags;
}
get_tag_valuesdescriptionprevnextTop
sub get_tag_values {
   my ($self,$tag) = @_;
   return wantarray ? @{$self->{'_tags'}->{$tag} || []} :
                     (@{$self->{'_tags'}->{$tag} || []})[0];
}
has_tagdescriptionprevnextTop
sub has_tag {
   my ($self,$tag) = @_;
   return exists $self->{'_tags'}->{$tag};
}
node_cleanupdescriptionprevnextTop
sub node_cleanup {
    my $self = shift;
    return unless defined $self;
    
    #*** below is wrong, cleanup doesn't actually occur. Will replace with:
    # $self->remove_all_Descendents; once further fixes in place..
    if( defined $self->{'_desc'} &&
        ref($self->{'_desc'}) =~ /ARRAY/i ) {
        while( my ($nodeid,$node) = each %{ $self->{'_desc'} } ) {
            $node->ancestor(undef); # insure no circular references
            $node = undef;
        }
    }
    $self->{'_desc'} = {};
}
reverse_edgedescriptionprevnextTop
sub reverse_edge {
    my ($self,$node) = @_;
    if( $self->delete_edge($node) ) {
      $node->add_Descendent($self);
      return 1;
    } 
    return 0;
}
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
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  http://bugzilla.open-bio.org/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
CONTRIBUTORSTop
Aaron Mackey, amackey-at-virginia-dot-edu
Sendu Bala, bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
get_all_DescendentsTop
 Title   : get_all_Descendents
 Usage   : my @nodes = $node->get_all_Descendents;
 Function: Recursively fetch all the nodes and their descendents
           *NOTE* This is different from each_Descendent
 Returns : Array or Bio::Tree::NodeI objects
 Args    : none
Helper FunctionsTop
id_outputTop
 Title   : id_output
 Usage   : my $id = $node->id_output;
 Function: Return an id suitable for output in format like newick
           so that if it contains spaces or ():; characters it is properly 
           quoted
 Returns : $id string if $node->id has a value
 Args    : none
Bio::Node::NodeI decorated interface implementedTop
The following methods are implemented by Bio::Node::NodeI decorated
interface.
to_stringTop
 Title   : to_string
 Usage   : my $str = $node->to_string()
 Function: For debugging, provide a node as a string
 Returns : string
 Args    : none