Bio::Tree Tree
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Summary
Bio::Tree::Tree - An implementation of the TreeI interface.
Package variables
No package variables defined.
Inherit
Bio::Root::Root Bio::Tree::TreeFunctionsI Bio::Tree::TreeI
Synopsis
    use Bio::TreeIO;
# like from a TreeIO my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'treefile.dnd'); my $tree = $treeio->next_tree; my @nodes = $tree->get_nodes; my $root = $tree->get_root_node;
Description
This object holds handles to Nodes which make up a tree.
Methods
newDescriptionCode
nodeleteDescriptionCode
get_nodesDescriptionCode
get_root_nodeDescriptionCode
set_root_nodeDescriptionCode
total_branch_lengthDescriptionCode
subtree_lengthDescriptionCode
idDescriptionCode
scoreDescriptionCode
as_textDescriptionCode
set_tag_valueDescriptionCode
add_tag_valueDescriptionCode
remove_tagDescriptionCode
remove_all_tagsDescriptionCode
get_all_tagsDescriptionCode
get_tag_valuesDescriptionCode
has_tagDescriptionCode
cloneDescriptionCode
cleanup_tree
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Tree::Tree->new();
Function: Builds a new Bio::Tree::Tree object
Returns : Bio::Tree::Tree
Args : -root => Bio::Tree::NodeI object which is the root
OR
-node => Bio::Tree::NodeI object from which the root will be
determined

-nodelete => boolean, whether or not to try and cleanup all
the nodes when this this tree goes out of scope.
-id => optional tree ID
-score => optional tree score value
nodeletecodeprevnextTop
 Title   : nodelete
Usage : $obj->nodelete($newval)
Function: Get/Set Boolean whether or not to delete the underlying
nodes when it goes out of scope. By default this is false
meaning trees are cleaned up.
Returns : boolean
Args : on set, new boolean value
get_nodescodeprevnextTop
 Title   : get_nodes
Usage : my @nodes = $tree->get_nodes()
Function: Return list of Bio::Tree::NodeI objects
Returns : array of Bio::Tree::NodeI objects
Args : (named values) hash with one value
order => 'b|breadth' first order or 'd|depth' first order
sortby => [optional] "height", "creation", "alpha", "revalpha",
or coderef to be used to sort the order of children nodes. See Bio::Tree::Node for details
get_root_nodecodeprevnextTop
 Title   : get_root_node
Usage : my $node = $tree->get_root_node();
Function: Get the Top Node in the tree, in this implementation
Trees only have one top node.
Returns : Bio::Tree::NodeI object
Args : none
set_root_nodecodeprevnextTop
 Title   : set_root_node
Usage : $tree->set_root_node($node)
Function: Set the Root Node for the Tree
Returns : Bio::Tree::NodeI
Args : Bio::Tree::NodeI
total_branch_lengthcodeprevnextTop
 Title   : total_branch_length
Usage : my $size = $tree->total_branch_length
Function: Returns the sum of the length of all branches
Returns : real
Args : none
subtree_lengthcodeprevnextTop
 Title   : subtree_length
Usage : my $subtree_size = $tree->subtree_length($internal_node)
Function: Returns the sum of the length of all branches in a subtree
under the node. Calculates the size of the whole tree
without an argument (but only if root node is defined)
Returns : real or undef
Args : Bio::Tree::NodeI object, defaults to the root node
idcodeprevnextTop
 Title   : id
Usage : my $id = $tree->id();
Function: An id value for the tree
Returns : scalar
Args : [optional] new value to set
scorecodeprevnextTop
 Title   : score
Usage : $obj->score($newval)
Function: Sets the associated score with this tree
This is a generic slot which is probably best used
for log likelihood or other overall tree score
Returns : value of score
Args : newvalue (optional)
as_textcodeprevnextTop
 Title   : as_text
Usage : my $tree_as_string = $tree->as_text($format)
Function: Returns the tree as a string representation in the
desired format (currently 'newick', 'nhx', or
'tabtree')
Returns : scalar string
Args : format type as specified by Bio::TreeIO
Note : This method loads the Bio::TreeIO::$format module
on the fly, and commandeers the _write_tree_Helper
routine therein to create the tree string.
set_tag_valuecodeprevnextTop
 Title   : set_tag_value
Usage : $tree->set_tag_value($tag,$value)
$tree->set_tag_value($tag,@values)
Function: Sets a tag value(s) to a tree. Replaces old values.
Returns : number of values stored for this tag
Args : $tag - tag name
$value - value to store for the tag
add_tag_valuecodeprevnextTop
 Title   : add_tag_value
Usage : $tree->add_tag_value($tag,$value)
Function: Adds a tag value to a tree
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 : $tree->remove_tag($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 : $tree->remove_all_tags()
Function: Removes all tags
Returns : None
Args : None
get_all_tagscodeprevnextTop
 Title   : get_all_tags
Usage : my @tags = $tree->get_all_tags()
Function: Gets all the tag names for this Tree
Returns : Array of tagnames
Args : None
get_tag_valuescodeprevnextTop
 Title   : get_tag_values
Usage : my @values = $tree->get_tag_values($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 : $tree->has_tag($tag)
Function: Boolean test if tag exists in the Tree
Returns : Boolean
Args : $tag - tagname
clonecodeprevnextTop
 Title   : clone
Alias : _clone
Usage : $tree_copy = $tree->clone();
$subtree_copy = $tree->clone($internal_node);
Function: Safe tree clone that doesn't segfault
Returns : Bio::Tree::Tree object
Args : [optional] $start_node, Bio::Tree::Node object
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
  
    my $self = $class->SUPER::new(@args);
    $self->{'_rootnode'} = undef;
    $self->{'_maxbranchlen'} = 0;
    $self->_register_for_cleanup(\&cleanup_tree);
    my ($root, $node, $nodel, $id, $score) =
        $self->_rearrange([qw(ROOT NODE NODELETE ID SCORE)], @args);
  
    if ($node && ! $root) {
        $self->throw("Must supply a Bio::Tree::NodeI") unless ref($node) && $node->isa('Bio::Tree::NodeI');
        my @lineage = $self->get_lineage_nodes($node);
        $root = shift(@lineage) || $node;
    
        # to stop us pulling in entire database of a Bio::Taxon when we later do
# get_nodes() or similar, specifically set ancestor() for each node
if ($node->isa('Bio::Taxon')) { push(@lineage, $node) unless $node eq $root; my $ancestor = $root; foreach my $lineage_node (@lineage) { $lineage_node->ancestor($ancestor); } continue { $ancestor = $lineage_node; } } } if ($root) { $self->set_root_node($root); } $self->nodelete($nodel || 0); $self->id($id) if defined $id; $self->score($score) if defined $score; return $self;
}
nodeletedescriptionprevnextTop
sub nodelete {
    my $self = shift;
    return $self->{'nodelete'} = shift if @_;
    return $self->{'nodelete'};
}
get_nodesdescriptionprevnextTop
sub get_nodes {
    my ($self, @args) = @_;
    my ($order, $sortby) = $self->_rearrange([qw(ORDER SORTBY)], @args);
    $order  ||= 'depth';
    $sortby ||= 'none';

    my @children;
    my $node = $self->get_root_node;
    if ($node) {
        if ($order =~ m/^b/oi) { # breadth-first
@children = ($node);
my @to_process = ($node); while( @to_process ) { my $n = shift @to_process; my @c = $n->each_Descendent($sortby); push @children, @c; push @to_process, @c; } } elsif ($order =~ m/^d/oi) { # depth-first
@children = ($node, $node->get_all_Descendents($sortby));
} else { $self->verbose(1); $self->warn("specified an order '$order' which I don't understan\n"); } } return @children;
}
get_root_nodedescriptionprevnextTop
sub get_root_node {
    my ($self) = @_;
    return $self->{'_rootnode'};
}
set_root_nodedescriptionprevnextTop
sub set_root_node {
    my $self = shift;
    if ( @_ ) { 
        my $value = shift;
        if ( defined $value && ! $value->isa('Bio::Tree::NodeI') ) { 
            $self->warn("Trying to set the root node to $value which is not a Bio::Tree::NodeI");
            return $self->get_root_node;
        }
        $self->{'_rootnode'} = $value;
    } 
    return $self->get_root_node;
}
total_branch_lengthdescriptionprevnextTop
sub total_branch_length {
 shift->subtree_length
}
subtree_lengthdescriptionprevnextTop
sub subtree_length {
    my $tree = shift;
    my $node = shift || $tree->get_root_node;
    return unless $node;
    my $sum = 0;
    for ( $node->get_all_Descendents ) {
        $sum += $_->branch_length || 0;
    }
    return $sum;
}
iddescriptionprevnextTop
sub id {
   my ($self, $val) = @_;
   if ( defined $val ) { 
       $self->{'_treeid'} = $val;
   }
   return $self->{'_treeid'};
}
scoredescriptionprevnextTop
sub score {
   my ($self, $val) = @_;
   if ( defined $val ) { 
       $self->{'_score'} = $val;
   }
   return $self->{'_score'};
}


# decorated interface TreeI Implements this
}
as_textdescriptionprevnextTop
sub as_text {
    my $self = shift;
    my $format = shift;
    my $params_input = shift || {};

    my $iomod = "Bio::TreeIO::$format";
    $self->_load_module($iomod);

    my $string = '';
    open(my $fh,">",\$string) or die ("Couldn't open $string as file: $!\n");
    my $test = $iomod->new( -format => $format, -fh => $fh );

    # Get the default params for the given IO module.
$test->set_params($params_input); $test->write_tree($self); close($fh); return $string;
}
set_tag_valuedescriptionprevnextTop
sub set_tag_value {
    my ($self, $tag, @values) = @_;
    if ( ! defined $tag || ! scalar @values ) {
        $self->warn("cannot call set_tag_value with an undefined value");
    }
    $self->remove_tag ($tag);
    map { push @{$self->{'_tags'}->{$tag}}, $_ } @values;
    return scalar @{$self->{'_tags'}->{$tag}};
}
add_tag_valuedescriptionprevnextTop
sub add_tag_value {
    my ($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};
}


# safe tree clone that doesn't seg fault
}
clonedescriptionprevnextTop
sub clone {
    my ($self, $parent, $parent_clone) = @_;
    $parent ||= $self->get_root_node;
    $parent_clone ||= $self->_clone_node($parent);

    foreach my $node ($parent->each_Descendent()) {
        my $child = $self->_clone_node($node);
        $child->ancestor($parent_clone);
        $self->_clone($node, $child);
    }
    $parent->ancestor && return;

    my $tree = $self->new(-root => $parent_clone);
    return $tree;
}


# -- private internal methods --
}
cleanup_treedescriptionprevnextTop
sub cleanup_tree {
    my $self = shift;
    unless( $self->nodelete ) {
        for my $node ($self->get_nodes(-order  => 'b', -sortby => 'none')) {
            $node->node_cleanup;
        }
    }
    $self->{'_rootnode'} = undef;
}

1;
}
General documentation
IMPLEMENTATION NOTETop
This implementation of Bio::Tree::Tree contains Bio::Tree:::NodeI; mainly linked
via the root node. As NodeI can potentially contain circular references (as
nodes will need to refer to both parent and child nodes), Bio::Tree::Tree will
remove those circular references when the object is garbage-collected. This has
some side effects; primarily, one must keep the Tree in scope or have at least
one reference to it if working with nodes. The fix is to count the references to
the nodes and if it is greater than expected retain all of them, but it requires
an additional prereq and thus may not be worth the effort. This only shows up
in minor edge cases, though (see Bug #2869).
Example of issue:
  # tree is not assigned to a variable, so passes from memory after
# root node is passed
my $root = Bio::TreeIO->new(-format => 'newick', -file => 'foo.txt')->next_tree
->get_root_node;
# gets nothing, as all Node links are broken when Tree is garbage-collected above my @descendents = $root->get_all_Descendents;
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
Support Top
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 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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
CONTRIBUTORSTop
Aaron Mackey amackey@virginia.edu
Sendu Bala bix@sendu.me.uk
Mark A. Jensen maj@fortinbras.us
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
heightTop
 Title   : height
Usage : my $height = $tree->height
Function: Gets the height of tree - this LOG_2($number_nodes)
WARNING: this is only true for strict binary trees. The TreeIO
system is capable of building non-binary trees, for which this
method will currently return an incorrect value!!
Returns : integer
Args : none
number_nodesTop
 Title   : number_nodes
Usage : my $size = $tree->number_nodes
Function: Returns the number of nodes in the tree
Returns : integer
Args : none
Methods for associating Tag/Values with a TreeTop
These methods associate tag/value pairs with a Tree