Bio::Tree
Tree
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Summary
Bio::Tree::Tree - An implementation of the TreeI interface.
Package variables
No package variables defined.
Inherit
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
Methods description
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 |
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 |
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 |
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 |
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 |
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 |
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 |
Title : id
Usage : my $id = $tree->id();
Function: An id value for the tree
Returns : scalar
Args : [optional] new value to set |
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) |
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. |
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 |
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 |
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 |
Title : remove_all_tags
Usage : $tree->remove_all_tags()
Function: Removes all tags
Returns : None
Args : None |
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 |
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 |
Title : has_tag
Usage : $tree->has_tag($tag)
Function: Boolean test if tag exists in the Tree
Returns : Boolean
Args : $tag - tagname |
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] $start_node, Bio::Tree::Node object |
Methods code
sub new
{ my ($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) || $node;
if ($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;} | sub nodelete
{ my $self = shift;
return $self->{'nodelete'} = shift if @_;
return $self->{'nodelete'};} | sub get_nodes
{ my ($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;} | sub get_root_node
{ my ($self) = @_;
return $self->{'_rootnode'};} | 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;} | sub total_branch_length
{ shift->subtree_length } | 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 $sum;} | sub id
{ my ($self, $val) = @_;
if ( defined $val ) {
$self->{'_treeid'} = $val;
}
return $self->{'_treeid'};} | sub score
{ my ($self, $val) = @_;
if ( defined $val ) {
$self->{'_score'} = $val;
}
return $self->{'_score'};
}
} | 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 );
$test->set_params($params_input);
$test->write_tree($self);
close($fh);
return $string;} | sub set_tag_value
{ my ($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'}->{$tag}};} | sub add_tag_value
{ my ($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'}->{$tag}};} | sub remove_tag
{ my ($self, $tag) = @_;
if ( exists $self->{'_tags'}->{$tag} ) {
$self->{'_tags'}->{$tag} = undef;
delete $self->{'_tags'}->{$tag};
return 1;
}
return 0;} | sub remove_all_tags
{ my ($self) = @_;
$self->{'_tags'} = {};
return;} | sub get_all_tags
{ my ($self) = @_;
my @tags = sort keys %{$self->{'_tags'} || {}};
return @tags;} | sub get_tag_values
{ my ($self, $tag) = @_;
return wantarray ? @{$self->{'_tags'}->{$tag} || []} :
(@{$self->{'_tags'}->{$tag} || []})[0];} | sub has_tag
{ my ($self, $tag) = @_;
return exists $self->{'_tags'}->{$tag};
}
} | 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;
}
} | 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
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;
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
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.
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 Stajich | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
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
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 Tree | Top |
These methods associate tag/value pairs with a Tree