Bio::Phylo::Forest::Node - Node in a phylogenetic tree
# some way to get nodes:
use Bio::Phylo::IO;
my $string = '((A,B),C);';
my $forest = Bio::Phylo::IO->parse(
-format => 'newick',
-string => $string
);
# prints 'Bio::Phylo::Forest'
print ref $forest;
foreach my $tree ( @{ $forest->get_entities } ) {
# prints 'Bio::Phylo::Forest::Tree'
print ref $tree;
foreach my $node ( @{ $tree->get_entities } ) {
# prints 'Bio::Phylo::Forest::Node'
print ref $node;
# node has a parent, i.e. is not root
if ( $node->get_parent ) {
$node->set_branch_length(1);
}
# node is root
else {
$node->set_branch_length(0);
}
}
}
This module defines a node object and its methods. The node is fairly syntactically rich in terms of navigation, and additional getters are provided to further ease navigation from node to node. Typical first daughter -> next sister traversal and recursion is possible, but there are also shrinkwrapped methods that return for example all terminal descendants of the focal node, or all internals, etc.
Node objects are inserted into tree objects, although technically the tree object is only a container holding all the nodes together. Unless there are orphans all nodes can be reached without recourse to the tree object.
Node constructor.
Type : Constructor
Title : new
Usage : my $node = Bio::Phylo::Forest::Node->new;
Function: Instantiates a Bio::Phylo::Forest::Node object
Returns : Bio::Phylo::Forest::Node
Args : All optional:
-parent => $parent,
-taxon => $taxon,
-branch_length => 0.423e+2,
-first_daughter => $f_daughter,
-last_daughter => $l_daughter,
-next_sister => $n_sister,
-previous_sister => $p_sister,
-name => 'node_name',
-desc => 'this is a node',
-score => 0.98,
-generic => {
-posterior => 0.98,
-bootstrap => 0.80
}
Node constructor from bioperl Bio::Tree::NodeI argument.
Type : Constructor
Title : new_from_bioperl
Usage : my $node =
Bio::Phylo::Forest::Node->new_from_bioperl(
$bpnode
);
Function: Instantiates a Bio::Phylo::Forest::Node object
from a bioperl node object.
Returns : Bio::Phylo::Forest::Node
Args : An objects that implements Bio::Tree::NodeI
Notes : The following BioPerl properties are copied:
BioPerl output: Bio::Phylo output:
------------------------------------------------
id get_name
branch_length get_branch_length
description get_desc
bootstrap get_generic('bootstrap')
In addition all BioPerl tags and values are copied
to set_generic( 'tag' => 'value' );
Sets argument as invocant's parent.
Type : Mutator Title : prune_child Usage : $parent->prune_child($child); Function: Removes $child (and its descendants) from $parent's children Returns : Modified object. Args : A valid argument is Bio::Phylo::Forest::Node object.
Collapse node.
Type : Mutator
Title : collapse
Usage : $node->collapse;
Function: Attaches invocant's children to invocant's parent.
Returns : Modified object.
Args : NONE
Comments: If defined, adds invocant's branch
length to that of its children. If
$node is in a tree, removes itself
from that tree.
Sets argument as invocant's parent.
Type : Mutator
Title : set_parent
Usage : $node->set_parent($parent);
Function: Assigns a node's parent.
Returns : Modified object.
Args : If no argument is given, the current
parent is set to undefined. A valid
argument is Bio::Phylo::Forest::Node
object.
Sets argument as invocant's first daughter.
Type : Mutator
Title : set_first_daughter
Usage : $node->set_first_daughter($f_daughter);
Function: Assigns a node's leftmost daughter.
Returns : Modified object.
Args : Undefines the first daughter if no
argument given. A valid argument is
a Bio::Phylo::Forest::Node object.
Sets argument as invocant's last daughter.
Type : Mutator
Title : set_last_daughter
Usage : $node->set_last_daughter($l_daughter);
Function: Assigns a node's rightmost daughter.
Returns : Modified object.
Args : A valid argument consists of a
Bio::Phylo::Forest::Node object. If
no argument is given, the value is
set to undefined.
Sets argument as invocant's previous sister.
Type : Mutator
Title : set_previous_sister
Usage : $node->set_previous_sister($p_sister);
Function: Assigns a node's previous sister (to the left).
Returns : Modified object.
Args : A valid argument consists of
a Bio::Phylo::Forest::Node object.
If no argument is given, the value
is set to undefined.
Sets argument as invocant's next sister.
Type : Mutator
Title : set_next_sister
Usage : $node->set_next_sister($n_sister);
Function: Assigns or retrieves a node's
next sister (to the right).
Returns : Modified object.
Args : A valid argument consists of a
Bio::Phylo::Forest::Node object.
If no argument is given, the
value is set to undefined.
Sets argument as invocant's child.
Type : Mutator
Title : set_child
Usage : $node->set_child($child);
Function: Assigns a new child to $node
Returns : Modified object.
Args : A valid argument consists of a
Bio::Phylo::Forest::Node object.
Sets argument as invocant's branch length.
Type : Mutator
Title : set_branch_length
Usage : $node->set_branch_length(0.423e+2);
Function: Assigns a node's branch length.
Returns : Modified object.
Args : If no argument is given, the
current branch length is set
to undefined. A valid argument
is a number in any of Perl's formats.
Sets new (unbranched) node below invocant.
Type : Mutator Title : set_node_below Usage : my $new_node = $node->set_node_below; Function: Creates a new node below $node Returns : New node if tree was modified, undef otherwise Args : NONE
Reroots below invocant.
Type : Mutator
Title : set_root_below
Usage : $node->set_root_below;
Function: Creates a new tree root below $node
Returns : New root if tree was modified, undef otherwise
Args : NONE
Comments: Implementation incomplete: returns spurious
results when $node is grandchild of current root.
Sets what tree invocant belongs to
Type : Mutator
Title : set_tree
Usage : $node->set_tree($tree);
Function: Sets what tree invocant belongs to
Returns : Invocant
Args : Bio::Phylo::Forest::Tree
Comments: This method is called automatically
when inserting or deleting nodes in
trees.
Gets invocant's parent.
Type : Accessor Title : get_parent Usage : my $parent = $node->get_parent; Function: Retrieves a node's parent. Returns : Bio::Phylo::Forest::Node Args : NONE
Gets invocant's first daughter.
Type : Accessor Title : get_first_daughter Usage : my $f_daughter = $node->get_first_daughter; Function: Retrieves a node's leftmost daughter. Returns : Bio::Phylo::Forest::Node Args : NONE
Gets invocant's last daughter.
Type : Accessor Title : get_last_daughter Usage : my $l_daughter = $node->get_last_daughter; Function: Retrieves a node's rightmost daughter. Returns : Bio::Phylo::Forest::Node Args : NONE
Gets invocant's previous sister.
Type : Accessor Title : get_previous_sister Usage : my $p_sister = $node->get_previous_sister; Function: Retrieves a node's previous sister (to the left). Returns : Bio::Phylo::Forest::Node Args : NONE
Gets invocant's next sister.
Type : Accessor Title : get_next_sister Usage : my $n_sister = $node->get_next_sister; Function: Retrieves a node's next sister (to the right). Returns : Bio::Phylo::Forest::Node Args : NONE
Gets invocant's branch length.
Type : Accessor
Title : get_branch_length
Usage : my $branch_length = $node->get_branch_length;
Function: Retrieves a node's branch length.
Returns : FLOAT
Args : NONE
Comments: Test for "defined($node->get_branch_length)"
for zero-length (but defined) branches. Testing
"if ( $node->get_branch_length ) { ... }"
yields false for zero-but-defined branches!
Gets invocant's ancestors.
Type : Query
Title : get_ancestors
Usage : my @ancestors = @{ $node->get_ancestors };
Function: Returns an array reference of ancestral nodes,
ordered from young to old (i.e. $ancestors[-1] is root).
Returns : Array reference of Bio::Phylo::Forest::Node
objects.
Args : NONE
Gets invocant's sisters.
Type : Query
Title : get_sisters
Usage : my @sisters = @{ $node->get_sisters };
Function: Returns an array reference of sisters,
ordered from left to right.
Returns : Array reference of
Bio::Phylo::Forest::Node objects.
Args : NONE
Gets invocant's immediate children.
Type : Query
Title : get_children
Usage : my @children = @{ $node->get_children };
Function: Returns an array reference of immediate
descendants, ordered from left to right.
Returns : Array reference of
Bio::Phylo::Forest::Node objects.
Args : NONE
Gets invocant's i'th child.
Type : Query
Title : get_child
Usage : my $child = $node->get_child($i);
Function: Returns the child at index $i
Returns : A Bio::Phylo::Forest::Node object.
Args : An index (integer) $i
Comments: if no index is specified, first
child is returned
Gets invocant's descendants.
Type : Query
Title : get_descendants
Usage : my @descendants = @{ $node->get_descendants };
Function: Returns an array reference of
descendants, recursively ordered
breadth first.
Returns : Array reference of
Bio::Phylo::Forest::Node objects.
Args : none.
Gets invocant's terminal descendants.
Type : Query
Title : get_terminals
Usage : my @terminals = @{ $node->get_terminals };
Function: Returns an array reference
of terminal descendants.
Returns : Array reference of
Bio::Phylo::Forest::Node objects.
Args : NONE
Gets invocant's internal descendants.
Type : Query
Title : get_internals
Usage : my @internals = @{ $node->get_internals };
Function: Returns an array reference
of internal descendants.
Returns : Array reference of
Bio::Phylo::Forest::Node objects.
Args : NONE
Gets invocant's most recent common ancestor shared with argument.
Type : Query
Title : get_mrca
Usage : my $mrca = $node->get_mrca($other_node);
Function: Returns the most recent common ancestor
of $node and $other_node.
Returns : Bio::Phylo::Forest::Node
Args : A Bio::Phylo::Forest::Node
object in the same tree.
Gets invocant's leftmost terminal descendant.
Type : Query
Title : get_leftmost_terminal
Usage : my $leftmost_terminal =
$node->get_leftmost_terminal;
Function: Returns the leftmost
terminal descendant of $node.
Returns : Bio::Phylo::Forest::Node
Args : NONE
Gets invocant's rightmost terminal descendant
Type : Query
Title : get_rightmost_terminal
Usage : my $rightmost_terminal =
$node->get_rightmost_terminal;
Function: Returns the rightmost
terminal descendant of $node.
Returns : Bio::Phylo::Forest::Node
Args : NONE
Returns the tree invocant belongs to
Type : Query Title : get_tree Usage : my $tree = $node->get_tree; Function: Returns the tree $node belongs to Returns : Bio::Phylo::Forest::Tree Args : NONE
Tests if invocant is a terminal node.
Type : Test
Title : is_terminal
Usage : if ( $node->is_terminal ) {
# do something
}
Function: Returns true if node has
no children (i.e. is terminal).
Returns : BOOLEAN
Args : NONE
Tests if invocant is an internal node.
Type : Test
Title : is_internal
Usage : if ( $node->is_internal ) {
# do something
}
Function: Returns true if node
has children (i.e. is internal).
Returns : BOOLEAN
Args : NONE
Tests if invocant is first sibling in left-to-right order.
Type : Test
Title : is_first
Usage : if ( $node->is_first ) {
# do something
}
Function: Returns true if first sibling
in left-to-right order.
Returns : BOOLEAN
Args : NONE
Tests if invocant is last sibling in left-to-right order.
Type : Test
Title : is_last
Usage : if ( $node->is_last ) {
# do something
}
Function: Returns true if last sibling
in left-to-right order.
Returns : BOOLEAN
Args : NONE
Tests if invocant is a root.
Type : Test
Title : is_root
Usage : if ( $node->is_root ) {
# do something
}
Function: Returns true if node is a root
Returns : BOOLEAN
Args : NONE
Tests if invocant is descendant of argument.
Type : Test
Title : is_descendant_of
Usage : if ( $node->is_descendant_of($grandparent) ) {
# do something
}
Function: Returns true if the node is
a descendant of the argument.
Returns : BOOLEAN
Args : putative ancestor - a
Bio::Phylo::Forest::Node object.
Tests if invocant is ancestor of argument.
Type : Test
Title : is_ancestor_of
Usage : if ( $node->is_ancestor_of($grandchild) ) {
# do something
}
Function: Returns true if the node
is an ancestor of the argument.
Returns : BOOLEAN
Args : putative descendant - a
Bio::Phylo::Forest::Node object.
Tests if invocant is sister of argument.
Type : Test
Title : is_sister_of
Usage : if ( $node->is_sister_of($sister) ) {
# do something
}
Function: Returns true if the node is
a sister of the argument.
Returns : BOOLEAN
Args : putative sister - a
Bio::Phylo::Forest::Node object.
Tests if invocant is child of argument.
Type : Test
Title : is_child_of
Usage : if ( $node->is_child_of($parent) ) {
# do something
}
Function: Returns true if the node is
a child of the argument.
Returns : BOOLEAN
Args : putative parent - a
Bio::Phylo::Forest::Node object.
Test if invocant is outgroup of argument nodes.
Type : Test
Title : is_outgroup_of
Usage : if ( $node->is_outgroup_of(\@ingroup) ) {
# do something
}
Function: Tests whether the set of
\@ingroup is monophyletic
with respect to the $node.
Returns : BOOLEAN
Args : A reference to an array of
Bio::Phylo::Forest::Node objects;
Comments: This method is essentially the same as
&Bio::Phylo::Forest::Tree::is_monophyletic.
Test if argument(s) can be a child/children of invocant.
Type : Test
Title : can_contain
Usage : if ( $parent->can_contain(@children) ) {
# do something
}
Function: Test if arguments can be children of invocant.
Returns : BOOLEAN
Args : An array of Bio::Phylo::Forest::Node objects;
Comments: This method is an override of
Bio::Phylo::Listable::can_contain. Since node
objects hold a list of their children, they
inherit from the listable class and so they
need to be able to validate the contents
of that list before they are inserted.
Calculates path to root.
Type : Calculation
Title : calc_path_to_root
Usage : my $path_to_root =
$node->calc_path_to_root;
Function: Returns the sum of branch
lengths from $node to the root.
Returns : FLOAT
Args : NONE
Calculates number of nodes to root.
Type : Calculation
Title : calc_nodes_to_root
Usage : my $nodes_to_root =
$node->calc_nodes_to_root;
Function: Returns the number of nodes
from $node to the root.
Returns : INT
Args : NONE
Calculates maximum number of nodes to tips.
Type : Calculation
Title : calc_max_nodes_to_tips
Usage : my $max_nodes_to_tips =
$node->calc_max_nodes_to_tips;
Function: Returns the maximum number
of nodes from $node to tips.
Returns : INT
Args : NONE
Calculates minimum number of nodes to tips.
Type : Calculation
Title : calc_min_nodes_to_tips
Usage : my $min_nodes_to_tips =
$node->calc_min_nodes_to_tips;
Function: Returns the minimum number of
nodes from $node to tips.
Returns : INT
Args : NONE
Calculates longest path to tips.
Type : Calculation
Title : calc_max_path_to_tips
Usage : my $max_path_to_tips =
$node->calc_max_path_to_tips;
Function: Returns the path length from
$node to the tallest tip.
Returns : FLOAT
Args : NONE
Calculates shortest path to tips.
Type : Calculation
Title : calc_min_path_to_tips
Usage : my $min_path_to_tips =
$node->calc_min_path_to_tips;
Function: Returns the path length from
$node to the shortest tip.
Returns : FLOAT
Args : NONE
Calculates patristic distance between invocant and argument.
Type : Calculation
Title : calc_patristic_distance
Usage : my $patristic_distance =
$node->calc_patristic_distance($other_node);
Function: Returns the patristic distance
between $node and $other_node.
Returns : FLOAT
Args : Bio::Phylo::Forest::Node
Calculates node distance between invocant and argument.
Type : Calculation
Title : calc_nodal_distance
Usage : my $nodal_distance =
$node->calc_nodal_distance($other_node);
Function: Returns the number of nodes
between $node and $other_node.
Returns : INT
Args : Bio::Phylo::Forest::Node
The methods below are similar in spirit to those by the same name in Bio::Phylo::Forest::Tree, except those in the tree class operate from the tree root, and those in this node class operate on an invocant node, and so these process a subtree.
Visits nodes depth first
Type : Visitor method
Title : visit_depth_first
Usage : $tree->visit_depth_first( -pre => sub{ ... }, -post => sub { ... } );
Function: Visits nodes in a depth first traversal, executes subs
Returns : $tree
Args : Optional:
# first event handler, is executed when node is reached in recursion
-pre => sub { print "pre: ", shift->get_name, "\n" },
# is executed if node has a daughter, but before that daughter is processed
-pre_daughter => sub { print "pre_daughter: ", shift->get_name, "\n" },
# is executed if node has a daughter, after daughter has been processed
-post_daughter => sub { print "post_daughter: ", shift->get_name, "\n" },
# is executed if node has no daughter
-no_daughter => sub { print "no_daughter: ", shift->get_name, "\n" },
# is executed whether or not node has sisters, if it does have sisters
# they're processed first
-in => sub { print "in: ", shift->get_name, "\n" },
# is executed if node has a sister, before sister is processed
-pre_sister => sub { print "pre_sister: ", shift->get_name, "\n" },
# is executed if node has a sister, after sister is processed
-post_sister => sub { print "post_sister: ", shift->get_name, "\n" },
# is executed if node has no sister
-no_sister => sub { print "no_sister: ", shift->get_name, "\n" },
# is executed last
-post => sub { print "post: ", shift->get_name, "\n" },
# specifies traversal order, default 'ltr' means first_daugher -> next_sister
# traversal, alternate value 'rtl' means last_daughter -> previous_sister traversal
-order => 'ltr', # ltr = left-to-right, 'rtl' = right-to-left
Comments:
Visits nodes breadth first
Type : Visitor method
Title : visit_breadth_first
Usage : $tree->visit_breadth_first( -pre => sub{ ... }, -post => sub { ... } );
Function: Visits nodes in a breadth first traversal, executes handlers
Returns : $tree
Args : Optional handlers in the order in which they would be executed on an internal node:
# first event handler, is executed when node is reached in recursion
-pre => sub { print "pre: ", shift->get_name, "\n" },
# is executed if node has a sister, before sister is processed
-pre_sister => sub { print "pre_sister: ", shift->get_name, "\n" },
# is executed if node has a sister, after sister is processed
-post_sister => sub { print "post_sister: ", shift->get_name, "\n" },
# is executed if node has no sister
-no_sister => sub { print "no_sister: ", shift->get_name, "\n" },
# is executed whether or not node has sisters, if it does have sisters
# they're processed first
-in => sub { print "in: ", shift->get_name, "\n" },
# is executed if node has a daughter, but before that daughter is processed
-pre_daughter => sub { print "pre_daughter: ", shift->get_name, "\n" },
# is executed if node has a daughter, after daughter has been processed
-post_daughter => sub { print "post_daughter: ", shift->get_name, "\n" },
# is executed if node has no daughter
-no_daughter => sub { print "no_daughter: ", shift->get_name, "\n" },
# is executed last
-post => sub { print "post: ", shift->get_name, "\n" },
# specifies traversal order, default 'ltr' means first_daugher -> next_sister
# traversal, alternate value 'rtl' means last_daughter -> previous_sister traversal
-order => 'ltr', # ltr = left-to-right, 'rtl' = right-to-left
Comments:
Visits nodes in a level order traversal.
Type : Visitor method
Title : visit_level_order
Usage : $tree->visit_level_order( sub{...} );
Function: Visits nodes in a level order traversal, executes sub
Returns : $tree
Args : A subroutine reference that operates on visited nodes.
Comments:
Clones invocant.
Type : Utility method
Title : clone
Usage : my $clone = $object->clone;
Function: Creates a copy of the invocant object.
Returns : A copy of the invocant.
Args : Optional: a hash of code references to
override reflection-based getter/setter copying
my $clone = $object->clone(
'set_forest' => sub {
my ( $self, $clone ) = @_;
for my $forest ( @{ $self->get_forests } ) {
$clone->set_forest( $forest );
}
},
'set_matrix' => sub {
my ( $self, $clone ) = @_;
for my $matrix ( @{ $self->get_matrices } ) {
$clone->set_matrix( $matrix );
}
);
Comments: Cloning is currently experimental, use with caution.
It works on the assumption that the output of get_foo
called on the invocant is to be provided as argument
to set_foo on the clone - such as
$clone->set_name( $self->get_name ). Sometimes this
doesn't work, for example where this symmetry doesn't
exist, or where the return value of get_foo isn't valid
input for set_foo. If such a copy fails, a warning is
emitted. To make sure all relevant attributes are copied
into the clone, additional code references can be
provided, as in the example above. Typically, this is
done by overrides of this method in child classes.
Serializes object to JSON string
Type : Serializer Title : to_json() Usage : print $obj->to_json(); Function: Serializes object to JSON string Returns : String Args : None Comments:
Serializes invocant to xml.
Type : Serializer Title : to_xml Usage : my $xml = $obj->to_xml; Function: Turns the invocant object (and its descendants )into an XML string. Returns : SCALAR Args : NONE
Serializes subtree subtended by invocant to newick string.
Type : Serializer Title : to_newick Usage : my $newick = $obj->to_newick; Function: Turns the invocant object into a newick string. Returns : SCALAR Args : takes same arguments as Bio::Phylo::Unparsers::Newick Comments: takes same arguments as Bio::Phylo::Unparsers::Newick
Bio::Phylo::Forest::Node inherits from one or more superclasses. This means that objects of class Bio::Phylo::Forest::Node also "do" the methods from the superclasses in addition to the ones implemented in this class. Below is the documentation for those additional methods, organized by superclass.
Bio::Phylo::Forest::Node inherits from superclass Bio::Phylo::Taxa::TaxonLinker. Below are the public methods (if any) from this superclass.
Retrieves the Bio::Phylo::Taxa::Taxon object linked to the invocant.
Type : Accessor
Title : get_taxon
Usage : my $taxon = $obj->get_taxon;
Function: Retrieves the Bio::Phylo::Taxa::Taxon
object linked to the invocant.
Returns : Bio::Phylo::Taxa::Taxon
Args : NONE
Comments:
Links the invocant object to a taxon object.
Type : Mutator
Title : set_taxon
Usage : $obj->set_taxon( $taxon );
Function: Links the invocant object
to a taxon object.
Returns : Modified $obj
Args : A Bio::Phylo::Taxa::Taxon object.
Unlinks the invocant object from any taxon object.
Type : Mutator
Title : unset_taxon
Usage : $obj->unset_taxon();
Function: Unlinks the invocant object
from any taxon object.
Returns : Modified $obj
Args : NONE
Bio::Phylo::Forest::Node inherits from superclass Bio::Phylo::Listable. Below are the public methods (if any) from this superclass.
Type : Mutator Title : add_set Usage : $obj->add_set($set) Function: Associates a Bio::Phylo::Set object with the invocant Returns : Invocant Args : A Bio::Phylo::Set object
Type : Mutator
Title : add_to_set
Usage : $listable->add_to_set($obj,$set);
Function: Adds first argument to the second argument
Returns : Invocant
Args : $obj - an object to add to $set
$set - the Bio::Phylo::Set object to add to
Notes : this method assumes that $obj is already
part of the invocant. If that assumption is
violated a warning message is printed.
Tests if argument can be inserted in invocant.
Type : Test Title : can_contain Usage : &do_something if $listable->can_contain( $obj ); Function: Tests if $obj can be inserted in $listable Returns : BOOL Args : An $obj to test
Empties container object.
Type : Object method Title : clear Usage : $obj->clear(); Function: Clears the container. Returns : A Bio::Phylo::Listable object. Args : Note. Note :
Clones invocant.
Type : Utility method Title : clone Usage : my $clone = $object->clone; Function: Creates a copy of the invocant object. Returns : A copy of the invocant. Args : None. Comments: Cloning is currently experimental, use with caution.
Tests whether the invocant object contains the argument object.
Type : Test
Title : contains
Usage : if ( $obj->contains( $other_obj ) ) {
# do something
}
Function: Tests whether the invocant object
contains the argument object
Returns : BOOLEAN
Args : A Bio::Phylo::* object
The cross_reference method links node and datum objects to the taxa they apply to. After crossreferencing a matrix with a taxa object, every datum object has a reference to a taxon object stored in its $datum->get_taxon field, and every taxon object has a list of references to datum objects stored in its $taxon->get_data field.
Type : Generic method
Title : cross_reference
Usage : $obj->cross_reference($taxa);
Function: Crossreferences the entities
in the invocant with names
in $taxa
Returns : string
Args : A Bio::Phylo::Taxa object
Comments:
Returns the current focal element of the listable object.
Type : Iterator
Title : current
Usage : my $current_obj = $obj->current;
Function: Retrieves the current focal
entity in the invocant.
Returns : A Bio::Phylo::* object
Args : none.
Returns the current internal index of the invocant.
Type : Generic query
Title : current_index
Usage : my $last_index = $obj->current_index;
Function: Returns the current internal
index of the invocant.
Returns : An integer
Args : none.
Deletes argument from invocant object.
Type : Object method
Title : delete
Usage : $obj->delete($other_obj);
Function: Deletes an object from its container.
Returns : A Bio::Phylo::Listable object.
Args : A Bio::Phylo::* object.
Note : Be careful with this method: deleting
a node from a tree like this will
result in undefined references in its
neighbouring nodes. Its children will
have their parent reference become
undef (instead of pointing to their
grandparent, as collapsing a node would
do). The same is true for taxon objects
that reference datum objects: if the
datum object is deleted from a matrix
(say), the taxon will now hold undefined
references.
Jumps to the first element contained by the listable object.
Type : Iterator
Title : first
Usage : my $first_obj = $obj->first;
Function: Retrieves the first
entity in the invocant.
Returns : A Bio::Phylo::* object
Args : none.
Gets element defined by argument index from invocant container.
Type : Query
Title : get_by_index
Usage : my $contained_obj = $obj->get_by_index($i);
Function: Retrieves the i'th entity
from a listable object.
Returns : An entity stored by a listable
object (or array ref for slices).
Args : An index or range. This works
the way you dereference any perl
array including through slices,
i.e. $obj->get_by_index(0 .. 10)>
$obj->get_by_index(0, -1)
and so on.
Comments: Throws if out-of-bounds
Gets first element that has argument name
Type : Visitor predicate
Title : get_by_name
Usage : my $found = $obj->get_by_name('foo');
Function: Retrieves the first contained object
in the current Bio::Phylo::Listable
object whose name is 'foo'
Returns : A Bio::Phylo::* object.
Args : A name (string)
Gets elements that match regular expression from invocant container.
Type : Visitor predicate
Title : get_by_regular_expression
Usage : my @objects = @{
$obj->get_by_regular_expression(
-value => $method,
-match => $re
) };
Function: Retrieves the data in the
current Bio::Phylo::Listable
object whose $method output
matches $re
Returns : A list of Bio::Phylo::* objects.
Args : -value => any of the string
datum props (e.g. 'get_type')
-match => a compiled regular
expression (e.g. qr/^[D|R]NA$/)
Gets elements that meet numerical rule from invocant container.
Type : Visitor predicate
Title : get_by_value
Usage : my @objects = @{ $obj->get_by_value(
-value => $method,
-ge => $number
) };
Function: Iterates through all objects
contained by $obj and returns
those for which the output of
$method (e.g. get_tree_length)
is less than (-lt), less than
or equal to (-le), equal to
(-eq), greater than or equal to
(-ge), or greater than (-gt) $number.
Returns : A reference to an array of objects
Args : -value => any of the numerical
obj data (e.g. tree length)
-lt => less than
-le => less than or equals
-eq => equals
-ge => greater than or equals
-gt => greater than
Returns a reference to an array of objects contained by the listable object.
Type : Generic query
Title : get_entities
Usage : my @entities = @{ $obj->get_entities };
Function: Retrieves all entities in the invocant.
Returns : A reference to a list of Bio::Phylo::*
objects.
Args : none.
Returns the index of the argument in the list, or undef if the list doesn't contain the argument
Type : Generic query
Title : get_index_of
Usage : my $i = $listable->get_index_of($obj)
Function: Returns the index of the argument in the list,
or undef if the list doesn't contain the argument
Returns : An index or undef
Args : A contained object
Gets a logger object.
Type : Accessor Title : get_logger Usage : my $logger = $obj->get_logger; Function: Returns a Bio::Phylo::Util::Logger object Returns : Bio::Phylo::Util::Logger Args : None
Type : Accessor
Title : get_sets
Usage : my @sets = @{ $obj->get_sets() };
Function: Retrieves all associated Bio::Phylo::Set objects
Returns : Invocant
Args : None
Pushes an object into its container.
Type : Object method Title : insert Usage : $obj->insert($other_obj); Function: Pushes an object into its container. Returns : A Bio::Phylo::Listable object. Args : A Bio::Phylo::* object.
Inserts argument object in invocant container at argument index.
Type : Object method Title : insert_at_index Usage : $obj->insert_at_index($other_obj, $i); Function: Inserts $other_obj at index $i in container $obj Returns : A Bio::Phylo::Listable object. Args : A Bio::Phylo::* object.
Type : Test
Title : is_in_set
Usage : @do_something if $listable->is_in_set($obj,$set);
Function: Returns whether or not the first argument is listed in the second argument
Returns : Boolean
Args : $obj - an object that may, or may not be in $set
$set - the Bio::Phylo::Set object to query
Notes : This method makes two assumptions:
i) the $set object is associated with the invocant,
i.e. add_set($set) has been called previously
ii) the $obj object is part of the invocant
If either assumption is violated a warning message
is printed.
Jumps to the last element contained by the listable object.
Type : Iterator
Title : last
Usage : my $last_obj = $obj->last;
Function: Retrieves the last
entity in the invocant.
Returns : A Bio::Phylo::* object
Args : none.
Returns the highest valid index of the invocant.
Type : Generic query
Title : last_index
Usage : my $last_index = $obj->last_index;
Function: Returns the highest valid
index of the invocant.
Returns : An integer
Args : none.
Returns the next focal element of the listable object.
Type : Iterator
Title : next
Usage : my $next_obj = $obj->next;
Function: Retrieves the next focal
entity in the invocant.
Returns : A Bio::Phylo::* object
Args : none.
Notifies listeners of changed contents.
Type : Utility method Title : notify_listeners Usage : $object->notify_listeners; Function: Notifies listeners of changed contents. Returns : Invocant. Args : NONE. Comments:
Returns the previous element of the listable object.
Type : Iterator
Title : previous
Usage : my $previous_obj = $obj->previous;
Function: Retrieves the previous
focal entity in the invocant.
Returns : A Bio::Phylo::* object
Args : none.
Type : Mutator
Title : remove_from_set
Usage : $listable->remove_from_set($obj,$set);
Function: Removes first argument from the second argument
Returns : Invocant
Args : $obj - an object to remove from $set
$set - the Bio::Phylo::Set object to remove from
Notes : this method assumes that $obj is already
part of the invocant. If that assumption is
violated a warning message is printed.
Type : Mutator Title : remove_set Usage : $obj->remove_set($set) Function: Removes association between a Bio::Phylo::Set object and the invocant Returns : Invocant Args : A Bio::Phylo::Set object
Attaches a listener (code ref) which is executed when contents change.
Type : Utility method
Title : set_listener
Usage : $object->set_listener( sub { my $object = shift; } );
Function: Attaches a listener (code ref) which is executed when contents change.
Returns : Invocant.
Args : A code reference.
Comments: When executed, the code reference will receive $object
(the invocant) as its first argument.
Iterates over objects contained by invocant, executes argument code reference on each.
Type : Visitor predicate
Title : visit
Usage : $obj->visit(
sub{ print $_[0]->get_name, "\n" }
);
Function: Implements visitor pattern
using code reference.
Returns : The invocant, possibly modified.
Args : a CODE reference.
Bio::Phylo::Forest::Node inherits from superclass Bio::Phylo::Util::XMLWritable. Below are the public methods (if any) from this superclass.
Type : Mutator Title : add_dictionary Usage : $obj->add_dictionary($dict); Function: Adds a dictionary attachment to the object Returns : $self Args : Bio::Phylo::Dictionary
Retrieves attributes for the element.
Type : Accessor
Title : get_attributes
Usage : my %attrs = %{ $obj->get_attributes };
Function: Gets the xml attributes for the object;
Returns : A hash reference
Args : None.
Comments: throws ObjectMismatch if no linked taxa object
can be found
Retrieves the dictionaries for the element.
Type : Accessor
Title : get_dictionaries
Usage : my @dicts = @{ $obj->get_dictionaries };
Function: Retrieves the dictionaries for the element.
Returns : An array ref of Bio::Phylo::Dictionary objects
Args : None.
Type : Accessor
Title : get_namespaces
Usage : my %ns = %{ $obj->get_namespaces };
Function: Retrieves the known namespaces
Returns : A hash of prefix/namespace key/value pairs, or
a single namespace if a single, optional
prefix was provided as argument
Args : Optional - a namespace prefix
Retrieves tag name for the element.
Type : Accessor Title : get_tag Usage : my $tag = $obj->get_tag; Function: Gets the xml tag name for the object; Returns : A tag name Args : None.
Retrieves xml id for the element.
Type : Accessor Title : get_xml_id Usage : my $id = $obj->get_xml_id; Function: Gets the xml id for the object; Returns : An xml id Args : None.
Retrieves tag string
Type : Accessor Title : get_xml_tag Usage : my $str = $obj->get_xml_tag; Function: Gets the xml tag for the object; Returns : A tag, i.e. pointy brackets Args : Optional: a true value, to close an empty tag
By default, all XMLWritable objects are identifiable when serialized, i.e. they have a unique id attribute. However, in some cases a serialized object may not have an id attribute (governed by the nexml schema). This method indicates whether that is the case.
Type : Test
Title : is_identifiable
Usage : if ( $obj->is_identifiable ) { ... }
Function: Indicates whether IDs are generated
Returns : BOOLEAN
Args : NONE
Type : Mutator Title : remove_dictionary Usage : $obj->remove_dictionary($dict); Function: Removes a dictionary attachment from the object Returns : $self Args : Bio::Phylo::Dictionary
Assigns attributes for the element.
Type : Mutator Title : set_attributes Usage : $obj->set_attributes( 'foo' => 'bar' ) Function: Sets the xml attributes for the object; Returns : $self Args : key/value pairs or a hash ref
By default, all XMLWritable objects are identifiable when serialized, i.e. they have a unique id attribute. However, in some cases a serialized object may not have an id attribute (governed by the nexml schema). For such objects, id generation can be explicitly disabled using this method. Typically, this is done internally - you will probably never use this method.
Type : Mutator Title : set_identifiable Usage : $obj->set_tag(0); Function: Enables/disables id generation Returns : $self Args : BOOLEAN
Type : Mutator Title : set_namespaces Usage : $obj->set_namespaces( 'dwc' => 'http://www.namespaceTBD.org/darwin2' ); Function: Adds one or more prefix/namespace pairs Returns : $self Args : One or more prefix/namespace pairs, as even-sized list, or as a hash reference, i.e.: $obj->set_namespaces( 'dwc' => 'http://www.namespaceTBD.org/darwin2' ); or $obj->set_namespaces( { 'dwc' => 'http://www.namespaceTBD.org/darwin2' } ); Notes : This is a global for the XMLWritable class, so that in a recursive to_xml call the outermost element contains the namespace definitions. This method can also be called as a static class method, i.e. Bio::Phylo::Util::XMLWritable->set_namespaces( 'dwc' => 'http://www.namespaceTBD.org/darwin2');
This method is usually only used internally, to define or alter the name of the tag into which the object is serialized. For example, for a Bio::Phylo::Forest::Node object, this method would be called with the 'node' argument, so that the object is serialized into an xml element structure called <node/>
Type : Mutator
Title : set_tag
Usage : $obj->set_tag('node');
Function: Sets the tag name
Returns : $self
Args : A tag name (must be a valid xml element name)
This method is usually only used internally, to store the xml id of an object as it is parsed out of a nexml file - this is for the purpose of round-tripping nexml info sets.
Type : Mutator
Title : set_xml_id
Usage : $obj->set_xml_id('node345');
Function: Sets the xml id
Returns : $self
Args : An xml id (must be a valid xml NCName)
Serializes invocant to XML.
Type : XML serializer Title : to_xml Usage : my $xml = $obj->to_xml; Function: Serializes $obj to xml Returns : An xml string Args : None
Bio::Phylo::Forest::Node inherits from superclass Bio::Phylo. Below are the public methods (if any) from this superclass.
Clones invocant.
Type : Utility method Title : clone Usage : my $clone = $object->clone; Function: Creates a copy of the invocant object. Returns : A copy of the invocant. Args : None. Comments: Cloning is currently experimental, use with caution.
Attempts to execute argument string as method on invocant.
Type : Accessor
Title : get
Usage : my $treename = $tree->get('get_name');
Function: Alternative syntax for safely accessing
any of the object data; useful for
interpolating runtime $vars.
Returns : (context dependent)
Args : a SCALAR variable, e.g. $var = 'get_name';
Gets invocant description.
Type : Accessor Title : get_desc Usage : my $desc = $obj->get_desc; Function: Returns the object's description (if any). Returns : A string Args : None
Gets generic hashref or hash value(s).
Type : Accessor
Title : get_generic
Usage : my $value = $obj->get_generic($key);
or
my %hash = %{ $obj->get_generic() };
Function: Returns the object's generic data. If an
argument is used, it is considered a key
for which the associated value is returned.
Without arguments, a reference to the whole
hash is returned.
Returns : A string or hash reference.
Args : None
Gets invocant's UID.
Type : Accessor Title : get_id Usage : my $id = $obj->get_id; Function: Returns the object's unique ID Returns : INT Args : None
Gets invocant's 'fallback' name (possibly autogenerated).
Type : Accessor
Title : get_internal_name
Usage : my $name = $obj->get_internal_name;
Function: Returns the object's name (if none was set, the name
is a combination of the $obj's class and its UID).
Returns : A string
Args : None
Gets a logger object.
Type : Accessor Title : get_logger Usage : my $logger = $obj->get_logger; Function: Returns a Bio::Phylo::Util::Logger object Returns : Bio::Phylo::Util::Logger Args : None
Gets invocant's name.
Type : Accessor Title : get_name Usage : my $name = $obj->get_name; Function: Returns the object's name. Returns : A string Args : None
Attempts to fetch an in-memory object by its UID
Type : Accessor Title : get_obj_by_id Usage : my $obj = Bio::Phylo->get_obj_by_id($uid); Function: Fetches an object from the IDPool cache Returns : A Bio::Phylo object Args : A unique id
Gets invocant's score.
Type : Accessor Title : get_score Usage : my $score = $obj->get_score; Function: Returns the object's numerical score (if any). Returns : A number Args : None
The Bio::Phylo root constructor, is rarely used directly. Rather, many other objects in Bio::Phylo internally go up the inheritance tree to this constructor. The arguments shown here can therefore also be passed to any of the child classes' constructors, which will pass them on up the inheritance tree. Generally, constructors in Bio::Phylo subclasses can process as arguments all methods that have set_* in their names. The arguments are named for the methods, but "set_" has been replaced with a dash "-", e.g. the method "set_name" becomes the argument "-name" in the constructor.
Type : Constructor
Title : new
Usage : my $phylo = Bio::Phylo->new;
Function: Instantiates Bio::Phylo object
Returns : a Bio::Phylo object
Args : Optional, any number of setters. For example,
Bio::Phylo->new( -name => $name )
will call set_name( $name ) internally
Sets invocant description.
Type : Mutator Title : set_desc Usage : $obj->set_desc($desc); Function: Assigns an object's description. Returns : Modified object. Args : Argument must be a string.
Sets generic key/value pair(s).
Type : Mutator
Title : set_generic
Usage : $obj->set_generic( %generic );
Function: Assigns generic key/value pairs to the invocant.
Returns : Modified object.
Args : Valid arguments constitute:
* key/value pairs, for example:
$obj->set_generic( '-lnl' => 0.87565 );
* or a hash ref, for example:
$obj->set_generic( { '-lnl' => 0.87565 } );
* or nothing, to reset the stored hash, e.g.
$obj->set_generic( );
Sets invocant name.
Type : Mutator
Title : set_name
Usage : $obj->set_name($name);
Function: Assigns an object's name.
Returns : Modified object.
Args : Argument must be a string, will be single
quoted if it contains [;|,|:\(|\)]
or spaces. Preceding and trailing spaces
will be removed.
Sets invocant score.
Type : Mutator
Title : set_score
Usage : $obj->set_score($score);
Function: Assigns an object's numerical score.
Returns : Modified object.
Args : Argument must be any of
perl's number formats, or undefined
to reset score.
Serializes object to JSON string
Type : Serializer Title : to_json() Usage : print $obj->to_json(); Function: Serializes object to JSON string Returns : String Args : None Comments:
Serializes object to general purpose string
Type : Serializer Title : to_string() Usage : print $obj->to_string(); Function: Serializes object to general purpose string Returns : String Args : None Comments: This is YAML
This object inherits from Bio::Phylo::Taxa::TaxonLinker, so methods defined there are also applicable here.
This object inherits from Bio::Phylo::Listable, so methods defined there are also applicable here.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
$Id: Node.pm 844 2009-03-05 00:07:26Z rvos $
