Bio::Phylo::Forest::Tree - Phylogenetic tree
# some way to get a tree
use Bio::Phylo::IO;
my $string = '((A,B),C);';
my $forest = Bio::Phylo::IO->parse(
-format => 'newick',
-string => $string
);
my $tree = $forest->first;
# do something:
print $tree->calc_imbalance;
# prints "1"
The object models a phylogenetic tree, a container of Bio::Phylo::Forest::Node objects. The tree object inherits from Bio::Phylo::Listable, so look there for more methods.
Tree constructor.
Type : Constructor Title : new Usage : my $tree = Bio::Phylo::Forest::Tree->new; Function: Instantiates a Bio::Phylo::Forest::Tree object. Returns : A Bio::Phylo::Forest::Tree object. Args : No required arguments.
Tree constructor from Bio::Tree::TreeI argument.
Type : Constructor
Title : new_from_bioperl
Usage : my $tree =
Bio::Phylo::Forest::Tree->new_from_bioperl(
$bptree
);
Function: Instantiates a
Bio::Phylo::Forest::Tree object.
Returns : A Bio::Phylo::Forest::Tree object.
Args : A tree that implements Bio::Tree::TreeI
Sets tree to be interpreted as unrooted.
Type : Mutator
Title : set_as_unrooted
Usage : $tree->set_as_unrooted;
Function: Sets tree to be interpreted as unrooted.
Returns : $tree
Args : NONE
Comments: This is a flag to indicate that the invocant
is interpreted to be unrooted (regardless of
topology). The object is otherwise unaltered,
this method is only here to capture things such
as the [&U] token in nexus files.
Sets tree to be the default tree in a forest
Type : Mutator
Title : set_as_default
Usage : $tree->set_as_default;
Function: Sets tree to be default tree in forest
Returns : $tree
Args : NONE
Comments: This is a flag to indicate that the invocant
is the default tree in a forest, i.e. to
capture the '*' token in nexus files.
Sets tree to NOT be the default tree in a forest
Type : Mutator
Title : set_not_default
Usage : $tree->set_not_default;
Function: Sets tree to not be default tree in forest
Returns : $tree
Args : NONE
Comments: This is a flag to indicate that the invocant
is the default tree in a forest, i.e. to
capture the '*' token in nexus files.
Get terminal nodes.
Type : Query
Title : get_terminals
Usage : my @terminals = @{ $tree->get_terminals };
Function: Retrieves all terminal nodes in
the Bio::Phylo::Forest::Tree object.
Returns : An array reference of
Bio::Phylo::Forest::Node objects.
Args : NONE
Comments: If the tree is valid, this method
retrieves the same set of nodes as
$node->get_terminals($root). However,
because there is no recursion it may
be faster. Also, the node method by
the same name does not see orphans.
Get internal nodes.
Type : Query
Title : get_internals
Usage : my @internals = @{ $tree->get_internals };
Function: Retrieves all internal nodes
in the Bio::Phylo::Forest::Tree object.
Returns : An array reference of
Bio::Phylo::Forest::Node objects.
Args : NONE
Comments: If the tree is valid, this method
retrieves the same set of nodes as
$node->get_internals($root). However,
because there is no recursion it may
be faster. Also, the node method by
the same name does not see orphans.
Get root node.
Type : Query
Title : get_root
Usage : my $root = $tree->get_root;
Function: Retrieves the first orphan in
the current Bio::Phylo::Forest::Tree
object - which should be the root.
Returns : Bio::Phylo::Forest::Node
Args : NONE
Retrieves the node furthest from the root.
Type : Query
Title : get_tallest_tip
Usage : my $tip = $tree->get_tallest_tip;
Function: Retrieves the node furthest from the
root in the current Bio::Phylo::Forest::Tree
object.
Returns : Bio::Phylo::Forest::Node
Args : NONE
Comments: If the tree has branch lengths, the tallest tip is
based on root-to-tip path length, else it is based
on number of nodes to root
Get most recent common ancestor of argument nodes.
Type : Query
Title : get_mrca
Usage : my $mrca = $tree->get_mrca(\@nodes);
Function: Retrieves the most recent
common ancestor of \@nodes
Returns : Bio::Phylo::Forest::Node
Args : A reference to an array of
Bio::Phylo::Forest::Node objects
in $tree.
Test if tree is default tree.
Type : Test
Title : is_default
Usage : if ( $tree->is_default ) {
# do something
}
Function: Tests whether the invocant
object is the default tree in the forest.
Returns : BOOLEAN
Args : NONE
Test if tree is rooted.
Type : Test
Title : is_rooted
Usage : if ( $tree->is_rooted ) {
# do something
}
Function: Tests whether the invocant
object is rooted.
Returns : BOOLEAN
Args : NONE
Comments: A tree is considered unrooted if:
- set_as_unrooted has been set, or
- the basal split is a polytomy
Test if tree is bifurcating.
Type : Test
Title : is_binary
Usage : if ( $tree->is_binary ) {
# do something
}
Function: Tests whether the invocant
object is bifurcating.
Returns : BOOLEAN
Args : NONE
Test if tree is ultrametric.
Type : Test
Title : is_ultrametric
Usage : if ( $tree->is_ultrametric(0.01) ) {
# do something
}
Function: Tests whether the invocant is
ultrametric.
Returns : BOOLEAN
Args : Optional margin between pairwise
comparisons (default = 0).
Comments: The test is done by performing
all pairwise comparisons for
root-to-tip path lengths. Since many
programs introduce rounding errors
in branch lengths the optional argument is
available to test TRUE for nearly
ultrametric trees. For example, a value
of 0.01 indicates that no pairwise
comparison may differ by more than 1%.
Note: behaviour is undefined for
negative branch lengths.
Tests if first argument (node array ref) is monophyletic with respect to second argument.
Type : Test
Title : is_monophyletic
Usage : if ( $tree->is_monophyletic(\@tips, $node) ) {
# do something
}
Function: Tests whether the set of \@tips is
monophyletic w.r.t. $outgroup.
Returns : BOOLEAN
Args : A reference to a list of nodes, and a node.
Comments: This method is essentially the
same as
&Bio::Phylo::Forest::Node::is_outgroup_of.
Type : Test
Title : is_paraphyletic
Usage : if ( $tree->is_paraphyletic(\@nodes,$node) ){ }
Function: Tests whether or not a given set of nodes are paraphyletic
(representing the full clade) given an outgroup
Returns : [-1,0,1] , -1 if the group is not monophyletic
0 if the group is not paraphyletic
1 if the group is paraphyletic
Args : Array ref of node objects which are in the tree,
Outgroup to compare the nodes to
Tests if argument (node array ref) forms a clade.
Type : Test
Title : is_clade
Usage : if ( $tree->is_clade(\@tips) ) {
# do something
}
Function: Tests whether the set of
\@tips forms a clade
Returns : BOOLEAN
Args : A reference to an array of
Bio::Phylo::Forest::Node objects.
Comments:
Tests if tree is a cladogram (i.e. no branch lengths)
Type : Test
Title : is_cladogram
Usage : if ( $tree->is_cladogram() ) {
# do something
}
Function: Tests whether the tree is a
cladogram (i.e. no branch lengths)
Returns : BOOLEAN
Args : NONE
Comments:
Calculates the sum of all branch lengths.
Type : Calculation
Title : calc_tree_length
Usage : my $tree_length =
$tree->calc_tree_length;
Function: Calculates the sum of all branch
lengths (i.e. the tree length).
Returns : FLOAT
Args : NONE
Calculates the height of the tree.
Type : Calculation
Title : calc_tree_height
Usage : my $tree_height =
$tree->calc_tree_height;
Function: Calculates the height
of the tree.
Returns : FLOAT
Args : NONE
Comments: For ultrametric trees this
method returns the height, but
this is done by averaging over
all root-to-tip path lengths, so
for additive trees the result
should consequently be interpreted
differently.
Calculates the number of nodes.
Type : Calculation
Title : calc_number_of_nodes
Usage : my $number_of_nodes =
$tree->calc_number_of_nodes;
Function: Calculates the number of
nodes (internals AND terminals).
Returns : INT
Args : NONE
Calculates the number of terminal nodes.
Type : Calculation
Title : calc_number_of_terminals
Usage : my $number_of_terminals =
$tree->calc_number_of_terminals;
Function: Calculates the number
of terminal nodes.
Returns : INT
Args : NONE
Calculates the number of internal nodes.
Type : Calculation
Title : calc_number_of_internals
Usage : my $number_of_internals =
$tree->calc_number_of_internals;
Function: Calculates the number
of internal nodes.
Returns : INT
Args : NONE
Calculates the sum of all root-to-tip path lengths.
Type : Calculation
Title : calc_total_paths
Usage : my $total_paths =
$tree->calc_total_paths;
Function: Calculates the sum of all
root-to-tip path lengths.
Returns : FLOAT
Args : NONE
Calculates the amount of shared (redundant) history on the total.
Type : Calculation
Title : calc_redundancy
Usage : my $redundancy =
$tree->calc_redundancy;
Function: Calculates the amount of shared
(redundant) history on the total.
Returns : FLOAT
Args : NONE
Comments: Redundancy is calculated as
1 / ( treelength - height / ( ntax * height - height ) )
Calculates Colless' coefficient of tree imbalance.
Type : Calculation
Title : calc_imbalance
Usage : my $imbalance = $tree->calc_imbalance;
Function: Calculates Colless' coefficient
of tree imbalance.
Returns : FLOAT
Args : NONE
Comments: As described in Colless, D.H., 1982.
The theory and practice of phylogenetic
systematics. Systematic Zoology 31(1): 100-104
Calculates I2 imbalance.
Type : Calculation Title : calc_i2 Usage : my $ci2 = $tree->calc_i2; Function: Calculates I2 imbalance. Returns : FLOAT Args : NONE Comments:
Calculates the Pybus gamma statistic.
Type : Calculation
Title : calc_gamma
Usage : my $gamma = $tree->calc_gamma();
Function: Calculates the Pybus gamma statistic
Returns : FLOAT
Args : NONE
Comments: As described in Pybus, O.G. and
Harvey, P.H., 2000. Testing
macro-evolutionary models using
incomplete molecular phylogenies.
Proc. R. Soc. Lond. B 267, 2267-2272
Calculates stemminess measure of Fiala and Sokal (1985).
Type : Calculation
Title : calc_fiala_stemminess
Usage : my $fiala_stemminess =
$tree->calc_fiala_stemminess;
Function: Calculates stemminess measure
Fiala and Sokal (1985).
Returns : FLOAT
Args : NONE
Comments: As described in Fiala, K.L. and
R.R. Sokal, 1985. Factors
determining the accuracy of
cladogram estimation: evaluation
using computer simulation.
Evolution, 39: 609-622
Calculates stemminess measure from Rohlf et al. (1990).
Type : Calculation
Title : calc_rohlf_stemminess
Usage : my $rohlf_stemminess =
$tree->calc_rohlf_stemminess;
Function: Calculates stemminess measure
from Rohlf et al. (1990).
Returns : FLOAT
Args : NONE
Comments: As described in Rohlf, F.J.,
W.S. Chang, R.R. Sokal, J. Kim,
1990. Accuracy of estimated
phylogenies: effects of tree
topology and evolutionary model.
Evolution, 44(6): 1671-1684
Calculates tree resolution.
Type : Calculation
Title : calc_resolution
Usage : my $resolution =
$tree->calc_resolution;
Function: Calculates the total number
of internal nodes over the
total number of internal nodes
on a fully bifurcating
tree of the same size.
Returns : FLOAT
Args : NONE
Calculates branching times.
Type : Calculation
Title : calc_branching_times
Usage : my $branching_times =
$tree->calc_branching_times;
Function: Returns a two-dimensional array.
The first dimension consists of
the "records", so that in the
second dimension $AoA[$first][0]
contains the internal node references,
and $AoA[$first][1] the branching
time of the internal node. The
records are orderered from root to
tips by time from the origin.
Returns : SCALAR[][] or FALSE
Args : NONE
Calculates lineage-through-time data points.
Type : Calculation
Title : calc_ltt
Usage : my $ltt = $tree->calc_ltt;
Function: Returns a two-dimensional array.
The first dimension consists of the
"records", so that in the second
dimension $AoA[$first][0] contains
the internal node references, and
$AoA[$first][1] the branching time
of the internal node, and $AoA[$first][2]
the cumulative number of lineages over
time. The records are orderered from
root to tips by time from the origin.
Returns : SCALAR[][] or FALSE
Args : NONE
Calculates the symmetric difference metric between invocant and argument.
Type : Calculation
Title : calc_symdiff
Usage : my $symdiff =
$tree->calc_symdiff($other_tree);
Function: Returns the symmetric difference
metric between $tree and $other_tree,
sensu Penny and Hendy, 1985.
Returns : SCALAR
Args : A Bio::Phylo::Forest::Tree object
Comments: Trees in comparison must span
the same set of terminal taxa
or results are meaningless.
Calculates the Fair Proportion value for each terminal.
Type : Calculation
Title : calc_fp
Usage : my $fp = $tree->calc_fp();
Function: Returns the Fair Proportion
value for each terminal
Returns : HASHREF
Args : NONE
Calculates the Equal Splits value for each terminal
Type : Calculation Title : calc_es Usage : my $es = $tree->calc_es(); Function: Returns the Equal Splits value for each terminal Returns : HASHREF Args : NONE
Calculates the Pendant Edge value for each terminal.
Type : Calculation Title : calc_pe Usage : my $es = $tree->calc_pe(); Function: Returns the Pendant Edge value for each terminal Returns : HASHREF Args : NONE
Calculates the Shapley value for each terminal.
Type : Calculation Title : calc_shapley Usage : my $es = $tree->calc_shapley(); Function: Returns the Shapley value for each terminal Returns : HASHREF Args : NONE
The following methods are a - not entirely true-to-form - implementation of the Visitor design pattern: the nodes in a tree are visited, and rather than having an object operate on them, a set of code references is used. This can be used, for example, to serialize a tree to a string format. To create a newick string without branch lengths you would use something like this (there is a more powerful 'to_newick' method, so this is just an example):
$tree->visit_depth_first(
'-pre_daughter' => sub { print '(' },
'-post_daughter' => sub { print ')' },
'-in' => sub { print shift->get_name },
'-pre_sister' => sub { print ',' },
);
print ';';
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 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 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 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 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 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 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:
Sets all root-to-tip path lengths equal.
Type : Tree manipulator
Title : ultrametricize
Usage : $tree->ultrametricize;
Function: Sets all root-to-tip path
lengths equal by stretching
all terminal branches to the
height of the tallest node.
Returns : The modified invocant.
Args : NONE
Comments: This method is analogous to
the 'ultrametricize' command
in Mesquite, i.e. no rate smoothing
or anything like that happens, just
a lengthening of terminal branches.
Scales the tree to the specified height.
Type : Tree manipulator
Title : scale
Usage : $tree->scale($height);
Function: Scales the tree to the
specified height.
Returns : The modified invocant.
Args : $height = a numerical value
indicating root-to-tip path length.
Comments: This method uses the
$tree->calc_tree_height method, and
so for additive trees the *average*
root-to-tip path length is scaled to
$height (i.e. some nodes might be
taller than $height, others shorter).
Randomly breaks polytomies.
Type : Tree manipulator
Title : resolve
Usage : $tree->resolve;
Function: Randomly breaks polytomies by inserting
additional internal nodes.
Returns : The modified invocant.
Args :
Comments:
Prunes argument nodes from invocant.
Type : Tree manipulator Title : prune_tips Usage : $tree->prune_tips(\@taxa); Function: Prunes specified taxa from invocant. Returns : A pruned Bio::Phylo::Forest::Tree object. Args : A reference to an array of taxon names. Comments:
Keeps argument nodes from invocant (i.e. prunes all others).
Type : Tree manipulator Title : keep_tips Usage : $tree->keep_tips(\@taxa); Function: Keeps specified taxa from invocant. Returns : The pruned Bio::Phylo::Forest::Tree object. Args : An array ref of taxon names or a Bio::Phylo::Taxa object Comments:
Converts negative branch lengths to zero.
Type : Tree manipulator
Title : negative_to_zero
Usage : $tree->negative_to_zero;
Function: Converts negative branch
lengths to zero.
Returns : The modified invocant.
Args : NONE
Comments:
Raises branch lengths to argument.
Type : Tree manipulator Title : exponentiate Usage : $tree->exponentiate($power); Function: Raises branch lengths to $power. Returns : The modified invocant. Args : A $power in any of perl's number formats.
Log argument base transform branch lengths.
Type : Tree manipulator Title : log_transform Usage : $tree->log_transform($base); Function: Log $base transforms branch lengths. Returns : The modified invocant. Args : A $base in any of perl's number formats.
Collapses internal nodes with fewer than 2 children.
Type : Tree manipulator
Title : remove_unbranched_internals
Usage : $tree->remove_unbranched_internals;
Function: Collapses internal nodes
with fewer than 2 children.
Returns : The modified invocant.
Args : NONE
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 invocant to newick string.
Type : Stringifier
Title : to_newick
Usage : my $string = $tree->to_newick;
Function: Turns the invocant tree object
into a newick string
Returns : SCALAR
Args : NONE
Serializes invocant to xml.
Type : Serializer Title : to_xml Usage : my $xml = $obj->to_xml; Function: Turns the invocant object into an XML string. Returns : SCALAR Args : NONE
Serializes invocant to SVG.
Type : Serializer Title : to_svg Usage : my $svg = $obj->to_svg; Function: Turns the invocant object into an SVG string. Returns : SCALAR Args : Same args as the Bio::Phylo::Treedrawer constructor
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:
Bio::Phylo::Forest::Tree inherits from one or more superclasses. This means that objects of class Bio::Phylo::Forest::Tree 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::Tree 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::Tree 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::Tree 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
The Bio::Phylo::Forest::Tree object inherits from the Bio::Phylo::Listable object, so the methods defined therein also apply to trees.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
$Id: Tree.pm 844 2009-03-05 00:07:26Z rvos $
