NAME

Bio::Phylo::Forest::Tree - Phylogenetic tree

SYNOPSIS

# 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"

DESCRIPTION

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.

METHODS

CONSTRUCTORS

new()

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.

new_from_bioperl()

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

MUTATORS

set_as_unrooted()

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.

set_as_default()

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.

set_not_default()

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.

QUERIES

get_terminals()

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_internals()

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()

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

get_tallest_tip()

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_mrca()

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.

TESTS

is_default()

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

is_rooted()

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

is_binary()

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

is_ultrametric()

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.

is_monophyletic()

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.

is_paraphyletic()

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

is_clade()

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:

is_cladogram()

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:

CALCULATIONS

calc_tree_length()

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

calc_tree_height()

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.

calc_number_of_nodes()

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

calc_number_of_terminals()

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

calc_number_of_internals()

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

calc_total_paths()

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

calc_redundancy()

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 ) )

calc_imbalance()

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

calc_i2()

Calculates I2 imbalance.

Type    : Calculation
Title   : calc_i2
Usage   : my $ci2 = $tree->calc_i2;
Function: Calculates I2 imbalance.
Returns : FLOAT
Args    : NONE
Comments:

calc_gamma()

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

calc_fiala_stemminess()

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

calc_rohlf_stemminess()

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

calc_resolution()

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

calc_branching_times()

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

calc_ltt()

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

calc_symdiff()

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.

calc_fp()

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

calc_es()

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

calc_pe()

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

calc_shapley()

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

VISITOR METHODS

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 ';';

visit_depth_first()

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:

visit_breadth_first()

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:

visit_level_order()

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:

TREE MANIPULATION

ultrametricize()

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.

scale()

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).

resolve()

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:

prune_tips()

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:

keep_tips()

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:

negative_to_zero()

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:

exponentiate()

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_transform()

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.

remove_unbranched_internals()

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:

UTILITY METHODS

clone()

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.

SERIALIZERS

to_newick()

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

to_xml()

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

to_svg()

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

to_json()

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:

INHERITED METHODS

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.

SUPERCLASS Bio::Phylo::Listable

Bio::Phylo::Forest::Tree inherits from superclass Bio::Phylo::Listable. Below are the public methods (if any) from this superclass.

add_set()

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

add_to_set()

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.

can_contain()

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

clear()

Empties container object.

Type    : Object method
Title   : clear
Usage   : $obj->clear();
Function: Clears the container.
Returns : A Bio::Phylo::Listable object.
Args    : Note.
Note    :

clone()

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.

contains()

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

cross_reference()

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:

current()

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.

current_index()

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.

delete()

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.

first()

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.

get_by_index()

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

get_by_name()

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)

get_by_regular_expression()

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 $re
Returns : A list of Bio::Phylo::* objects.
Args    : -value => any of the string 
                    datum props (e.g. 'get_type')
          -match => a compiled regular 
                    expression (e.g. qr/^[D|R]NA$/)

get_by_value()

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

get_entities()

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.

get_index_of()

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

get_logger()

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

get_sets()

Type    : Accessor
Title   : get_sets
Usage   : my @sets = @{ $obj->get_sets() };
Function: Retrieves all associated Bio::Phylo::Set objects
Returns : Invocant
Args    : None

insert()

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.

insert_at_index()

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.

is_in_set()

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.

last()

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.

last_index()

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.

next()

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.

notify_listeners()

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:

previous()

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.

remove_from_set()

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.

remove_set()

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

set_listener()

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.

visit()

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.

SUPERCLASS Bio::Phylo::Util::XMLWritable

Bio::Phylo::Forest::Tree inherits from superclass Bio::Phylo::Util::XMLWritable. Below are the public methods (if any) from this superclass.

add_dictionary()

Type    : Mutator
Title   : add_dictionary
Usage   : $obj->add_dictionary($dict);
Function: Adds a dictionary attachment to the object
Returns : $self
Args    : Bio::Phylo::Dictionary

get_attributes()

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

get_dictionaries()

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.

get_namespaces()

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

get_tag()

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.

get_xml_id()

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.

get_xml_tag()

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

is_identifiable()

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

remove_dictionary()

Type    : Mutator
Title   : remove_dictionary
Usage   : $obj->remove_dictionary($dict);
Function: Removes a dictionary attachment from the object
Returns : $self
Args    : Bio::Phylo::Dictionary

set_attributes()

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

set_identifiable()

Type    : Mutator
Title   : set_identifiable
Usage   : $obj->set_tag(0);
Function: Enables/disables id generation
Returns : $self
Args    : BOOLEAN

set_namespaces()

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');

set_tag()

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)

set_xml_id()

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)

to_xml()

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

SUPERCLASS Bio::Phylo

Bio::Phylo::Forest::Tree inherits from superclass Bio::Phylo. Below are the public methods (if any) from this superclass.

clone()

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.

get()

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';

get_desc()

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

get_generic()

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

get_id()

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

get_internal_name()

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

get_logger()

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

get_name()

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

get_obj_by_id()

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

get_score()

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

new()

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

set_desc()

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.

set_generic()

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( );

set_name()

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.

set_score()

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.

to_json()

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:

to_string()

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

REVISION

$Id: Tree.pm 844 2009-03-05 00:07:26Z rvos $

To install Bio::Phylo, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Phylo

CPAN shell

perl -MCPAN -e shell
install Bio::Phylo

For more information on module installation, please visit the detailed CPAN module installation guide.

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NAME

SYNOPSIS

DESCRIPTION

METHODS

CONSTRUCTORS

MUTATORS

QUERIES

TESTS

CALCULATIONS

VISITOR METHODS

TREE MANIPULATION

UTILITY METHODS

SERIALIZERS

INHERITED METHODS

SUPERCLASS Bio::Phylo::Listable

SUPERCLASS Bio::Phylo::Util::XMLWritable

SUPERCLASS Bio::Phylo

SEE ALSO

REVISION

Module Install Instructions