Bio::Tree TreeFunctionsI
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Summary
Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods
Package variables
No package variables defined.
Inherit
Bio::Tree::TreeI
Synopsis
  use Bio::TreeIO;
my $in = Bio::TreeIO->new(-format => 'newick', -file => 'tree.tre');
my $tree = $in->next_tree; my @nodes = $tree->find_node('id1'); if( $tree->is_monophyletic(-nodes => \@nodes, -outgroup => $outnode) ){ #... }
Description
This interface provides a set of implementated Tree functions which
only use the defined methods in the TreeI or NodeI interface.
Methods
find_nodeDescriptionCode
remove_NodeDescriptionCode
get_lineage_nodesDescriptionCode
get_lineage_stringDescriptionCode
spliceDescriptionCode
get_lcaDescriptionCode
merge_lineageDescriptionCode
contract_linear_pathsDescriptionCode
is_binaryDescriptionCode
force_binaryDescriptionCode
simplify_to_leaves_stringDescriptionCode
_clone_node
No description
Code
_simplify_helper
No description
Code
distanceDescriptionCode
is_monophyleticDescriptionCode
is_paraphyleticDescriptionCode
rerootDescriptionCode
reroot_at_midpointDescriptionCode
findnode_by_idDescriptionCode
move_id_to_bootstrapDescriptionCode
_read_trait_file
No description
Code
add_traitDescriptionCode
Methods description
find_nodecode    nextTop
 Title   : find_node
Usage : my @nodes = $self->find_node(-id => 'node1');
Function: returns all nodes that match a specific field, by default this
is id, but different branch_length,
Returns : List of nodes which matched search
Args : text string to search for
OR
-fieldname => $textstring
remove_NodecodeprevnextTop
 Title   : remove_Node
Usage : $tree->remove_Node($node)
Function: Removes a node from the tree
Returns : boolean represent status of success
Args : either Bio::Tree::NodeI or string of the node id
get_lineage_nodescodeprevnextTop
 Title   : get_lineage_nodes
Usage : my @nodes = $tree->get_lineage_nodes($node);
Function: Given a node or its ID, get its full lineage, i.e. all its ancestors,
from the root to the most recent ancestor. Only use the node ID as
input if the nodes have been added to the tree.
Returns : list of nodes
Args : either Bio::Tree::NodeI (or string of the node id)
get_lineage_stringcodeprevnextTop
 Title   : get_lineage_string
Usage : my $lineage = $tree->get_lineage_string($node);
Function: Get the string representation of the full lineage of a node, e.g.
for the Enterobacteriales node, return
Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales.
This method uses get_lineage_nodes internally and therefore inherits
of all of its caveats.
Returns : string
Args : * either Bio::Tree::NodeI (or string of the node id)
* an optional separator (default: ';')
splicecodeprevnextTop
 Title   : splice
Usage : $tree->splice(-remove_id => \@ids);
Function: Remove all the nodes from a tree that correspond to the supplied
args, making all the descendents of a removed node the descendents
of the removed node's ancestor.
You can ask to explicitly remove certain nodes by using -remove_*,
remove them conditionally by using -remove_* in combination with
-keep_*, or remove everything except certain nodes by using only
-keep_*.
Returns : n/a
Args : just a list of Bio::Tree::NodeI objects to remove, OR
-key => value pairs, where -key has the prefix 'remove' or 'keep',
followed by an underscore, followed by a fieldname (like for the
method find_node). Value should be a scalar or an array ref of
scalars (again, like you might supply to find_node).
So (-remove_id => [1, 2]) will remove all nodes from the tree that have an id() of '1' or '2', while (-remove_id => [1, 2], -keep_id => [2]) will remove all nodes with an id() of '1'. (-keep_id => [2]) will remove all nodes unless they have an id() of '2' (note, no -remove_*). -preserve_lengths => 1 : setting this argument will splice out intermediate nodes, preserving the original total length between the ancestor and the descendants of the spliced node. Undef by default.
get_lcacodeprevnextTop
 Title   : get_lca
Usage : get_lca(-nodes => \@nodes ); OR
get_lca(@nodes);
Function: given two or more nodes, returns the lowest common ancestor (aka most
recent common ancestor)
Returns : node object or undef if there is no common ancestor
Args : -nodes => arrayref of nodes to test, OR
just a list of nodes
merge_lineagecodeprevnextTop
 Title   : merge_lineage
Usage : merge_lineage($node)
Function: Merge a lineage of nodes with this tree.
Returns : n/a
Args : Bio::Tree::TreeI with only one leaf, OR
Bio::Tree::NodeI which has an ancestor
For example, if we are the tree $tree: +---B | A | +---C and we want to merge the lineage $other_tree: A---C---D After calling $tree->merge_lineage($other_tree), $tree looks like: +---B | A | +---C---D
contract_linear_pathscodeprevnextTop
 Title   : contract_linear_paths
Usage : contract_linear_paths()
Function: Splices out all nodes in the tree that have an ancestor and only one
descendent.
Returns : n/a
Args : none for normal behaviour, true to dis-regard the ancestor requirment
and re-root the tree as necessary
For example, if we are the tree $tree: +---E | A---B---C---D | +---F After calling $tree->contract_linear_paths(), $tree looks like: +---E | A---D | +---F Instead, $tree->contract_linear_paths(1) would have given: +---E | D | +---F
is_binarycodeprevnextTop
  Example    : is_binary(); is_binary($node);
Description: Finds if the tree or subtree defined by
the internal node is a true binary tree
without polytomies
Returns : boolean
Exceptions :
Args : Internal node Bio::Tree::NodeI, optional
force_binarycodeprevnextTop
 Title   : force_binary
Usage : force_binary()
Function: Forces the tree into a binary tree, splitting branches arbitrarily
and creating extra nodes as necessary, such that all nodes have
exactly two or zero descendants.
Returns : n/a
Args : none
For example, if we are the tree $tree: +---G | +---F | +---E | A | +---D | +---C | +---B (A has 6 descendants B-G) After calling $tree->force_binary(), $tree looks like: +---X | +---X | | | +---X | +---X | | | | +---G | | | | +---X | | | +---F A | +---E | | | +---X | | | | | +---D | | +---X | | +---C | | +---X | +---B (Where X are artificially created nodes with ids 'artificial_n', where n is an integer making the id unique within the tree)
simplify_to_leaves_stringcodeprevnextTop
 Title   : simplify_to_leaves_string
Usage : my $leaves_string = $tree->simplify_to_leaves_string()
Function: Creates a simple textual representation of the relationship between
leaves in self. It forces the tree to be binary, so the result may
not strictly correspond to the tree (if the tree wasn't binary), but
will be as close as possible. The tree object is not altered. Only
leaf node ids are output, in a newick-like format.
Returns : string
Args : none
distancecodeprevnextTop
 Title   : distance
Usage : distance(-nodes => \@nodes )
Function: returns the distance between two given nodes
Returns : numerical distance
Args : -nodes => arrayref of nodes to test
or ($node1, $node2)
is_monophyleticcodeprevnextTop
 Title   : is_monophyletic
Usage : if( $tree->is_monophyletic(-nodes => \@nodes,
-outgroup => $outgroup)
Function: Will do a test of monophyly for the nodes specified
in comparison to a chosen outgroup
Returns : boolean
Args : -nodes => arrayref of nodes to test
-outgroup => outgroup to serve as a reference
is_paraphyleticcodeprevnextTop
 Title   : is_paraphyletic
Usage : if( $tree->is_paraphyletic(-nodes =>\@nodes,
-outgroup => $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 : -nodes => Array of Bio::Tree::NodeI objects which are in the tree
-outgroup => a Bio::Tree::NodeI to compare the nodes to
rerootcodeprevnextTop
 Title   : reroot
Usage : $tree->reroot($node);
Function: Reroots a tree making a new node the root
Returns : 1 on success, 0 on failure
Args : Bio::Tree::NodeI that is in the tree, but is not the current root
reroot_at_midpointcodeprevnextTop
 Title   : reroot_at_midpoint
Usage : $tree->reroot_at_midpoint($node, $new_root_id);
Function: Reroots a tree on a new node created halfway between the
argument and its ancestor
Returns : the new midpoint Bio::Tree::NodeIon success, 0 on failure
Args : non-root Bio::Tree::NodeI currently in $tree
scalar string, id for new node (optional)
findnode_by_idcodeprevnextTop
 Title   : findnode_by_id
Usage : my $node = $tree->findnode_by_id($id);
Function: Get a node by its id (which should be
unique for the tree)
Returns : Bio::Tree::NodeI
Args : node id
move_id_to_bootstrapcodeprevnextTop
 Title   : move_id_to_bootstrap
Usage : $tree->move_id_to_bootstrap
Function: Move internal IDs to bootstrap slot
Returns : undef
Args : undef
add_traitcodeprevnextTop
 Title   : add_trait
Usage : my $key = $tree->add_trait($trait_file, 3);
Function: Add traits to the leaf nodes of a Bio::Tree:Tree from a file.
The trait file is a tab-delimited text file and needs to have a
header line giving names to traits. The first column contains the
leaf node ids. Subsequent columns contain different trait value sets.
Single or double quotes are removed from the trait values. Traits
are added to leaf nodes as a tag named $key using the add_tag_value()
method. This means that you can retrieve the trait values using the
get_tag_values() method (see the documentation for Bio::Tree::Node).
Returns : Trait name (a scalar) on success, undef on failure (for example, if
the column index requested was too large).
Args : * Name of trait file (scalar string).
* Index of trait file column (scalar int). Note that numbering starts
at 0. Default: 1 (second column).
* Ignore missing values. Typically, if a leaf node has no value in
the trait file, an exception is thrown. If you set this option to
1, then no trait will be given to the node (no exception thrown).
Methods code
find_nodedescriptionprevnextTop
sub find_node {
   my ($self, $type, $field) = @_;
   if( ! defined $type ) { 
       $self->warn("Must request a either a string or field and string when searching");
   }

   # all this work for a '-' named field
# is so that we could potentially
# expand to other constraints in
# different implementations
# like 'find all nodes with boostrap < XX'
if( ! defined $field ) { # only 1 argument, default to searching by id
$field = $type; $type = 'id'; } else { $type =~ s/^-//; } # could actually do this by testing $rootnode->can($type) but
# it is possible that a tree is implemeted with different node types
# - although it is unlikely that the root node would be richer than the
# leaf nodes. Can't handle NHX tags right now
my @nodes = grep { $_->can($type) && defined $_->$type() && $_->$type() eq $field } $self->get_nodes(); if ( wantarray) { return @nodes; } else { if( @nodes > 1 ) { $self->warn("More than 1 node found but caller requested scalar, only returning first node"); } return shift @nodes; }
}
remove_NodedescriptionprevnextTop
sub remove_Node {
   my ($self,$input) = @_;
   my $node = undef;
   unless( ref($input) ) {
       $node = $self->find_node($input);
   }  elsif( ! $input->isa('Bio::Tree::NodeI') ) {
       $self->warn("Did not provide either a valid Bio::Tree::NodeI object or id to remove_node");
       return 0;
   } else { 
       $node = $input;
   }
   if( ! $node->ancestor && 
       $self->get_root_node->internal_id != $node->internal_id) {
     $self->warn("Node (".$node->to_string . ") has no ancestor, can't remove!");
   } else { 
     $node->ancestor->remove_Descendent($node);
   }
}
get_lineage_nodesdescriptionprevnextTop
sub get_lineage_nodes {
    my ($self, $input) = @_;
    my $node;

    # Sanity checks
if (ref $input) { if (not $input->isa('Bio::Tree::NodeI')) { $self->throw("Did not provide a valid Bio::Tree::NodeI object or ID string to get_lineage_nodes"); } $node = $input; } else { $node = $self->find_node($input); } # When dealing with Bio::Taxon objects with databases, the root will always
# be the database's root, ignoring this Tree's set root node; prefer the
# Tree's idea of root.
my $root = $self->get_root_node || ''; my @lineage; while ($node) { $node = $node->ancestor || last; unshift(@lineage, $node); $node eq $root && last; } return @lineage;
}
get_lineage_stringdescriptionprevnextTop
sub get_lineage_string {
    my ($self, $input, $sep) = @_;
    $sep ||= ';';
    my $node;
    unless (ref $input) {
        $node = $self->find_node($input);
    }
    elsif (! $input->isa('Bio::Tree::NodeI')) {
        $self->warn("Did not provide either a valid Bio::Tree::NodeI object or id to get_lineage_nodes");
        return;
    }
    else {
        $node = $input;
    }
    my @nodes = ($self->get_lineage_nodes($node), $node);
    for my $i (0 .. scalar @nodes - 1) {
        my $node_name = $nodes[$i]->node_name || '';
        if ($node_name =~ m/$sep/) {
$self->warn("Separator '$sep' is not safe to use because the node ".
"called '
$node_name' contains it. Consider using another separator".
" or sanitizing the node name.");
} $nodes[$i] = $node_name; } return join $sep, @nodes;
}
splicedescriptionprevnextTop
sub splice {
    my ($self, @args) = @_;
    $self->throw("Must supply some arguments") unless @args > 0;
    my $preserve_lengths = 0;
    my @nodes_to_remove;
    if (ref($args[0])) {
        $self->throw("When supplying just a list of Nodes, they must be Bio::Tree::NodeI objects") unless $args[0]->isa('Bio::Tree::NodeI');
        @nodes_to_remove = @args;
    }
    else {
        $self->throw("When supplying -key => value pairs, must be an even number of args") unless @args % 2 == 0;
        my %args = @args;
        my @keep_nodes;
        my @remove_nodes;
        my $remove_all = 1;
        while (my ($key, $value) = each %args) {
            my @values = ref($value) ? @{$value} : ($value);

            if ($key =~ s/remove_//) {
                $remove_all = 0;
                foreach my $value (@values) {
                    push(@remove_nodes, $self->find_node($key => $value));
                }
            }
            elsif ($key =~ s/keep_//) {
                foreach my $value (@values) {
                    push(@keep_nodes, $self->find_node($key => $value));
                }
            }
            elsif ($key =~ /preserve/) {
                $preserve_lengths = $value;
            }
        }

        if ($remove_all) {
            if (@keep_nodes == 0) {
                $self->warn("Requested to remove everything except certain nodes, but those nodes were not found; doing nothing instead");
                return;
            }

            @remove_nodes = $self->get_nodes;
        }
        if (@keep_nodes > 0) {
            my %keep_iids = map { $_->internal_id => 1 } @keep_nodes;
            foreach my $node (@remove_nodes) {
                push(@nodes_to_remove, $node) unless exists $keep_iids{$node->internal_id};
            }
        }
        else {
            @nodes_to_remove = @remove_nodes;
        }
    }
    # do the splicing
#*** the algorithm here hasn't really been thought through and tested much,
# will probably need revising
my %root_descs; my $reroot = 0; foreach my $node (@nodes_to_remove) { my @descs = $node->each_Descendent; my $ancestor = $node->ancestor; if (! $ancestor && ! $reroot) { # we're going to remove the tree root, so will have to re-root the
# tree later
$reroot = 1; %root_descs = map { $_->internal_id => $_ } @descs; $node->remove_all_Descendents; next; } if (exists $root_descs{$node->internal_id}) { # well, this one can't be the future root anymore
delete $root_descs{$node->internal_id}; # but maybe one of this one's descs will become the root
foreach my $desc (@descs) { $root_descs{$desc->internal_id} = $desc; } } # make the ancestor of our descendents our own ancestor, and give us
# no ancestor of our own to remove us from the tree
foreach my $desc (@descs) { $desc->ancestor($ancestor); $desc->branch_length($desc->branch_length + $node->branch_length) if $preserve_lengths; } $node->ancestor(undef); } if ($reroot) { my @candidates = values %root_descs; $self->throw("After splicing, there was no tree root!") unless @candidates > 0; $self->throw("After splicing, the original root was removed but there are multiple candidates for the new root!") unless @candidates == 1; $self->set_root_node($candidates[0]); # not sure its valid to use the reroot() method
}
}
get_lcadescriptionprevnextTop
sub get_lca {
    my ($self, @args) = @_;
    my ($nodes) = $self->_rearrange([qw(NODES)],@args);
    my @nodes;
    if (ref($nodes) eq 'ARRAY') {
        @nodes = @{$nodes};
    }
    else {
        @nodes = @args;
    }
    @nodes >= 2 or $self->throw("At least 2 nodes are required");
    # We must go root->leaf to get the correct answer to lca (in a world where
# internal_id might not be uniquely assigned), but leaf->root is more
# forgiving (eg. lineages may not all have the same root, or they may have
# different numbers of 'minor' taxa inbeteen 'major' ones).
#
# I use root->leaf so that we can easily do multiple nodes at once - no
# matter what taxa are below the lca, the lca and all its ancestors ought to
# be identical.
my @paths; foreach my $node (@nodes) { unless(ref($node) && $node->isa('Bio::Tree::NodeI')) { $self->throw("Cannot process get_lca() with a non-NodeI object ($node)\n"); } my @path = ($self->get_lineage_nodes($node), $node); push(@paths,\@ path); } return unless @paths >= 2; my $lca; LEVEL: while ($paths[0] > 0) { my %node_ids; my $node; foreach my $path (@paths) { $node = shift(@{$path}) || last LEVEL; my $node_id = $node->internal_id; unless (defined $node_id) { $self->warn("One of the lineages had a node with no internal_id, can't calculate the common ancestor"); return; } $node_ids{$node_id}++; } if (keys %node_ids == 1) { $lca = $node; } else { # at this point in the lineage the nodes are different; the previous
# loop had the lca
last LEVEL; } } # If the tree that we are contains the lca (get_lca could have been called
# on an empty tree, since it works with plain Nodes), prefer to return the
# node object that belongs to us
if ($lca && $self->number_nodes > 0) { my $own_lca = $self->find_node(-internal_id => $lca->internal_id); $lca = $own_lca if $own_lca; } return $lca;
}
merge_lineagedescriptionprevnextTop
sub merge_lineage {
    my ($self, $thing) = @_;
    $self->throw("Must supply an object reference") unless ref($thing);

    my ($lineage_tree, $lineage_leaf);
    if ($thing->isa('Bio::Tree::TreeI')) {
        my @leaves = $thing->get_leaf_nodes;
        $self->throw("The supplied Tree can only have one leaf") unless @leaves == 1;
        $lineage_tree = $thing;
        $lineage_leaf = shift(@leaves);
    }
    elsif ($thing->isa('Bio::Tree::NodeI')) {
        $self->throw("The supplied Node must have an ancestor") unless $thing->ancestor;
        $lineage_tree = $self->new(-node => $thing);
        $lineage_leaf = $thing;
    }

    # see if any node in the supplied lineage is in our tree - that will be
# our lca and we can merge at the node below
my @lineage = ($lineage_leaf, reverse($self->get_lineage_nodes($lineage_leaf))); my $merged = 0; for my $i (0..$#lineage) { my $lca = $self->find_node(-internal_id => $lineage[$i]->internal_id) || next; if ($i == 0) { # the supplied thing to merge is already in the tree, nothing to do
return; } # $i is the lca, so the previous node is new to the tree and should
# be merged on
$lca->add_Descendent($lineage[$i-1]); $merged = 1; last; } $merged || ($self->warn("Couldn't merge the lineage of ".$lineage_leaf->id." with the rest of the tree!\n") && return);
}
contract_linear_pathsdescriptionprevnextTop
sub contract_linear_paths {
    my $self = shift;
    my $reroot = shift;
    my @remove;
    foreach my $node ($self->get_nodes) {
        if ($node->ancestor && $node->each_Descendent == 1) {
            push(@remove, $node);
        }
    }
    $self->splice(@remove) if @remove;
    if ($reroot) {
        my $root = $self->get_root_node;
        my @descs = $root->each_Descendent;
        if (@descs == 1) {
            my $new_root = shift(@descs);
            $self->set_root_node($new_root);
            $new_root->ancestor(undef);
        }
    }
}
is_binarydescriptionprevnextTop
sub is_binary {
    my $self = shift;
    my $node = shift || $self->get_root_node;

    my $binary = 1;
    my @descs = $node->each_Descendent;
    $binary = 0 unless @descs == 2 or @descs == 0;
    #print "$binary, ", scalar @descs, "\n";
# recurse
foreach my $desc (@descs) { $binary += $self->is_binary($desc) -1; } $binary = 0 if $binary < 0; return $binary;
}
force_binarydescriptionprevnextTop
sub force_binary {
    my $self = shift;
    my $node = shift || $self->get_root_node;

    my @descs = $node->each_Descendent;
    if (@descs > 2) {
        # Removed overly verbose warning - cjfields 3-12-11
# Many nodes have no identifying names, a simple warning is probably
# enough.
$self->warn("Node has more than two descendants\nWill do an arbitrary balanced split"); my @working = @descs; # create an even set of artifical nodes on which to later hang the descs
my $half = @working / 2;
$half++ if $half > int($half); $half = int($half); my @artificials; while ($half > 1) { my @this_level; foreach my $top_node (@artificials || $node) { for (1..2) { my $art = $top_node->new(-id => "artificial_".++$self->{_art_num}); $top_node->add_Descendent($art); push(@this_level, $art); } } @artificials = @this_level; $half--; } # attach two descs to each artifical leaf
foreach my $art (@artificials) { for (1..2) { my $desc = shift(@working) || $node->new(-id => "artificial_".++$self->{_art_num}); $desc->ancestor($art); } } } elsif (@descs == 1) { # ensure that all nodes have 2 descs
$node->add_Descendent($node->new(-id => "artificial_".++$self->{_art_num})); } # recurse
foreach my $desc (@descs) { $self->force_binary($desc); }
}
simplify_to_leaves_stringdescriptionprevnextTop
sub simplify_to_leaves_string {
    my $self = shift;

    # Before contracting and forcing binary we need to clone self, but Clone.pm
# clone() seg faults and fails to make the clone, whilst Storable dclone
# needs $self->{_root_cleanup_methods} deleted (code ref) and seg faults at
# end of script. Let's make our own clone...
my $tree = $self->_clone; $tree->contract_linear_paths(1); $tree->force_binary; foreach my $node ($tree->get_nodes) { my $id = $node->id; $id = ($node->is_Leaf && $id !~ /^artificial/) ? $id : ''; $node->id($id); } my %paired; my @data = $self->_simplify_helper($tree->get_root_node,\% paired); return join(',', @data); } # alias
}
_clone_nodedescriptionprevnextTop
sub _clone_node {
    my ($self, $node) = @_;
    my $clone = $node->new;

    while (my ($key, $val) = each %{$node}) {
        if ($key eq '_desc' || $key eq '_ancestor') {
            next;
        }
        ${$clone}{$key} = $val;
    }

    return $clone;
}


# tree string generator for simplify_to_leaves_string, based on
# Bio::TreeIO::newick::_write_tree_Helper
}
_simplify_helperdescriptionprevnextTop
sub _simplify_helper {
    my ($self, $node, $paired) = @_;
    return () if (!defined $node);

    my @data = ();
    foreach my $node ($node->each_Descendent()) {
        push(@data, $self->_simplify_helper($node, $paired));
    }

    my $id = $node->id_output || '';
    if (@data) {
        unless (exists ${$paired}{"@data"} || @data == 1)  {
            $data[0] = "(" . $data[0];
            $data[-1] .= ")";
            ${$paired}{"@data"} = 1;
        }
    }
    elsif ($id) {
        push(@data, $id);
    }

    return @data;
}
distancedescriptionprevnextTop
sub distance {
    my ($self,@args) = @_;
    my ($nodes) = $self->_rearrange([qw(NODES)],@args);
    if( ! defined $nodes ) {
        $self->warn("Must supply two nodes or -nodes parameter to distance() method");
        return;
    }
    elsif (ref($nodes) eq 'ARRAY') {
        1;
    }
    elsif ( @args == 2) { # assume these are nodes...
$nodes =\@ args; } else { $self->warn("Must supply two nodes or -nodes parameter to distance() method"); return; } $self->throw("Must provide 2 nodes") unless @{$nodes} == 2; my $lca = $self->get_lca(@{$nodes}); unless($lca) { $self->warn("could not find the lca of supplied nodes; can't find distance either"); return; } my $cumul_dist = 0; my $warned = 0; foreach my $current_node (@{$nodes}) { while (1) { last if $current_node eq $lca; if ($current_node->branch_length) { $cumul_dist += $current_node->branch_length; } elsif (! $warned) { $self->warn("At least some nodes do not have a branch length, the distance returned could be wrong"); $warned = 1; } $current_node = $current_node->ancestor || last; } } return $cumul_dist;
}
is_monophyleticdescriptionprevnextTop
sub is_monophyletic {
   my ($self,@args) = @_;
   my ($nodes,$outgroup) = $self->_rearrange([qw(NODES OUTGROUP)],@args);

   if( ! defined $nodes || ! defined $outgroup ) {
       $self->warn("Must supply -nodes and -outgroup parameters to the method
is_monophyletic");
       return;
   }
   if( ref($nodes) !~ /ARRAY/i ) {
       $self->warn("Must provide a valid array reference for -nodes");
   }

   my $clade_root = $self->get_lca(@{$nodes});
   unless( defined $clade_root ) { 
       $self->warn("could not find clade root via lca");
       return;
   }

   my $og_ancestor = $outgroup->ancestor;
   while( defined ($og_ancestor ) ) {
       if( $og_ancestor->internal_id == $clade_root->internal_id ) {
           # monophyly is violated
return 0; } $og_ancestor = $og_ancestor->ancestor; } return 1;
}
is_paraphyleticdescriptionprevnextTop
sub is_paraphyletic {
   my ($self,@args) = @_;
   my ($nodes,$outgroup) = $self->_rearrange([qw(NODES OUTGROUP)],@args);

   if( ! defined $nodes || ! defined $outgroup ) {
       $self->warn("Must suply -nodes and -outgroup parameters to the method is_paraphyletic");
       return;
   }
   if( ref($nodes) !~ /ARRAY/i ) { 
       $self->warn("Must provide a valid array reference for -nodes");
       return;
   }

   # Algorithm
# Find the lca
# Find all the nodes beneath the lca
# Test to see that none are missing from the nodes list
my %nodehash; foreach my $n ( @$nodes ) { $nodehash{$n->internal_id} = $n; } my $clade_root = $self->get_lca(-nodes => $nodes ); unless( defined $clade_root ) { $self->warn("could not find clade root via lca"); return; } my $og_ancestor = $outgroup->ancestor; # Is this necessary/correct for paraphyly test?
while( defined ($og_ancestor ) ) { if( $og_ancestor->internal_id == $clade_root->internal_id ) { # monophyly is violated, could be paraphyletic
return -1; } $og_ancestor = $og_ancestor->ancestor; } my $tree = Bio::Tree::Tree->new(-root => $clade_root, -nodelete => 1); foreach my $n ( $tree->get_nodes() ) { next unless $n->is_Leaf(); # if any leaf node is not in the list
# then it is part of the clade and so the list
# must be paraphyletic
return 1 unless ( $nodehash{$n->internal_id} ); } return 0;
}
rerootdescriptionprevnextTop
sub reroot {
    my ($self,$new_root) = @_;
    unless (defined $new_root && $new_root->isa("Bio::Tree::NodeI")) {
        $self->warn("Must provide a valid Bio::Tree::NodeI when rerooting");
        return 0;
    }

    my $old_root = $self->get_root_node;
    if( $new_root == $old_root ) {
        $self->warn("Node requested for reroot is already the root node!");
        return 0;
    }
    my $anc = $new_root->ancestor;
    unless( $anc ) {
        # this is already the root
$self->warn("Node requested for reroot is already the root node!"); return 0; } my $tmp_node = $new_root->create_node_on_branch(-position=>0,-force=>1); # reverse the ancestor & children pointers
my $former_anc = $tmp_node->ancestor; my @path_from_oldroot = ($self->get_lineage_nodes($tmp_node), $tmp_node); for (my $i = 0; $i < $#path_from_oldroot; $i++) { my $current = $path_from_oldroot[$i]; my $next = $path_from_oldroot[$i + 1]; $current->remove_Descendent($next); $current->branch_length($next->branch_length); $current->bootstrap($next->bootstrap) if defined $next->bootstrap; $next->remove_tag('B'); $next->add_Descendent($current); } $new_root->add_Descendent($former_anc); $tmp_node->remove_Descendent($former_anc); $tmp_node = undef; $new_root->branch_length(undef); $old_root = undef; $self->set_root_node($new_root); return 1;
}
reroot_at_midpointdescriptionprevnextTop
sub reroot_at_midpoint {
    my $self = shift;
    my $node = shift;
    my $id = shift;

    unless (defined $node && $node->isa("Bio::Tree::NodeI")) {
        $self->warn("Must provide a valid Bio::Tree::NodeI when rerooting");
        return 0;
    }

    my $midpt = $node->create_node_on_branch(-FRACTION=>0.5);
    if (defined $id) {
        $self->warn("ID argument is not a scalar") if (ref $id);
        $midpt->id($id) if defined($id) && !ref($id);
    }
    $self->reroot($midpt);
    return $midpt;
}
findnode_by_iddescriptionprevnextTop
sub findnode_by_id {
    my $tree = shift;
    $tree->deprecated("use of findnode_by_id() is deprecated; ".
                      "use find_node() instead");
    my $id = shift;
    my $rootnode = $tree->get_root_node;
    if ( ($rootnode->id) and ($rootnode->id eq $id) ) {
        return $rootnode;
    }
    # process all the children
foreach my $node ( $rootnode->get_Descendents ) { if ( ($node->id) and ($node->id eq $id ) ) { return $node; } }
}
move_id_to_bootstrapdescriptionprevnextTop
sub move_id_to_bootstrap {
   my ($tree) = shift;
   for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
       $node->bootstrap($node->id || '');
       $node->id('');
   }
}
_read_trait_filedescriptionprevnextTop
sub _read_trait_file {
    my ($self, $file, $column) = @_;
    $column ||= 1;

    my $trait_name;
    my $trait_values;
    open my $TRAIT, '<', $file or $self->throw("Could not open file $file: $!\n");

    my $first_line = 1;
    while (<$TRAIT>) {
        chomp;
        s/['"]//g;
        my @line = split /\t/;
        if ($first_line) {
            $first_line = 0;
            $trait_name = $line[$column];
            next;
        }

        my $id = $line[0];
        last if (not defined $id) or ($id eq '');

        # Skip empty trait values
my $value = $line[$column]; next if (not defined $value) or ($value eq ''); $trait_values->{$id} = $value; } close $TRAIT; return $trait_name, $trait_values;
}
add_traitdescriptionprevnextTop
sub add_trait {
    my ($self, $file, $column, $ignore) = @_;
    $ignore = 0 if not defined $ignore;

    my ($trait_name, $trait_values) = $self->_read_trait_file($file, $column);

    if (defined $trait_name) {

        for my $node ($self->get_leaf_nodes) {

            # strip quotes from the node id
$node->id($1) if $node->id =~ /^['"]+(.*)['"]+$/; if ( not exists $trait_values->{$node->id} ) { if ($ignore) { next; } else { $self->throw("No trait for node [".$node->id."/".$node->internal_id."]"); } } $node->add_tag_value($trait_name, $trait_values->{ $node->id } ); } } return $trait_name; } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich, Aaron Mackey, Justin ReeseTop
Email jason-at-bioperl-dot-org
Email amackey-at-virginia.edu
Email jtr4v-at-virginia.edu
CONTRIBUTORSTop
Sendu Bala, bix@sendu.me.uk
Rerooting code was worked on by
  Daniel Barker d.barker-at-reading.ac.uk
Ramiro Barrantes Ramiro.Barrantes-at-uvm.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _