Bio::Tree TreeI
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Summary
Bio::Tree::TreeI - A Tree object suitable for lots of things, designed
originally for Phylogenetic Trees.
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
  # get a Bio::Tree::TreeI somehow
# like from a TreeIO
my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'treefile.dnd');
my $tree = $treeio->next_tree;
my @nodes = $tree->get_nodes;
my @leaves = $tree->get_leaf_nodes;
my $root = $tree->get_root_node;
Description
This object holds a pointer to the Root of a Tree which is a
Bio::Tree::NodeI.
Methods
get_nodesDescriptionCode
get_root_nodeDescriptionCode
number_nodesDescriptionCode
total_branch_lengthDescriptionCode
heightDescriptionCode
idDescriptionCode
scoreDescriptionCode
get_leaf_nodesDescriptionCode
set_tag_valueDescriptionCode
add_tag_valueDescriptionCode
remove_tagDescriptionCode
remove_all_tagsDescriptionCode
get_all_tagsDescriptionCode
get_tag_valuesDescriptionCode
has_tagDescriptionCode
Methods description
get_nodescode    nextTop
 Title   : get_nodes
Usage : my @nodes = $tree->get_nodes()
Function: Return list of Tree::NodeI objects
Returns : array of Tree::NodeI objects
Args : (named values) hash with one value
order => 'b|breadth' first order or 'd|depth' first order
get_root_nodecodeprevnextTop
 Title   : get_root_node
Usage : my $node = $tree->get_root_node();
Function: Get the Top Node in the tree, in this implementation
Trees only have one top node.
Returns : Bio::Tree::NodeI object
Args : none
number_nodescodeprevnextTop
 Title   : number_nodes
Usage : my $size = $tree->number_nodes
Function: Find the number of nodes in the tree.
Returns : int
Args : none
total_branch_lengthcodeprevnextTop
 Title   : total_branch_length
Usage : my $size = $tree->total_branch_length
Function: Returns the sum of the length of all branches
Returns : integer
Args : none
heightcodeprevnextTop
 Title   : height
Usage : my $height = $tree->height
Function: Gets the height of tree - this LOG_2($number_nodes)
WARNING: this is only true for strict binary trees. The TreeIO
system is capable of building non-binary trees, for which this
method will currently return an incorrect value!!
Returns : integer
Args : none
idcodeprevnextTop
 Title   : id
Usage : my $id = $tree->id();
Function: An id value for the tree
Returns : scalar
Args :
scorecodeprevnextTop
 Title   : score
Usage : $obj->score($newval)
Function: Sets the associated score with this tree
This is a generic slot which is probably best used
for log likelihood or other overall tree score
Returns : value of score
Args : newvalue (optional)
get_leaf_nodescodeprevnextTop
 Title   : get_leaf_nodes
Usage : my @leaves = $tree->get_leaf_nodes()
Function: Returns the leaves (tips) of the tree
Returns : Array of Bio::Tree::NodeI objects
Args : none
set_tag_valuecodeprevnextTop
 Title   : set_tag_value
Usage : $tree->set_tag_value($tag,$value)
$tree->set_tag_value($tag,@values)
Function: Sets a tag value(s) to a tree. Replaces old values.
Returns : number of values stored for this tag
Args : $tag - tag name
$value - value to store for the tag
add_tag_valuecodeprevnextTop
 Title   : add_tag_value
Usage : $tree->add_tag_value($tag,$value)
Function: Adds a tag value to a tree
Returns : number of values stored for this tag
Args : $tag - tag name
$value - value to store for the tag
remove_tagcodeprevnextTop
 Title   : remove_tag
Usage : $tree->remove_tag($tag)
Function: Remove the tag and all values for this tag
Returns : boolean representing success (0 if tag does not exist)
Args : $tag - tagname to remove
remove_all_tagscodeprevnextTop
 Title   : remove_all_tags
Usage : $tree->remove_all_tags()
Function: Removes all tags
Returns : None
Args : None
get_all_tagscodeprevnextTop
 Title   : get_all_tags
Usage : my @tags = $tree->get_all_tags()
Function: Gets all the tag names for this Tree
Returns : Array of tagnames
Args : None
get_tag_valuescodeprevnextTop
 Title   : get_tag_values
Usage : my @values = $tree->get_tag_values($tag)
Function: Gets the values for given tag ($tag)
Returns : Array of values or empty list if tag does not exist
Args : $tag - tag name
has_tagcodeprevnextTop
 Title   : has_tag
Usage : $tree->has_tag($tag)
Function: Boolean test if tag exists in the Tree
Returns : Boolean
Args : $tag - tagname
Methods code
get_nodesdescriptionprevnextTop
sub get_nodes {
   my ($self) = @_;
   $self->throw_not_implemented();
}
get_root_nodedescriptionprevnextTop
sub get_root_node {
   my ($self) = @_;
   $self->throw_not_implemented();
}
number_nodesdescriptionprevnextTop
sub number_nodes {
   my ($self) = @_;
   my $root = $self->get_root_node;
   if( defined $root && $root->isa('Bio::Tree::NodeI'))  {
       return ($root->descendent_count + 1);
   }
   return 0;
}
total_branch_lengthdescriptionprevnextTop
sub total_branch_length {
   my ($self) = @_;
   $self->throw_not_implemented();
}
heightdescriptionprevnextTop
sub height {
   my ($self) = @_;
   my $nodect =  $self->number_nodes;
   return 0 if( ! $nodect ); 
   return log($nodect) / log(2);
}
iddescriptionprevnextTop
sub id {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
scoredescriptionprevnextTop
sub score {
   my ($self,$value) = @_;
   $self->throw_not_implemented();
}
get_leaf_nodesdescriptionprevnextTop
sub get_leaf_nodes {
   my ($self) = @_;
   return grep { $_->is_Leaf() } $self->get_nodes(-sortby  => 'none');
}
set_tag_valuedescriptionprevnextTop
sub set_tag_value {
    shift->throw_not_implemented();
}
add_tag_valuedescriptionprevnextTop
sub add_tag_value {
    shift->throw_not_implemented();
}
remove_tagdescriptionprevnextTop
sub remove_tag {
    shift->throw_not_implemented();
}
remove_all_tagsdescriptionprevnextTop
sub remove_all_tags {
    shift->throw_not_implemented();
}
get_all_tagsdescriptionprevnextTop
sub get_all_tags {
    shift->throw_not_implemented();
}
get_tag_valuesdescriptionprevnextTop
sub get_tag_values {
    shift->throw_not_implemented();
}
has_tagdescriptionprevnextTop
sub has_tag {
    shift->throw_not_implemented();
}

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 StajichTop
Email jason@bioperl.org
CONTRIBUTORSTop
Aaron Mackey, amackey@virginia.edu
Elia Stupka, elia@fugu-sg.org
Sendu Bala, bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Methods for associating Tag/Values with a TreeTop
These methods associate tag/value pairs with a Tree