Bio::Tree::NodeI(3pm)

NAME

Bio::Tree::NodeI - Interface describing a Tree Node

SYNOPSIS

    # get a Tree::NodeI somehow
    # like from a TreeIO
    use Bio::TreeIO;
    # read in a clustalw NJ in phylip/newick format
    my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'file.dnd');
    my $tree = $treeio->next_tree; # we'll assume it worked for demo purposes
                                   # you might want to test that it was defined
    my $rootnode = $tree->get_root_node;
    # process just the next generation
    foreach my $node ( $rootnode->each_Descendent() ) {
        print "branch len is ", $node->branch_length, "\n";
    }
    # process all the children
    my $example_leaf_node;
    foreach my $node ( $rootnode->get_all_Descendents() ) {
        if( $node->is_Leaf ) { 
            print "node is a leaf ... "; 
            # for example use below
            $example_leaf_node = $node unless defined $example_leaf_node; 
        }
        print "branch len is ", $node->branch_length, "\n";
    }
    # The ancestor() method points to the parent of a node
    # A node can only have one parent
    my $parent = $example_leaf_node->ancestor;
    # parent won't likely have an description because it is an internal node
    # but child will because it is a leaf
    print "Parent id: ", $parent->id," child id: ", 
          $example_leaf_node->id, "\n";

DESCRIPTION

A NodeI is capable of the basic structure of building a tree and storing the branch length between nodes. The branch length is the length of the branch between the node and its ancestor, thus a root node in a Tree will not typically have a valid branch length.

Various implementations of NodeI may extend the basic functions and allow storing of other information (like attaching a species object or full sequences used to build a tree or alternative sequences). If you don't know how to extend a Bioperl object please ask, happy to help, we would also greatly appreciate contributions with improvements or extensions of the objects back to the Bioperl code base so that others don't have to reinvent your ideas.

FEEDBACK

Mailing Lists

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 Bugs

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email [email protected]

CONTRIBUTORS

Aaron Mackey [email protected]

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

add_Descendent

 Title   : add_Descendent
 Usage   : $node->add_Descendent($node);
 Function: Adds a descendent to a node
 Returns : number of current descendents for this node
 Args    : Bio::Node::NodeI

each_Descendent

 Title   : each_Descendent
 Usage   : my @nodes = $node->each_Descendent;
 Function: all the descendents for this Node (but not their descendents 
                                              i.e. not a recursive fetchall)
 Returns : Array of Bio::Tree::NodeI objects
 Args    : none

Decorated Interface methods

get_all_Descendents

 Title   : get_all_Descendents($sortby)
 Usage   : my @nodes = $node->get_all_Descendents;
 Function: Recursively fetch all the nodes and their descendents
           *NOTE* This is different from each_Descendent
 Returns : Array or Bio::Tree::NodeI objects
 Args    : $sortby [optional] "height", "creation", "alpha", "revalpha", 
           or a coderef to be used to sort the order of children nodes.

is_Leaf

 Title   : is_Leaf
 Usage   : if( $node->is_Leaf ) 
 Function: Get Leaf status
 Returns : boolean
 Args    : none

descendent_count

 Title   : descendent_count
 Usage   : my $count = $node->descendent_count;
 Function: Counts the number of descendents a node has 
           (and all of their subnodes)
 Returns : integer
 Args    : none

to_string

 Title   : to_string
 Usage   : my $str = $node->to_string()
 Function: For debugging, provide a node as a string
 Returns : string
 Args    : none

height

 Title   : height
 Usage   : my $len = $node->height
 Function: Returns the height of the tree starting at this
           node.  Height is the maximum branchlength to get to the tip.
 Returns : The longest length (weighting branches with branch_length) to a leaf
 Args    : none

depth

 Title   : depth
 Usage   : my $len = $node->depth
 Function: Returns the depth of the tree starting at this
           node.  Depth is the distance from this node to the root.
 Returns : The branch length to the root.
 Args    : none

Get/Set methods

branch_length

 Title   : branch_length
 Usage   : $obj->branch_length()
 Function: Get/Set the branch length
 Returns : value of branch_length
 Args    : newvalue (optional)

id

 Title   : id
 Usage   : $obj->id($newval)
 Function: The human readable identifier for the node 
 Returns : value of human readable id
 Args    : newvalue (optional)

internal_id

 Title   : internal_id
 Usage   : my $internalid = $node->internal_id
 Function: Returns the internal unique id for this Node
 Returns : unique id
 Args    : none

description

 Title   : description
 Usage   : $obj->description($newval)
 Function: Get/Set the description string
 Returns : value of description
 Args    : newvalue (optional)

bootstrap

 Title   : bootstrap
 Usage   : $obj->bootstrap($newval)
 Function: Get/Set the bootstrap value
 Returns : value of bootstrap
 Args    : newvalue (optional)

ancestor

 Title   : ancestor
 Usage   : my $node = $node->ancestor;
 Function: Get/Set the ancestor node pointer for a Node
 Returns : Null if this is top level node
 Args    : none

invalidate_height

 Title   : invalidate_height
 Usage   : private helper method
 Function: Invalidate our cached value of the node height in the tree
 Returns : nothing
 Args    : none

Methods for associating Tag/Values with a Node

These methods associate tag/value pairs with a Node

set_tag_value

 Title   : set_tag_value
 Usage   : $node->set_tag_value($tag,$value)
           $node->set_tag_value($tag,@values)
 Function: Sets a tag value(s) to a node. Replaces old values.
 Returns : number of values stored for this tag
 Args    : $tag   - tag name
           $value - value to store for the tag

add_tag_value

 Title   : add_tag_value
 Usage   : $node->add_tag_value($tag,$value)
 Function: Adds a tag value to a node 
 Returns : number of values stored for this tag
 Args    : $tag   - tag name
           $value - value to store for the tag

remove_tag

 Title   : remove_tag
 Usage   : $node->remove_tag($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_tags

 Title   : remove_all_tags
 Usage   : $node->remove_all_tags()
 Function: Removes all tags 
 Returns : None
 Args    : None

get_all_tags

 Title   : get_all_tags
 Usage   : my @tags = $node->get_all_tags()
 Function: Gets all the tag names for this Node
 Returns : Array of tagnames
 Args    : None

get_tag_values

 Title   : get_tag_values
 Usage   : my @values = $node->get_tag_values($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_tag

 Title   : has_tag
 Usage   : $node->has_tag($tag)
 Function: Boolean test if tag exists in the Node
 Returns : Boolean
 Args    : $tag - tagname

Helper Functions

id_output

 Title   : id_output
 Usage   : my $id = $node->id_output;
 Function: Return an id suitable for output in format like newick
           so that if it contains spaces or ():; characters it is properly 
           quoted
 Returns : $id string if $node->id has a value
 Args    : none