Linux Certif

Toute la documentation sur la certification Linux LPI

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 attatching 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.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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 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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Aaron Mackey amackey@virginia.edu

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