Raw content of Bio::Tree::NodeI # $Id: NodeI.pm,v 2003/09/14 19:00:35 jason Exp $ # # BioPerl module for Bio::Tree::NodeI # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::NodeI - Interface describing a Tree Node =head1 SYNOPSIS # get a Tree::NodeI somehow # like from a TreeIO use Bio::TreeIO; # read in a clustalw NJ in phylip/newick format my $treeio = new Bio::TreeIO(-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"; =head1 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. =head1 FEEDBACK =head2 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/MailList.shtml - About the mailing lists =head2 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.bioperl.org/ =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Aaron Mackey amackey@virginia.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tree::NodeI; use vars qw(@ISA); use strict; use Bio::Root::RootI; @ISA = qw(Bio::Root::RootI); =head2 add_Descendent Title : add_Descendent Usage : $node->add_Descendant($node); Function: Adds a descendent to a node Returns : number of current descendents for this node Args : Bio::Node::NodeI =cut sub add_Descendent{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 each_Descendent Title : each_Descendent Usage : my @nodes = $node->each_Descendent; Function: all the descendents for this Node (but not their descendents i.e. not a recursive fetchall) Returns : Array of Bio::Tree::NodeI objects Args : none =cut sub each_Descendent{ my ($self) = @_; $self->throw_not_implemented(); } =head2 Decorated Interface methods =cut =head2 get_all_Descendents Title : get_all_Descendents($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 : $sortby [optional] "height", "creation" or coderef to be used to sort the order of children nodes. =cut sub get_all_Descendents{ my ($self, $sortby) = @_; $sortby ||= 'height'; my @nodes; foreach my $node ( $self->each_Descendent($sortby) ) { push @nodes, ($node->get_all_Descendents($sortby), $node); } return @nodes; } *get_Descendents = \&get_all_Descendents; =head2 is_Leaf Title : is_Leaf Usage : if( $node->is_Leaf ) Function: Get Leaf status Returns : boolean Args : none =cut sub is_Leaf{ my ($self) = @_; $self->throw_not_implemented(); } =head2 descendent_count Title : descendent_count Usage : my $count = $node->descendent_count; Function: Counts the number of descendents a node has (and all of their subnodes) Returns : integer Args : none =cut sub descendent_count{ my ($self) = @_; my $count = 0; foreach my $node ( $self->each_Descendent ) { $count += 1; $node->can('descendent_count') ? $count += $node->descendent_count : next; } return $count; } =head2 to_string Title : to_string Usage : my $str = $node->to_string() Function: For debugging, provide a node as a string Returns : string Args : none =cut sub to_string{ my ($self) = @_; return sprintf("%s%s%s", defined $self->id ? $self->id : '', defined $self->branch_length ? ':' . $self->branch_length : ' ', $self->is_Leaf() ? '(leaf)' : '' ); } =head2 height Title : height Usage : my $len = $node->height Function: Returns the height of the tree starting at this node. Height is the maximum branchlength. Returns : The longest length (weighting branches with branch_length) to a leaf Args : none =cut sub height{ my ($self) = @_; if( $self->is_Leaf ) { if( !defined $self->branch_length ) { $self->debug(sprintf("Trying to calculate height of a node when a Node (%s) has an undefined branch_length\n",$self->id || '?' )); return 0; } return $self->branch_length; } my $max = 0; foreach my $subnode ( $self->each_Descendent ) { my $s = $subnode->height; if( $s > $max ) { $max = $s; } } return $max + ($self->branch_length || 1); } =head2 Get/Set methods =cut =head2 branch_length Title : branch_length Usage : $obj->branch_length() Function: Get/Set the branch length Returns : value of branch_length Args : newvalue (optional) =cut sub branch_length{ my ($self)= @_; $self->throw_not_implemented(); } =head2 id Title : id Usage : $obj->id($newval) Function: The human readable identifier for the node Returns : value of human readable id Args : newvalue (optional) =cut sub id{ my ($self)= @_; $self->throw_not_implemented(); } =head2 internal_id Title : internal_id Usage : my $internalid = $node->internal_id Function: Returns the internal unique id for this Node Returns : unique id Args : none =cut sub internal_id{ my ($self) = @_; $self->throw_not_implemented(); } =head2 description Title : description Usage : $obj->description($newval) Function: Get/Set the description string Returns : value of description Args : newvalue (optional) =cut sub description{ my ($self) = @_; $self->throw_not_implemented(); } =head2 bootstrap Title : bootstrap Usage : $obj->bootstrap($newval) Function: Get/Set the bootstrap value Returns : value of bootstrap Args : newvalue (optional) =cut sub bootstrap{ my ($self) = @_; $self->throw_not_implemented(); } =head2 ancestor Title : ancestor Usage : my $node = $node->ancestor; Function: Get/Set the ancestor node pointer for a Node Returns : Null if this is top level node Args : none =cut sub ancestor{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 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 =cut sub invalidate_height { shift->throw_not_implemented(); } =head2 Methods for associating Tag/Values with a Node These methods associate tag/value pairs with a Node =head2 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 =cut sub add_tag_value{ shift->throw_not_implemented(); } =head2 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 =cut sub remove_tag { shift->throw_not_implemented(); } =head2 remove_all_tags Title : remove_all_tags Usage : $node->remove_all_tags() Function: Removes all tags Returns : None Args : None =cut sub remove_all_tags{ shift->throw_not_implemented(); } =head2 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 =cut sub get_all_tags { shift->throw_not_implemented(); } =head2 get_tag_values Title : get_tag_values Usage : my @values = $node->get_tag_value($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 =cut sub get_tag_values{ shift->throw_not_implemented(); } =head2 has_tag Title : has_tag Usage : $node->has_tag($tag) Function: Boolean test if tag exists in the Node Returns : Boolean Args : $tag - tagname =cut sub has_tag{ shift->throw_not_implemented(); } 1;