Bio::Tree::AlleleNode - A Node with Alleles attached use Bio::Tree::AlleleNode; AlleleNodes are basic Bio::Tree::Nodes with the added ability to add Genotypes alleles as defined by the Bio::PopGen::IndividualI interface. Genotypes are defined by the Bio::PopGen::GenotypeI interface, you will probably want to use the Bio::PopGen::Genotype implementation. This is implemented via containment to avoid multiple inheritance problems. Their is a Bio::PopGen::Individual object which handles the Bio::PopGen::IndividualI interface, and is accessible via the Bio::Tree::AlleleNode::individual method.

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email jason-at-bioperl-dot-org Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ This module was re-written to be a combination of Bio::PopGen::Individual and Bio::Tree::Node primarily for use in Bio::PopGen::Simulation::Coalescent simulations.

new
Title : new Usage : my $obj = new Bio::Tree::AlleleNode(); Function: Builds a new Bio::Tree::AlleleNode() object Returns : an instance of Bio::Tree::AlleleNode Args : -unique_id => $id, -genotypes => \@genotypes -left => pointer to Left descendent (optional) -right => pointer to Right descenent (optional) -branch_length => branch length [integer] (optional) -bootstrap => value bootstrap value (string) -description => description of node -id => human readable (unique) id for node Should NOT contain the characters '();:' =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->individual( Bio::PopGen::Individual->new(@args)); return $self; }

individual
Title : individual Usage : $obj->individual($newval) Function: Get/Set Access to the underlying individual object Returns : L<Bio::PopGen::Individual> object Args : on set, new value (L<Bio::PopGen::Individual>)

Bio::PopGen::Individual methods
Methods required by Bio::PopGen::IndividualI.

unique_id
Title : unique_id Usage : my $id = $individual->unique_id Function: Unique Identifier Returns : string representing unique identifier Args : string

num_of_results
Title : num_of_results Usage : my $count = $person->num_results; Function: returns the count of the number of Results for a person Returns : integer Args : none

add_Genotype
Title : add_Genotype Usage : $individual->add_Genotype Function: add a genotype value, only a single genotype may be associated Returns : count of the number of genotypes associated with this individual Args : @genotypes - Bio::PopGen::GenotypeI object(s) containing alleles plus a marker name

reset_Genotypes
Title : reset_Genotypes Usage : $individual->reset_Genotypes; Function: Reset the genotypes stored for this individual Returns : none Args : none

remove_Genotype
Title : remove_Genotype Usage : $individual->remove_Genotype(@names) Function: Removes the genotypes for the requested markers Returns : none Args : Names of markers

get_Genotypes
Title : get_Genotypes Usage : my @genotypes = $ind->get_Genotypes(-marker => $markername); Function: Get the genotypes for an individual, based on a criteria Returns : Array of genotypes Args : either none (return all genotypes) or -marker => name of marker to return (exact match, case matters)

has_Marker
Title : has_Marker Usage : if( $ind->has_Marker($name) ) {} Function: Boolean test to see if an Individual has a genotype for a specific marker Returns : Boolean (true or false) Args : String representing a marker name

get_marker_names
Title : get_marker_names Usage : my @names = $individual->get_marker_names; Function: Returns the list of known marker names Returns : List of strings Args : none

Bio::Tree::Node methods
Methods inherited from Bio::Tree::Node.

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 boolean flag, true if you want to ignore the fact that you are adding a second node with the same unique id (typically memory location reference in this implementation). default is false and will throw an error if you try and overwrite an existing node.

each_Descendent
Title : each_Descendent($sortby) 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 : $sortby [optional] "height", "creation" or coderef to be used to sort the order of children nodes.

remove_Descendent
Title : remove_Descendent Usage : $node->remove_Descedent($node_foo); Function: Removes a specific node from being a Descendent of this node Returns : nothing Args : An array of Bio::Node::NodeI objects which have be previously passed to the add_Descendent call of this object.

remove_all_Descendents
Title : remove_all_Descendents Usage : $node->remove_All_Descendents() Function: Cleanup the node's reference to descendents and reset their ancestor pointers to undef, if you don't have a reference to these objects after this call they will be cleaned up - so a get_nodes from the Tree object would be a safe thing to do first Returns : nothing Args : none

get_all_Descendents
Title : get_all_Descendents 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 : none

ancestor
Title : ancestor Usage : $obj->ancestor($newval) Function: Set the Ancestor Returns : value of ancestor Args : newvalue (optional)

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

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

description
Title : description Usage : $obj->description($newval) Function: Get/Set the description string Returns : value of description 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) Note : id cannot contain the chracters '();:' "A name can be any string of printable characters except blanks, colons, semicolons, parentheses, and square brackets. Because you may want to include a blank in a name, it is assumed that an underscore character ("_") stands for a blank; any of these in a name will be converted to a blank when it is read in." from <http://evolution.genetics.washington.edu/phylip/newicktree.html>

internal_id
Title : internal_id Usage : my $internalid = $node->internal_id Function: Returns the internal unique id for this Node (a monotonically increasing number for this in-memory implementation but could be a database determined unique id in other implementations) Returns : unique id Args : none

Bio::Node::NodeI decorated interface implemented
The following methods are implemented by Bio::Node::NodeI decorated interface.

is_Leaf
Title : is_Leaf Usage : if( $node->is_Leaf ) Function: Get Leaf status Returns : boolean 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. Returns : The longest length (weighting branches with branch_length) to a leaf Args : none

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

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 = $node->get_tag_value($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

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