NAME

       Bio::Tree::AlleleNode - A Node with Alleles attached

SYNOPSIS

         use Bio::Tree::AlleleNode;

DESCRIPTION

       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.

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:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org

APPENDIX

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

HISTORY

       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 = Bio::Tree::AlleleNode->new();
        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
                                    '();:'

   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   : $node->add_Descendent($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