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.

  [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 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