/ 
bioperl-1.5.2_005-RCb
/ Bio::Tree::AlleleNode

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

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-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 = 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 
                             '();:'

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