Bio::Tree::AlleleNode.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   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 = 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