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Bio::Tree::AlleleNode(User Contributed Perl DocumentatBio::Tree::AlleleNode(3)

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://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

perl v5.24.1			  2017-07-08	      Bio::Tree::AlleleNode(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX | HISTORY

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::Tree::AlleleNode&sektion=3&manpath=FreeBSD+12.0-RELEASE+and+Ports>

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