| Bio::Tree::AlleleNode(3pm) | User Contributed Perl Documentation | Bio::Tree::AlleleNode(3pm) |
Bio::Tree::AlleleNode - A Node with Alleles attached
use Bio::Tree::AlleleNode;
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.
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
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.
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
Email jason-at-bioperl-dot-org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
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
'();:'
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>)
Methods required by Bio::PopGen::IndividualI.
Title : unique_id Usage : my $id = $individual->unique_id Function: Unique Identifier Returns : string representing unique identifier Args : string
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
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
Title : reset_Genotypes Usage : $individual->reset_Genotypes; Function: Reset the genotypes stored for this individual Returns : none Args : none
Title : remove_Genotype Usage : $individual->remove_Genotype(@names) Function: Removes the genotypes for the requested markers Returns : none Args : Names of markers
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)
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
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
Methods inherited from Bio::Tree::Node.
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.
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.
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.
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
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
Title : ancestor Usage : $obj->ancestor($newval) Function: Set the Ancestor Returns : value of ancestor Args : newvalue (optional)
Title : branch_length Usage : $obj->branch_length() Function: Get/Set the branch length Returns : value of branch_length Args : newvalue (optional)
Title : bootstrap Usage : $obj->bootstrap($newval) Function: Get/Set the bootstrap value Returns : value of bootstrap Args : newvalue (optional)
Title : description Usage : $obj->description($newval) Function: Get/Set the description string Returns : value of description Args : newvalue (optional)
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 characters '();:'
"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>
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
The following methods are implemented by Bio::Node::NodeI decorated interface.
Title : is_Leaf Usage : if( $node->is_Leaf ) Function: Get Leaf status Returns : boolean Args : none
Title : to_string Usage : my $str = $node->to_string() Function: For debugging, provide a node as a string Returns : string Args : none
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
Title : invalidate_height Usage : private helper method Function: Invalidate our cached value of the node's height in the tree Returns : nothing Args : none
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
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
Title : remove_all_tags Usage : $node->remove_all_tags() Function: Removes all tags Returns : None Args : None
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
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
Title : has_tag Usage : $node->has_tag($tag) Function: Boolean test if tag exists in the Node Returns : Boolean Args : $tag - tagname
| 2018-10-27 | perl v5.26.2 |