Bio::Tree
AlleleNode
Summary
Bio::Tree::AlleleNode - A Node with Alleles attached
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::Tree::AlleleNode;
Description
Methods
Methods description
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
'();:' |
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 = $individual->get_marker_names;
Function: Returns the list of known marker names
Returns : List of strings
Args : none |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->individual( Bio::PopGen::Individual->new(@args));
return $self;} |
sub individual
{ my ($self,$newval) = @_;
if( defined $newval || ! defined $self->{'individual'} ) {
$newval = Bio::PopGen::Individual->new() unless defined $newval;
$self->{'individual'} = $newval;
}
return $self->{'individual'};} |
sub unique_id
{ my $self = shift;
$self->individual->unique_id(@_);} |
sub num_of_results
{ my $self = shift;
$self->individual->num_of_results(@_);} |
sub add_Genotype
{ my $self = shift;
$self->individual->add_Genotype(@_);} |
sub reset_Genotypes
{ my $self = shift;
$self->individual->reset_Genotypes(@_);} |
sub remove_Genotype
{ my $self = shift;
$self->individual->remove_Genotype(@_);} |
sub get_Genotypes
{ my $self = shift;
$self->individual->get_Genotypes(@_);} |
sub has_Marker
{ my $self = shift;
$self->individual->has_Marker(@_);} |
sub get_marker_names
{ my $self = shift;
$self->individual->get_marker_names(@_); } |
General documentation
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/MailList.shtml - About the mailing lists
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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
| AUTHOR - Jason Stajich | Top |
Email jason-at-bioperl-dot-org
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
| Bio::PopGen::Individual methods | Top |
| Bio::Tree::Node methods | Top |
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.
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.
| remove_all_Descendents | Top |
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 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
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 | Top |
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