NAME

Bio::Phylo - Phylogenetic analysis using perl.

DESCRIPTION

This is the base class for the Bio::Phylo package. All other modules inherit from it, the methods defined here are applicable to all. Consult the manual for usage examples: Bio::Phylo::Manual.

METHODS

CONSTRUCTOR

new()

The Bio::Phylo object itself, and thus its constructor, is rarely, if ever, used directly. Rather, all other objects in this package inherit its methods, and call its constructor internally.

Type    : Constructor
Title   : new
Usage   : my $phylo = Bio::Phylo->new;
Function: Instantiates Bio::Phylo object
Returns : a Bio::Phylo object
Args    : -name    => (object name)
          -desc    => (object description)
          -score   => (numerical score)
          -generic => (generic key/value pair)

MUTATORS

set_name()

Type    : Mutator
Title   : set_name
Usage   : $obj->set_name($name);
Function: Assigns an object's name.
Returns : Modified object.
Args    : Argument must be a string that doesn't contain [;|,|:\(|\)]

set_desc()

Type    : Mutator
Title   : set_desc
Usage   : $obj->set_desc($desc);
Function: Assigns an object's description.
Returns : Modified object.
Args    : Argument must be a string.

set_score()

Type    : Mutator
Title   : set_score
Usage   : $obj->set_score($score);
Function: Assigns an object's numerical score.
Returns : Modified object.
Args    : Argument must be any of perl's number formats.

set_generic()

Type    : Mutator
Title   : set_generic
Usage   : $obj->set_generic(%generic);
Function: Assigns generic key/value pairs to the invocant.
Returns : Modified object.
Args    : Valid arguments constitute key/value pairs, for example:
          $node->set_generic(posterior => 0.87565);

ACCESSORS

get_name()

Type    : Accessor
Title   : get_name
Usage   : my $name = $obj->get_name;
Function: Returns the object's name (if any).
Returns : A string
Args    : None

get_desc()

Type    : Accessor
Title   : get_desc
Usage   : my $desc = $obj->get_desc;
Function: Returns the object's description (if any).
Returns : A string
Args    : None

get_score()

Type    : Accessor
Title   : get_score
Usage   : my $score = $obj->get_score;
Function: Returns the object's numerical score (if any).
Returns : A number
Args    : None

get_generic()

Type    : Accessor
Title   : get_generic
Usage   : my $value = $obj->get_generic($key);
          or
          my %hash = %{ $obj->get_generic($key) };
Function: Returns the object's generic data. If an
          argument is used, it is considered a key
          for which the associated value is return.
          Without arguments, a reference to the whole
          hash is returned.
Returns : A string or hash reference.
Args    : None

PACKAGE METHODS

get()

All objects in the package subclass the Bio::Phylo object, and so, for example, you can do $node->get('get_branch_length'); instead of $node->get_branch_length. This is a useful feature for listable objects especially, as they have the get_by_value method, which allows you to retrieve, for instance, a list of nodes whose branch length exceeds a certain value. That method (and get_by_regular_expression) uses this $obj->get method.

Type    : Accessor
Title   : get
Usage   : my $treelength = $tree->get('calc_tree_length');
Function: Alternative syntax for safely accessing any of the object data;
          useful for interpolating runtime $vars.
Returns : (context dependent)
Args    : a SCALAR variable, e.g. $var = 'calc_tree_length';

clone()

Type    : Utility method
Title   : clone
Usage   : my $clone = $object->clone;
Function: Creates a copy of the invocant object.
Returns : A copy of the invocant.
Args    : none.

VERBOSE()

Getter and setter for the verbose level. Currently it's just 0=no messages, 1=messages, but perhaps there could be more levels? For caller diagnostics and so on?

Type    : Accessor
Title   : VERBOSE(0|1)
Usage   : Phylo->VERBOSE(0|1)
Function: Sets/gets verbose level
Alias   :
Returns : Verbose level
Args    : 0=no messages; 1=error messages
Comments:

CITATION()

Type    : Accessor
Title   : CITATION
Usage   : $phylo->CITATION;
Function: Returns suggested citation.
Alias   :
Returns : Returns suggested citation.
Args    : None
Comments:

VERSION()

Type    : Accessor
Title   : VERSION
Usage   : $phylo->VERSION;
Function: Returns version number (including revision number).
Alias   :
Returns : SCALAR
Args    : NONE
Comments:

DESTRUCTOR

DESTROY()

The destructor doesn't actually do anything yet, but it may be used, in the future, for additional debugging messages.

Type    : Destructor
Title   : DESTROY
Usage   : $phylo->DESTROY
Function: Destroys Phylo object
Alias   :
Returns : TRUE
Args    : none
Comments: You don't really need this, perl takes care of memory
          management and garbage collection.

SEE ALSO

Also see the manual: Bio::Phylo::Manual.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: Phylo.pm,v 1.20 2005/09/29 20:31:16 rvosa Exp $

AUTHOR

Rutger Vos,

email: rvosa@sfu.ca

web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.