NAME
Bio::Phylo - Phylogenetic analysis using perl.
SYNOPSIS
# verbosity goes from 0, only fatal messages, to 4: everything from
# fatal -> error -> warning -> info -> debug (which is a lot)
use Bio::Phylo verbose => 1;DESCRIPTION
This is the base class for the Bio::Phylo package. Most other modules inherit from it, the methods defined here are applicable to them. 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. The arguments shown here can thus also be passed to any of the child classes' constructors, which will pass them on up the inheritance tree.
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, hash ref)
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, will be single quoted if it contains [;|,|:\(|\)] or spaces. Preceding and trailing spaces will be removed. - 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, or undefined to reset score. - 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: $obj->set_generic( '-lnl' => 0.87565 ); * or a hash ref, for example: $obj->set_generic( { '-lnl' => 0.87565 } ); * or nothing, to reset the stored hash, e.g. $obj->set_generic( );
ACCESSORS
- get_name()
-
Type : Accessor Title : get_name Usage : my $name = $obj->get_name; Function: Returns the object's name (if none was set, the name is a combination of the $obj's class and its UID). 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() }; Function: Returns the object's generic data. If an argument is used, it is considered a key for which the associated value is returned. Without arguments, a reference to the whole hash is returned. Returns : A string or hash reference. Args : None - get_id()
-
Type : Accessor Title : get_id Usage : my $id = $obj->get_id; Function: Returns the object's unique ID Returns : INT 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 $treename = $tree->get('get_name'); 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 = 'get_name'; - debug()
-
Type : logging method Title : debug Usage : $object->debug( "debugging message" ); Function: prints debugging message, depending on verbosity Returns : invocant Args : logging message - info()
-
Type : logging method Title : info Usage : $object->info( "info message" ); Function: prints info message, depending on verbosity Returns : invocant Args : logging message - warn()
-
Type : logging method Title : warn Usage : $object->warn( "warning message" ); Function: prints warning message, depending on verbosity Returns : invocant Args : logging message - error()
-
Type : logging method Title : error Usage : $object->error( "error message" ); Function: prints error message, depending on verbosity Returns : invocant Args : logging message - fatal()
-
Type : logging method Title : fatal Usage : $object->fatal( "fatal message" ); Function: prints fatal message, depending on verbosity Returns : invocant Args : logging message - 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. Comments: Currently not implemented - VERBOSE()
-
Getter and setter for the verbose level. This comes in five levels: 0 = only fatal messages (though, when something fatal happens, you'll most likely get an exception object), 1 = errors (hopefully recoverable), 2 = warnings (recoverable), 3 = info (useful diagnostics), 4 = debug (every method call)
Type : Accessor Title : VERBOSE() Usage : Bio::Phylo->VERBOSE( -level => $level ) Function: Sets/gets verbose level Returns : Verbose level Args : 0 <= $level && $level <= 4 Comments: - CITATION()
-
Type : Accessor Title : CITATION Usage : $phylo->CITATION; Function: Returns suggested citation. Returns : Returns suggested citation. Args : None Comments: - VERSION()
-
Type : Accessor Title : VERSION Usage : $phylo->VERSION; Function: Returns version number (including SVN revision number). Alias : Returns : SCALAR Args : NONE Comments: - to_xml()
-
Type : Format converter Title : to_xml Usage : my $xml = $obj->to_xml; Function: Returns an XML representation of the invocant object. Returns : SCALAR Args : NONE
DESTRUCTOR
- DESTROY()
-
Type : Destructor Title : DESTROY Usage : $phylo->DESTROY Function: Destroys Phylo object Alias : Returns : TRUE Args : none Comments: You don't really need this, it is called automatically when the object goes out of scope.
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 3319 2007-03-20 01:39:35Z rvosa $
AUTHOR
Rutger Vos,
- email: mailto://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.