Bio::Phylo
Bio::Phylo
Bio::Phylo - Phylogenetic analysis using perl.
# 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;
This is the base class for the Bio::Phylo OO package. In this file, methods are defined that are performed by other objects in the Bio::Phylo release, i.e. objects that inherit from this class.
For general information on how to use Bio::Phylo, consult the manual (Bio::Phylo::Manual); for information on using Bio::Phylo in combination with Bioperl (http://www.bioperl.org) and Bio::Nexus (http://search.cpan.org/~tjhladish/Bio-NEXUS), consult the object compatibility document (Bio::ObjectCompat).
If you come here because you are trying to debug a problem you run into in using Bio::Phylo, you may be interested in the "exceptions" system as discussed in Bio::Phylo::Util::Exceptions. In addition, you may find the logging system that is discussed below of use.
Documentation on the various scripts included in this release is embedded in
their respective source files, which, like all perldoc can be viewed in
various ways using the nroff-like formatter perldoc <filename> or using
one of the many pod2* convertors such as pod2text, pod2html, pod2latex and so
on. In addition, the scripts generally have a -h or --help or -?
option.
The Bio::Phylo root 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. Generally, constructors in Bio::Phylo subclasses can process as arguments all methods that have set_* in their names. The arguments are named for the methods, but "set_" has been replaced with a dash "-", e.g. the method "set_name" becomes the argument "-name" in the constructor.
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)
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.
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.
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.
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( );
Type : Accessor Title : get_name Usage : my $name = $obj->get_name; Function: Returns the object's name. Returns : A string Args : None
Type : Accessor
Title : get_internal_name
Usage : my $name = $obj->get_internal_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
Type : Accessor Title : get_desc Usage : my $desc = $obj->get_desc; Function: Returns the object's description (if any). Returns : A string Args : None
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
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
Type : Accessor Title : get_id Usage : my $id = $obj->get_id; Function: Returns the object's unique ID Returns : INT Args : None
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';
Type : logging method Title : debug Usage : $object->debug( "debugging message" ); Function: prints debugging message, depending on verbosity Returns : invocant Args : logging message
Type : logging method Title : info Usage : $object->info( "info message" ); Function: prints info message, depending on verbosity Returns : invocant Args : logging message
Type : logging method Title : warn Usage : $object->warn( "warning message" ); Function: prints warning message, depending on verbosity Returns : invocant Args : logging message
Type : logging method Title : error Usage : $object->error( "error message" ); Function: prints error message, depending on verbosity Returns : invocant Args : logging message
Type : logging method Title : fatal Usage : $object->fatal( "fatal message" ); Function: prints fatal message, depending on verbosity Returns : invocant Args : logging message
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
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:
Type : Accessor Title : CITATION Usage : $phylo->CITATION; Function: Returns suggested citation. Returns : Returns suggested citation. Args : None Comments:
Type : Accessor
Title : VERSION
Usage : $phylo->VERSION;
Function: Returns version number
(including SVN revision number).
Alias :
Returns : SCALAR
Args : NONE
Comments:
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.
Also see the manual: Bio::Phylo::Manual.
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
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 3409 2007-03-27 21:27:44Z rvosa $
Rutger Vos,
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 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.