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Bio::Phylo(3)	      User Contributed Perl Documentation	 Bio::Phylo(3)

NAME
       Bio::Phylo - Phylogenetic analysis using	perl

SYNOPSIS
	# Actually, you	would almost never use this module directly. This is
	# the base class for other modules.
	use Bio::Phylo;

	# sets global verbosity	to 'error'
	Bio::Phylo->VERBOSE( -level => Bio::Phylo::Util::Logger::ERROR );

	# sets verbosity for forest ojects to 'debug'
	Bio::Phylo->VERBOSE(
	       -level => Bio::Phylo::Util::Logger::DEBUG,
	       -class => 'Bio::Phylo::Forest'
	);

	# prints version, including SVN	revision number
	print Bio::Phylo->VERSION;

	# prints suggested citation
	print Bio::Phylo->CITATION;

DESCRIPTION
       This is the base	class for the Bio::Phylo package for phylogenetic
       analysis	using object-oriented perl5. In	this file, methods are defined
       that are	performed by other objects in the Bio::Phylo release that
       inherit from this base class (which you normally	wouldn't use
       directly).

       For general information on how to use Bio::Phylo, consult the manual
       (Bio::Phylo::Manual).

       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 in Bio::Phylo::Util::Logger of use to	localize
       problems.

METHODS
   CONSTRUCTOR
       new()
	   The Bio::Phylo root constructor is rarely used directly. Rather,
	   many	other objects in Bio::Phylo internally go up the inheritance
	   tree	to this	constructor.  The arguments shown here can therefore
	   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    : Optional,	any number of setters. For example,
			      Bio::Phylo->new( -name =>	$name )
			      will call	set_name( $name	) internally

   MUTATORS
       set_guid()
	   Sets	invocant GUID.

	    Type    : Mutator
	    Title   : set_guid
	    Usage   : $obj->set_guid($guid);
	    Function: Assigns an object's GUID.
	    Returns : Modified object.
	    Args    : A	scalar
	    Notes   : This field can be	used for storing an identifier that is
		      unambiguous within a given content. For example, an LSID,
		      a	genbank	accession number, etc.

       set_desc()
	   Sets	invocant description.

	    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()
	   Sets	invocant 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()
	   Sets	generic	key/value pair(s).

	    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_guid()
	   Gets	invocant GUID.

	    Type    : Accessor
	    Title   : get_guid
	    Usage   : my $guid = $obj->get_guid;
	    Function: Assigns an object's GUID.
	    Returns : Scalar.
	    Args    : None
	    Notes   : This field can be	used for storing an identifier that is
		      unambiguous within a given content. For example, an LSID,
		      a	genbank	accession number, etc.

       get_desc()
	   Gets	invocant description.

	    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()
	   Gets	invocant's 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()
	   Gets	generic	hashref	or hash	value(s).

	    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	value or an array reference of values
	    Args    : A	key (string) or	an array reference of keys

   PACKAGE METHODS
       get_obj_by_id()
	   Attempts to fetch an	in-memory object by its	UID

	    Type    : Accessor
	    Title   : get_obj_by_id
	    Usage   : my $obj =	Bio::Phylo->get_obj_by_id($uid);
	    Function: Fetches an object	from the IDPool	cache
	    Returns : A	Bio::Phylo object
	    Args    : A	unique id

       get_logger()
	   Returns a singleton reference to a Bio::Phylo::Util::Logger object

	    Type    : Accessor
	    Title   : get_logger
	    Usage   : my $logger = Bio::Phylo->get_logger
	    Function: Returns logger
	    Returns : A	Bio::Phylo::Util::Logger object
	    Args    : None

       VERSION()
	   Returns the $VERSION	string of this Bio::Phylo release

	    Type    : Accessor
	    Title   : VERSION
	    Usage   : my $version = Bio::Phylo->VERSION
	    Function: Returns version string
	    Returns : A	string
	    Args    : None

       clone()
	   Clones invocant.

	    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: Cloning is currently experimental, use with caution.

SEE ALSO
       There is	a mailing list at
       <https://groups.google.com/forum/#!forum/bio-phylo> for any user	or
       developer questions and discussions.

       Also see	the manual: Bio::Phylo::Manual and
       <http://rutgervos.blogspot.com>

CITATION
       If you use Bio::Phylo in	published research, please cite	it:

       Rutger A	Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase
       Miller, 2011. Bio::Phylo	- phyloinformatic analysis using Perl.	BMC
       Bioinformatics 12:63.  <http://dx.doi.org/10.1186/1471-2105-12-63>

perl v5.24.1			  2014-03-27			 Bio::Phylo(3)

NAME | SYNOPSIS | DESCRIPTION | METHODS | SEE ALSO | CITATION

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::Phylo&sektion=3&manpath=FreeBSD+12.1-RELEASE+and+Ports>

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