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.

to_js()
    Serializes to simple JSON. For a conversion to NeXML/JSON, use "to_json".

     Type    : Serializer
     Title   : to_js
     Usage   : my $json = $object->to_js;
     Function: Serializes to JSON
     Returns : A JSON string
     Args    : None.
     Comments:

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>