Bio::Phylo - Phylogenetic analysis using perl
# 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;
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.
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
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.
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.
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.
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( );
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.
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
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
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
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
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
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
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.
Serializes to simple JSON. For a conversion to NeXML/JSON, use to_json.
to_json
Type : Serializer Title : to_js Usage : my $json = $object->to_js; Function: Serializes to JSON Returns : A JSON string Args : None. Comments:
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
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
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.