Bio::PhyloRole - Extra behaviours for the base class
# 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.
Gets invocant's name, modified to be safely used in nexus files. This means that:
Type : Accessor Title : get_nexus_name Usage : my $name = $obj->get_nexus_name; Function: Returns the object's name. Returns : A string Args : (Optional) if provided a true value, the returned name may be the null string, in cases where no name for the object has been set. The default value (i.e. if no argument was provided) is to return an autogenerated name for any anonymous object.
Gets invocant's 'fallback' name (possibly autogenerated).
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
Attempts to execute argument string as method on invocant.
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';
Serializes object to general purpose string
Type : Serializer Title : to_string() Usage : print $obj->to_string(); Function: Serializes object to general purpose string Returns : String Args : None Comments: This is YAML
Getter and setter for the verbosity level. Refer to Bio::Phylo::Util::Logger for more info on available verbosity levels.
Type : Accessor Title : VERBOSE() Usage : Bio::Phylo->VERBOSE( -level => $level ) Function: Sets/gets verbose level Returns : Verbose level Args : -level => $level Comments:
Returns suggested citation.
Type : Accessor Title : CITATION Usage : $phylo->CITATION; Function: Returns suggested citation. Returns : Returns suggested citation. 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.
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