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 : None
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.
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.