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Author image Rutger Vos
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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'
        -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:

names with spaces in them that aren't 'single quoted' have their spaces replaced with underscores
names with any of the following characters in them are single quoted: -^*(){}[]+=;:"\<>/,
names with single quotes inside them (i.e. not around them) are "double quoted"
 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

Returns suggested citation.

 Type    : Accessor
 Title   : CITATION
 Usage   : $phylo->CITATION;
 Function: Returns suggested citation.
 Returns : Returns suggested citation.
 Args    : None


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