NAME

Bio::PhyloRole - Extra behaviours for the base class

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

ACCESSORS

get_nexus_name()

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.

get_internal_name()

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

PACKAGE METHODS

get()

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';

to_string()

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

VERBOSE()

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:

CITATION()

Returns suggested citation.

Type    : Accessor
Title   : CITATION
Usage   : $phylo->CITATION;
Function: Returns suggested citation.
Returns : Returns suggested citation.
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