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    : None

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