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Man Pages


Manual Reference Pages  -  BIO::PHYLOROLE (3)

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NAME

Bio::PhyloRole - Extra behaviours for the base class

CONTENTS

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 objects 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 objects name (if none was set, the name
           is a combination of the $objs 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:

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

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perl v5.20.3 BIO::PHYLOROLE (3) 2014-02-08

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