The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
Bio-Phylo-0.17_RC3
River stage two • 9 direct dependents • 18 total dependents
/ Bio::Phylo

NAME

Bio::Phylo - Phylogenetic analysis using perl.

SYNOPSIS

 # verbosity goes from 0, only fatal messages, to 4: everything from
 # fatal -> error -> warning -> info -> debug (which is a lot)
 use Bio::Phylo verbose => 1;

DESCRIPTION

This is the base class for the Bio::Phylo OO package. In this file, methods are defined that are performed by other objects in the Bio::Phylo release, i.e. objects that inherit from this class.

For general information on how to use Bio::Phylo, consult the manual (Bio::Phylo::Manual); for information on using Bio::Phylo in combination with Bioperl (http://www.bioperl.org) and Bio::Nexus (http://search.cpan.org/~tjhladish/Bio-NEXUS), consult the object compatibility document (Bio::ObjectCompat).

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 that is discussed in this base class of use.

Documentation on the various scripts included in this release is embedded in their respective source files, which, like all perldoc can be viewed in various ways using the nroff-like formatter perldoc <filename> or using one of the many pod2* convertors such as pod2text, pod2html, pod2latex and so on. In addition, the scripts generally have a -h or --help or -? option.

METHODS

CONSTRUCTOR

new()

The Bio::Phylo root object itself, and thus its constructor, is rarely, if ever, used directly. Rather, all other objects in this package inherit its methods, and call its constructor internally. The arguments shown here can thus also be passed to any of the child classes' constructors, which will pass them on up the inheritance tree. Generally, constructors in Bio::Phylo subclasses can process as arguments all methods that have set_* in their names. The arguments are named for the methods, but "set_" has been replaced with a dash "-", e.g. the method "set_name" becomes the argument "-name" in the constructor.

 Type    : Constructor
 Title   : new
 Usage   : my $phylo = Bio::Phylo->new;
 Function: Instantiates Bio::Phylo object
 Returns : a Bio::Phylo object
 Args    : -name    => (object name)
           -desc    => (object description)
           -score   => (numerical score)
           -generic => (generic key/value pair, hash ref)

MUTATORS

set_name()

Sets invocant name.

 Type    : Mutator
 Title   : set_name
 Usage   : $obj->set_name($name);
 Function: Assigns an object's name.
 Returns : Modified object.
 Args    : Argument must be a string, will be single 
           quoted if it contains [;|,|:\(|\)] 
           or spaces. Preceding and trailing spaces
           will be removed.
set_desc()

Sets invocant description.

 Type    : Mutator
 Title   : set_desc
 Usage   : $obj->set_desc($desc);
 Function: Assigns an object's description.
 Returns : Modified object.
 Args    : Argument must be a string.
set_score()

Sets invocant score.

 Type    : Mutator
 Title   : set_score
 Usage   : $obj->set_score($score);
 Function: Assigns an object's numerical score.
 Returns : Modified object.
 Args    : Argument must be any of
           perl's number formats, or undefined
           to reset score.
set_generic()

Sets generic key/value pair(s).

 Type    : Mutator
 Title   : set_generic
 Usage   : $obj->set_generic( %generic );
 Function: Assigns generic key/value pairs to the invocant.
 Returns : Modified object.
 Args    : Valid arguments constitute:

           * key/value pairs, for example:
             $obj->set_generic( '-lnl' => 0.87565 );

           * or a hash ref, for example:
             $obj->set_generic( { '-lnl' => 0.87565 } );

           * or nothing, to reset the stored hash, e.g.
                $obj->set_generic( );

ACCESSORS

get_name()

Gets invocant's name.

 Type    : Accessor
 Title   : get_name
 Usage   : my $name = $obj->get_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
get_desc()

Gets invocant description.

 Type    : Accessor
 Title   : get_desc
 Usage   : my $desc = $obj->get_desc;
 Function: Returns the object's description (if any).
 Returns : A string
 Args    : None
get_score()

Gets invocant's score.

 Type    : Accessor
 Title   : get_score
 Usage   : my $score = $obj->get_score;
 Function: Returns the object's numerical score (if any).
 Returns : A number
 Args    : None
get_generic()

Gets generic hashref or hash value(s).

 Type    : Accessor
 Title   : get_generic
 Usage   : my $value = $obj->get_generic($key);
           or
           my %hash = %{ $obj->get_generic() };
 Function: Returns the object's generic data. If an
           argument is used, it is considered a key
           for which the associated value is returned.
           Without arguments, a reference to the whole
           hash is returned.
 Returns : A string or hash reference.
 Args    : None
get_id()

Gets invocant's UID.

 Type    : Accessor
 Title   : get_id
 Usage   : my $id = $obj->get_id;
 Function: Returns the object's unique ID
 Returns : INT
 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';
debug()

Prints argument debugging message, depending on verbosity.

 Type    : logging method
 Title   : debug
 Usage   : $object->debug( "debugging message" );
 Function: prints debugging message, depending on verbosity
 Returns : invocant
 Args    : logging message
info()

Prints argument informational message, depending on verbosity.

 Type    : logging method
 Title   : info
 Usage   : $object->info( "info message" );
 Function: prints info message, depending on verbosity
 Returns : invocant
 Args    : logging message
warn()

Prints argument warning message, depending on verbosity.

 Type    : logging method
 Title   : warn
 Usage   : $object->warn( "warning message" );
 Function: prints warning message, depending on verbosity
 Returns : invocant
 Args    : logging message
error()

Prints argument error message, depending on verbosity.

 Type    : logging method
 Title   : error
 Usage   : $object->error( "error message" );
 Function: prints error message, depending on verbosity
 Returns : invocant
 Args    : logging message
fatal()

Prints argument fatal message, depending on verbosity.

 Type    : logging method
 Title   : fatal
 Usage   : $object->fatal( "fatal message" );
 Function: prints fatal message, depending on verbosity
 Returns : invocant
 Args    : logging message
clone()

Clones invocant.

 Type    : Utility method
 Title   : clone
 Usage   : my $clone = $object->clone;
 Function: Creates a copy of the invocant object.
 Returns : A copy of the invocant.
 Args    : none.
 Comments: Currently not implemented
VERBOSE()

Getter and setter for the verbose level. This comes in five levels: 0 = only fatal messages (though, when something fatal happens, you'll most likely get an exception object), 1 = errors (hopefully recoverable), 2 = warnings (recoverable), 3 = info (useful diagnostics), 4 = debug (every method call)

 Type    : Accessor
 Title   : VERBOSE()
 Usage   : Bio::Phylo->VERBOSE( -level => $level )
 Function: Sets/gets verbose level
 Returns : Verbose level
 Args    : 0 <= $level && $level <= 4
 Comments:
CITATION()

Returns suggested citation.

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

Gets version number (including revision number).

 Type    : Accessor
 Title   : VERSION
 Usage   : $phylo->VERSION;
 Function: Returns version number
           (including SVN revision number).
 Alias   :
 Returns : SCALAR
 Args    : NONE
 Comments:

DESTRUCTOR

DESTROY()

Invocant destructor.

 Type    : Destructor
 Title   : DESTROY
 Usage   : $phylo->DESTROY
 Function: Destroys Phylo object
 Alias   :
 Returns : TRUE
 Args    : none
 Comments: You don't really need this,
           it is called automatically when
           the object goes out of scope.

SEE ALSO

Also see the manual: Bio::Phylo::Manual.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: Phylo.pm 4196 2007-07-12 03:04:01Z rvosa $

AUTHOR

Rutger Vos,

email: mailto://rvosa@sfu.ca
web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.