Bio::Phylo - Phylogenetic analysis using perl.
# 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; # or: Bio::Phylo->VERBOSE( -level => 1 ); # sets global verbosity to 'error' # sets verbosity for forest ojects to 'debug' Bio::Phylo->VERBOSE( -level => 4, -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); 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 in Bio::Phylo::Util::Logger of use to localize problems.
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.
The Bio::Phylo root object itself, and thus its constructor, is rarely, if ever, used directly. Rather, many other objects in Bio::Phylo 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)
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.
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.
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.
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( );
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
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
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
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
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
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
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';
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
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:
Returns suggested citation.
Type : Accessor Title : CITATION Usage : $phylo->CITATION; Function: Returns suggested citation. Returns : Returns suggested citation. Args : None Comments:
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:
Also see the manual: Bio::Phylo::Manual.
$Id: Phylo.pm 4265 2007-07-20 14:14:44Z rvosa $
