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';
- 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.
REVISION
$Id: Phylo.pm 4251 2007-07-19 14:21:33Z rvosa $