NAME

Bio::Phylo::Util::Exceptions - Errors ($@) that are objects

SYNOPSIS

use Bio::Phylo::Forest::Node;
my $node = Bio::Phylo::Forest::Node->new;

# now let's try something illegal
eval {
   $node->set_branch_length( 'non-numerical value' );
};

# have an error
if ( my $e = Bio::Phylo::Util::Exceptions::BadNumber->caught ) {

   # print out where the error came from
   print $@->trace->as_string;
   
   # caught() returns $@, so $e and $@ are the 
   # same object in this example. 
   # Therefore, the same thing would be:
   print $e->trace->as_string;
}

DESCRIPTION

Sometimes, Bio::Phylo dies. If this happens because you did something that brought Bio::Phylo into an undefined and dangerous state (such as might happen if you provide a non-numerical value for a setter that needs numbers), Bio::Phylo will throw an "exception", a special form of the $@ variable that is a blessed object with useful methods to help you diagnose the problem.

This package defines the exceptions that can be thrown by Bio::Phylo. There are no serviceable parts inside. Refer to the Exception::Class perldoc for more examples on how to catch exceptions and show traces.

EXCEPTION CLASSES

Bio::Phylo::Util::Exceptions::BadNumber

Thrown when anything other than a number that passes Scalar::Util's looks_like_number test is given as an argument to a method that expects a number.

Bio::Phylo::Util::Exceptions::BadString

Thrown when an incorrectly formatted string argument is provided, for example a string that would be split into substrings under NEXUS tokenization rules, a string that isn't an xs:NCName or a string that isn't a binomial CURIE

Bio::Phylo::Util::Exceptions::BadFormat

Thrown when a non-existing parser or unparser format is requested, in calls such as parse( -format => 'newik', -string => $string ), where 'newik' doesn't exist.

Bio::Phylo::Util::Exceptions::OddHash

Thrown when an odd number of arguments has been specified. This might happen if you call a method that requires named arguments and the key/value pairs don't seem to match up.

Bio::Phylo::Util::Exceptions::ObjectMismatch

Thrown when a method is called that requires an object as an argument, and the wrong type of object is specified.

Bio::Phylo::Util::Exceptions::UnknownMethod

Trown when an indirect method call is attempted through the $obj->get('unknown_method') interface, and the object doesn't seem to implement the requested method.

Bio::Phylo::Util::Exceptions::BadArgs

Thrown when something undefined is wrong with the supplied arguments.

Bio::Phylo::Util::Exceptions::FileError

Thrown when a file specified as an argument does not exist or is not readable.

Bio::Phylo::Util::Exceptions::ExtensionError

Thrown when there is an error loading a requested extension.

Bio::Phylo::Util::Exceptions::OutOfBounds

Thrown when an entity is requested that falls outside of the range of objects contained by a Bio::Phylo::Listable subclass, probably through the $obj->get_by_index($i) method call.

Bio::Phylo::Util::Exceptions::NotImplemented

Thrown when an interface method is called instead of the implementation by the child class.

Bio::Phylo::Util::Exceptions::Deprecated

Thrown when a deprecated method is called.

METHODS

new()

Constructor

Type    : Constructor
Title   : new
Usage   : $class->new( error => 'An exception was thrown!' );
Function: Constructs exception
Returns : A Bio::Phylo::Util::Exceptions object
Args    : error => 'Error message'

throw()

Throws exception.

Type    : Exception
Title   : throw
Usage   : $class->throw( error => 'An exception was thrown!' );
Function: Throws exception
Returns : A Bio::Phylo::Util::Exceptions object
Args    : error => 'Error message'

caught()

Catches an exception by class.

Type    : Handler
Title   : caught
Usage   : my $e = Bio::Phylo::Util::Exceptions->caught;
Function: Catches an exception
Returns : A Bio::Phylo::Util::Exceptions object
Args    : None

rethrow()

Rethrows a caught exception.

Type    : Exception
Title   : rethrow
Usage   : $@->rethrow;
Function: Rethrows exception
Returns : A Bio::Phylo::Util::Exceptions object
Args    : None

as_string()

Serializes exception.

Type    : Serializer
Title   : as_string
Usage   : print $@->as_string;
Function: Serializes exception with description and stack trace.
Returns : String
Args    : None

SEE ALSO

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

Bio::Phylo::Manual

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