NAME

Bio::NEXUS::Util::Exceptions - Exception classes for Bio::NEXUS.

SYNOPSIS

            

              
              
use Bio::NEXUS::Node;
my $node = Bio::NEXUS::Node->new;
# now let's try something illegal
eval {
   $node->set_branch_length( 'non-numerical value' );
};
# have an error
if ( $@ && UNIVERSAL::isa( $@, 'Bio::NEXUS::Util::Exception' ) ) {
   # print out where the error came from
   print $@->trace->as_string;
}
            
          

DESCRIPTION

Sometimes, Bio::NEXUS dies. If this happens because you did something that brought Bio::NEXUS into an undefined and dangerous state (such as might happen if you provide a non-numerical value for a setter that needs numbers), Bio::NEXUS 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::NEXUS. There are no serviceable parts inside. Refer to the Exception::Class perldoc for more examples on how to catch exceptions and show traces.

AUTHORS

Original conception by Rutger Vos.

EXCEPTION CLASSES

Bio::NEXUS::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::NEXUS::Util::Exceptions::BadString

Thrown when a string that contains any of the characters ():;, is given as an argument to a method that expects a name.

Bio::NEXUS::Util::Exceptions::BadFormat

Thrown when a file format error is encountered (e.g. unknown or invalid format).

Bio::NEXUS::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::NEXUS::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::NEXUS::Util::Exceptions::UnknownMethod

Thrown when an unknown method is called (e.g. through AUTOLOAD).

Bio::NEXUS::Util::Exceptions::BadArgs

Thrown when something undefined is wrong with the supplied arguments.

Bio::NEXUS::Util::Exceptions::FileError

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

Bio::NEXUS::Util::Exceptions::ExtensionError

Thrown when there is an error loading a requested extension.

Bio::NEXUS::Util::Exceptions::OutOfBounds

Thrown when an index is supplied that falls outside of an allowed range.

Bio::NEXUS::Util::Exceptions::NotImplemented

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

Bio::NEXUS::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::NEXUS::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::NEXUS::Util::Exceptions object
Args    : error => 'Error message'
            
          

caught()

Catches an exception by class.

            

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

rethrow()

Rethrows a caught exception.

            

              
              
Type    : Exception
Title   : rethrow
Usage   : $@->rethrow;
Function: Rethrows exception
Returns : A Bio::NEXUS::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
            
          

REVISION

            

              
              
$Id: Exceptions.pm,v 1.5 2012/02/07 21:49:27 astoltzfus Exp $