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Manual Reference Pages  -  BIO::NEXUS::UTIL::EXCEPTIONS (3)

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



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

 # now lets 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;


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.


Original conception by Rutger Vos.


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.


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


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

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perl v5.20.3 BIO::NEXUS::UTIL::EXCEPTIONS (3) 2012-02-07

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