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Bio::Root::Exception.3pm

NAME

Bio::Root::Exception - Generic exception objects for Bioperl

SYNOPSIS

Throwing exceptions using Error.pm throw:

     use Bio::Root::Exception;
     use Error;
 
     # Set Error::Debug to include stack trace data in the error messages
     $Error::Debug = 1;
 
     $file = shift;
     open (IN, $file) ||
             throw Bio::Root::FileOpenException ( "Can't open file $file for reading", $!);
 
 

Throwing exceptions using Bioperl throw:

      # Here we have an object that ISA Bio::Root::Root, so it inherits throw().
 
      open (IN, $file) || 
                 $object->throw(-class => 'Bio::Root::FileOpenException',
                                -text => "Can't open file $file for reading",
                                -value => $!);
 
 

Catching and handling exceptions using Error.pm try:

     use Bio::Root::Exception;
     use Error qw(:try);
 
     # Note that we need to import the 'try' tag from Error.pm
 
     # Set Error::Debug to include stack trace data in the error messages
     $Error::Debug = 1;
 
     $file = shift;
     try {
         open (IN, $file) ||
             throw Bio::Root::FileOpenException ( "Can't open file $file for reading", $!);
     }
     catch Bio::Root::FileOpenException with {
         my $err = shift;
         print STDERR "Using default input file: $default_file\n";
         open (IN, $default_file) || die "Can't open $default_file";
     }
     otherwise {
         my $err = shift;
         print STDERR "An unexpected exception occurred: \n$err";
 
         # By placing an the error object reference within double quotes,
         # you're invoking its stringify() method.
     }
    finally {
        # Any code that you want to execute regardless of whether or not
        # an exception occurred.
    };  
    # the ending semicolon is essential!
 
 

Defining a new Exception type as a subclass of Bio::Root::Exception:

     @Bio::TestException::ISA = qw( Bio::Root::Exception );
 
 

DESCRIPTION

Exceptions defined in Bio::Root::Exception

These are generic exceptions for typical problem situations that could arise in any module or script.

Bio::Root::Exception()

Bio::Root::NotImplemented()

Bio::Root::IOException()

Bio::Root::FileOpenException()

Bio::Root::SystemException()

Bio::Root::BadParameter()

Bio::Root::OutOfRange()

Bio::Root::NoSuchThing()

Using defined exception classes like these is a good idea because it indicates the basic nature of what went wrong in a convenient, computable way.

If there is a type of exception that you want to throw that is not covered by the classes listed above, it is easy to define a new one that fits your needs. Just write a line like the following in your module or script where you want to use it (or put it somewhere that is accessible to your code):

     @NoCanDoException::ISA = qw( Bio::Root::Exception );
 
 

All of the exceptions defined in this module inherit from a common base class exception, Bio::Root::Exception. This allows a user to write a handler for all Bioperl-derived exceptions as follows:

            use Bio::Whatever;
            use Error qw(:try);
 
            try {
                 # some code that depends on Bioperl
            }
            catch Bio::Root::Exception with {
                my $err = shift;
                print "A Bioperl exception occurred:\n$err\n";
            };
 
 

So if you do create your own exceptions, just be sure they inherit from Bio::Root::Exception directly, or indirectly by inheriting from a Bio::Root::Exception subclass.

The exceptions in Bio::Root::Exception are extensions of Graham Barr's Error module available from CPAN. Despite this dependency, the Bio::Root::Exception module does not explicitly "require Error". This permits Bio::Root::Exception to be loaded even when Error.pm is not available.

Throwing exceptions within Bioperl modules

Error.pm is not part of the Bioperl distibution, and may not be present within any given perl installation. So, when you want to throw an exception in a Bioperl module, the safe way to throw it is to use ``throw'' in Bio::Root::Root which can use Error.pm when it's available. See documentation in Bio::Root::Root for details.

SEE ALSO

See the "examples/exceptions" directory of the Bioperl distribution for working demo code.

``throw'' in Bio::Root::Root for information about throwing Bio::Root::Exception-based exceptions.

Error (available from CPAN, author: GBARR)

Error.pm is helping to guide the design of exception handling in Perl 6. See these RFC's:

      http://dev.perl.org/rfc/63.pod 
 
      http://dev.perl.org/rfc/88.pod
 
 

AUTHOR

Steve Chervitz <sac@bioperl.org>

COPYRIGHT

Copyright (c) 2001 Steve Chervitz. All Rights Reserved.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided ``as is'' without warranty of any kind.

EXCEPTIONS

Bio::Root::Exception

  Purpose : A generic base class for all BioPerl exceptions.
            By including a "catch Bio::Root::Exception" block, you
            should be able to trap all BioPerl exceptions.
  Example : throw Bio::Root::Exception("A generic exception", $!);
 
 

Methods defined by Bio::Root::Exception

new

  Purpose : Guarantees that -value is set properly before
            calling Error::new().
 
  Arguments: key-value style arguments same as for Error::new()
 
      You can also specify plain arguments as ($message, $value)
      where $value is optional.
 
      -value, if defined, must be non-zero and not an empty string 
      in order for eval{}-based exception handlers to work. 
      These require that if($@) evaluates to true, which will not 
      be the case if the Error has no value (Error overloads 
      numeric operations to the Error::value() method).
 
      It is OK to create Bio::Root::Exception objects without
      specifing -value. In this case, an invisible dummy value is used.
 
      If you happen to specify a -value of zero (0), it will
      be replaced by the string "The number zero (0)".
 
      If you happen to specify a -value of empty string (""), it will
      be replaced by the string "An empty string ("")".
 
 

pretty_format()

  Purpose : Get a nicely formatted string containing information about the 
            exception. Format is similar to that produced by 
            Bio::Root::Root::throw(), with the addition of the name of
            the exception class in the EXCEPTION line and some other
            data available via the Error object.
  Example : print $error->pretty_format;
 
 

stringify()

  Purpose : Overrides Error::stringify() to call pretty_format(). 
            This is called automatically when an exception object 
            is placed between double quotes.
  Example : catch Bio::Root::Exception with {
               my $error = shift;
               print "$error";
            }
 
 

See Also: pretty_format()

Subclasses of Bio::Root::Exception

Bio::Root::NotImplemented

  Purpose : Indicates that a method has not been implemented.
  Example : throw Bio::Root::NotImplemented( 
                -text   => "Method \"foo\" not implemented in module FooBar.",
                -value  => "foo" );
 
 

Bio::Root::IOException

  Purpose : Indicates that some input/output-related trouble has occurred.
  Example : throw Bio::Root::IOException( 
                -text   => "Can't save data to file $file.",
                -value  => $! );
 
 

Bio::Root::FileOpenException

  Purpose : Indicates that a file could not be opened.
  Example : throw Bio::Root::FileOpenException( 
                -text   => "Can't open file $file for reading.",
                -value  => $! );
 
 

Bio::Root::SystemException

  Purpose : Indicates that a system call failed.
  Example : unlink($file) or throw Bio::Root::SystemException( 
                -text   => "Can't unlink file $file.",
                -value  => $! );
 
 

Bio::Root::BadParameter

  Purpose : Indicates that one or more parameters supplied to a method 
            are invalid, unspecified, or conflicting.
  Example : throw Bio::Root::BadParameter( 
                -text   => "Required parameter \"-foo\" was not specified",
                -value  => "-foo" );
 
 

Bio::Root::OutOfRange

  Purpose : Indicates that a specified (start,end) range or 
            an index to an array is outside the permitted range.
  Example : throw Bio::Root::OutOfRange( 
                -text   => "Start coordinate ($start) cannot be less than zero.",
                -value  => $start  );
 
 

Bio::Root::NoSuchThing

  Purpose : Indicates that a requested thing cannot be located 
            and therefore could possibly be bogus.
  Example : throw Bio::Root::NoSuchThing( 
                -text   => "Accession M000001 could not be found.",
                -value  => "M000001"  );