Bio::Root::Exception(3pm)				User Contributed Perl Documentation				 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
";
	       open (IN, $default_file) || die "Can't open $default_file";
	   }
	   otherwise {
	       my $err = shift;
	       print STDERR "An unexpected exception occurred: 
$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:
$err
";
		  };

       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
	    specifying -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"  );

perl v5.14.2							    2012-03-02						 Bio::Root::Exception(3pm)