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", $!);

     # 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 => $!);

    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!

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

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

           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";
           };

    my $self = shift;
    my $msg = $self->text;
    my $stack = $self->stacktrace();
    $stack =~ s/\Q$msg//;
    my @stack = split( /\n/, $stack);
    my @new_stack = ();
    my ($method, $file, $linenum, $prev_file, $prev_linenum);
    my $stack_count = 0;
    foreach my $i( 0..$#stack ) {
        # print "STACK-ORIG: $stack[$i]\n";
        if( ($stack[$i] =~ /^\s*([^(]+)\s*\(.*\) called at (\S+) line (\d+)/) ||
             ($stack[$i] =~ /^\s*(require 0) called at (\S+) line (\d+)/)) {
            ($method, $file, $linenum) = ($1, $2, $3);
            $stack_count++;
        }
        else{
            next;
        }
        if( $stack_count == 1 ) {
            push @new_stack, "STACK: $method";
            ($prev_file, $prev_linenum) = ($file, $linenum);
            next;
        }

        if( $method =~ /__ANON__/ ) {
            $method = "try{} block";
        }
        if( ($method =~ /^require/ and $file =~ /Error\.pm/ ) ||
            ($method =~ /^Error::subs::try/ ) )   {
            last;
        }
        push @new_stack, "STACK: $method $prev_file:$prev_linenum";
        ($prev_file, $prev_linenum) = ($file, $linenum);
    }
    push @new_stack, "STACK: $prev_file:$prev_linenum";

    return join "\n", @new_stack;

    my ($class, @args) = @_; 
    my ($value, %params);
    if( @args % 2 == 0 && $args[0] =~ /^-/) {
        %params = @args;
        $value = $params{'-value'};
    }
    else {
        $params{-text} = $args[0];
        $value = $args[1];
    }

    if( defined $value and not $value) {
	$value = "The number zero (0)" if $value == 0;
	$value = "An empty string (\"\")" if $value eq "";
    }
    else {
	$value ||= $DEFAULT_VALUE;
    }
    $params{-value} = $value;

    my $self = $class->SUPER::new( %params );
    return $self;

    my $self = shift;
    my $msg = $self->text;
    my $stack = '';
    if( $Error::Debug ) {
      $stack = $self->_reformat_stacktrace();
    }
    my $value_string = $self->value ne $DEFAULT_VALUE ? "VALUE: ".$self->value."\n" : "";
    my $class = ref($self);

    my $title = "------------- EXCEPTION: $class -------------";
    my $footer = "\n" . '-' x CORE::length($title);
    my $out = "\n$title\n" .
       "MSG: $msg\n". $value_string. $stack. $footer . "\n";
    return $out;
}


# Reformatting of the stack performed by  _reformat_stacktrace:
#   1. Shift the file:line data in line i to line i+1.
#   2. change xxx::__ANON__() to "try{} block"
#   3. skip the "require" and "Error::subs::try" stack entries (boring)
# This means that the first line in the stack won't have any file:line data
# But this isn't a big issue since it's for a Bio::Root::-based method 
# that doesn't vary from exception to exception.

    my ($self, @args) = @_;
    return $self->pretty_format( @args );

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

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

 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", $!);

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

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

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

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

 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" );

 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  );

 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"  );