Ewan Birney


Bio::Root::Root - Hash-based implementation of Bio::Root::RootI


  # any bioperl or bioperl compliant object is a RootI 
  # compliant object

  # Here's how to throw and catch an exception using the eval-based syntax.

  $obj->throw("This is an exception");

  eval {
      $obj->throw("This is catching an exception");

  if( $@ ) {
      print "Caught exception";
  } else {
      print "no exception";

  # Alternatively, using the new typed exception syntax in the throw() call:

    $obj->throw( -class => 'Bio::Root::BadParameter',
                 -text  => "Can't open file $file",
                 -value  => $file);

  # Exceptions can be used in an eval{} block as shown above or within
  # a try{} block if you have installed the Error.pm module.
  # Here's a brief example. For more, see Bio::Root::Exception

  use Error qw(:try);

    try {
    $obj->throw(  # arguments as above );
    catch Bio::Root::FileOpenException with {
        my $err = shift;
        print "Handling exception $err\n";


This is a hashref-based implementation of the Bio::Root::RootI interface. Most bioperl objects should inherit from this.

See the documentation for Bio::Root::RootI for most of the methods implemented by this module. Only overridden methods are described here.

Throwing Exceptions

One of the functionalities that Bio::Root::RootI provides is the ability throw() exceptions with pretty stack traces. Bio::Root::Root enhances this with the ability to use Error.pm (available from CPAN) if it has also been installed.

If Error.pm has been installed, throw() will use it. This causes an Error.pm-derived object to be thrown. This can be caught within a catch{} block, from wich you can extract useful bits of information. If Error.pm is not installed, it will use the Bio::Root::RootI-based exception throwing facilty.

Typed Exception Syntax

The typed exception syntax of throw() has the advantage of plainly indicating the nature of the trouble, since the name of the class is included in the title of the exception output.

To take advantage of this capability, you must specify arguments as named parameters in the throw() call. Here are the parameters:


name of the class of the exception. This should be one of the classes defined in Bio::Root::Exception, or a custom error of yours that extends one of the exceptions defined in Bio::Root::Exception.


a sensible message for the exception


the value causing the exception or $!, if appropriate.

Note that Bio::Root::Exception does not need to be imported into your module (or script) namespace in order to throw exceptions via Bio::Root::Root::throw(), since Bio::Root::Root imports it.

Try-Catch-Finally Support

In addition to using an eval{} block to handle exceptions, you can also use a try-catch-finally block structure if Error.pm has been installed in your system (available from CPAN). See the documentation for Error for more details.

Here's an example. See the Bio::Root::Exception module for other pre-defined exception types:

   try {
    open( IN, $file) || $obj->throw( -class => 'Bio::Root::FileOpenException',
                                     -text => "Cannot open file $file for reading",
                                     -value => $!);
   catch Bio::Root::BadParameter with {
       my $err = shift;   # get the Error object
       # Perform specific exception handling code for the FileOpenException
   catch Bio::Root::Exception with {
       my $err = shift;   # get the Error object
       # Perform general exception handling code for any Bioperl exception.
   otherwise {
       # A catch-all for any other type of exception
   finally {
       # Any code that you want to execute regardless of whether or not
       # an exception occurred.
   # the ending semicolon is essential!


Functions originally from Steve Chervitz. Refactored by Ewan Birney. Re-refactored by Lincoln Stein.


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : _create_object()
 Usage   : $obj->create_object(@args)
 Function: Method which actually creates the blessed  hashref
 Returns : Blessed hashref
 Args    : Ignored

Override this method, the new() method, or _initialize() to make a custom constructor.


 Title   : throw
 Usage   : $obj->throw("throwing exception message");
           $obj->throw( -class => 'Bio::Root::Exception',
                        -text  => "throwing exception message",
                        -value => $bad_value  );
 Function: Throws an exception, which, if not caught with an eval or
           a try block will provide a nice stack trace to STDERR 
           with the message.
           If Error.pm is installed, and if a -class parameter is
           provided, Error::throw will be used, throwing an error 
           of the type specified by -class.
           If Error.pm is installed and no -class parameter is provided
           (i.e., a simple string is given), A Bio::Root::Exception 
           is thrown.
 Returns : n/a
 Args    : A string giving a descriptive error message
           Named parameters:
           '-class'  a string for the name of a class that derives 
                     from Error.pm, such as any of the exceptions 
                     defined in Bio::Root::Exception.
                     Default class: Bio::Root::Exception
           '-text'   a string giving a descriptive error message
           '-value'  the value causing the exception, or $! (optional)

           Thus, if only a string argument is given, and Error.pm is available,
           this is equivalent to the arguments:
                 -text  => "message",
                 -class => Bio::Root::Exception
 Comments : If Error.pm is installed, and you don't want to use it
            for some reason, you can block the use of Error.pm by
           Bio::Root::Root::throw() by defining a scalar named
           $main::DONT_USE_ERROR (define it in your main script
           and you don't need the main:: part) and setting it to 
           a true value.