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


  # Any 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 not open file $file",
               -value  => $file );

  # Want to see debug() outputs for this object

  my $obj = Bio::Object->new(-verbose=>1);

  my $obj = Bio::Object->new(%args);

  # Print debug messages which honour current verbosity setting

  $obj->debug("Boring output only to be seen if verbose > 0\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 to throw() exceptions with pretty stack traces. Bio::Root::Root enhances this with the ability to use Error (available from CPAN) if it has also been installed.

If Error 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 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 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!


Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists.

Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:



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 _


 Purpose   : generic instantiation function can be overridden if 
             special needs of a module cannot be done in _initialize


 Title   : verbose
 Usage   : $self->verbose(1)
 Function: Sets verbose level for how ->warn behaves
           -1 = no warning
            0 = standard, small warning
            1 = warning with stack trace
            2 = warning becomes throw
 Returns : The current verbosity setting (integer between -1 to 2)
 Args    : -1,0,1 or 2


 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, optional
           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; you must do this within a BEGIN subroutine.


 Title   : debug
 Usage   : $obj->debug("This is debugging output");
 Function: Prints a debugging message when verbose is > 0
 Returns : none
 Args    : message string(s) to print to STDERR


 Title   : _load_module
 Usage   : $self->_load_module("Bio::SeqIO::genbank");
 Function: Loads up (like use) the specified module at run time on demand.
 Example : 
 Returns : TRUE on success. Throws an exception upon failure.
 Args    : The module to load (_without_ the trailing .pm).