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Bio::Root::Root - implementation of Bio::Root::RootI interface


  # 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");

  # Deep-object copy

  my $clone = $obj->clone;


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 object to be thrown. This can be caught within a catch{} block, from which 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:

   my $IN;
   try {
    open $IN, '<', $file or $obj->throw( -class => 'Bio::Root::FileOpenException',
                                         -text  => "Cannot read file '$file'",
                                         -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!

AUTHOR Steve Chervitz

Ewan Birney, Lincoln Stein


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


 Title   : clone
 Usage   : my $clone = $obj->clone();
           my $clone = $obj->clone( -start => 110 );
 Function: Deep recursion copying of any object via Storable dclone()
 Returns : A cloned object.
 Args    : Any named parameters provided will be set on the new object.
           Unnamed parameters are ignored.
 Comments: Where possible, faster clone methods are used, in order:
           Clone::Fast::clone(), Clone::clone(), Storable::dclone.  If neither
           is present, a pure perl fallback (not very well tested) is used
           instead. Storable dclone() cannot clone CODE references.  Therefore,
           any CODE reference in your original object will remain, but will not
           exist in the cloned object.  This should not be used for anything
           other than cloning of simple objects. Developers of subclasses are
           encouraged to override this method with one of their own.


 Title   : clone
 Usage   : my $clone = $obj->_dclone($ref);
           my $clone = $obj->_dclone($ref);
 Function: Returns a copy of the object passed to it (a deep clone)
 Returns : clone of passed argument
 Args    : Anything
 NOTE    : This differs from clone significantly in that it does not clone
           self, but the data passed to it.  This code may need to be optimized
           or overridden as needed.
 Comments: This is set in the BEGIN block to take advantage of optimized
           cloning methods if Clone or Storable is present, falling back to a
           pure perl kludge. May be moved into a set of modules if the need
           arises. At the moment, code ref cloning is not supported.


 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 is installed, and if a -class parameter is
           provided, Error::throw will be used, throwing an error
           of the type specified by -class.
           If 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, 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 is available,
           this is equivalent to the arguments:
                 -text  => "message",
                 -class => Bio::Root::Exception
 Comments : If is installed, and you don't want to use it
            for some reason, you can block the use of 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).