Bio::Root::Root(3pm)

🌸 NAME 🌸

okay bestie, welcome to Bio::Root::Root(3pm) — that's the manual name, and it's part of the User Contributed Perl Documentation collection. The NAME line is giving:

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

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✨ SYNOPSIS ✨

here's the vibe in code form, no cap:

  # 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);
  $obj->verbose(2);

  # 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;

---

💖 DESCRIPTION 💖

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

For most of the methods implemented by this module, you should check the documentation for Bio::Root::RootI. Only the overridden methods are described right here, bestie.

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 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:

• -class — 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.
• -text — a sensible message for the exception.
• -value — 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. Slay.

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!

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👑 AUTHOR 👑

Steve Chervitz Ewan Birney, Lincoln Stein

absolute icons, no cap.

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🧚 METHODS 🧚

okay bestie, here come the method deets, and yes we're keeping every single one.

new

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

clone

• Title: clone
• Usage:

my $clone = $obj->clone();

or

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.

_dclone

• Title: clone (yes, the title says clone, not _dclone — iconic)
• Usage:

my $clone = $obj->_dclone($ref);

or

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.

verbose

• 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

_register_for_cleanup

the original page doesn't give a description for this one, bestie — just the method name. same energy for the next two.

_unregister_for_cleanup

no description, just the name. periodt.

_cleanup_methods

no description, just the name. keep it moving.

throw

• Title: throw
• Usage:

$obj->throw("throwing exception message");

or

$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.

debug

• 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

_load_module

• Title: _load_module
• Usage: $self->_load_module("Bio::SeqIO::genbank");
• Function: Loads up (like use) the specified module at run time on demand.
• Example: (the original leaves this blank, bestie — no example given)
• Returns: TRUE on success. Throws an exception upon failure.
• Args: The module to load (_without_ the trailing .pm).

DESTROY

no description, just the name. it's giving mysterious main character energy.

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and that's the whole page, bestie! this manual page is from perl v5.32.1 dated 2021-08-15 and the manual name is Bio::Root::Root(3pm). now go clone something deep and slay. 💅