Bio::Root::RootI(3p)

NAME
Bio::Root::RootI - base interface for all BioPerl classes

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

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

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

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

  # Using throw_not_implemented() within a RootI-based interface module:

  package Foo;
  use base qw(Bio::Root::RootI);

  sub foo {
      my $self = shift;
      $self->throw_not_implemented;
  }

DESCRIPTION
This is just a set of methods which do not assume anything about the object they are on. The methods provide the ability to throw exceptions with nice stack traces.

This is what should be inherited by all Bioperl compliant interfaces, even if they are exotic XS/CORBA/Other perl systems.

  Using throw_not_implemented()
The method throw_not_implemented() should be called by all methods within interface modules that extend RootI so that if an implementation fails to override them, an exception will be thrown.

For example, say there is an interface module called "FooI" that provides a method called foo(). Since this method is considered abstract within FooI and should be implemented by any module claiming to implement "FooI", the FooI::foo() method should consist of the following:

    sub foo {
        my $self = shift;
        $self->throw_not_implemented;
    }

So, if an implementer of "FooI" forgets to implement foo() and a user of the implementation calls foo(), a Bio::Exception::NotImplemented exception will result.

Unfortunately, failure to implement a method can only be determined at run time (i.e., you can't verify that an implementation is complete by running "perl -wc" on it). So it should be standard practice for a test of an implementation to check each method and verify that it doesn't throw a Bio::Exception::NotImplemented.

AUTHOR Steve Chervitz
Ewan Birney, Lincoln Stein, Steve Chervitz, Sendu Bala, Jason Stajich

  new

  throw
 Title   : throw
 Usage   : $obj->throw("throwing exception message")
 Function: Throws an exception, which, if not caught with an eval brace
           will provide a nice stack trace to STDERR with the message
 Returns : nothing
 Args    : A string giving a descriptive error message

  warn
 Title   : warn
 Usage   : $object->warn("Warning message");
 Function: Places a warning. What happens now is down to the
           verbosity of the object  (value of $obj->verbose)
            verbosity 0 or not set => small warning
            verbosity -1 => no warning
            verbosity 1 => warning with stack trace
            verbosity 2 => converts warnings into throw
 Returns : n/a
 Args    : string (the warning message)

  deprecated
 Title   : deprecated
 Usage   : $obj->deprecated("Method X is deprecated");
           $obj->deprecated("Method X is deprecated", 1.007);
           $obj->deprecated(-message => "Method X is deprecated");
           $obj->deprecated(-message => "Method X is deprecated",
                            -version => 1.007);
 Function: Prints a message about deprecation unless verbose is < 0
           (which means be quiet)
 Returns : none
 Args    : Message string to print to STDERR
           Version of BioPerl where use of the method results in an exception

 Notes   : This is deprecated.  Use Carp::carp to warn about a
           deprecated method.  Just remove the method when it comes to
           error.  If you really want to throw an error insyead of
           removing, use Carp::croak.

           The irony of deprecating deprecated() is not lost on us.
           We hope you also find it more funny that frustrating.

  stack_trace_dump
 Title   : stack_trace_dump
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

  stack_trace
 Title   : stack_trace
 Usage   : @stack_array_ref= $self->stack_trace
 Function: gives an array to a reference of arrays with stack trace info
           each coming from the caller(stack_number) call
 Returns : array containing a reference of arrays
 Args    : none

  _rearrange
 Usage     : $object->_rearrange( array_ref, list_of_arguments)
 Purpose   : Rearranges named parameters to requested order.
 Example   : $self->_rearrange([qw(SEQUENCE ID DESC)],@param);
           : Where @param = (-sequence => $s,
           :                 -desc     => $d,
           :                 -id       => $i);
 Returns   : @params - an array of parameters in the requested order.
           : The above example would return ($s, $i, $d).
           : Unspecified parameters will return undef. For example, if
           :        @param = (-sequence => $s);
           : the above _rearrange call would return ($s, undef, undef)
 Argument  : $order : a reference to an array which describes the desired
           :          order of the named parameters.
           : @param : an array of parameters, either as a list (in
           :          which case the function simply returns the list),
           :          or as an associative array with hyphenated tags
           :          (in which case the function sorts the values
           :          according to @{$order} and returns that new array.)
           :          The tags can be upper, lower, or mixed case
           :          but they must start with a hyphen (at least the
           :          first one should be hyphenated.)
 Source    : This function was taken from CGI.pm, written by Dr. Lincoln
           : Stein, and adapted for use in Bio::Seq by Richard Resnick and
           : then adapted for use in Bio::Root::Object.pm by Steve Chervitz,
           : then migrated into Bio::Root::RootI.pm by Ewan Birney.
 Comments  :
           : Uppercase tags are the norm,
           : (SAC)
           : This method may not be appropriate for method calls that are
           : within in an inner loop if efficiency is a concern.
           :
           : Parameters can be specified using any of these formats:
           :  @param = (-name=>'me', -color=>'blue');
           :  @param = (-NAME=>'me', -COLOR=>'blue');
           :  @param = (-Name=>'me', -Color=>'blue');
           :  @param = ('me', 'blue');
           : A leading hyphenated argument is used by this function to
           : indicate that named parameters are being used.
           : Therefore, the ('me', 'blue') list will be returned as-is.
           :
           : Note that Perl will confuse unquoted, hyphenated tags as
           : function calls if there is a function of the same name
           : in the current namespace:
           :    -name => 'foo' is interpreted as -&name => 'foo'
           :
           : For ultimate safety, put single quotes around the tag:
           : ('-name'=>'me', '-color' =>'blue');
           : This can be a bit cumbersome and I find not as readable
           : as using all uppercase, which is also fairly safe:
           : (-NAME=>'me', -COLOR =>'blue');
           :
           : Personal note (SAC): I have found all uppercase tags to
           : be more manageable: it involves less single-quoting,
           : the key names stand out better, and there are no method naming
           : conflicts.
           : The drawbacks are that it's not as easy to type as lowercase,
           : and lots of uppercase can be hard to read.
           :
           : Regardless of the style, it greatly helps to line
           : the parameters up vertically for long/complex lists.
           :
           : Note that if @param is a single string that happens to start with
           : a dash, it will be treated as a hash key and probably fail to
           : match anything in the array_ref, so not be returned as normally
           : happens when @param is a simple list and not an associative array.

  _set_from_args
 Usage     : $object->_set_from_args(\%args, -methods => \@methods)
 Purpose   : Takes a hash of user-supplied args whose keys match method names,
           : and calls the method supplying it the corresponding value.
 Example   : $self->_set_from_args(\%args, -methods => [qw(sequence id desc)]);
           : Where %args = (-sequence    => $s,
           :                -description => $d,
           :                -ID          => $i);
           :
           : the above _set_from_args calls the following methods:
           : $self->sequence($s);
           : $self->id($i);
           : ( $self->description($i) is not called because 'description' wasn't
           :   one of the given methods )
 Argument  : \%args | \@args : a hash ref or associative array ref of arguments
           :                   where keys are any-case strings corresponding to
           :                   method names but optionally prefixed with
           :                   hyphens, and values are the values the method
           :                   should be supplied. If keys contain internal
           :                   hyphens (eg. to separate multi-word args) they
           :                   are converted to underscores, since method names
           :                   cannot contain dashes.
           : -methods => []  : (optional) only call methods with names in this
           :                   array ref. Can instead supply a hash ref where
           :                   keys are method names (of real existing methods
           :                   unless -create is in effect) and values are array
           :                   refs of synonyms to allow access to the method
           :                   using synonyms. If there is only one synonym it
           :                   can be supplied as a string instead of a single-
           :                   element array ref
           : -force => bool  : (optional, default 0) call methods that don't
           :                   seem to exist, ie. let AUTOLOAD handle them
           : -create => bool : (optional, default 0) when a method doesn't
           :                   exist, create it as a simple getter/setter
           :                   (combined with -methods it would create all the
           :                   supplied methods that didn't exist, even if not
           :                   mentioned in the supplied %args)
           : -code => '' | {}: (optional) when creating methods use the supplied
           :                   code (a string which will be evaulated as a sub).
           :                   The default code is a simple get/setter.
           :                   Alternatively you can supply a hash ref where
           :                   the keys are method names and the values are
           :                   code strings. The variable '$method' will be
           :                   available at evaluation time, so can be used in
           :                   your code strings. Beware that the strict pragma
           :                   will be in effect.
           : -case_sensitive => bool : require case sensitivity on the part of
           :                           user (ie. a() and A() are two different
           :                           methods and the user must be careful
           :                           which they use).
 Comments  :
           : The \%args argument will usually be the args received during new()
           : from the user. The user is allowed to get the case wrong, include
           : 0 or more than one hyphens as a prefix, and to include hyphens as
           : multi-word arg separators: '--an-arg' => 1, -an_arg => 1 and
           : An_Arg => 1 are all equivalent, calling an_arg(1). However, in
           : documentation users should only be told to use the standard form
           : -an_arg to avoid confusion. A possible exception to this is a
           : wrapper module where '--an-arg' is what the user is used to
           : supplying to the program being wrapped.
           :
           : Another issue with wrapper modules is that there may be an
           : argument that has meaning both to Bioperl and to the program, eg.
           : -verbose. The recommended way of dealing with this is to leave
           : -verbose to set the Bioperl verbosity whilst requesting users use
           : an invented -program_verbose (or similar) to set the program
           : verbosity. This can be resolved back with
           : Bio::Tools::Run::WrapperBase's _setparams() method and code along
           : the lines of:
           : my %methods = map { $_ => $_ } @LIST_OF_ALL_ALLOWED_PROGRAM_ARGS
           : delete $methods{'verbose'};
           : $methods{'program_verbose'} = 'verbose';
           : my $param_string = $self->_setparams(-methods => \%methods);
           : system("$exe $param_string");

  _rearrange_old

  _register_for_cleanup
 Title   : _register_for_cleanup
 Usage   : -- internal --
 Function: Register a method to be called at DESTROY time. This is useful
           and sometimes essential in the case of multiple inheritance for
           classes coming second in the sequence of inheritance.
 Returns :
 Args    : a code reference

The code reference will be invoked with the object as the first argument, as per a method. You may register an unlimited number of cleanup methods.

  _unregister_for_cleanup
 Title   : _unregister_for_cleanup
 Usage   : -- internal --
 Function: Remove a method that has previously been registered to be called
           at DESTROY time.  If called with a method to be called at DESTROY time.
           Has no effect if the code reference has not previously been registered.
 Returns : nothing
 Args    : a code reference

  _cleanup_methods
 Title   : _cleanup_methods
 Usage   : -- internal --
 Function: Return current list of registered cleanup methods.
 Returns : list of coderefs
 Args    : none

  throw_not_implemented
 Purpose : Throws a Bio::Root::NotImplemented exception.
           Intended for use in the method definitions of
           abstract interface modules where methods are defined
           but are intended to be overridden by subclasses.
 Usage   : $object->throw_not_implemented();
 Example : sub method_foo {
             $self = shift;
             $self->throw_not_implemented();
           }
 Returns : n/a
 Args    : n/a
 Throws  : A Bio::Root::NotImplemented exception.
           The message of the exception contains
             - the name of the method
             - the name of the interface
             - the name of the implementing class

           If this object has a throw() method, $self->throw will be used.
           If the object doesn't have a throw() method,
           Carp::confess() will be used.

  warn_not_implemented
 Purpose : Generates a warning that a method has not been implemented.
           Intended for use in the method definitions of
           abstract interface modules where methods are defined
           but are intended to be overridden by subclasses.
           Generally, throw_not_implemented() should be used,
           but warn_not_implemented() may be used if the method isn't
           considered essential and convenient no-op behavior can be
           provided within the interface.
 Usage   : $object->warn_not_implemented( method-name-string );
 Example : $self->warn_not_implemented( "get_foobar" );
 Returns : Calls $self->warn on this object, if available.
           If the object doesn't have a warn() method,
           Carp::carp() will be used.
 Args    : n/a

  _not_implemented_msg
Unify 'not implemented' message. -Juguang