Bio::Root RootI
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Bio::Root::RootI - Abstract interface to root object code
Package variables
No package variables defined.
Included modules
Carp ' confess ' , ' carp '
  # 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; @ISA = qw( Bio::Root::RootI ); sub foo { my $self = shift; $self->throw_not_implemented; }
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. 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
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
    sub foo {
my $self = shift;
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.
No description
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Methods description
_cleanup_methodscode    nextTop
 Title   : _cleanup_methods
Usage : -- internal --
Function: Return current list of registered cleanup methods.
Returns : list of coderefs
Args : none
 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, written by Dr. Lincoln
: Stein, and adapted for use in Bio::Seq by Richard Resnick and
: then adapted for use in by Steve Chervitz,
: then migrated into 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 managable: 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.
 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.
 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 methoda 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
 Title   : deprecated
Usage : $obj->deprecated("Method X is deprecated");
Function: Prints a message about deprecation
unless verbose is < 0 (which means be quiet)
Returns : none
Args : Message string to print to STDERR
 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
 Title   : stack_trace_dump
Usage :
Example :
Returns :
Args :
 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
 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;
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.
 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
Example :
Returns :
Args :
 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
Methods code
     $ID        = 'Bio::Root::RootI';
    $VERSION   = 1.0;
    $Revision  = '$Id:,v 1.61 2002/12/16 09:44:28 birney Exp $ ';
    $DEBUG     = 0;
    $VERBOSITY = 0;
sub _cleanup_methods {
  my $self = shift;
  unless ( $ENV{'BIOPERLDEBUG'} || $self->verbose  > 0 ) {
      carp("Use of Bio::Root::RootI is deprecated.  Please use Bio::Root::Root instead");
sub _initialize {
    my($self,@args) = @_;
    return 1;
sub _rearrange {
    my $dummy = shift;
    my $order = shift;

    return @_ unless (substr($_[0]||'',0,1) eq '-');
    push @_,undef unless $#_ %2;
    my %param;
    while( @_ ) {
	(my $key = shift) =~ tr/a-z\055/A-Z/d; #deletes all dashes!
$param{$key} = shift; } map { $_ = uc($_) } @$order; # for bug #1343, but is there perf hit here?
return @param{@$order}; } #----------------'
sub _rearrange_old {
my($self,$order,@param) = @_; # JGRG -- This is wrong, because we don't want
# to assign empty string to anything, and this
# code is actually returning an array 1 less
# than the length of @param:
## If there are no parameters, we simply wish to return
## an empty array which is the size of the @{$order} array.
#return ('') x $#{$order} unless @param;
# ...all we need to do is return an empty array:
# return unless @param;
# If we've got parameters, we need to check to see whether
# they are named or simply listed. If they are listed, we
# can just return them.
# The mod test fixes bug where a single string parameter beginning with '-' gets lost.
# This tends to happen in error messages such as: $obj->throw("-id not defined")
return @param unless (defined($param[0]) && $param[0]=~/^-/o && ($#param % 2)); # Tester
# print "\n_rearrange() named parameters:\n";
# my $i; for ($i=0;$i<@param;$i+=2) { printf "%20s => %s\n", $param[$i],$param[$i+1]; }; <STDIN>;
# Now we've got to do some work on the named parameters.
# The next few lines strip out the '-' characters which
# preceed the keys, and capitalizes them.
for (my $i=0;$i<@param;$i+=2) { $param[$i]=~s/^\-//;
} # Now we'll convert the @params variable into an associative array.
# local($^W) = 0; # prevent "odd number of elements" warning with -w.
my(%param) = @param; # my(@return_array);
# What we intend to do is loop through the @{$order} variable,
# and for each value, we use that as a key into our associative
# array, pushing the value at that key onto our return array.
# my($key);
#foreach (@{$order}) {
# my($value) = $param{$key};
# delete $param{$key};
return @param{@{$order}}; # print "\n_rearrange() after processing:\n";
# my $i; for ($i=0;$i<@return_array;$i++) { printf "%20s => %s\n", ${$order}[$i], $return_array[$i]; } <STDIN>;
# return @return_array;
sub _register_for_cleanup {
  my ($self,$method) = @_;
sub _unregister_for_cleanup {
  my ($self,$method) = @_;
sub deprecated {
   my ($self,$msg) = @_;
   if( $self->verbose >= 0 ) { 
       print STDERR $msg, "\n", $self->stack_trace_dump;
sub new {
  my $class = shift;
  my @args = @_;
  unless ( $ENV{'BIOPERLDEBUG'} ) {
      carp("Use of new in Bio::Root::RootI is deprecated.  Please use Bio::Root::Root instead");
  eval "require Bio::Root::Root";
  return Bio::Root::Root->new(@args);

# for backwards compatibility
sub stack_trace {
   my ($self) = @_;

   my $i = 0;
   my @out;
   my $prev;
   while( my @call = caller($i++)) {
       # major annoyance that caller puts caller context as
# function name. Hence some monkeying around...
$prev->[3] = $call[3]; push(@out,$prev); $prev =\@ call; } $prev->[3] = 'toplevel'; push(@out,$prev); return @out;
sub stack_trace_dump {
   my ($self) = @_;

   my @stack = $self->stack_trace();

   shift @stack;
   shift @stack;
   shift @stack;

   my $out;
   my ($module,$function,$file,$position);

   foreach my $stack ( @stack) {
       ($module,$file,$position,$function) = @{$stack};
       $out .= "STACK $function $file:$position\n";

   return $out;
sub throw {
   my ($self,$string) = @_;

   my $std = $self->stack_trace_dump();

   my $out = "\n-------------------- EXCEPTION --------------------\n".
       "MSG: ".$string."\n".$std."-------------------------------------------\n";
   die $out;
sub throw_not_implemented {
    my $self = shift;
    my $package = ref $self;
    my $iface = caller(0);
    my @call = caller(1);
    my $meth = $call[3];

    my $message = "Abstract method\" $meth\" is not implemented by package $package.\n" .
		   "This is not your fault - author of $package should be blamed!\n";

    # Checking if is available in case the object isn't decended from
# Bio::Root::Root, which knows how to check for
# EB - this wasn't working and I couldn't figure out!
# SC - OK, since most RootI objects will be,
# and can deal with
# Still, I'd like to know why it wasn't working...
if( $self->can('throw') ) { $self->throw( -text => $message, -class => 'Bio::Root::NotImplemented'); } else { confess $message ; }
sub warn {
    my ($self,$string) = @_;
    my $verbose;
    if( $self->can('verbose') ) {
	$verbose = $self->verbose;
    } else {
	$verbose = 0;

    if( $verbose == 2 ) {
    } elsif( $verbose == -1 ) {
    } elsif( $verbose == 1 ) {
	my $out = "\n-------------------- WARNING ---------------------\n".
		"MSG: ".$string."\n";
	$out .= $self->stack_trace_dump;
	print STDERR $out;

    my $out = "\n-------------------- WARNING ---------------------\n".
       "MSG: ".$string."\n".
    print STDERR $out;
sub warn_not_implemented {
    my $self = shift;
    my $package = ref $self;
    my $iface = caller(0);
    my @call = caller(1);
    my $meth = $call[3];

    my $message = "Abstract method\" $meth\" is not implemented by package $package.\n" .
		   "This is not your fault - author of $package should be blamed!\n";

    if( $self->can('warn') ) {
        $self->warn( $message );
    else {
	carp $message ;

General documentation
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 _