Bio::Root
RootI
Summary
Bio::Root::RootI - Abstract interface to root object code
Package variables
No package variables defined.
Included modules
Carp ' confess ' , ' carp '
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;
@ISA = 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.
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.
Methods
Methods description
Purpose : generic instantiation function can be overridden if
special needs of a module cannot be done in _initialize |
Title : _create_object()
Usage : $obj->create_object(@args)
Function: Abstract method which actually creates the blessed object reference
Returns : Blessed object (hashref, arrayref, scalarref)
Args : Implementation-specific |
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 |
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 : |
Title : debug
Usage : $obj->debug("This is debugging output");
Function: Prints a debugging message when verbose is > 0
Returns : none
Args : message string to print to STDERR |
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 : 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 : stack_trace_dump
Usage :
Function:
Example :
Returns :
Args : |
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 |
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,
: -id => $i,
: -desc => $d);
Returns : @params - an array of parameters in the requested order.
: The above example would return ($s, $i, $d)
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.
Comments : (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 code is more readable, and there are no method naming conlicts.
: 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 : _cleanup_methods
Usage : -- internal --
Function: Return current list of registered cleanup methods.
Returns : list of coderefs
Args : none |
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. |
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
BEGIN { $ID = 'Bio::Root::RootI';
$VERSION = 1.0;
$Revision = '$Id: RootI.pm,v 1.47.2.5 2002/06/06 21:36:59 jason Exp $ ';
$VERSION = 1.0;
$DEBUG = 0;
$VERBOSITY = 0;} | sub new
{ local($^W) = 0;
my ($caller, @args) = @_;
my $self = $caller->_create_object(@args);
my %param = @args;
my $verbose = $param{'-VERBOSE'} || $param{'-verbose'};
$self->verbose($verbose);
return $self;} | sub _initialize
{ my($self,@args) = @_;
return 1;} | sub _create_object
{ my $class = shift;
my @args = @_;
unless ( $ENV{'BIOPERLDEBUG'} ) {
carp("Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead");
}
eval "require Bio::Root::Root";
return Bio::Root::Root->new(@args);} | sub throw
{ my ($self,$string) = @_;
my $std = $self->stack_trace_dump();
my $out = "-------------------- EXCEPTION --------------------\n".
"MSG: ".$string."\n".$std."-------------------------------------------\n";
die $out;} | sub warn
{ my ($self,$string) = @_;
my $verbose = $self->verbose;
if( $verbose == 2 ) {
$self->throw($string);
} elsif( $verbose == -1 ) {
return;
} elsif( $verbose == 1 ) {
my $out = "-------------------- WARNING ---------------------\n".
"MSG: ".$string."\n";
$out .= $self->stack_trace_dump;
print STDERR $out;
return;
}
my $out = "-------------------- WARNING ---------------------\n".
"MSG: ".$string."\n".
"---------------------------------------------------\n";
print STDERR $out;} | sub debug
{ my ($self,$msg) = @_;
if( $self->verbose > 0 ) {
print STDERR $msg;
}} | sub deprecated
{ my ($self,$msg) = @_;
if( $self->verbose >= 0 ) {
print STDERR $msg, "\n", $self->stack_trace_dump;
}} | sub verbose
{ my ($self,$value) = @_;
$self->throw_not_implemented(); } | sub stack_trace_dump
{ my ($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 $out;} | sub stack_trace
{ my ($self) = @_;
my $i = 0;
my @out;
my $prev;
while( my @call = caller($i++)) {
$prev->[3] = $call[3];
push(@out,$prev);
$prev =\@ call;
}
$prev->[3] = 'toplevel';
push(@out,$prev);
return @out;} | sub _rearrange
{
my($self,$order,@param) = @_;
return unless @param;
return @param unless (defined($param[0]) && $param[0]=~/^-/);
my $i;
for ($i=0;$i<@param;$i+=2) {
$param[$i]=~s/^\-//;
$param[$i]=~tr/a-z/A-Z/;
}
local($^W) = 0;
my(%param) = @param;
my(@return_array);
my($key);
foreach $key (@{$order}) {
my($value) = $param{$key};
delete $param{$key};
push(@return_array,$value);
}
return @return_array;
} | sub _register_for_cleanup
{ my ($self,$method) = @_;
$self->throw_not_implemented(); } | sub _unregister_for_cleanup
{ my ($self,$method) = @_;
$self->throw_not_implemented(); } | 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");
}
return;} | 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";
if( $self->can('throw') ) {
$self->throw( -text => $message,
-class => 'Bio::Root::NotImplemented');
}
else {
confess $message ;
}} | 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 ;
}} | sub DESTROY
{ my $self = shift;
my @cleanup_methods = $self->_cleanup_methods or return;
for my $method (@cleanup_methods) {
$method->($self);
}} | 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 _