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#
# Bio::MAGE::Base
#
##############################
# C O P Y R I G H T N O T I C E
# Copyright (c) 2001-2006 by:
# * The MicroArray Gene Expression Database Society (MGED)
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge,
# publish, distribute, sublicense, and/or sell copies of the Software,
# and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
package Bio::MAGE::Base;
use strict;
use Carp;
=head1 NAME
Bio::MAGE::Base - generic base class
=head1 SYNOPSIS
use Bio::MAGE::Base;
# create an empty instance
my $obj = Bio::MAGE::Base->new();
# create an instance and populate with data
my $obj = Bio::MAGE::Base->new(attr1=>$val1, attr2=>$val2);
# copy an existing instance
my $obj_copy = $obj->new();
=head1 DESCRIPTION
The base class for all other Bio::MAGE classes
=head1 CLASS METHODS
The following methods can all be called without first having an
instance of the class via the Namespace::Class->methodname()
syntax, i.e. the class name B<must> be given as an argument to the
method.
=over
=item $obj = class->new(%params)
The C<new()> method is the class constructor.
B<Parameters>: if given a list of name/value parameters the
corresponding slots, attributes, or associations will have their
initial values set by the constructor.
B<Return value>: It returns a reference to an object of the class.
B<Side effects>: It invokes the C<initialize()> method if it is defined
by the class.
=cut
sub new {
my $class = shift;
my $obj;
if (ref($class)) {
# copy an existing object
$obj = $class;
$class = ref($class);
}
my $self = bless {}, $class;
if (defined $obj) {
$self->set_slots([$obj->get_slot_names],
[$obj->get_slots($obj->get_slot_names)],
);
} else {
$self->set_slots(@_) if @_;
}
my $rc = $self->initialize;
return undef if $rc == -1;
return $self;
}
sub __get_superclass {
my $class = shift;
{
no strict 'refs';
my $var = $class . '::ISA';
my @isa = @$var;
if (scalar @isa) {
return $isa[0];
} else {
return undef;
}
}
}
sub __get_slot_array {
my $class = shift;
my $slot_name = shift;
# allow the $obj->method() syntax
$class = ref($class) if ref($class);
{
no strict 'refs';
my $var = $class . '::' . $slot_name;
my $val = $$var;
while (not defined $val) {
$class = $class->__get_superclass($class);
last unless defined $class;
$var = $class . '::' . $slot_name;
$val = $$var;
}
if (defined $val) {
return @{$val};
} else {
return ();
}
}
}
sub __get_slot_val {
my $class = shift;
my $slot_name = shift;
# allow the $obj->method() syntax
$class = ref($class) if ref($class);
{
no strict 'refs';
my $var = $class . '::' . $slot_name;
my $val = $$var;
while (not defined $val) {
$class = $class->__get_superclass($class);
last unless defined $class;
$var = $class . '::' . $slot_name;
$val = $$var;
}
return $val;
}
}
=back
The following methods can all be called with either the
Namespace::Class->methodname() and $obj->methodname() syntaxes.
=over
=item @names = get_slot_names()
The C<get_slot_names()> method is used to retrieve the name of all
slots defined for a given object.
B<NOTE>: the list of names does not include attribute or association
names.
B<Return value>: A list of the names of all slots defined for this class.
B<Side effects>: none
=cut
sub get_slot_names {
my $class = shift;
return $class->__get_slot_array('__SLOT_NAMES');
}
=item @name_list = get_attribute_names()
returns the list of attribute data members for this class.
=cut
sub get_attribute_names {
my $class = shift;
return $class->__get_slot_array('__ATTRIBUTE_NAMES');
}
=item @name_list = get_association_names()
returns the list of association data members for this class.
=cut
sub get_association_names {
my $class = shift;
return $class->__get_slot_array('__ASSOCIATION_NAMES');
}
=item @class_list = get_superclasses()
returns the list of superclasses for this class.
=cut
sub get_superclasses {
my $class = shift;
return $class->__get_slot_array('__SUPERCLASSES');
}
=item @class_list = get_subclasses()
returns the list of subclasses for this class.
=cut
sub get_subclasses {
my $class = shift;
return $class->__get_slot_array('__SUBCLASSES');
}
=item $name = class_name()
Returns the full class name for this class.
=cut
sub class_name {
my $class = shift;
return $class->__get_slot_val('__CLASS_NAME');
}
=item $package_name = package_name()
Returns the base package name (i.e. no 'namespace::') of the package
that contains this class.
=cut
sub package_name {
my $class = shift;
return $class->__get_slot_val('__PACKAGE_NAME');
}
=item %assns = associations()
returns the association meta-information in a hash where the keys are
the association names and the values are C<Association> objects that
provide the meta-information for the association.
=cut
sub associations {
my $class = shift;
# allow the $obj->method() syntax
$class = ref($class) if ref($class);
my @list = ();
# superclasses first
my @superclasses = $class->get_superclasses();
foreach my $super (@superclasses) {
push(@list, $super->associations());
}
# then associations from this class
push(@list, $class->__get_slot_array('__ASSOCIATIONS'));
return @list;
}
=back
=head1 INSTANCE METHODS
These methods must be invoked with the direct object syntax using an
existing instance, i.e. $object->method_name().
=over
=item $obj_copy = $obj->new()
When invoked with an existing object reference and not a class name,
the C<new()> method acts as a copy constructor - with the new object's
initial values set to be those of the existing object.
B<Parameters>: No input parameters are used in the copy constructor,
the initial values are taken directly from the object to be copied.
B<Return value>: It returns a reference to an object of the class.
B<Side effects>: It invokes the C<initialize()> method if it is defined
by the class.
=cut
#
# see above in new()
#
=item $obj->set_slots(%parameters)
=item $obj->set_slots(\@name_list, \@value_list)
The C<set_slots()> method is used to set a number of slots at the same
time. It has two different invocation methods. The first takes a named
parameter list, and the second takes two array references.
B<Return value>: none
B<Side effects>: will call C<croak()> if a slot_name is used that the class
does not define.
=cut
sub set_slots {
my $self = shift;
my %slots;
if (ref($_[0])) {
my @slot_names = @{shift()};
my @slot_values = @{shift()};
@slots{@slot_names} = @slot_values;
} else {
%slots = @_;
}
while (my ($slot_name,$slot_val) = each %slots) {
$self->set_slot($slot_name,$slot_val);
}
}
=item $obj->get_slots(@name_list)
The C<get_slots()> method is used to get the values of a number of
slots at the same time.
B<Return value>: a list of instance objects
B<Side effects>: none
=cut
sub get_slots {
my ($self, @slot_names) = @_;
my @return;
foreach my $slot (@slot_names) {
push(@return,$self->get_slot($slot));
}
return @return;
}
=item $val = $obj->set_slot($name,$val)
The C<set_slot()> method sets the slot C<$name> to the value C<$val>
B<Return value>: the new value of the slot, i.e. C<$val>
B<Side effects>: none
=cut
sub set_slot {
my ($self, $slot_name, $slot_val) = @_;
my $method = 'set' . ucfirst($slot_name);
unless ($self->can($method)) {
unless ($self->can($slot_name)) {
croak(__PACKAGE__ . "::set_slot: slot $slot_name doesn't exist");
}
# this is a class slot, not an attribute or association. They still
# use the confusing polymorphic setter/getter methods.
$method = $slot_name;
}
{
no strict 'refs';
# invoke the setter directly to gain type checking
return $self->$method($slot_val);
}
}
=item $val = $obj->get_slot($name)
The C<get_slot()> method is used to get the values of a number of
slots at the same time.
B<Return value>: a single slot value, or undef if the slot has not been
initialized.
B<Side effects>: none
=cut
sub get_slot {
my ($self, $slot_name) = @_;
my $method = 'get' . ucfirst($slot_name);
unless ($self->can($method)) {
unless ($self->can($slot_name)) {
croak(__PACKAGE__ . "::get_slot: slot $slot_name doesn't exist");
}
# this is a class slot, not an attribute or association. They still
# use the confusing polymorphic setter/getter methods.
$method = $slot_name;
}
{
no strict 'refs';
# invoke the getter directly
return $self->$method();
}
}
sub initialize {
return 1;
}
=item throw
Title : throw
Usage :
Function:
Example :
Returns :
Args :
=cut
sub throw {
my ($self, $msg) = @_;
die(caller().': '.$msg);
}
=item throw_not_implemented
Title : throw_not_implemented
Usage :
Function:
Example :
Returns :
Args :
=cut
sub throw_not_implemented {
my ($self) = @_;
die("Abstract method ".caller()." implementing class did not provide method");
}
=back
=head1 BUGS
Please send bug reports to the project mailing list: ()
=head1 AUTHOR
=head1 SEE ALSO
perl(1).
=cut
# all perl modules must be true...
1;
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