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##############################
#
# Bio::MAGE::Identifiable
#
##############################
package Bio::MAGE::Identifiable;
use strict;
use Carp;
use Bio::MAGE::Base;
use Bio::MAGE::Association;
use Bio::MAGE::Describable;
use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $__ASSOCIATIONS);
require Exporter;
@ISA = qw(Bio::MAGE::Base Bio::MAGE::Describable Exporter);
$VERSION = q[$Id: Identifiable.pm,v 1.5 2002/08/24 16:12:21 jason_e_stewart Exp $];
# Items to export into callers namespace by default. Note: do not export
# names by default without a very good reason. Use EXPORT_OK instead.
# Do not simply export all your public functions/methods/constants.
@EXPORT_OK = qw();
HideShow 31 lines of Pod
=head1 Bio::MAGE::Identifiable
=head2 SYNOPSIS
  use Bio::MAGE::Identifiable;
    # creating an empty instance
  my $identifiable = Bio::MAGE::Identifiable->new();
    # creating an already populated instance
  my $identifiable = Bio::MAGE::Identifiable->new(identifier=>$identifier_value,
                        name=>$name_value);
    # setting and retrieving object attributes
  my $identifier_val = $identifiable->identifier();
  $identifiable->identifier($value);
  my $name_val = $identifiable->name();
  $identifiable->name($value);
=head2 DESCRIPTION
From the MAGE-OM documentation for the C<Identifiable> class:
An Identifiable class is one that has an unambiguous reference within the scope.  It also has a potentially ambiguous name.
=cut
HideShow 162 lines of Pod
=head2 INHERITANCE
Bio::MAGE::Identifiable has the following super classes
=over 
=item * Bio::MAGE::Describable
=back
Bio::MAGE::Identifiable has the following subclasses
=over 
=item * Bio::MAGE::BioMaterial::Compound
=item * Bio::MAGE::BioEvent::BioEvent
=item * Bio::MAGE::ArrayDesign::DesignElementGroup
=item * Bio::MAGE::QuantitationType::QuantitationType
=item * Bio::MAGE::ArrayDesign::Zone
=item * Bio::MAGE::BioAssayData::BioAssayDimension
=item * Bio::MAGE::BioAssayData::QuantitationTypeDimension
=item * Bio::MAGE::ArrayDesign::ArrayDesign
=item * Bio::MAGE::AuditAndSecurity::Contact
=item * Bio::MAGE::Experiment::FactorValue
=item * Bio::MAGE::BioAssayData::BioAssayData
=item * Bio::MAGE::Array::ArrayManufacture
=item * Bio::MAGE::DesignElement::DesignElement
=item * Bio::MAGE::BioAssayData::DesignElementDimension
=item * Bio::MAGE::Description::Database
=item * Bio::MAGE::Experiment::Experiment
=item * Bio::MAGE::Array::ArrayGroup
=item * Bio::MAGE::AuditAndSecurity::Security
=item * Bio::MAGE::BioAssay::Channel
=item * Bio::MAGE::Protocol::Parameterizable
=item * Bio::MAGE::AuditAndSecurity::SecurityGroup
=item * Bio::MAGE::Array::Array
=item * Bio::MAGE::BioAssay::Image
=item * Bio::MAGE::Protocol::Parameter
=item * Bio::MAGE::BioAssay::BioAssay
=item * Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster
=item * Bio::MAGE::Experiment::ExperimentalFactor
=item * Bio::MAGE::BioSequence::BioSequence
=item * Bio::MAGE::BioMaterial::BioMaterial
=back
=head2 CLASS METHODS
The following methods can all be called without first having an
instance of the class via the Bio::MAGE::Identifiable->methodname() syntax.
=item new()
=item new(%args)
The object constructor C<new()> accepts the following optional
named-value style arguments:
=over
=item * identifier
Sets the value of the identifier attribute (from C<Bio::MAGE::Identifiable>).
=item * name
Sets the value of the name attribute (from C<Bio::MAGE::Identifiable>).
=item * security
Sets the value of the security association (from C<Bio::MAGE::Describable>).
=item * auditTrail
Sets the value of the auditTrail association (from C<Bio::MAGE::Describable>).
=item * descriptions
Sets the value of the descriptions association (from C<Bio::MAGE::Describable>).
=item * propertySets
Sets the value of the propertySets association (from C<Bio::MAGE::Extendable>).
=back
=cut
#
# code for new() inherited from Base.pm
#
HideShow 15 lines of Pod
=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
#
# code for set_slots() inherited from Base.pm
#
HideShow 11 lines of Pod
=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
#
# code for get_slots() inherited from Base.pm
#
HideShow 10 lines of Pod
=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
#
# code for set_slot() inherited from Base.pm
#
HideShow 12 lines of Pod
=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
#
# code for get_slot() inherited from Base.pm
#
HideShow 12 lines of Pod
=item @names = $obj->get_slot_names()
The C<get_slot_names()> method is used to retrieve the name of all
slots defined for a given object.
B<Return value>: a single slot value, or undef if the slot has not been
initialized.
B<Side effects>: none
=cut
#
# code for get_slot_names() inherited from Base.pm
#
HideShow 6 lines of Pod
=item $name = class_name()
Returns the full class name for this class, Bio::MAGE::Identifiable.
=cut
sub class_name {
  return q[Bio::MAGE::Identifiable];
}
HideShow 7 lines of Pod
=item $package_name = package()
Returns the unresolved package name (i.e. no 'Bio::MAGE::') of the
package that contains class, Bio::MAGE::Identifiable.
=cut
sub package {
  return q[MAGE];
}
HideShow 6 lines of Pod
=item @classes = subclasses()
returns the list of subclasses for this class.
=cut
sub subclasses {
  my @list = ('Bio::MAGE::BioMaterial::Compound', 'Bio::MAGE::BioEvent::BioEvent', 'Bio::MAGE::ArrayDesign::DesignElementGroup', 'Bio::MAGE::QuantitationType::QuantitationType', 'Bio::MAGE::ArrayDesign::Zone', 'Bio::MAGE::BioAssayData::BioAssayDimension', 'Bio::MAGE::BioAssayData::QuantitationTypeDimension', 'Bio::MAGE::ArrayDesign::ArrayDesign', 'Bio::MAGE::AuditAndSecurity::Contact', 'Bio::MAGE::Experiment::FactorValue', 'Bio::MAGE::BioAssayData::BioAssayData', 'Bio::MAGE::Array::ArrayManufacture', 'Bio::MAGE::DesignElement::DesignElement', 'Bio::MAGE::BioAssayData::DesignElementDimension', 'Bio::MAGE::Description::Database', 'Bio::MAGE::Experiment::Experiment', 'Bio::MAGE::Array::ArrayGroup', 'Bio::MAGE::AuditAndSecurity::Security', 'Bio::MAGE::BioAssay::Channel', 'Bio::MAGE::Protocol::Parameterizable', 'Bio::MAGE::AuditAndSecurity::SecurityGroup', 'Bio::MAGE::Array::Array', 'Bio::MAGE::BioAssay::Image', 'Bio::MAGE::Protocol::Parameter', 'Bio::MAGE::BioAssay::BioAssay', 'Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster', 'Bio::MAGE::Experiment::ExperimentalFactor', 'Bio::MAGE::BioSequence::BioSequence', 'Bio::MAGE::BioMaterial::BioMaterial');
  return @list;
}
HideShow 6 lines of Pod
=item @classes = superclasses()
returns the list of superclasses for this class.
=cut
sub superclasses {
  my @list = ('Bio::MAGE::Describable');
  return @list;
}
HideShow 6 lines of Pod
=item @methods = attribute_methods()
returns the list of attribute accessor methods for this class.
=cut
sub attribute_methods {
  my $class = shift;
  my @list = ('identifier', 'name');
  if ($class->superclasses()) {
    foreach ($class->superclasses()) {
      push(@list,$_->attribute_methods());
    }
  }
  return @list;
}
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=item @methods = association_methods()
returns the list of association accessor methods for this class.
=cut
sub association_methods {
  my $class = shift;
  my @list = ();
  if ($class->superclasses()) {
    foreach ($class->superclasses()) {
      push(@list,$_->association_methods());
    }
  }
  return @list;
}
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=item %assns = associations()
returns the association meta-information in a hash where the keys are
the association names and the values are C<Bio::MAGE::Association>
objects that provide the meta-information for the association.
=cut
sub associations {
  my $class = shift;
  my @list = ();
  # superclasses first
  if ($class->superclasses()) {
    foreach ($class->superclasses()) {
      push(@list,$_->associations());
    }
  }
  # then associations from this class
  if (defined $__ASSOCIATIONS) {
    push(@list,@{$__ASSOCIATIONS})
  }
  return @list;
}
HideShow 38 lines of Pod
=head2 ATTRIBUTES
Attributes are simple data types that belong to a single instance of a
class. In the Perl implementation of the MAGE-OM classes, the
interface to attributes is implemented using separate setter and
getter methods for each attribute.
Bio::MAGE::Identifiable: has the following attribute accessor methods:
=over
=item identifier
From the MAGE-OM documentation for the C<identifier> attribute:
An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
=over
=item $val = $identifiable->setIdentifier($val)
The restricted setter method for the identifier attribute.
Input parameters: the value to which the identifier attribute will be set 
Return value: the current value of the identifier attribute 
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified 
=cut
sub setIdentifier {
  my $self = shift;
  croak(__PACKAGE__ . "::setIdentifier: no arguments passed to setter")
    unless @_;
  croak(__PACKAGE__ . "::setIdentifier: too many arguments passed to setter")
    if @_ > 1;
  my $val = shift;
   
  return $self->{__IDENTIFIER} = $val;
}
HideShow 14 lines of Pod
=item $val = $identifiable->getIdentifier()
The restricted getter method for the identifier attribute.
Input parameters: none
Return value: the current value of the identifier attribute 
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getIdentifier {
  my $self = shift;
  croak(__PACKAGE__ . "::getIdentifier: arguments passed to getter")
    if @_;
  return $self->{__IDENTIFIER};
}
HideShow 29 lines of Pod
=back
=item name
From the MAGE-OM documentation for the C<name> attribute:
The potentially ambiguous common identifier.
=over
=item $val = $identifiable->setName($val)
The restricted setter method for the name attribute.
Input parameters: the value to which the name attribute will be set 
Return value: the current value of the name attribute 
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified 
=cut
sub setName {
  my $self = shift;
  croak(__PACKAGE__ . "::setName: no arguments passed to setter")
    unless @_;
  croak(__PACKAGE__ . "::setName: too many arguments passed to setter")
    if @_ > 1;
  my $val = shift;
   
  return $self->{__NAME} = $val;
}
HideShow 14 lines of Pod
=item $val = $identifiable->getName()
The restricted getter method for the name attribute.
Input parameters: none
Return value: the current value of the name attribute 
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getName {
  my $self = shift;
  croak(__PACKAGE__ . "::getName: arguments passed to getter")
    if @_;
  return $self->{__NAME};
}
HideShow 9 lines of Pod
=back
=back
=cut
sub initialize {
  carp "Bio::MAGE::Identifiable::initialize: abstract base classes should not be instantiated";
}
HideShow 14 lines of Pod
=head1 BUGS
Please send bug reports to mged-mage@lists.sf.net
=head1 AUTHOR
Jason E. Stewart (jason@openinformatics.com)
=head1 SEE ALSO
perl(1).
=cut
#
# End the module by returning a true value
#
1;