##############################
#
# Bio::MAGE::QuantitationType::Error
#
##############################
# C O P Y R I G H T   N O T I C E
#  Copyright (c) 2001-2002 by:
#    * The MicroArray Gene Expression Database Society (MGED)
#    * Rosetta Inpharmatics
#
# 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::QuantitationType::Error;

use strict;
use Carp;
use Bio::MAGE::Base;
use Bio::MAGE::Association;
use Bio::MAGE::QuantitationType::ConfidenceIndicator;


use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $__ASSOCIATIONS);

require Exporter;

@ISA = qw(Bio::MAGE::Base Bio::MAGE::QuantitationType::ConfidenceIndicator Exporter);
$VERSION = 20020902.6;

# 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();


=head1 Bio::MAGE::QuantitationType::Error

=head2 SYNOPSIS

  use Bio::MAGE::QuantitationType::Error;

    # creating an empty instance
  my $error = Bio::MAGE::QuantitationType::Error->new();


=head2 DESCRIPTION

From the MAGE-OM documentation for the C<Error> class:

Error measurement of a quantitation.  Of type float.



=cut


=head2 INHERITANCE


Bio::MAGE::QuantitationType::Error has the following super classes

=over 


=item * Bio::MAGE::QuantitationType::ConfidenceIndicator


=back


=head2 CLASS METHODS

The following methods can all be called without first having an
instance of the class via the Bio::MAGE::QuantitationType::Error->methodname() syntax.


=item new()

=item new(%args)


The object constructor C<new()> accepts the following optional
named-value style arguments:

=over


=item * targetQuantitationType

Sets the value of the targetQuantitationType association (this association was inherited
from class C<Bio::MAGE::QuantitationType::ConfidenceIndicator>).

The value will be of type C<QuantitationType>.


=item * isBackground

Sets the value of the isBackground attribute (this attribute was inherited
from class C<Bio::MAGE::QuantitationType::QuantitationType>).



=item * quantitationTypeMaps

Sets the value of the quantitationTypeMaps association (this association was inherited
from class C<Bio::MAGE::QuantitationType::QuantitationType>).

The value will be of type C<QuantitationTypeMap>.


=item * dataType

Sets the value of the dataType association (this association was inherited
from class C<Bio::MAGE::QuantitationType::QuantitationType>).

The value will be of type C<OntologyEntry>.


=item * scale

Sets the value of the scale association (this association was inherited
from class C<Bio::MAGE::QuantitationType::QuantitationType>).

The value will be of type C<OntologyEntry>.


=item * channel

Sets the value of the channel association (this association was inherited
from class C<Bio::MAGE::QuantitationType::QuantitationType>).

The value will be of type C<Channel>.


=item * confidenceIndicators

Sets the value of the confidenceIndicators association (this association was inherited
from class C<Bio::MAGE::QuantitationType::QuantitationType>).

The value will be of type C<ConfidenceIndicator>.


=item * identifier

Sets the value of the identifier attribute (this attribute was inherited
from class C<Bio::MAGE::Identifiable>).



=item * name

Sets the value of the name attribute (this attribute was inherited
from class C<Bio::MAGE::Identifiable>).



=item * descriptions

Sets the value of the descriptions association (this association was inherited
from class C<Bio::MAGE::Describable>).

The value will be of type C<Description>.


=item * security

Sets the value of the security association (this association was inherited
from class C<Bio::MAGE::Describable>).

The value will be of type C<Security>.


=item * auditTrail

Sets the value of the auditTrail association (this association was inherited
from class C<Bio::MAGE::Describable>).

The value will be of type C<Audit>.


=item * propertySets

Sets the value of the propertySets association (this association was inherited
from class C<Bio::MAGE::Extendable>).

The value will be of type C<NameValueType>.


=back



=cut

#
# code for new() inherited from Base.pm
#

=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
#

=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
#

=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
#

=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
#

=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
#



=item $name = class_name()

Returns the full class name for this class, Bio::MAGE::QuantitationType::Error.

=cut

sub class_name {
  return q[Bio::MAGE::QuantitationType::Error];
}

=item $package_name = package()

Returns the unresolved package name (i.e. no 'Bio::MAGE::') of the
package that contains class, Bio::MAGE::QuantitationType::Error.

=cut

sub package {
  return q[QuantitationType];
}

=item @classes = subclasses()

returns the list of subclasses for this class.

=cut

sub subclasses {
  my @list = ();
  return @list;
}

=item @classes = superclasses()

returns the list of superclasses for this class.

=cut

sub superclasses {
  my @list = ('Bio::MAGE::QuantitationType::ConfidenceIndicator');
  return @list;
}

=item @methods = attribute_methods()

returns the list of attribute accessor methods for this class.

=cut

sub attribute_methods {
  my $class = shift;
  my @list = ();
  if ($class->superclasses()) {
    foreach ($class->superclasses()) {
      push(@list,$_->attribute_methods());
    }
  }
  return @list;
}

=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;
}

=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;
}


=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::QuantitationType::Error: has the following attribute accessor methods:

=over

Attributes Inherited from Bio::MAGE::QuantitationType::QuantitationType


=item isBackground

From the MAGE-OM documentation for the C<isBackground> attribute:

Indicates whether the quantitation has been measured from the background or from the feature itself.



=over


=item $val = $quantitationtype->setIsBackground($val)

The restricted setter method for the isBackground attribute.

Input parameters: the value to which the isBackground attribute will be set 

Return value: the current value of the isBackground attribute 

Side effects: none

Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified 

=cut


=item $val = $quantitationtype->getIsBackground()

The restricted getter method for the isBackground attribute.

Input parameters: none

Return value: the current value of the isBackground attribute 

Side effects: none

Exceptions: will call C<croak()> if any input parameters are specified

=cut



=back

Attributes Inherited from Bio::MAGE::Identifiable


=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


=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



=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


=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



=back



=back


=cut



sub initialize {
  my $self = shift;
  return 1;
}



=head1 BUGS

Please send bug reports to mged-mage@lists.sf.net

=head1 AUTHOR

Jason E. Stewart (www.openinformatics.com)

=head1 SEE ALSO

perl(1).

=cut

#
# End the module by returning a true value
#
1;

