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##############################
#
# Bio::MAGE::Array::FeatureDefect
#
##############################
package Bio::MAGE::Array::FeatureDefect;
use strict;
use Carp;
use Bio::MAGE::Base;
use Bio::MAGE::Association;
use Bio::MAGE::Extendable;
use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $__ASSOCIATIONS);
require Exporter;
@ISA = qw(Bio::MAGE::Base Bio::MAGE::Extendable Exporter);
$VERSION = q[$Id: FeatureDefect.pm,v 1.4 2002/08/24 16:12:11 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 35 lines of Pod
=head1 Bio::MAGE::Array::FeatureDefect
=head2 SYNOPSIS
  use Bio::MAGE::Array::FeatureDefect;
    # creating an empty instance
  my $featuredefect = Bio::MAGE::Array::FeatureDefect->new();
    # creating an already populated instance
  my $featuredefect = Bio::MAGE::Array::FeatureDefect->new(feature=>$feature_value,
                        positionDelta=>$positionDelta_value,
                        defectType=>$defectType_value);
    # setting and retrieving object associations
  my $feature_val = $featuredefect->feature();
  $featuredefect->feature($value);
  my $positionDelta_val = $featuredefect->positionDelta();
  $featuredefect->positionDelta($value);
  my $defectType_val = $featuredefect->defectType();
  $featuredefect->defectType($value);
=head2 DESCRIPTION
From the MAGE-OM documentation for the C<FeatureDefect> class:
Stores the defect information for a feature.
=cut
HideShow 57 lines of Pod
=head2 INHERITANCE
Bio::MAGE::Array::FeatureDefect has the following super classes
=over 
=item * Bio::MAGE::Extendable
=back
=head2 CLASS METHODS
The following methods can all be called without first having an
instance of the class via the Bio::MAGE::Array::FeatureDefect->methodname() syntax.
=item new()
=item new(%args)
The object constructor C<new()> accepts the following optional
named-value style arguments:
=over
=item * feature
Sets the value of the feature association (from C<Bio::MAGE::Array::FeatureDefect>).
=item * positionDelta
Sets the value of the positionDelta association (from C<Bio::MAGE::Array::FeatureDefect>).
=item * defectType
Sets the value of the defectType association (from C<Bio::MAGE::Array::FeatureDefect>).
=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::Array::FeatureDefect.
=cut
sub class_name {
  return q[Bio::MAGE::Array::FeatureDefect];
}
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::Array::FeatureDefect.
=cut
sub package {
  return q[Array];
}
HideShow 6 lines of Pod
=item @classes = subclasses()
returns the list of subclasses for this class.
=cut
sub subclasses {
  my @list = ();
  return @list;
}
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=item @classes = superclasses()
returns the list of superclasses for this class.
=cut
sub superclasses {
  my @list = ('Bio::MAGE::Extendable');
  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 $class = shift;
  my @list = ();
  if ($class->superclasses()) {
    foreach ($class->superclasses()) {
      push(@list,$_->attribute_methods());
    }
  }
  return @list;
}
HideShow 6 lines of Pod
=item @methods = association_methods()
returns the list of association accessor methods for this class.
=cut
sub association_methods {
  my $class = shift;
  my @list = ('feature', 'positionDelta', 'defectType');
  if ($class->superclasses()) {
    foreach ($class->superclasses()) {
      push(@list,$_->association_methods());
    }
  }
  return @list;
}
HideShow 8 lines of Pod
=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 18 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::Array::FeatureDefect: has the following attribute accessor methods:
=over
=back
=cut
BEGIN {
  $__ASSOCIATIONS = [
          'defectType',
          bless( {
                   '__NAME' => 'defectType',
                   '__IS_REF' => 0,
                   '__CARDINALITY' => '1',
                   '__CLASS_NAME' => 'OntologyEntry',
                   '__RANK' => '1',
                   '__DESCRIPTION' => 'Indicates the type of defect (e.g. a missing feature or a moved feature).',
                   '__ORDERED' => 0
                 }, 'Bio::MAGE::Association' ),
          'positionDelta',
          bless( {
                   '__NAME' => 'positionDelta',
                   '__IS_REF' => 0,
                   '__CARDINALITY' => '0..1',
                   '__CLASS_NAME' => 'PositionDelta',
                   '__RANK' => '2',
                   '__DESCRIPTION' => 'How the feature deviates in position from the ArrayDesign.',
                   '__ORDERED' => 0
                 }, 'Bio::MAGE::Association' ),
          'feature',
          bless( {
                   '__NAME' => 'feature',
                   '__IS_REF' => 1,
                   '__CARDINALITY' => '1',
                   '__CLASS_NAME' => 'Feature',
                   '__RANK' => '3',
                   '__DESCRIPTION' => 'The feature that was manufactured defectively.',
                   '__ORDERED' => 0
                 }, 'Bio::MAGE::Association' )
        ]
}
HideShow 61 lines of Pod
=head2 ASSOCIATIONS
Associations are references to other class objects which can be shared
by multiple class instances at the same time. In the Perl
implementation of MAGE-OM classes, associations are implemented using
three separate methods:
=over
=item get*
Retrieves the current value. If the association has list cardinality,
an array reference is returned.
=item set*
Sets the current value B<replacing> any existing value. If the
association has list cardinality, the argument must be an array
reference. Unless you know what you are doing, you probably should be
using the add* methods.
=item add*
This method exists only for associations with list cardinality. It
appends a list of objects to any values that may already be stored in
the association.
=back
Bio::MAGE::Array::FeatureDefect: has the following association accessor methods:
=over
=item feature
From the MAGE-OM documentation for the C<feature> association:
The feature that was manufactured defectively.
=over
=item $val = $featuredefect->setFeature($val)
The restricted setter method for the feature association.
Input parameters: the value to which the feature association will be set : an instance of type C<Bio::MAGE::DesignElement::Feature>.
Return value: the current value of the feature association : an instance of type C<Bio::MAGE::DesignElement::Feature>.
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified , or if $val is not an instance of class C<Bio::MAGE::DesignElement::Feature>
=cut
sub setFeature {
  my $self = shift;
  croak(__PACKAGE__ . "::setFeature: no arguments passed to setter")
    unless @_;
  croak(__PACKAGE__ . "::setFeature: too many arguments passed to setter")
    if @_ > 1;
  my $val = shift;
  croak(__PACKAGE__ . "::setFeature: wrong type: " . ref($val) . " expected Bio::MAGE::DesignElement::Feature") unless UNIVERSAL::isa($val,'Bio::MAGE::DesignElement::Feature');
  return $self->{__FEATURE} = $val;
}
HideShow 14 lines of Pod
=item $val = $featuredefect->getFeature()
The restricted getter method for the feature association.
Input parameters: none
Return value: the current value of the feature association : an instance of type C<Bio::MAGE::DesignElement::Feature>.
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getFeature {
  my $self = shift;
  croak(__PACKAGE__ . "::getFeature: arguments passed to getter")
    if @_;
  return $self->{__FEATURE};
}
HideShow 30 lines of Pod
=back
=item positionDelta
From the MAGE-OM documentation for the C<positionDelta> association:
How the feature deviates in position from the ArrayDesign.
=over
=item $val = $featuredefect->setPositionDelta($val)
The restricted setter method for the positionDelta association.
Input parameters: the value to which the positionDelta association will be set : an instance of type C<Bio::MAGE::Array::PositionDelta>.
Return value: the current value of the positionDelta association : an instance of type C<Bio::MAGE::Array::PositionDelta>.
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified , or if $val is not an instance of class C<Bio::MAGE::Array::PositionDelta>
=cut
sub setPositionDelta {
  my $self = shift;
  croak(__PACKAGE__ . "::setPositionDelta: no arguments passed to setter")
    unless @_;
  croak(__PACKAGE__ . "::setPositionDelta: too many arguments passed to setter")
    if @_ > 1;
  my $val = shift;
  croak(__PACKAGE__ . "::setPositionDelta: wrong type: " . ref($val) . " expected Bio::MAGE::Array::PositionDelta") unless UNIVERSAL::isa($val,'Bio::MAGE::Array::PositionDelta');
  return $self->{__POSITIONDELTA} = $val;
}
HideShow 14 lines of Pod
=item $val = $featuredefect->getPositionDelta()
The restricted getter method for the positionDelta association.
Input parameters: none
Return value: the current value of the positionDelta association : an instance of type C<Bio::MAGE::Array::PositionDelta>.
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getPositionDelta {
  my $self = shift;
  croak(__PACKAGE__ . "::getPositionDelta: arguments passed to getter")
    if @_;
  return $self->{__POSITIONDELTA};
}
HideShow 30 lines of Pod
=back
=item defectType
From the MAGE-OM documentation for the C<defectType> association:
Indicates the type of defect (e.g. a missing feature or a moved feature).
=over
=item $val = $featuredefect->setDefectType($val)
The restricted setter method for the defectType association.
Input parameters: the value to which the defectType association will be set : an instance of type C<Bio::MAGE::Description::OntologyEntry>.
Return value: the current value of the defectType association : an instance of type C<Bio::MAGE::Description::OntologyEntry>.
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified , or if $val is not an instance of class C<Bio::MAGE::Description::OntologyEntry>
=cut
sub setDefectType {
  my $self = shift;
  croak(__PACKAGE__ . "::setDefectType: no arguments passed to setter")
    unless @_;
  croak(__PACKAGE__ . "::setDefectType: too many arguments passed to setter")
    if @_ > 1;
  my $val = shift;
  croak(__PACKAGE__ . "::setDefectType: wrong type: " . ref($val) . " expected Bio::MAGE::Description::OntologyEntry") unless UNIVERSAL::isa($val,'Bio::MAGE::Description::OntologyEntry');
  return $self->{__DEFECTTYPE} = $val;
}
HideShow 14 lines of Pod
=item $val = $featuredefect->getDefectType()
The restricted getter method for the defectType association.
Input parameters: none
Return value: the current value of the defectType association : an instance of type C<Bio::MAGE::Description::OntologyEntry>.
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getDefectType {
  my $self = shift;
  croak(__PACKAGE__ . "::getDefectType: arguments passed to getter")
    if @_;
  return $self->{__DEFECTTYPE};
}
HideShow 32 lines of Pod
=back
Associations Inherited from Bio::MAGE::Extendable
=item propertySets
From the MAGE-OM documentation for the C<propertySets> association:
Allows specification of name/value pairs.  Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.
=over
=item $array_ref = $extendable->setPropertySets($array_ref)
The restricted setter method for the propertySets association.
Input parameters: the value to which the propertySets association will be set : a reference to an array of objects of type C<Bio::MAGE::NameValueType>
Return value: the current value of the propertySets association : a reference to an array of objects of type C<Bio::MAGE::NameValueType>
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified , or if $array_ref is not a reference to an array class C<Bio::MAGE::NameValueType> instances
=cut
HideShow 14 lines of Pod
=item $array_ref = $extendable->getPropertySets()
The restricted getter method for the propertySets association.
Input parameters: none
Return value: the current value of the propertySets association : a reference to an array of objects of type C<Bio::MAGE::NameValueType>
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
HideShow 18 lines of Pod
=item $extendable->addPropertySets(@vals)
Because the propertySets association has list cardinality, it may store more
than one value. This method adds the current list of objects in the propertySets
association.
Input parameters: the list of values C<@vals> to add to the propertySets
association. B<NOTE>: submitting a single value is permitted.
Return value: none
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified
, or if any of the objects in @vals is not an instance of class C<Bio::MAGE::NameValueType>
=cut
HideShow 9 lines of Pod
=back
=back
=cut
sub initialize {
  my $self = shift;
  return 1;
}
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;