Bio::MAGE - Container module for classes in the MAGE package: MAGE

Bio-MAGE documentation Contained in the Bio-MAGE distribution.

Index

Code Index:

NAME

Top

Bio::MAGE - Container module for classes in the MAGE package: MAGE

SYNOPSIS

Top

  use Bio::MAGE;

DESCRIPTION

Top

This is a package module that encapsulates a number of classes in the Bio::MAGE hierarchy. These classes belong to the MAGE package of the MAGE-OM object model.

CLASSES

Top

The Bio::MAGE module contains the following Bio::MAGE classes:

* NameValueType
* Extendable
* Identifiable
* Describable

CLASS METHODS

Top

@class_list = Bio::MAGE::classes();

This method returns a list of non-fully qualified class names (i.e. they do not have 'Bio::MAGE::' as a prefix) in this package.

@list_names = Bio::MAGE::xml_packages();

This method returns an ordered list of the MAGE-ML packages that exist in the top level MAGE-ML element.

$hash_ref = Bio::MAGE::class2fullclass();

This method returns a hash table that maps the fully qualified class name of a class given the abbreviated name for the complete Bio::MAGE class hierarchy.

$obj = class->new(%parameters)

The new() method is the class constructor.

Parameters: if given a list of name/value parameters the corresponding slots, attributes, or associations will have their initial values set by the constructor.

Return value: It returns a reference to an object of the class.

Side effects: It invokes the initialize() method if it is defined by the class.

@names = class->get_slot_names()

The get_slot_names() method is used to retrieve the name of all slots defined in a given class.

NOTE: the list of names does not include attribute or association names.

Return value: A list of the names of all slots defined for this class.

Side effects: none

@name_list = get_attribute_names()

returns the list of attribute data members for this class.

@name_list = get_association_names()

returns the list of association data members for this class.

@class_list = get_superclasses()

returns the list of superclasses for this class.

@class_list = get_subclasses()

returns the list of subclasses for this class.

$name = class_name()

Returns the full class name for this class.

$package_name = package_name()

Returns the base package name (i.e. no 'namespace::') of the package that contains this class.

%assns = associations()

returns the association meta-information in a hash where the keys are the association names and the values are Association objects that provide the meta-information for the association.

INSTANCE METHODS

Top

$obj_copy = $obj->new()

When invoked with an existing object reference and not a class name, the new() method acts as a copy constructor - with the new object's initial values set to be those of the existing object.

Parameters: No input parameters are used in the copy constructor, the initial values are taken directly from the object to be copied.

Return value: It returns a reference to an object of the class.

Side effects: It invokes the initialize() method if it is defined by the class.

$obj->set_slots(%parameters)
$obj->set_slots(\@name_list, \@value_list)

The 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.

Return value: none

Side effects: will call croak() if a slot_name is used that the class does not define.

@obj_list = $obj->get_slots(@name_list)

The get_slots() method is used to get the values of a number of slots at the same time.

Return value: a list of instance objects

Side effects: none

$val = $obj->set_slot($name,$val)

The set_slot() method sets the slot $name to the value $val

Return value: the new value of the slot, i.e. $val

Side effects: none

$val = $obj->get_slot($name)

The get_slot() method is used to get the values of a number of slots at the same time.

Return value: a single slot value, or undef if the slot has not been initialized.

Side effects: none

$val = $mage->objects()
$inval = $mage->objects($inval)

This is the unified setter/getter method for the objects slot.

If $inval is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $inval will invoke the setter method.

Return value: for both setter and getter the current value of the objects slot

Side effects: none

Exceptions: none

$val = $mage->tagname()
$inval = $mage->tagname($inval)

This is the unified setter/getter method for the tagname slot.

If $inval is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $inval will invoke the setter method.

Return value: for both setter and getter the current value of the tagname slot

Side effects: none

Exceptions: none

$val = $mage->identifier()
$inval = $mage->identifier($inval)

This is the unified setter/getter method for the identifier slot.

If $inval is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $inval will invoke the setter method.

Return value: for both setter and getter the current value of the identifier slot

Side effects: none

Exceptions: none

$val = $mage->registered_objects()
$inval = $mage->registered_objects($inval)

This is the unified setter/getter method for the registered_objects slot.

If $inval is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $inval will invoke the setter method.

Return value: for both setter and getter the current value of the registered_objects slot

Side effects: none

Exceptions: none

$val = $mage->identifiers()
$inval = $mage->identifiers($inval)

This is the unified setter/getter method for the identifiers slot.

If $inval is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $inval will invoke the setter method.

Return value: for both setter and getter the current value of the identifiers slot

Side effects: none

Exceptions: none

$val = $mage->packages()
$inval = $mage->packages($inval)

This is the unified setter/getter method for the packages slot.

If $inval is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $inval will invoke the setter method.

Return value: for both setter and getter the current value of the packages slot

Side effects: none

Exceptions: none

$mage->add_objects(@list)

The objects in @list are added to the MAGE object. This method will recursively descend that association hierarcy of each object and place all Identifiable objects in their appropriate lists for writing as MAGE-ML.

$pkg_obj = $mage->getHigherLevelAnalysis_package()

This method manages the handling of the singleton class object for the Bio::MAGE::HigherLevelAnalysis class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getBioEvent_package()

This method manages the handling of the singleton class object for the Bio::MAGE::BioEvent class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getBioMaterial_package()

This method manages the handling of the singleton class object for the Bio::MAGE::BioMaterial class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getBioSequence_package()

This method manages the handling of the singleton class object for the Bio::MAGE::BioSequence class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getAuditAndSecurity_package()

This method manages the handling of the singleton class object for the Bio::MAGE::AuditAndSecurity class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getBioAssayData_package()

This method manages the handling of the singleton class object for the Bio::MAGE::BioAssayData class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getBQS_package()

This method manages the handling of the singleton class object for the Bio::MAGE::BQS class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getArray_package()

This method manages the handling of the singleton class object for the Bio::MAGE::Array class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getQuantitationType_package()

This method manages the handling of the singleton class object for the Bio::MAGE::QuantitationType class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getExperiment_package()

This method manages the handling of the singleton class object for the Bio::MAGE::Experiment class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getBioAssay_package()

This method manages the handling of the singleton class object for the Bio::MAGE::BioAssay class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getDesignElement_package()

This method manages the handling of the singleton class object for the Bio::MAGE::DesignElement class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getProtocol_package()

This method manages the handling of the singleton class object for the Bio::MAGE::Protocol class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getDescription_package()

This method manages the handling of the singleton class object for the Bio::MAGE::Description class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getArrayDesign_package()

This method manages the handling of the singleton class object for the Bio::MAGE::ArrayDesign class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$pkg_obj = $mage->getMeasurement_package()

This method manages the handling of the singleton class object for the Bio::MAGE::Measurement class. When called it will return the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

$mage->obj2xml($writer)

Write out this object, and all sub-objects, as XML using the supplied $writer to actually do the XML formatting.

Input parameters: $writer must be an XML writer, e.g. an instance of Bio::MAGE::XML::Writer. It must have methods: write_start_tag() and write_end_tag().

Return value: none

Side effects: all writing is delegated to the $writer - it's write_start_tag() and write_end_tag() methods are invoked with the appropriate data, and all package sub-objects of the Bio::MAGE instance will have their obj2xml() methods invoked in turn. By allowing the $writer to do the actual formatting of the output XML, it enables the user to precisely control the format.

Exceptions: will call croak() if no identifier has been set for the Bio::MAGE instance.

$mage->register($obj)

Store an object for later writing as XML.

Input parameters: object to be added to the list of registered objects.

Return value: none

Side effects: if $obj needs to be stored by this class, a reference will be stored in the correct XML list for this class.

Exceptions: die() will be called if the object does not have it's identifier set, or if the object has incorrectly set an association of list cardinality to a single object.

SLOTS, ATTRIBUTES, AND ASSOCIATIONS

Top

In the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations.

SLOTS

This API uses the term slot to indicate a data member of the class that was not present in the UML model and is used for mainly internal purposes - use only if you understand the inner workings of the API. Most often slots are used by generic methods such as those in the XML writing and reading classes.

Slots are implemented using unified getter/setter methods:

$var = $obj->slot_name();

Retrieves the current value of the slot.

$new_var = $obj->slot_name($new_var);

Store $new_var in the slot - the return value is also $new_var.

@names = $obj->get_slot_names()

Returns the list of all slots in the class.

DATA CHECKING: No data type checking is made for these methods.

ATTRIBUTES AND ASSOCIATIONS

The terms attribute and association indicate data members of the class that were specified directly from the UML model.

In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:

get*

Retrieves the current value.

NOTE: For associations, if the association has list cardinality, an array reference is returned.

DATA CHECKING: Ensure that no argument is provided.

set*

Sets the current value, replacing any existing value.

NOTE: For associations, if the association has list cardinality, the argument must be an array reference. Because of this, you probably should be using the add* methods.

DATA CHECKING: For attributes, ensure that a single value is provided as the argument. For associations, if the association has list cardinality, ensure that the argument is a reference to an array of instances of the correct MAGE-OM class, otherwise ensure that there is a single argument of the correct MAGE-OM class.

add*

NOTE: Only present in associations with list cardinality.

Appends a list of objects to any values that may already be stored in the association.

DATA CHECKING: Ensure that all arguments are of the correct MAGE-OM class.

GENERIC METHODS

The unified base class of all MAGE-OM classes, Bio::MAGE::Base, provides a set of generic methods that will operate on slots, attributes, and associations:

$val = $obj->get_slot($name)
\@list_ref = $obj->get_slots(@name_list);
$val = $obj->set_slot($name,$val)
$obj->set_slots(%parameters)
$obj->set_slots(\@name_list, \@value_list)

See elsewhere in this page for a detailed description of these methods.

BUGS

Top

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)

AUTHOR

Top

Jason E. Stewart (jasons 'at' cpan 'dot' org)

SEE ALSO

Top

perl(1).

Bio-MAGE documentation Contained in the Bio-MAGE distribution. 
##############################
#
# Bio::MAGE
#
##############################
# 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;

use strict;

use base qw(Bio::MAGE::Base);

use Carp;
use Tie::IxHash;

use Bio::MAGE::NameValueType;
use Bio::MAGE::Extendable;
use Bio::MAGE::Identifiable;
use Bio::MAGE::Describable;

use base qw(Exporter);
use vars qw(%EXPORT_TAGS $__XML_PACKAGES $__CLASS2FULLCLASS $__XML_LISTS $VERSION);

$VERSION = 20030502.3;

 %EXPORT_TAGS = (ALL => ['']);

sub import {
  my ($pkg,@tags) = @_;
  foreach (@tags) {
    if ($_ =~ /ALL/) {
      import_all();
    }
  }
}

sub import_all {
  eval qq[
                    require Bio::MAGE::HigherLevelAnalysis;
                    require Bio::MAGE::BioEvent;
                    require Bio::MAGE::BioMaterial;
                    require Bio::MAGE::BioSequence;
                    require Bio::MAGE::AuditAndSecurity;
                    require Bio::MAGE::BioAssayData;
                    require Bio::MAGE::BQS;
                    require Bio::MAGE::Array;
                    require Bio::MAGE::QuantitationType;
                    require Bio::MAGE::Experiment;
                    require Bio::MAGE::BioAssay;
                    require Bio::MAGE::DesignElement;
                    require Bio::MAGE::Protocol;
                    require Bio::MAGE::Description;
                    require Bio::MAGE::ArrayDesign;
                    require Bio::MAGE::Measurement;
	 	 ];
  if ($@) {
    die __PACKAGE__ . "::import_all: load error: $@\n";
  }
}

sub initialize {
  my ($self) = shift;
  $self->identifiers({});
  $self->packages({});		# create packages on a per-need basis
  $self->registered_objects({});
  $self->tagname('MAGE-ML')
    unless defined $self->tagname();
  $self->add_objects($self->objects())
    if defined $self->objects();
  return 1;
}




sub classes {
  return ('NameValueType','Extendable','Identifiable','Describable');
}

BEGIN {
  $__XML_PACKAGES = [
          'AuditAndSecurity',
          'Description',
          'Measurement',
          'BQS',
          'BioEvent',
          'Protocol',
          'BioMaterial',
          'BioSequence',
          'DesignElement',
          'ArrayDesign',
          'Array',
          'BioAssay',
          'QuantitationType',
          'BioAssayData',
          'Experiment',
          'HigherLevelAnalysis'
        ]
;
  $__CLASS2FULLCLASS = {
          'ReporterGroup' => 'Bio::MAGE::ArrayDesign::ReporterGroup',
          'SeqFeatureLocation' => 'Bio::MAGE::BioSequence::SeqFeatureLocation',
          'BibliographicReference' => 'Bio::MAGE::BQS::BibliographicReference',
          'BioDataTuples' => 'Bio::MAGE::BioAssayData::BioDataTuples',
          'ArrayGroup' => 'Bio::MAGE::Array::ArrayGroup',
          'DistanceUnit' => 'Bio::MAGE::Measurement::DistanceUnit',
          'ProtocolApplication' => 'Bio::MAGE::Protocol::ProtocolApplication',
          'ManufactureLIMS' => 'Bio::MAGE::Array::ManufactureLIMS',
          'FeatureReporterMap' => 'Bio::MAGE::DesignElement::FeatureReporterMap',
          'Hybridization' => 'Bio::MAGE::BioAssay::Hybridization',
          'Security' => 'Bio::MAGE::AuditAndSecurity::Security',
          'PositionDelta' => 'Bio::MAGE::Array::PositionDelta',
          'DerivedBioAssayData' => 'Bio::MAGE::BioAssayData::DerivedBioAssayData',
          'CompositePosition' => 'Bio::MAGE::DesignElement::CompositePosition',
          'Hardware' => 'Bio::MAGE::Protocol::Hardware',
          'ParameterValue' => 'Bio::MAGE::Protocol::ParameterValue',
          'CompositeCompositeMap' => 'Bio::MAGE::DesignElement::CompositeCompositeMap',
          'Audit' => 'Bio::MAGE::AuditAndSecurity::Audit',
          'BioAssay' => 'Bio::MAGE::BioAssay::BioAssay',
          'HardwareApplication' => 'Bio::MAGE::Protocol::HardwareApplication',
          'Unit' => 'Bio::MAGE::Measurement::Unit',
          'BioSource' => 'Bio::MAGE::BioMaterial::BioSource',
          'CompositeSequence' => 'Bio::MAGE::DesignElement::CompositeSequence',
          'PValue' => 'Bio::MAGE::QuantitationType::PValue',
          'BioAssayDimension' => 'Bio::MAGE::BioAssayData::BioAssayDimension',
          'StandardQuantitationType' => 'Bio::MAGE::QuantitationType::StandardQuantitationType',
          'MismatchInformation' => 'Bio::MAGE::DesignElement::MismatchInformation',
          'DesignElementDimension' => 'Bio::MAGE::BioAssayData::DesignElementDimension',
          'Parameter' => 'Bio::MAGE::Protocol::Parameter',
          'Feature' => 'Bio::MAGE::DesignElement::Feature',
          'FeatureGroup' => 'Bio::MAGE::ArrayDesign::FeatureGroup',
          'QuantitationType' => 'Bio::MAGE::QuantitationType::QuantitationType',
          'ExternalReference' => 'Bio::MAGE::Description::ExternalReference',
          'SequencePosition' => 'Bio::MAGE::BioSequence::SequencePosition',
          'BioEvent' => 'Bio::MAGE::BioEvent::BioEvent',
          'MeasuredBioAssay' => 'Bio::MAGE::BioAssay::MeasuredBioAssay',
          'CompositeGroup' => 'Bio::MAGE::ArrayDesign::CompositeGroup',
          'BioAssayDatum' => 'Bio::MAGE::BioAssayData::BioAssayDatum',
          'BioAssayTreatment' => 'Bio::MAGE::BioAssay::BioAssayTreatment',
          'Extendable' => 'Bio::MAGE::Extendable',
          'SoftwareApplication' => 'Bio::MAGE::Protocol::SoftwareApplication',
          'Node' => 'Bio::MAGE::HigherLevelAnalysis::Node',
          'NodeValue' => 'Bio::MAGE::HigherLevelAnalysis::NodeValue',
          'DerivedBioAssay' => 'Bio::MAGE::BioAssay::DerivedBioAssay',
          'DatabaseEntry' => 'Bio::MAGE::Description::DatabaseEntry',
          'Compound' => 'Bio::MAGE::BioMaterial::Compound',
          'ArrayDesign' => 'Bio::MAGE::ArrayDesign::ArrayDesign',
          'BioMaterialMeasurement' => 'Bio::MAGE::BioMaterial::BioMaterialMeasurement',
          'ConcentrationUnit' => 'Bio::MAGE::Measurement::ConcentrationUnit',
          'Transformation' => 'Bio::MAGE::BioAssayData::Transformation',
          'BioMaterial' => 'Bio::MAGE::BioMaterial::BioMaterial',
          'Treatment' => 'Bio::MAGE::BioMaterial::Treatment',
          'BioAssayData' => 'Bio::MAGE::BioAssayData::BioAssayData',
          'BioAssayCreation' => 'Bio::MAGE::BioAssay::BioAssayCreation',
          'ReporterDimension' => 'Bio::MAGE::BioAssayData::ReporterDimension',
          'ConfidenceIndicator' => 'Bio::MAGE::QuantitationType::ConfidenceIndicator',
          'Failed' => 'Bio::MAGE::QuantitationType::Failed',
          'ArrayManufactureDeviation' => 'Bio::MAGE::Array::ArrayManufactureDeviation',
          'SpecializedQuantitationType' => 'Bio::MAGE::QuantitationType::SpecializedQuantitationType',
          'FeatureInformation' => 'Bio::MAGE::DesignElement::FeatureInformation',
          'ExperimentDesign' => 'Bio::MAGE::Experiment::ExperimentDesign',
          'PhysicalArrayDesign' => 'Bio::MAGE::ArrayDesign::PhysicalArrayDesign',
          'PhysicalBioAssay' => 'Bio::MAGE::BioAssay::PhysicalBioAssay',
          'Ratio' => 'Bio::MAGE::QuantitationType::Ratio',
          'FeatureLocation' => 'Bio::MAGE::DesignElement::FeatureLocation',
          'DesignElement' => 'Bio::MAGE::DesignElement::DesignElement',
          'QuantitationTypeDimension' => 'Bio::MAGE::BioAssayData::QuantitationTypeDimension',
          'DerivedSignal' => 'Bio::MAGE::QuantitationType::DerivedSignal',
          'Fiducial' => 'Bio::MAGE::Array::Fiducial',
          'BioSequence' => 'Bio::MAGE::BioSequence::BioSequence',
          'ReporterPosition' => 'Bio::MAGE::DesignElement::ReporterPosition',
          'QuantitationTypeMapping' => 'Bio::MAGE::BioAssayData::QuantitationTypeMapping',
          'MeasuredBioAssayData' => 'Bio::MAGE::BioAssayData::MeasuredBioAssayData',
          'Identifiable' => 'Bio::MAGE::Identifiable',
          'Position' => 'Bio::MAGE::DesignElement::Position',
          'Array' => 'Bio::MAGE::Array::Array',
          'ExperimentalFactor' => 'Bio::MAGE::Experiment::ExperimentalFactor',
          'BioAssayMap' => 'Bio::MAGE::BioAssayData::BioAssayMap',
          'SeqFeature' => 'Bio::MAGE::BioSequence::SeqFeature',
          'OntologyEntry' => 'Bio::MAGE::Description::OntologyEntry',
          'ImageAcquisition' => 'Bio::MAGE::BioAssay::ImageAcquisition',
          'FeatureExtraction' => 'Bio::MAGE::BioAssay::FeatureExtraction',
          'Error' => 'Bio::MAGE::QuantitationType::Error',
          'ArrayManufacture' => 'Bio::MAGE::Array::ArrayManufacture',
          'Map' => 'Bio::MAGE::BioEvent::Map',
          'Organization' => 'Bio::MAGE::AuditAndSecurity::Organization',
          'Database' => 'Bio::MAGE::Description::Database',
          'SecurityGroup' => 'Bio::MAGE::AuditAndSecurity::SecurityGroup',
          'CompositeSequenceDimension' => 'Bio::MAGE::BioAssayData::CompositeSequenceDimension',
          'Image' => 'Bio::MAGE::BioAssay::Image',
          'Zone' => 'Bio::MAGE::ArrayDesign::Zone',
          'NodeContents' => 'Bio::MAGE::HigherLevelAnalysis::NodeContents',
          'Reporter' => 'Bio::MAGE::DesignElement::Reporter',
          'FeatureDimension' => 'Bio::MAGE::BioAssayData::FeatureDimension',
          'Protocol' => 'Bio::MAGE::Protocol::Protocol',
          'Describable' => 'Bio::MAGE::Describable',
          'ExpectedValue' => 'Bio::MAGE::QuantitationType::ExpectedValue',
          'Contact' => 'Bio::MAGE::AuditAndSecurity::Contact',
          'CompoundMeasurement' => 'Bio::MAGE::BioMaterial::CompoundMeasurement',
          'MassUnit' => 'Bio::MAGE::Measurement::MassUnit',
          'FactorValue' => 'Bio::MAGE::Experiment::FactorValue',
          'ZoneDefect' => 'Bio::MAGE::Array::ZoneDefect',
          'VolumeUnit' => 'Bio::MAGE::Measurement::VolumeUnit',
          'DesignElementGroup' => 'Bio::MAGE::ArrayDesign::DesignElementGroup',
          'ReporterCompositeMap' => 'Bio::MAGE::DesignElement::ReporterCompositeMap',
          'LabeledExtract' => 'Bio::MAGE::BioMaterial::LabeledExtract',
          'TimeUnit' => 'Bio::MAGE::Measurement::TimeUnit',
          'FeatureDefect' => 'Bio::MAGE::Array::FeatureDefect',
          'QuantityUnit' => 'Bio::MAGE::Measurement::QuantityUnit',
          'BioAssayMapping' => 'Bio::MAGE::BioAssayData::BioAssayMapping',
          'ZoneGroup' => 'Bio::MAGE::ArrayDesign::ZoneGroup',
          'BioAssayDataCluster' => 'Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster',
          'DesignElementMapping' => 'Bio::MAGE::BioAssayData::DesignElementMapping',
          'Parameterizable' => 'Bio::MAGE::Protocol::Parameterizable',
          'BioDataValues' => 'Bio::MAGE::BioAssayData::BioDataValues',
          'DesignElementMap' => 'Bio::MAGE::BioAssayData::DesignElementMap',
          'QuantitationTypeMap' => 'Bio::MAGE::BioAssayData::QuantitationTypeMap',
          'Person' => 'Bio::MAGE::AuditAndSecurity::Person',
          'ZoneLayout' => 'Bio::MAGE::ArrayDesign::ZoneLayout',
          'ParameterizableApplication' => 'Bio::MAGE::Protocol::ParameterizableApplication',
          'Channel' => 'Bio::MAGE::BioAssay::Channel',
          'BioDataCube' => 'Bio::MAGE::BioAssayData::BioDataCube',
          'MeasuredSignal' => 'Bio::MAGE::QuantitationType::MeasuredSignal',
          'ManufactureLIMSBiomaterial' => 'Bio::MAGE::Array::ManufactureLIMSBiomaterial',
          'BioSample' => 'Bio::MAGE::BioMaterial::BioSample',
          'NameValueType' => 'Bio::MAGE::NameValueType',
          'TemperatureUnit' => 'Bio::MAGE::Measurement::TemperatureUnit',
          'Experiment' => 'Bio::MAGE::Experiment::Experiment',
          'Software' => 'Bio::MAGE::Protocol::Software',
          'PresentAbsent' => 'Bio::MAGE::QuantitationType::PresentAbsent',
          'Measurement' => 'Bio::MAGE::Measurement::Measurement',
          'Description' => 'Bio::MAGE::Description::Description'
        }
;
}


sub xml_packages {
  return @{$__XML_PACKAGES};
}


sub class2fullclass {
  return %{$__CLASS2FULLCLASS};
}





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


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


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


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


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


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


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


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


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




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


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


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


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


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





sub objects {
  my $self = shift;
  if (@_) {
    $self->{__OBJECTS} = shift;
  }
  return $self->{__OBJECTS};
}







sub tagname {
  my $self = shift;
  if (@_) {
    $self->{__TAGNAME} = shift;
  }
  return $self->{__TAGNAME};
}







sub identifier {
  my $self = shift;
  if (@_) {
    $self->{__IDENTIFIER} = shift;
  }
  return $self->{__IDENTIFIER};
}







sub registered_objects {
  my $self = shift;
  if (@_) {
    $self->{__REGISTERED_OBJECTS} = shift;
  }
  return $self->{__REGISTERED_OBJECTS};
}







sub identifiers {
  my $self = shift;
  if (@_) {
    $self->{__IDENTIFIERS} = shift;
  }
  return $self->{__IDENTIFIERS};
}







sub packages {
  my $self = shift;
  if (@_) {
    $self->{__PACKAGES} = shift;
  }
  return $self->{__PACKAGES};
}







sub add_objects {
  my ($self,$list_ref) = @_;
  croak __PACKAGE__ . "::add_objects: Expected array reference but got $list_ref"
    unless UNIVERSAL::isa($list_ref,'ARRAY');
  foreach my $object (@{$list_ref}) {
    # we've been asked to register the objects, so we do it
    $self->register($object,1);
  }
}



sub getHigherLevelAnalysis_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'HigherLevelAnalysis'}) {
    eval "require Bio::MAGE::HigherLevelAnalysis";
    die "Couldn't require Bio::MAGE::HigherLevelAnalysis"
      if $@;
    $self->{__PACKAGES}{'HigherLevelAnalysis'} = Bio::MAGE::HigherLevelAnalysis->new();
  }
  return $self->{__PACKAGES}{'HigherLevelAnalysis'};
}



sub getBioEvent_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'BioEvent'}) {
    eval "require Bio::MAGE::BioEvent";
    die "Couldn't require Bio::MAGE::BioEvent"
      if $@;
    $self->{__PACKAGES}{'BioEvent'} = Bio::MAGE::BioEvent->new();
  }
  return $self->{__PACKAGES}{'BioEvent'};
}



sub getBioMaterial_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'BioMaterial'}) {
    eval "require Bio::MAGE::BioMaterial";
    die "Couldn't require Bio::MAGE::BioMaterial"
      if $@;
    $self->{__PACKAGES}{'BioMaterial'} = Bio::MAGE::BioMaterial->new();
  }
  return $self->{__PACKAGES}{'BioMaterial'};
}



sub getBioSequence_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'BioSequence'}) {
    eval "require Bio::MAGE::BioSequence";
    die "Couldn't require Bio::MAGE::BioSequence"
      if $@;
    $self->{__PACKAGES}{'BioSequence'} = Bio::MAGE::BioSequence->new();
  }
  return $self->{__PACKAGES}{'BioSequence'};
}



sub getAuditAndSecurity_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'AuditAndSecurity'}) {
    eval "require Bio::MAGE::AuditAndSecurity";
    die "Couldn't require Bio::MAGE::AuditAndSecurity"
      if $@;
    $self->{__PACKAGES}{'AuditAndSecurity'} = Bio::MAGE::AuditAndSecurity->new();
  }
  return $self->{__PACKAGES}{'AuditAndSecurity'};
}



sub getBioAssayData_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'BioAssayData'}) {
    eval "require Bio::MAGE::BioAssayData";
    die "Couldn't require Bio::MAGE::BioAssayData"
      if $@;
    $self->{__PACKAGES}{'BioAssayData'} = Bio::MAGE::BioAssayData->new();
  }
  return $self->{__PACKAGES}{'BioAssayData'};
}



sub getBQS_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'BQS'}) {
    eval "require Bio::MAGE::BQS";
    die "Couldn't require Bio::MAGE::BQS"
      if $@;
    $self->{__PACKAGES}{'BQS'} = Bio::MAGE::BQS->new();
  }
  return $self->{__PACKAGES}{'BQS'};
}



sub getArray_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'Array'}) {
    eval "require Bio::MAGE::Array";
    die "Couldn't require Bio::MAGE::Array"
      if $@;
    $self->{__PACKAGES}{'Array'} = Bio::MAGE::Array->new();
  }
  return $self->{__PACKAGES}{'Array'};
}



sub getQuantitationType_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'QuantitationType'}) {
    eval "require Bio::MAGE::QuantitationType";
    die "Couldn't require Bio::MAGE::QuantitationType"
      if $@;
    $self->{__PACKAGES}{'QuantitationType'} = Bio::MAGE::QuantitationType->new();
  }
  return $self->{__PACKAGES}{'QuantitationType'};
}



sub getExperiment_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'Experiment'}) {
    eval "require Bio::MAGE::Experiment";
    die "Couldn't require Bio::MAGE::Experiment"
      if $@;
    $self->{__PACKAGES}{'Experiment'} = Bio::MAGE::Experiment->new();
  }
  return $self->{__PACKAGES}{'Experiment'};
}



sub getBioAssay_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'BioAssay'}) {
    eval "require Bio::MAGE::BioAssay";
    die "Couldn't require Bio::MAGE::BioAssay"
      if $@;
    $self->{__PACKAGES}{'BioAssay'} = Bio::MAGE::BioAssay->new();
  }
  return $self->{__PACKAGES}{'BioAssay'};
}



sub getDesignElement_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'DesignElement'}) {
    eval "require Bio::MAGE::DesignElement";
    die "Couldn't require Bio::MAGE::DesignElement"
      if $@;
    $self->{__PACKAGES}{'DesignElement'} = Bio::MAGE::DesignElement->new();
  }
  return $self->{__PACKAGES}{'DesignElement'};
}



sub getProtocol_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'Protocol'}) {
    eval "require Bio::MAGE::Protocol";
    die "Couldn't require Bio::MAGE::Protocol"
      if $@;
    $self->{__PACKAGES}{'Protocol'} = Bio::MAGE::Protocol->new();
  }
  return $self->{__PACKAGES}{'Protocol'};
}



sub getDescription_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'Description'}) {
    eval "require Bio::MAGE::Description";
    die "Couldn't require Bio::MAGE::Description"
      if $@;
    $self->{__PACKAGES}{'Description'} = Bio::MAGE::Description->new();
  }
  return $self->{__PACKAGES}{'Description'};
}



sub getArrayDesign_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'ArrayDesign'}) {
    eval "require Bio::MAGE::ArrayDesign";
    die "Couldn't require Bio::MAGE::ArrayDesign"
      if $@;
    $self->{__PACKAGES}{'ArrayDesign'} = Bio::MAGE::ArrayDesign->new();
  }
  return $self->{__PACKAGES}{'ArrayDesign'};
}



sub getMeasurement_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'Measurement'}) {
    eval "require Bio::MAGE::Measurement";
    die "Couldn't require Bio::MAGE::Measurement"
      if $@;
    $self->{__PACKAGES}{'Measurement'} = Bio::MAGE::Measurement->new();
  }
  return $self->{__PACKAGES}{'Measurement'};
}



sub obj2xml {
  my ($self,$writer) = @_;

  # require and identifier for the top-level XML element
  my $identifier = $self->identifier();
  croak __PACKAGE__ . '::obj2xml: Identifier not specified for topmost level object'
    unless defined $identifier;
  my @attrs = (identifier=>$identifier);

  my $empty = 0;
  my $tag = $self->tagname();
  $writer->write_start_tag($tag,$empty,@attrs);

  my %packages = %{$self->packages()};
  foreach my $package ($self->xml_packages()) {
    next unless exists $packages{$package};
    my $pkg_obj = $packages{$package};
    $pkg_obj->obj2xml($writer);
  }

  # and we're done
  $writer->write_end_tag($tag);
}


sub register {
  my ($self,$obj,$register) = @_;

  # to avoid circular references keep track of objects that
  # we have already or are in the process of registering
  #

  my $registered = $self->registered_objects();
  return if exists $registered->{$obj};
  $registered->{$obj}++;

  # objects only register themselves if they are Identifiable
  # and we have been told to register them
  my $known_identifiers = $self->identifiers();
  if ($register and $obj->isa('Bio::MAGE::Identifiable')) {
    my $id = $obj->getIdentifier();
    die __PACKAGE__ . "::register: object must have identifier: $obj"
      unless $id;
    unless (exists $known_identifiers->{$id}) {
      my $packages = $self->packages();
      my $package_name = $obj->package_name();
      my $pkg_obj = $packages->{$package_name};
      unless (defined $pkg_obj) {
	# we only create the package objects if we need them.
	# register is the first time they will be needed
	my $class = "Bio::MAGE::$package_name";
	$pkg_obj = $class->new();
	$packages->{$package_name} = $pkg_obj;
      }
      $pkg_obj->register($obj);
      $known_identifiers->{$id}++;
    }
  }

  # regardless, they must enable their sub objects to register themselves
  my %assns_hash = $obj->associations();
  foreach my $association ($obj->get_association_names()) {
    my $association_obj;
    {
      no strict 'refs';
      my $assoc_name = 'get' . ucfirst($association);
      $association_obj = $obj->$assoc_name();
    }
    next unless defined $association_obj;

    # we need to know what kind of an association this is if it is an
    # aggregate association we don't want to register it whether it is
    # Identifiable or not, but we still want to register it's
    # sub-objects so we need to alert register()
    #
    # to decide if the association is aggregate, we look at
    # the 'self' end of the association
    my $register = $assns_hash{$association}->self->is_ref();

    # register a list of sub objects or a single one
    if ($assns_hash{$association}->other->cardinality() eq "0..N" or
	$assns_hash{$association}->other->cardinality() eq "1..N") {
      if (UNIVERSAL::isa($association_obj, 'ARRAY')) {
	foreach my $element (@$association_obj) {
	  $self->register($element,$register)
	    if defined $element;
	}
      } else {
	die __PACKAGE__ . "::register: expected array ref: $obj, association: $association, got $association_obj\n";
      }
    } else {
      $self->register($association_obj,$register);
    }
  }
}





# all perl modules must be true...
1;