Provided by: libbio-mage-perl_20030502.3-5_all bug

NAME

       Bio::MAGE::Identifiable - Class for the MAGE-OM API

SYNOPSIS

         use Bio::MAGE::Identifiable

         # Bio::MAGE::Identifiable is an abstract base class and should not
         # be directly instantiated. These examples indicate how subclass
         # objects will behave

         # 'name' attribute
         my $name_val = $identifiable->name(); # getter
         $identifiable->name($value); # setter

         # 'identifier' attribute
         my $identifier_val = $identifiable->identifier(); # getter
         $identifiable->identifier($value); # setter

         # 'auditTrail' association
         my $audit_array_ref = $identifiable->auditTrail(); # getter
         $identifiable->auditTrail(\@audit_list); # setter

         # 'propertySets' association
         my $namevaluetype_array_ref = $identifiable->propertySets(); # getter
         $identifiable->propertySets(\@namevaluetype_list); # setter

         # 'descriptions' association
         my $description_array_ref = $identifiable->descriptions(); # getter
         $identifiable->descriptions(\@description_list); # setter

         # 'security' association
         my $security_ref = $identifiable->security(); # getter
         $identifiable->security($security_ref); # setter

DESCRIPTION

       From the MAGE-OM documentation for the "Identifiable" class:

       An Identifiable class is one that has an unambiguous reference within the scope.  It also
       has a potentially ambiguous name.

       Bio::MAGE::Identifiable is an abstract base class and should not be directly instantiated.
       Instead it serves as an interface definition for its subclasses.

INHERITANCE

       Bio::MAGE::Identifiable has the following superclasses:

       ·   Bio::MAGE::Describable

       Bio::MAGE::Identifiable has the following subclasses:

       ·   Bio::MAGE::QuantitationType::QuantitationType

       ·   Bio::MAGE::ArrayDesign::ArrayDesign

       ·   Bio::MAGE::Description::Database

       ·   Bio::MAGE::BioAssay::Image

       ·   Bio::MAGE::BioAssay::BioAssay

       ·   Bio::MAGE::BioAssay::Channel

       ·   Bio::MAGE::AuditAndSecurity::Security

       ·   Bio::MAGE::DesignElement::DesignElement

       ·   Bio::MAGE::ArrayDesign::Zone

       ·   Bio::MAGE::AuditAndSecurity::SecurityGroup

       ·   Bio::MAGE::AuditAndSecurity::Contact

       ·   Bio::MAGE::ArrayDesign::DesignElementGroup

       ·   Bio::MAGE::BioAssayData::BioAssayData

       ·   Bio::MAGE::BioAssayData::QuantitationTypeDimension

       ·   Bio::MAGE::BioAssayData::DesignElementDimension

       ·   Bio::MAGE::Array::Array

       ·   Bio::MAGE::Array::ArrayGroup

       ·   Bio::MAGE::BioAssayData::BioAssayDimension

       ·   Bio::MAGE::Array::ArrayManufacture

       ·   Bio::MAGE::BioEvent::BioEvent

       ·   Bio::MAGE::Experiment::Experiment

       ·   Bio::MAGE::Experiment::ExperimentalFactor

       ·   Bio::MAGE::Experiment::FactorValue

       ·   Bio::MAGE::Protocol::Parameter

       ·   Bio::MAGE::BioMaterial::BioMaterial

       ·   Bio::MAGE::BioMaterial::Compound

       ·   Bio::MAGE::BioSequence::BioSequence

       ·   Bio::MAGE::Protocol::Parameterizable

       ·   Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster

CLASS METHODS

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

       new()
       new(%args)
           Bio::MAGE::Identifiable is an abstract base class and should not be directly
           instantiated using the "new()" constructor. It is listed here to indicate what
           arguments will be accepted for its subclasses.

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

           ·   name

               Sets the value of the "name" attribute

           ·   identifier

               Sets the value of the "identifier" attribute

           ·   auditTrail

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

               The value must be of type: array of "Bio::MAGE::AuditAndSecurity::Audit".

           ·   propertySets

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

               The value must be of type: array of "Bio::MAGE::NameValueType".

           ·   descriptions

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

               The value must be of type: array of "Bio::MAGE::Description::Description".

           ·   security

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

               The value must be of type: instance of "Bio::MAGE::AuditAndSecurity::Security".

       $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

       $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

   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:

       name
           Methods for the "name" attribute.

           From the MAGE-OM documentation:

           The potentially ambiguous common identifier.

           $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 "croak()" if no input parameters are specified, or if too
               many input parameters are specified

           $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 "croak()" if any input parameters are specified

       identifier
           Methods for the "identifier" attribute.

           From the MAGE-OM documentation:

           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.

           $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 "croak()" if no input parameters are specified, or if too
               many input parameters are specified

           $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 "croak()" if any input parameters are specified

   ASSOCIATIONS
       Associations are references to other classes. Associations in MAGE-OM have a cardinality
       that determines the minimum and maximum number of instances of the 'other' class that
       maybe included in the association:

       1.  There must be exactly one item in the association, i.e. this is a mandatory data
           field.

       2.  0..1

           There may be one item in the association, i.e. this is an optional data field.

       3.  1..N

           There must be one or more items in the association, i.e. this is a mandatory data
           field, with list cardinality.

       4.  0..N

           There may be one or more items in the association, i.e. this is an optional data
           field, with list cardinality.

       Bio::MAGE::Identifiable has the following association accessor methods:

       auditTrail
           Methods for the "auditTrail" association.

           From the MAGE-OM documentation:

           A list of Audit instances that track changes to the instance of Describable.

           $array_ref = $identifiable->setAuditTrail($array_ref)
               The restricted setter method for the "auditTrail" association.

               Input parameters: the value to which the "auditTrail" association will be set : a
               reference to an array of objects of type "Bio::MAGE::AuditAndSecurity::Audit"

               Return value: the current value of the "auditTrail" association : a reference to
               an array of objects of type "Bio::MAGE::AuditAndSecurity::Audit"

               Side effects: none

               Exceptions: will call "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 "Bio::MAGE::AuditAndSecurity::Audit" instances

           $array_ref = $identifiable->getAuditTrail()
               The restricted getter method for the "auditTrail" association.

               Input parameters: none

               Return value: the current value of the "auditTrail" association : a reference to
               an array of objects of type "Bio::MAGE::AuditAndSecurity::Audit"

               Side effects: none

               Exceptions: will call "croak()" if any input parameters are specified

           $val = $identifiable->addAuditTrail(@vals)
               Because the auditTrail association has list cardinality, it may store more than
               one value. This method adds the current list of objects in the auditTrail
               association.

               Input parameters: the list of values @vals to add to the auditTrail association.
               NOTE: submitting a single value is permitted.

               Return value: the number of items stored in the slot after adding @vals

               Side effects: none

               Exceptions: will call "croak()" if no input parameters are specified, or if any of
               the objects in @vals is not an instance of class
               "Bio::MAGE::AuditAndSecurity::Audit"

       propertySets
           Methods for the "propertySets" association.

           From the MAGE-OM documentation:

           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.

           $array_ref = $identifiable->setPropertySets($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 "Bio::MAGE::NameValueType"

               Return value: the current value of the "propertySets" association : a reference to
               an array of objects of type "Bio::MAGE::NameValueType"

               Side effects: none

               Exceptions: will call "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 "Bio::MAGE::NameValueType" instances

           $array_ref = $identifiable->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 "Bio::MAGE::NameValueType"

               Side effects: none

               Exceptions: will call "croak()" if any input parameters are specified

           $val = $identifiable->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 @vals to add to the propertySets association.
               NOTE: submitting a single value is permitted.

               Return value: the number of items stored in the slot after adding @vals

               Side effects: none

               Exceptions: will call "croak()" if no input parameters are specified, or if any of
               the objects in @vals is not an instance of class "Bio::MAGE::NameValueType"

       descriptions
           Methods for the "descriptions" association.

           From the MAGE-OM documentation:

           Free hand text descriptions.  Makes available the associations of Description to an
           instance of Describable.

           $array_ref = $identifiable->setDescriptions($array_ref)
               The restricted setter method for the "descriptions" association.

               Input parameters: the value to which the "descriptions" association will be set :
               a reference to an array of objects of type "Bio::MAGE::Description::Description"

               Return value: the current value of the "descriptions" association : a reference to
               an array of objects of type "Bio::MAGE::Description::Description"

               Side effects: none

               Exceptions: will call "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 "Bio::MAGE::Description::Description" instances

           $array_ref = $identifiable->getDescriptions()
               The restricted getter method for the "descriptions" association.

               Input parameters: none

               Return value: the current value of the "descriptions" association : a reference to
               an array of objects of type "Bio::MAGE::Description::Description"

               Side effects: none

               Exceptions: will call "croak()" if any input parameters are specified

           $val = $identifiable->addDescriptions(@vals)
               Because the descriptions association has list cardinality, it may store more than
               one value. This method adds the current list of objects in the descriptions
               association.

               Input parameters: the list of values @vals to add to the descriptions association.
               NOTE: submitting a single value is permitted.

               Return value: the number of items stored in the slot after adding @vals

               Side effects: none

               Exceptions: will call "croak()" if no input parameters are specified, or if any of
               the objects in @vals is not an instance of class
               "Bio::MAGE::Description::Description"

       security
           Methods for the "security" association.

           From the MAGE-OM documentation:

           Information on the security for the instance of the class.

           $val = $identifiable->setSecurity($val)
               The restricted setter method for the "security" association.

               Input parameters: the value to which the "security" association will be set : one
               of the accepted enumerated values.

               Return value: the current value of the "security" association : one of the
               accepted enumerated values.

               Side effects: none

               Exceptions: will call "croak()" if no input parameters are specified, or if too
               many input parameters are specified, or if $val is not an instance of class
               "Bio::MAGE::AuditAndSecurity::Security"

           $val = $identifiable->getSecurity()
               The restricted getter method for the "security" association.

               Input parameters: none

               Return value: the current value of the "security" association : an instance of
               type "Bio::MAGE::AuditAndSecurity::Security".

               Side effects: none

               Exceptions: will call "croak()" if any input parameters are specified

           sub initialize {

             carp __PACKAGE__ . "::initialize: abstract base classes should not be instantiated";

           }

SLOTS, ATTRIBUTES, AND ASSOCIATIONS

       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

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

AUTHOR

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

SEE ALSO

       perl(1).

POD ERRORS

       Hey! The above document had some coding errors, which are explained below:

       Around line 409:
           '=item' outside of any '=over'

       Around line 494:
           You forgot a '=back' before '=head2'

       Around line 666:
           Expected '=item 2'

       Around line 671:
           Expected '=item 3'

       Around line 676:
           Expected '=item 4'