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

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

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

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

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

           •   URI

               Sets the value of the "URI" attribute

           •   text

               Sets the value of the "text" attribute

           •   databaseReferences

               Sets the value of the "databaseReferences" association

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

           •   externalReference

               Sets the value of the "externalReference" association

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

           •   bibliographicReferences

               Sets the value of the "bibliographicReferences" association

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

           •   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".

           •   annotations

               Sets the value of the "annotations" association

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

           •   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.

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

           Sideeffects: 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.

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

           Sideeffects: 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.

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

       A free text description of an object.

       Bio::MAGE::Description::Description has the following superclasses:

       •   Bio::MAGE::Describable

       $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.

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

           Sideeffects: 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.

           Returnvalue: none

           Sideeffects: 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.

           Returnvalue: a list of instance objects

           Sideeffects: none

       $val = $obj->set_slot($name,$val)
           The "set_slot()" method sets the slot $name to the value $val

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

           Sideeffects: 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.

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

           Sideeffects: 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::Description::Description" has the following attribute accessor methods:

       URI Methods for the "URI" attribute.

           From the MAGE-OM documentation:

           A reference to the location and type of an outside resource.

           $val = $description->setURI($val)
               The restricted setter method for the "URI" attribute.

               Input parameters: the value to which the "URI" attribute will be set

               Return value: the current value of the "URI" attribute

               Side effects: none

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

           $val = $description->getURI()
               The restricted getter method for the "URI" attribute.

               Input parameters: none

               Return value: the current value of the "URI" attribute

               Side effects: none

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

       text
           Methods for the "text" attribute.

           From the MAGE-OM documentation:

           The description.

           $val = $description->setText($val)
               The restricted setter method for the "text" attribute.

               Input parameters: the value to which the "text" attribute will be set

               Return value: the current value of the "text" attribute

               Side effects: none

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

           $val = $description->getText()
               The restricted getter method for the "text" attribute.

               Input parameters: none

               Return value: the current value of the "text" 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::Description::Description has the following association accessor methods:

       databaseReferences
           Methods for the "databaseReferences" association.

           From the MAGE-OM documentation:

           References to entries in databases.

           $array_ref = $description->setDatabaseReferences($array_ref)
               The restricted setter method for the "databaseReferences" association.

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

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

               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::DatabaseEntry" instances

           $array_ref = $description->getDatabaseReferences()
               The restricted getter method for the "databaseReferences" association.

               Input parameters: none

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

               Side effects: none

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

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

               Input  parameters:  the  list of values @vals to add to the databaseReferences 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::DatabaseEntry"

       externalReference
           Methods for the "externalReference" association.

           From the MAGE-OM documentation:

           Specifies where the described instance was originally obtained from.

           $val = $description->setExternalReference($val)
               The restricted setter method for the "externalReference" association.

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

               Return value: the current value of the "externalReference" 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::Description::ExternalReference"

           $val = $description->getExternalReference()
               The restricted getter method for the "externalReference" association.

               Input parameters: none

               Return  value:  the  current  value  of the "externalReference" association : an instance of type
               "Bio::MAGE::Description::ExternalReference".

               Side effects: none

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

       bibliographicReferences
           Methods for the "bibliographicReferences" association.

           From the MAGE-OM documentation:

           References to existing literature.

           $array_ref = $description->setBibliographicReferences($array_ref)
               The restricted setter method for the "bibliographicReferences" association.

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

               Return  value: the current value of the "bibliographicReferences" association : a reference to an
               array of objects of type "Bio::MAGE::BQS::BibliographicReference"

               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::BQS::BibliographicReference" instances

           $array_ref = $description->getBibliographicReferences()
               The restricted getter method for the "bibliographicReferences" association.

               Input parameters: none

               Return value: the current value of the "bibliographicReferences" association : a reference to  an
               array of objects of type "Bio::MAGE::BQS::BibliographicReference"

               Side effects: none

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

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

               Input parameters: the list of values @vals to add  to  the  bibliographicReferences  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::BQS::BibliographicReference"

       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 = $description->setAuditTrail($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 = $description->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 = $description->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 = $description->setPropertySets($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 = $description->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 = $description->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"

       annotations
           Methods for the "annotations" association.

           From the MAGE-OM documentation:

           Allows specification of ontology entries related to the instance being described.

           $array_ref = $description->setAnnotations($array_ref)
               The restricted setter method for the "annotations" association.

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

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

               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::OntologyEntry" instances

           $array_ref = $description->getAnnotations()
               The restricted getter method for the "annotations" association.

               Input parameters: none

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

               Side effects: none

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

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

               Input  parameters:  the  list  of  values  @vals  to  add  to  the annotations 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::OntologyEntry"

       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 = $description->setDescriptions($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 = $description->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 = $description->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 = $description->setSecurity($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 = $description->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 {

             my $self = shift;
             return 1;

           }

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

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perl v5.32.0                                       2020-11-27                MAGE::Description::Description(3pm)

perl(1).

       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.

       DATACHECKING: No data type checking is made for these methods.

   ATTRIBUTESANDASSOCIATIONS
       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.

           DATACHECKING: 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.

           DATACHECKING:  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.

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

   GENERICMETHODS
       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.

         use Bio::MAGE::Description::Description

         # creating an empty instance
         my $description = Bio::MAGE::Description::Description->new();

         # creating an instance with existing data
         my $description = Bio::MAGE::Description::Description->new(
               URI=>$uri_val,
               text=>$text_val,
               databaseReferences=>\@databaseentry_list,
               externalReference=>$externalreference_ref,
               bibliographicReferences=>\@bibliographicreference_list,
               auditTrail=>\@audit_list,
               propertySets=>\@namevaluetype_list,
               annotations=>\@ontologyentry_list,
               descriptions=>\@description_list,
               security=>$security_ref,
         );

         # 'URI' attribute
         my $URI_val = $description->URI(); # getter
         $description->URI($value); # setter

         # 'text' attribute
         my $text_val = $description->text(); # getter
         $description->text($value); # setter

         # 'databaseReferences' association
         my $databaseentry_array_ref = $description->databaseReferences(); # getter
         $description->databaseReferences(\@databaseentry_list); # setter

         # 'externalReference' association
         my $externalreference_ref = $description->externalReference(); # getter
         $description->externalReference($externalreference_ref); # setter

         # 'bibliographicReferences' association
         my $bibliographicreference_array_ref = $description->bibliographicReferences(); # getter
         $description->bibliographicReferences(\@bibliographicreference_list); # setter

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

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

         # 'annotations' association
         my $ontologyentry_array_ref = $description->annotations(); # getter
         $description->annotations(\@ontologyentry_list); # setter

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

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