use Bio::MAGE::Description::Description;
# creating an empty instance my $description = Bio::MAGE::Description::Description->new();
# creating an already populated instance my $description = Bio::MAGE::Description::Description->new(URI=>$URI_value, text=>$text_value, databaseReferences=>$databaseReferences_value, externalReference=>$externalReference_value, bibliographicReferences=>$bibliographicReferences_value, annotations=>$annotations_value);
# setting and retrieving object attributes my $URI_val = $description->URI(); $description->URI($value);
my $text_val = $description->text(); $description->text($value);
# setting and retrieving object associations my $databaseReferences_val = $description->databaseReferences(); $description->databaseReferences($value);
my $externalReference_val = $description->externalReference(); $description->externalReference($value);
my $bibliographicReferences_val = $description->bibliographicReferences(); $description->bibliographicReferences($value);
my $annotations_val = $description->annotations(); $description->annotations($value);
From the MAGE-OM documentation for the Description
class:
A free text description of an object.
Bio::MAGE::Description::Description has the following super classes
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)
new()
accepts the following optional
named-value style arguments:
Bio::MAGE::Description::Description
).
Bio::MAGE::Description::Description
).
Bio::MAGE::Description::Description
).
Bio::MAGE::Description::Description
).
Bio::MAGE::Description::Description
).
Bio::MAGE::Description::Description
).
Bio::MAGE::Describable
).
Bio::MAGE::Describable
).
Bio::MAGE::Describable
).
Bio::MAGE::Extendable
).
set_slots(%parameters)
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.
get_slots(@name_list)
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
set_slot($name,$val)
set_slot()
method sets the slot $name
to the value $val
Return value: the new value of the slot, i.e. $val
Side effects: none
get_slot($name)
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
get_slot_names()
get_slot_names()
method is used to retrieve the name of all
slots defined for a given object.
Return value: a single slot value, or undef if the slot has not been initialized.
Side effects: none
class_name()
package()
subclasses()
superclasses()
attribute_methods()
association_methods()
associations()
Bio::MAGE::Association
objects that provide the meta-information for the association.
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
attribute:
A reference to the location and type of an outside resource.
setURI($val)
Input parameters: the value to which the URI attribute will be set
Return value: the current value of the URI attribute
Side effects: none
Exceptions: will call croak()
if no input parameters are specified, or
if too many input parameters are specified
getURI()
Input parameters: none
Return value: the current value of the URI attribute
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
text
attribute:
The description.
setText($val)
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
getText()
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 are references to other class objects which can be shared by multiple class instances at the same time. In the Perl implementation of MAGE-OM classes, associations are implemented using three separate methods:
Bio::MAGE::Description::Description: has the following association accessor methods:
databaseReferences
association:
References to entries in databases.
setDatabaseReferences($array_ref)
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 $array_ref is not a reference to an array class Bio::MAGE::Description::DatabaseEntry
instances
getDatabaseReferences()
Input parameters: none
Return value: the current value of the databaseReferences association : a reference to an array of objects of type Bio::MAGE::Description::DatabaseEntry
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
addDatabaseReferences(@vals)
Input parameters: the list of values @vals
to add to the databaseReferences
association. NOTE: submitting a single value is permitted.
Return value: none
Side effects: none
Exceptions: will call croak()
if no input parameters are specified
, or if any of the objects in @vals is not an instance of class Bio::MAGE::Description::DatabaseEntry
externalReference
association:
Specifies where the described instance was originally obtained from.
setExternalReference($val)
Input parameters: the value to which the externalReference association will be set : an instance of type Bio::MAGE::Description::ExternalReference
.
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 no input parameters are specified, or
if too many input parameters are specified , or if $val is not an instance of class Bio::MAGE::Description::ExternalReference
getExternalReference()
Input parameters: none
Return value: the current value of the externalReference association : an instance of type Bio::MAGE::Description::ExternalReference
.
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
bibliographicReferences
association:
References to existing literature.
setBibliographicReferences($array_ref)
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 $array_ref is not a reference to an array class Bio::MAGE::BQS::BibliographicReference
instances
getBibliographicReferences()
Input parameters: none
Return value: the current value of the bibliographicReferences association : a reference to an array of objects of type Bio::MAGE::BQS::BibliographicReference
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
addBibliographicReferences(@vals)
Input parameters: the list of values @vals
to add to the bibliographicReferences
association. NOTE: submitting a single value is permitted.
Return value: none
Side effects: none
Exceptions: will call croak()
if no input parameters are specified
, or if any of the objects in @vals is not an instance of class Bio::MAGE::BQS::BibliographicReference
annotations
association:
Allows specification of ontology entries related to the instance being described.
setAnnotations($array_ref)
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 $array_ref is not a reference to an array class Bio::MAGE::Description::OntologyEntry
instances
getAnnotations()
Input parameters: none
Return value: the current value of the annotations association : a reference to an array of objects of type Bio::MAGE::Description::OntologyEntry
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
addAnnotations(@vals)
Input parameters: the list of values @vals
to add to the annotations
association. NOTE: submitting a single value is permitted.
Return value: none
Side effects: none
Exceptions: will call croak()
if no input parameters are specified
, or if any of the objects in @vals is not an instance of class Bio::MAGE::Description::OntologyEntry
Associations Inherited from Bio::MAGE::Describable
security
association:
Information on the security for the instance of the class.
setSecurity($val)
Input parameters: the value to which the security association will be set : an instance of type Bio::MAGE::AuditAndSecurity::Security
.
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 no input parameters are specified, or
if too many input parameters are specified , or if $val is not an instance of class Bio::MAGE::AuditAndSecurity::Security
getSecurity()
Input parameters: none
Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security
.
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
auditTrail
association:
A list of Audit instances that track changes to the instance of Describable.
setAuditTrail($array_ref)
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 $array_ref is not a reference to an array class Bio::MAGE::AuditAndSecurity::Audit
instances
getAuditTrail()
Input parameters: none
Return value: the current value of the auditTrail association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
addAuditTrail(@vals)
Input parameters: the list of values @vals
to add to the auditTrail
association. NOTE: submitting a single value is permitted.
Return value: none
Side effects: none
Exceptions: will call croak()
if no input parameters are specified
, or if any of the objects in @vals is not an instance of class Bio::MAGE::AuditAndSecurity::Audit
descriptions
association:
Free hand text descriptions. Makes available the associations of Description to an instance of Describable.
setDescriptions($array_ref)
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 $array_ref is not a reference to an array class Bio::MAGE::Description::Description
instances
getDescriptions()
Input parameters: none
Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
addDescriptions(@vals)
Input parameters: the list of values @vals
to add to the descriptions
association. NOTE: submitting a single value is permitted.
Return value: none
Side effects: none
Exceptions: will call croak()
if no input parameters are specified
, or if any of the objects in @vals is not an instance of class Bio::MAGE::Description::Description
Associations Inherited from Bio::MAGE::Extendable
propertySets
association:
Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.
setPropertySets($array_ref)
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
getPropertySets()
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
addPropertySets(@vals)
Input parameters: the list of values @vals
to add to the propertySets
association. NOTE: submitting a single value is permitted.
Return value: none
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
Please send bug reports to mged-mage@lists.sf.net
Jason E. Stewart (www.openinformatics.com)
perl(1).