Bio::MAGE::Description::OntologyEntry - Class for the MAGE-OM API
use Bio::MAGE::Description::OntologyEntry # creating an empty instance my $ontologyentry = Bio::MAGE::Description::OntologyEntry->new(); # creating an instance with existing data my $ontologyentry = Bio::MAGE::Description::OntologyEntry->new( value=>$value_val, description=>$description_val, category=>$category_val, ontologyReference=>$databaseentry_ref, propertySets=>\@namevaluetype_list, associations=>\@ontologyentry_list, ); # 'value' attribute my $value_val = $ontologyentry->value(); # getter $ontologyentry->value($value); # setter # 'description' attribute my $description_val = $ontologyentry->description(); # getter $ontologyentry->description($value); # setter # 'category' attribute my $category_val = $ontologyentry->category(); # getter $ontologyentry->category($value); # setter # 'ontologyReference' association my $databaseentry_ref = $ontologyentry->ontologyReference(); # getter $ontologyentry->ontologyReference($databaseentry_ref); # setter # 'propertySets' association my $namevaluetype_array_ref = $ontologyentry->propertySets(); # getter $ontologyentry->propertySets(\@namevaluetype_list); # setter # 'associations' association my $ontologyentry_array_ref = $ontologyentry->associations(); # getter $ontologyentry->associations(\@ontologyentry_list); # setter
From the MAGE-OM documentation for the OntologyEntry class:
OntologyEntry
A single entry from an ontology or a controlled vocabulary. For instance, category could be 'species name', value could be 'homo sapiens' and ontology would be taxonomy database, NCBI.
Bio::MAGE::Description::OntologyEntry has the following superclasses:
Bio::MAGE::Extendable
The following methods can all be called without first having an instance of the class via the Bio::MAGE::Description::OntologyEntry->methodname() syntax.
The object constructor new() accepts the following optional named-value style arguments:
new()
value
Sets the value of the value attribute
description
Sets the value of the description attribute
category
Sets the value of the category attribute
ontologyReference
Sets the value of the ontologyReference association
The value must be of type: instance of Bio::MAGE::Description::DatabaseEntry.
Bio::MAGE::Description::DatabaseEntry
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.
Bio::MAGE::NameValueType
associations
Sets the value of the associations association
The value must be of type: array of Bio::MAGE::Description::OntologyEntry.
Bio::MAGE::Description::OntologyEntry
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.
initialize()
The get_slot_names() method is used to retrieve the name of all slots defined in a given class.
get_slot_names()
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
returns the list of attribute data members for this class.
returns the list of association data members for this class.
returns the list of superclasses for this class.
returns the list of subclasses for this class.
Returns the full class name for this class.
Returns the base package name (i.e. no 'namespace::') of the package that contains this class.
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.
Association
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.
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.
set_slots()
Return value: none
Side effects: will call croak() if a slot_name is used that the class does not define.
croak()
The get_slots() method is used to get the values of a number of slots at the same time.
get_slots()
Return value: a list of instance objects
The set_slot() method sets the slot $name to the value $val
set_slot()
$name
$val
Return value: the new value of the slot, i.e. $val
The get_slot() method is used to get the values of a number of slots at the same time.
get_slot()
Return value: a single slot value, or undef if the slot has not been initialized.
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::OntologyEntry has the following attribute accessor methods:
Methods for the value attribute.
From the MAGE-OM documentation:
The value for this entry in this category.
The restricted setter method for the value attribute.
Input parameters: the value to which the value attribute will be set
Return value: the current value of the value attribute
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified
The restricted getter method for the value attribute.
Input parameters: none
Exceptions: will call croak() if any input parameters are specified
Methods for the description attribute.
The description of the meaning for this entry.
The restricted setter method for the description attribute.
Input parameters: the value to which the description attribute will be set
Return value: the current value of the description attribute
The restricted getter method for the description attribute.
Methods for the category attribute.
The category to which this entry belongs.
The restricted setter method for the category attribute.
Input parameters: the value to which the category attribute will be set
Return value: the current value of the category attribute
The restricted getter method for the category attribute.
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:
There must be exactly one item in the association, i.e. this is a mandatory data field.
0..1
There may be one item in the association, i.e. this is an optional data field.
1..N
There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.
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::OntologyEntry has the following association accessor methods:
Methods for the ontologyReference association.
Many ontology entries will not yet have formalized ontologies. In those cases, they will not have a database reference to the ontology.
In the future it is highly encouraged that these ontologies be developed and ontologyEntry be subclassed from DatabaseReference.
The restricted setter method for the ontologyReference association.
Input parameters: the value to which the ontologyReference association will be set : one of the accepted enumerated values.
Return value: the current value of the ontologyReference association : one of the accepted enumerated values.
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::DatabaseEntry
The restricted getter method for the ontologyReference association.
Return value: the current value of the ontologyReference association : an instance of type Bio::MAGE::Description::DatabaseEntry.
Methods for the 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.
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
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
The restricted getter method for the propertySets association.
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.
@vals
Return value: the number of items stored in the slot after adding @vals
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
Methods for the associations association.
Allows an instance of an OntologyEntry to be further qualified.
The restricted setter method for the associations association.
Input parameters: the value to which the associations association will be set : a reference to an array of objects of type Bio::MAGE::Description::OntologyEntry
Return value: the current value of the associations association : a reference to an array of objects of type Bio::MAGE::Description::OntologyEntry
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
The restricted getter method for the associations association.
Because the associations association has list cardinality, it may store more than one value. This method adds the current list of objects in the associations association.
Input parameters: the list of values @vals to add to the associations association. NOTE: submitting a single value is permitted.
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
sub initialize {
my $self = shift; return 1;
}
In the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations.
slots
attributes
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.
slot
Slots are implemented using unified getter/setter methods:
Retrieves the current value of the slot.
Store $new_var in the slot - the return value is also $new_var.
Returns the list of all slots in the class.
DATA CHECKING: No data type checking is made for these methods.
The terms attribute and association indicate data members of the class that were specified directly from the UML model.
attribute
association
In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:
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.
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.
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.
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:
Bio::MAGE::Base
See elsewhere in this page for a detailed description of these methods.
Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)
Jason E. Stewart (jasons 'at' cpan 'dot' org)
perl(1).
5 POD Errors
The following errors were encountered while parsing the POD:
'=item' outside of any '=over'
You forgot a '=back' before '=head2'
Expected '=item 2'
Expected '=item 3'
Expected '=item 4'
To install Bio::MAGE, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::MAGE
CPAN shell
perl -MCPAN -e shell install Bio::MAGE
For more information on module installation, please visit the detailed CPAN module installation guide.