Ubuntu Manpage: Bio::MAGE::BioAssayData::BioDataValues

Provided by: libbio-mage-perl_20030502.3-4_all

NAME

       Bio::MAGE::BioAssayData::BioDataValues - Class for the MAGE-OM API

SYNOPSIS

         use Bio::MAGE::BioAssayData::BioDataValues

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

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

DESCRIPTION

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

       The actual values for the BioAssayCube.

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

INHERITANCE

       Bio::MAGE::BioAssayData::BioDataValues has the following superclasses:

       •   Bio::MAGE::Extendable

       Bio::MAGE::BioAssayData::BioDataValues has the following subclasses:

       •   Bio::MAGE::BioAssayData::BioDataCube

       •   Bio::MAGE::BioAssayData::BioDataTuples

CLASS METHODS

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

       new()
       new(%args)
           Bio::MAGE::BioAssayData::BioDataValues 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:

           •   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".

       $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::BioAssayData::BioDataValues" has the following attribute accessor methods:

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::BioAssayData::BioDataValues has the following association accessor methods:

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 = $biodatavalues->setPropertySets($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 = $biodatavalues->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 = $biodatavalues->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"

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)

POD ERRORS

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

       Around line 276:
           '=item' outside of any '=over'

       Around line 361:
           You forgot a '=back' before '=head2'

       Around line 389:
           Expected '=item 2'

       Around line 394:
           Expected '=item 3'

       Around line 399:
           Expected '=item 4'

NAME

SYNOPSIS

DESCRIPTION

INHERITANCE

CLASS METHODS

INSTANCE METHODS

SLOTS, ATTRIBUTES, AND ASSOCIATIONS

BUGS

AUTHOR

SEE ALSO

POD ERRORS