NAME

       Bio::MAGE::BioMaterial - Container module for classes in the MAGE package: BioMaterial

SYNOPSIS

         use Bio::MAGE::BioMaterial;

DESCRIPTION

       This is a package module that encapsulates a number of classes in the Bio::MAGE hierarchy.
       These classes belong to the BioMaterial package of the MAGE-OM object model.

CLASSES

       The Bio::MAGE::BioMaterial module contains the following Bio::MAGE classes:

       •   BioSource

       •   BioMaterial

       •   LabeledExtract

       •   BioSample

       •   Compound

       •   CompoundMeasurement

       •   BioMaterialMeasurement

       •   Treatment

CLASS METHODS

       @class_list = Bio::MAGE::BioMaterial::classes();
           This method returns a list of non-fully qualified class names (i.e. they do not have
           'Bio::MAGE::' as a prefix) in this package.

       $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

       $val = $biomaterial->xml_lists()
       $inval = $biomaterial->xml_lists($inval)
           This is the unified setter/getter method for the xml_lists slot.

           If $inval is specified, the setter method is invoked, with no parameters, the getter
           method is invoked.

           Input parameters: the optional $inval will invoke the setter method.

           Return value: for both setter and getter the current value of the xml_lists slot

           Side effects: none

           Exceptions: none

       $val = $biomaterial->tagname()
       $inval = $biomaterial->tagname($inval)
           This is the unified setter/getter method for the tagname slot.

           If $inval is specified, the setter method is invoked, with no parameters, the getter
           method is invoked.

           Input parameters: the optional $inval will invoke the setter method.

           Return value: for both setter and getter the current value of the tagname slot

           Side effects: none

           Exceptions: none

       $val = $biomaterial->compound_list()
       $inval = $biomaterial->compound_list($inval)
           This is the unified setter/getter method for the compound_list slot.

           If $inval is specified, the setter method is invoked, with no parameters, the getter
           method is invoked.

           Input parameters: the optional $inval will invoke the setter method.

           Return value: for both setter and getter the current value of the compound_list slot

           Side effects: none

           Exceptions: none

       $val = $biomaterial->biomaterial_list()
       $inval = $biomaterial->biomaterial_list($inval)
           This is the unified setter/getter method for the biomaterial_list slot.

           If $inval is specified, the setter method is invoked, with no parameters, the getter
           method is invoked.

           Input parameters: the optional $inval will invoke the setter method.

           Return value: for both setter and getter the current value of the biomaterial_list
           slot

           Side effects: none

           Exceptions: none

       $array_ref = $biomaterial->getCompound_list()
           This method handles the list for the "Bio::MAGE::BioMaterial::Compound" class. It
           returns a reference to an array of the class objects that have been associated with
           the package instance.

           This is useful when retrieving data from parsed MAGE-ML file.

       $biomaterial->addCompound(@vals)
           This method is an interface for adding "Bio::MAGE::BioMaterial::Compound" objects to
           the "compound_list" list. It is generally used by generic methods such as those in the
           XMLWriter.

           Input parameters: the list of values @vals to add to the owner 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 a subclass of class "Bio::MAGE::BioMaterial::Compound"

       $array_ref = $biomaterial->getBioMaterial_list()
           This method handles the list for the "Bio::MAGE::BioMaterial::BioMaterial" class. It
           returns a reference to an array of the class objects that have been associated with
           the package instance.

           This is useful when retrieving data from parsed MAGE-ML file.

       $biomaterial->addBioMaterial(@vals)
           This method is an interface for adding "Bio::MAGE::BioMaterial::BioMaterial" objects
           to the "biomaterial_list" list. It is generally used by generic methods such as those
           in the XMLWriter.

           Input parameters: the list of values @vals to add to the owner 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 a subclass of class "Bio::MAGE::BioMaterial::BioMaterial"

       $biomaterial->obj2xml($writer)
           Write out this object, and all sub-objects, as XML using the supplied $writer to
           actually do the XML formatting.

           Input parameters: $writer must be an XML writer, e.g. an instance of
           Bio::MAGE::XML::Writer. It must have methods: write_start_tag(), write_end_tag(), and
           obj2xml().

           Return value: none

           Side effects: all writing is delegated to the $writer - it's write_start_tag() and
           write_end_tag() methods are invoked with the appropriate data, and all class sub-
           objects of the "Bio::MAGE::BioMaterial" instance will have their obj2xml() methods
           invoked in turn. By allowing the $writer to do the actual formatting of the output
           XML, it enables the user to precisely control the format.

           Exceptions: will call "croak()" if no identifier has been set for the
           "Bio::MAGE::BioMaterial" instance.

       $biomaterial->register($obj)
           Store an object for later writing as XML.

           Input parameters: object to be added to the list of registered objects.

           Return value: none

           Side effects: if $obj needs to be stored by this class, a reference will be stored in
           the correct XML list for this class.

           Exceptions: none

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).