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

       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)

       @class_list = Bio::MAGE::DesignElement::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.

           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.

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

       •   DesignElement

       •   Position

       •   Reporter

       •   ReporterPosition

       •   CompositePosition

       •   CompositeSequence

       •   Feature

       •   MismatchInformation

       •   FeatureInformation

       •   CompositeCompositeMap

       •   FeatureReporterMap

       •   ReporterCompositeMap

       •   FeatureLocation

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

       $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

       $val = $designelement->xml_lists()
       $inval = $designelement->xml_lists($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 = $designelement->tagname()
       $inval = $designelement->tagname($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 = $designelement->compositesequence_list()
       $inval = $designelement->compositesequence_list($inval)
           This is the unified setter/getter method for the compositesequence_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 compositesequence_list slot

           Side effects: none

           Exceptions: none

       $val = $designelement->reporter_list()
       $inval = $designelement->reporter_list($inval)
           This is the unified setter/getter method for the reporter_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 reporter_list slot

           Side effects: none

           Exceptions: none

       $val = $designelement->compositecompositemap_list()
       $inval = $designelement->compositecompositemap_list($inval)
           This is the unified setter/getter method for the compositecompositemap_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 compositecompositemap_list slot

           Side effects: none

           Exceptions: none

       $val = $designelement->reportercompositemap_list()
       $inval = $designelement->reportercompositemap_list($inval)
           This is the unified setter/getter method for the reportercompositemap_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 reportercompositemap_list slot

           Side effects: none

           Exceptions: none

       $val = $designelement->featurereportermap_list()
       $inval = $designelement->featurereportermap_list($inval)
           This is the unified setter/getter method for the featurereportermap_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 featurereportermap_list slot

           Side effects: none

           Exceptions: none

       $array_ref = $designelement->getCompositeSequence_list()
           This method handles the list for the "Bio::MAGE::DesignElement::CompositeSequence" 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.

       $designelement->addCompositeSequence(@vals)
           This  method  is an interface for adding "Bio::MAGE::DesignElement::CompositeSequence" objects to the
           "compositesequence_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::DesignElement::CompositeSequence"

       $array_ref = $designelement->getReporter_list()
           This method handles the  list  for  the  "Bio::MAGE::DesignElement::Reporter"  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.

       $designelement->addReporter(@vals)
           This   method  is  an  interface  for  adding  "Bio::MAGE::DesignElement::Reporter"  objects  to  the
           "reporter_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::DesignElement::Reporter"

       $array_ref = $designelement->getCompositeCompositeMap_list()
           This  method  handles  the  list  for the "Bio::MAGE::DesignElement::CompositeCompositeMap" 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.

       $designelement->addCompositeCompositeMap(@vals)
           This  method  is an interface for adding "Bio::MAGE::DesignElement::CompositeCompositeMap" objects to
           the "compositecompositemap_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::DesignElement::CompositeCompositeMap"

       $array_ref = $designelement->getReporterCompositeMap_list()
           This method handles the  list  for  the  "Bio::MAGE::DesignElement::ReporterCompositeMap"  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.

       $designelement->addReporterCompositeMap(@vals)
           This method is an interface for adding  "Bio::MAGE::DesignElement::ReporterCompositeMap"  objects  to
           the  "reportercompositemap_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::DesignElement::ReporterCompositeMap"

       $array_ref = $designelement->getFeatureReporterMap_list()
           This method handles the list for the "Bio::MAGE::DesignElement::FeatureReporterMap" 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.

       $designelement->addFeatureReporterMap(@vals)
           This  method is an interface for adding "Bio::MAGE::DesignElement::FeatureReporterMap" objects to the
           "featurereportermap_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::DesignElement::FeatureReporterMap"

       $designelement->obj2xml($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::DesignElement" 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::DesignElement"
           instance.

       $designelement->register($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

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

perl(1).

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

       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::DesignElement;