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.\" ========================================================================
.\"
.IX Title "MAGE::Array 3pm"
.TH MAGE::Array 3pm "2020-11-27" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::MAGE::Array \- Container module for classes in the MAGE package: Array
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::MAGE::Array;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a \fIpackage\fR module that encapsulates a number of classes in
the Bio::MAGE hierarchy. These classes belong to the
Array package of the MAGE-OM object model.
.SH "CLASSES"
.IX Header "CLASSES"
The Bio::MAGE::Array module contains the following
Bio::MAGE classes:
.IP "\(bu" 4
Array
.IP "\(bu" 4
FeatureDefect
.IP "\(bu" 4
ArrayGroup
.IP "\(bu" 4
ArrayManufacture
.IP "\(bu" 4
ArrayManufactureDeviation
.IP "\(bu" 4
Fiducial
.IP "\(bu" 4
ManufactureLIMS
.IP "\(bu" 4
ManufactureLIMSBiomaterial
.IP "\(bu" 4
PositionDelta
.IP "\(bu" 4
ZoneDefect
.SH "CLASS METHODS"
.IX Header "CLASS METHODS"
.ie n .IP "@class_list = \fBBio::MAGE::Array::classes()\fR;" 4
.el .IP "\f(CW@class_list\fR = \fBBio::MAGE::Array::classes()\fR;" 4
.IX Item "@class_list = Bio::MAGE::Array::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.
.ie n .IP "$obj = class\->new(%parameters)" 4
.el .IP "\f(CW$obj\fR = class\->new(%parameters)" 4
.IX Item "$obj = class->new(%parameters)"
The \f(CW\*(C`new()\*(C'\fR method is the class constructor.
.Sp
\&\fBParameters\fR: if given a list of name/value parameters the
corresponding slots, attributes, or associations will have their
initial values set by the constructor.
.Sp
\&\fBReturn value\fR: It returns a reference to an object of the class.
.Sp
\&\fBSide effects\fR: It invokes the \f(CW\*(C`initialize()\*(C'\fR method if it is defined
by the class.
.ie n .IP "@names = class\->\fBget_slot_names()\fR" 4
.el .IP "\f(CW@names\fR = class\->\fBget_slot_names()\fR" 4
.IX Item "@names = class->get_slot_names()"
The \f(CW\*(C`get_slot_names()\*(C'\fR method is used to retrieve the name of all
slots defined in a given class.
.Sp
\&\fB\s-1NOTE\s0\fR: the list of names does not include attribute or association
names.
.Sp
\&\fBReturn value\fR: A list of the names of all slots defined for this class.
.Sp
\&\fBSide effects\fR: none
.ie n .IP "@name_list = \fBget_attribute_names()\fR" 4
.el .IP "\f(CW@name_list\fR = \fBget_attribute_names()\fR" 4
.IX Item "@name_list = get_attribute_names()"
returns the list of attribute data members for this class.
.ie n .IP "@name_list = \fBget_association_names()\fR" 4
.el .IP "\f(CW@name_list\fR = \fBget_association_names()\fR" 4
.IX Item "@name_list = get_association_names()"
returns the list of association data members for this class.
.ie n .IP "@class_list = \fBget_superclasses()\fR" 4
.el .IP "\f(CW@class_list\fR = \fBget_superclasses()\fR" 4
.IX Item "@class_list = get_superclasses()"
returns the list of superclasses for this class.
.ie n .IP "@class_list = \fBget_subclasses()\fR" 4
.el .IP "\f(CW@class_list\fR = \fBget_subclasses()\fR" 4
.IX Item "@class_list = get_subclasses()"
returns the list of subclasses for this class.
.ie n .IP "$name = \fBclass_name()\fR" 4
.el .IP "\f(CW$name\fR = \fBclass_name()\fR" 4
.IX Item "$name = class_name()"
Returns the full class name for this class.
.ie n .IP "$package_name = \fBpackage_name()\fR" 4
.el .IP "\f(CW$package_name\fR = \fBpackage_name()\fR" 4
.IX Item "$package_name = package_name()"
Returns the base package name (i.e. no 'namespace::') of the package
that contains this class.
.ie n .IP "%assns = \fBassociations()\fR" 4
.el .IP "\f(CW%assns\fR = \fBassociations()\fR" 4
.IX Item "%assns = associations()"
returns the association meta-information in a hash where the keys are
the association names and the values are \f(CW\*(C`Association\*(C'\fR objects that
provide the meta-information for the association.
.SH "INSTANCE METHODS"
.IX Header "INSTANCE METHODS"
.ie n .IP "$obj_copy = $obj\->\fBnew()\fR" 4
.el .IP "\f(CW$obj_copy\fR = \f(CW$obj\fR\->\fBnew()\fR" 4
.IX Item "$obj_copy = $obj->new()"
When invoked with an existing object reference and not a class name,
the \f(CW\*(C`new()\*(C'\fR method acts as a copy constructor \- with the new object's
initial values set to be those of the existing object.
.Sp
\&\fBParameters\fR: No input parameters  are used in the copy  constructor,
the initial values are taken directly from the object to be copied.
.Sp
\&\fBReturn value\fR: It returns a reference to an object of the class.
.Sp
\&\fBSide effects\fR: It invokes the \f(CW\*(C`initialize()\*(C'\fR method if it is defined
by the class.
.ie n .IP "$obj\->set_slots(%parameters)" 4
.el .IP "\f(CW$obj\fR\->set_slots(%parameters)" 4
.IX Item "$obj->set_slots(%parameters)"
.PD 0
.ie n .IP "$obj\->set_slots(\e@name_list, \e@value_list)" 4
.el .IP "\f(CW$obj\fR\->set_slots(\e@name_list, \e@value_list)" 4
.IX Item "$obj->set_slots(@name_list, @value_list)"
.PD
The \f(CW\*(C`set_slots()\*(C'\fR 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.
.Sp
\&\fBReturn value\fR: none
.Sp
\&\fBSide effects\fR: will call \f(CW\*(C`croak()\*(C'\fR if a slot_name is used that the class
does not define.
.ie n .IP "@obj_list = $obj\->get_slots(@name_list)" 4
.el .IP "\f(CW@obj_list\fR = \f(CW$obj\fR\->get_slots(@name_list)" 4
.IX Item "@obj_list = $obj->get_slots(@name_list)"
The \f(CW\*(C`get_slots()\*(C'\fR method is used to get the values of a number of
slots at the same time.
.Sp
\&\fBReturn value\fR: a list of instance objects
.Sp
\&\fBSide effects\fR: none
.ie n .IP "$val = $obj\->set_slot($name,$val)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->set_slot($name,$val)" 4
.IX Item "$val = $obj->set_slot($name,$val)"
The \f(CW\*(C`set_slot()\*(C'\fR method sets the slot \f(CW$name\fR to the value \f(CW$val\fR
.Sp
\&\fBReturn value\fR: the new value of the slot, i.e. \f(CW$val\fR
.Sp
\&\fBSide effects\fR: none
.ie n .IP "$val = $obj\->get_slot($name)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->get_slot($name)" 4
.IX Item "$val = $obj->get_slot($name)"
The \f(CW\*(C`get_slot()\*(C'\fR method is used to get the values of a number of
slots at the same time.
.Sp
\&\fBReturn value\fR: a single slot value, or undef if the slot has not been
initialized.
.Sp
\&\fBSide effects\fR: none
.ie n .IP "$val = $array\->\fBxml_lists()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$array\fR\->\fBxml_lists()\fR" 4
.IX Item "$val = $array->xml_lists()"
.PD 0
.ie n .IP "$inval = $array\->xml_lists($inval)" 4
.el .IP "\f(CW$inval\fR = \f(CW$array\fR\->xml_lists($inval)" 4
.IX Item "$inval = $array->xml_lists($inval)"
.PD
This is the unified setter/getter method for the xml_lists slot.
.Sp
If \f(CW$inval\fR is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
.Sp
Input parameters: the optional \f(CW$inval\fR will invoke the setter method.
.Sp
Return value: for both setter and getter the current value of the xml_lists
slot
.Sp
Side effects: none
.Sp
Exceptions: none
.ie n .IP "$val = $array\->\fBtagname()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$array\fR\->\fBtagname()\fR" 4
.IX Item "$val = $array->tagname()"
.PD 0
.ie n .IP "$inval = $array\->tagname($inval)" 4
.el .IP "\f(CW$inval\fR = \f(CW$array\fR\->tagname($inval)" 4
.IX Item "$inval = $array->tagname($inval)"
.PD
This is the unified setter/getter method for the tagname slot.
.Sp
If \f(CW$inval\fR is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
.Sp
Input parameters: the optional \f(CW$inval\fR will invoke the setter method.
.Sp
Return value: for both setter and getter the current value of the tagname
slot
.Sp
Side effects: none
.Sp
Exceptions: none
.ie n .IP "$val = $array\->\fBarraygroup_list()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$array\fR\->\fBarraygroup_list()\fR" 4
.IX Item "$val = $array->arraygroup_list()"
.PD 0
.ie n .IP "$inval = $array\->arraygroup_list($inval)" 4
.el .IP "\f(CW$inval\fR = \f(CW$array\fR\->arraygroup_list($inval)" 4
.IX Item "$inval = $array->arraygroup_list($inval)"
.PD
This is the unified setter/getter method for the arraygroup_list slot.
.Sp
If \f(CW$inval\fR is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
.Sp
Input parameters: the optional \f(CW$inval\fR will invoke the setter method.
.Sp
Return value: for both setter and getter the current value of the arraygroup_list
slot
.Sp
Side effects: none
.Sp
Exceptions: none
.ie n .IP "$val = $array\->\fBarray_list()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$array\fR\->\fBarray_list()\fR" 4
.IX Item "$val = $array->array_list()"
.PD 0
.ie n .IP "$inval = $array\->array_list($inval)" 4
.el .IP "\f(CW$inval\fR = \f(CW$array\fR\->array_list($inval)" 4
.IX Item "$inval = $array->array_list($inval)"
.PD
This is the unified setter/getter method for the array_list slot.
.Sp
If \f(CW$inval\fR is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
.Sp
Input parameters: the optional \f(CW$inval\fR will invoke the setter method.
.Sp
Return value: for both setter and getter the current value of the array_list
slot
.Sp
Side effects: none
.Sp
Exceptions: none
.ie n .IP "$val = $array\->\fBarraymanufacture_list()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$array\fR\->\fBarraymanufacture_list()\fR" 4
.IX Item "$val = $array->arraymanufacture_list()"
.PD 0
.ie n .IP "$inval = $array\->arraymanufacture_list($inval)" 4
.el .IP "\f(CW$inval\fR = \f(CW$array\fR\->arraymanufacture_list($inval)" 4
.IX Item "$inval = $array->arraymanufacture_list($inval)"
.PD
This is the unified setter/getter method for the arraymanufacture_list slot.
.Sp
If \f(CW$inval\fR is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
.Sp
Input parameters: the optional \f(CW$inval\fR will invoke the setter method.
.Sp
Return value: for both setter and getter the current value of the arraymanufacture_list
slot
.Sp
Side effects: none
.Sp
Exceptions: none
.ie n .IP "$array_ref = $array\->\fBgetArrayGroup_list()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$array\fR\->\fBgetArrayGroup_list()\fR" 4
.IX Item "$array_ref = $array->getArrayGroup_list()"
This method handles the list for the \f(CW\*(C`Bio::MAGE::Array::ArrayGroup\*(C'\fR class. It
returns a reference to an array of the class objects that have been
associated with the package instance.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$array\->addArrayGroup(@vals)" 4
.el .IP "\f(CW$array\fR\->addArrayGroup(@vals)" 4
.IX Item "$array->addArrayGroup(@vals)"
This method is an interface for adding \f(CW\*(C`Bio::MAGE::Array::ArrayGroup\*(C'\fR objects to
the \f(CW\*(C`arraygroup_list\*(C'\fR list. It is generally used by generic methods such
as those in the XMLWriter.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the owner
association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: none
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified
, or if any of the objects in \f(CW@vals\fR is not a subclass of class \f(CW\*(C`Bio::MAGE::Array::ArrayGroup\*(C'\fR
.ie n .IP "$array_ref = $array\->\fBgetArray_list()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$array\fR\->\fBgetArray_list()\fR" 4
.IX Item "$array_ref = $array->getArray_list()"
This method handles the list for the \f(CW\*(C`Bio::MAGE::Array::Array\*(C'\fR class. It
returns a reference to an array of the class objects that have been
associated with the package instance.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$array\->addArray(@vals)" 4
.el .IP "\f(CW$array\fR\->addArray(@vals)" 4
.IX Item "$array->addArray(@vals)"
This method is an interface for adding \f(CW\*(C`Bio::MAGE::Array::Array\*(C'\fR objects to
the \f(CW\*(C`array_list\*(C'\fR list. It is generally used by generic methods such
as those in the XMLWriter.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the owner
association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: none
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified
, or if any of the objects in \f(CW@vals\fR is not a subclass of class \f(CW\*(C`Bio::MAGE::Array::Array\*(C'\fR
.ie n .IP "$array_ref = $array\->\fBgetArrayManufacture_list()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$array\fR\->\fBgetArrayManufacture_list()\fR" 4
.IX Item "$array_ref = $array->getArrayManufacture_list()"
This method handles the list for the \f(CW\*(C`Bio::MAGE::Array::ArrayManufacture\*(C'\fR class. It
returns a reference to an array of the class objects that have been
associated with the package instance.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$array\->addArrayManufacture(@vals)" 4
.el .IP "\f(CW$array\fR\->addArrayManufacture(@vals)" 4
.IX Item "$array->addArrayManufacture(@vals)"
This method is an interface for adding \f(CW\*(C`Bio::MAGE::Array::ArrayManufacture\*(C'\fR objects to
the \f(CW\*(C`arraymanufacture_list\*(C'\fR list. It is generally used by generic methods such
as those in the XMLWriter.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the owner
association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: none
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified
, or if any of the objects in \f(CW@vals\fR is not a subclass of class \f(CW\*(C`Bio::MAGE::Array::ArrayManufacture\*(C'\fR
.ie n .IP "$array\->obj2xml($writer)" 4
.el .IP "\f(CW$array\fR\->obj2xml($writer)" 4
.IX Item "$array->obj2xml($writer)"
Write out this object, and all sub-objects, as \s-1XML\s0 using the supplied
\&\f(CW$writer\fR to actually do the \s-1XML\s0 formatting.
.Sp
Input parameters: \f(CW$writer\fR must be an \s-1XML\s0 writer, e.g. an instance of
Bio::MAGE::XML::Writer. It must have methods: \fBwrite_start_tag()\fR,
\&\fBwrite_end_tag()\fR, and \fBobj2xml()\fR.
.Sp
Return value: none
.Sp
Side effects: all writing is delegated to the \f(CW$writer\fR \- it's
\&\fBwrite_start_tag()\fR and \fBwrite_end_tag()\fR methods are invoked with the
appropriate data, and all class sub-objects of the \f(CW\*(C`Bio::MAGE::Array\*(C'\fR instance will have their \fBobj2xml()\fR methods
invoked in turn. By allowing the \f(CW$writer\fR to do the actual formatting
of the output \s-1XML,\s0 it enables the user to precisely control the
format.
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no identifier has been set for the
\&\f(CW\*(C`Bio::MAGE::Array\*(C'\fR instance.
.ie n .IP "$array\->register($obj)" 4
.el .IP "\f(CW$array\fR\->register($obj)" 4
.IX Item "$array->register($obj)"
Store an object for later writing as \s-1XML.\s0
.Sp
Input parameters: object to be added to the list of registered objects.
.Sp
Return value: none
.Sp
Side effects: if \f(CW$obj\fR needs to be stored by this class, a reference
will be stored in the correct \s-1XML\s0 list for this class.
.Sp
Exceptions: none
.SH "SLOTS, ATTRIBUTES, AND ASSOCIATIONS"
.IX Header "SLOTS, ATTRIBUTES, AND ASSOCIATIONS"
In the Perl implementation of MAGE-OM classes, there are
three types of class data members: \f(CW\*(C`slots\*(C'\fR, \f(CW\*(C`attributes\*(C'\fR, and
\&\f(CW\*(C`associations\*(C'\fR.
.SS "\s-1SLOTS\s0"
.IX Subsection "SLOTS"
This \s-1API\s0 uses the term \f(CW\*(C`slot\*(C'\fR to indicate a data member of the class
that was not present in the \s-1UML\s0 model and is used for mainly internal
purposes \- use only if you understand the inner workings of the
\&\s-1API.\s0 Most often slots are used by generic methods such as those in the
\&\s-1XML\s0 writing and reading classes.
.PP
Slots are implemented using unified getter/setter methods:
.ie n .IP "$var = $obj\->\fBslot_name()\fR;" 4
.el .IP "\f(CW$var\fR = \f(CW$obj\fR\->\fBslot_name()\fR;" 4
.IX Item "$var = $obj->slot_name();"
Retrieves the current value of the slot.
.ie n .IP "$new_var = $obj\->slot_name($new_var);" 4
.el .IP "\f(CW$new_var\fR = \f(CW$obj\fR\->slot_name($new_var);" 4
.IX Item "$new_var = $obj->slot_name($new_var);"
Store \f(CW$new_var\fR in the slot \- the return value is also \f(CW$new_var\fR.
.ie n .IP "@names = $obj\->\fBget_slot_names()\fR" 4
.el .IP "\f(CW@names\fR = \f(CW$obj\fR\->\fBget_slot_names()\fR" 4
.IX Item "@names = $obj->get_slot_names()"
Returns the list of all slots in the class.
.PP
\&\fB\s-1DATA CHECKING\s0\fR: No data type checking is made for these methods.
.SS "\s-1ATTRIBUTES AND ASSOCIATIONS\s0"
.IX Subsection "ATTRIBUTES AND ASSOCIATIONS"
The terms \f(CW\*(C`attribute\*(C'\fR and \f(CW\*(C`association\*(C'\fR indicate data members of the
class that were specified directly from the \s-1UML\s0 model.
.PP
In the Perl implementation of MAGE-OM classes,
association and attribute accessors are implemented using three
separate methods:
.IP "get*" 4
.IX Item "get*"
Retrieves the current value.
.Sp
\&\fB\s-1NOTE\s0\fR: For associations, if the association has list cardinality, an
array reference is returned.
.Sp
\&\fB\s-1DATA CHECKING\s0\fR: Ensure that no argument is provided.
.IP "set*" 4
.IX Item "set*"
Sets the current value, \fBreplacing\fR any existing value.
.Sp
\&\fB\s-1NOTE\s0\fR: For associations, if the association has list cardinality,
the argument must be an array reference. Because of this, you probably
should be using the add* methods.
.Sp
\&\fB\s-1DATA CHECKING\s0\fR: For attributes, ensure that a single value is
provided as the argument. For associations, if the association has
list cardinality, ensure that the argument is a reference to an array
of instances of the correct MAGE-OM class, otherwise
ensure that there is a single argument of the correct MAGE-OM class.
.IP "add*" 4
.IX Item "add*"
\&\fB\s-1NOTE\s0\fR: Only present in associations with list cardinality.
.Sp
Appends a list of objects to any values that may already be stored
in the association.
.Sp
\&\fB\s-1DATA CHECKING\s0\fR: Ensure that all arguments are of the correct MAGE-OM class.
.SS "\s-1GENERIC METHODS\s0"
.IX Subsection "GENERIC METHODS"
The unified base class of all MAGE-OM classes, \f(CW\*(C`Bio::MAGE::Base\*(C'\fR, provides a set of generic methods that
will operate on slots, attributes, and associations:
.ie n .IP "$val = $obj\->get_slot($name)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->get_slot($name)" 4
.IX Item "$val = $obj->get_slot($name)"
.PD 0
.ie n .IP "\e@list_ref = $obj\->get_slots(@name_list);" 4
.el .IP "\e@list_ref = \f(CW$obj\fR\->get_slots(@name_list);" 4
.IX Item "@list_ref = $obj->get_slots(@name_list);"
.ie n .IP "$val = $obj\->set_slot($name,$val)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->set_slot($name,$val)" 4
.IX Item "$val = $obj->set_slot($name,$val)"
.ie n .IP "$obj\->set_slots(%parameters)" 4
.el .IP "\f(CW$obj\fR\->set_slots(%parameters)" 4
.IX Item "$obj->set_slots(%parameters)"
.ie n .IP "$obj\->set_slots(\e@name_list, \e@value_list)" 4
.el .IP "\f(CW$obj\fR\->set_slots(\e@name_list, \e@value_list)" 4
.IX Item "$obj->set_slots(@name_list, @value_list)"
.PD
See elsewhere in this page for a detailed description of these
methods.
.SH "BUGS"
.IX Header "BUGS"
Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)
.SH "AUTHOR"
.IX Header "AUTHOR"
Jason E. Stewart (jasons 'at' cpan 'dot' org)
.SH "SEE ALSO"
.IX Header "SEE ALSO"
\&\fBperl\fR\|(1).